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Sökning: WFRF:(Genheden Samuel)

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1.
  • Bettiga, Maurizio, 1978, et al. (författare)
  • Plasma membrane as a crucial player in acetic acid effect on yeast
  • 2017
  • Ingår i: IMYA12- 12th International Meeting on Yeast Apoptosis, Bari, Italy • 14-18 May 2017.
  • Konferensbidrag (övrigt vetenskapligt/konstnärligt)abstract
    • Weak organic acids such as formic, acetic or lactic acid are known inhibitors of microbial growth and fermentation. Acetic acid toxicity to yeast cells has been explained by different theories, involving specific signaling effects triggering an active cell death program, reduction of intracellular pH and acetate anion accumulation. Regardless of the fact whether the actual effect of acetate involves one of these mechanisms or a combination thereof, acetic acid inhibits yeast metabolism and affects yeast viability. This has a high impact on the feasibility of the new generation of fermentation processes, based on the naturally acetic acid-rich lignocellulosic substrates. It is therefore highly desirable to obtain a strain with increased capacity of coping with high acetic acid concentrations in the fermentation medium. Acetic acid is thought to be internalized by yeast cells in its undissociated form, by crossing the hydrophobic barrier of plasma membrane. Thus, in our work we focused on the investigation of membrane properties and how these influence the tolerance of yeast to acetic acid. First, we demonstrated with lipidomics analysis of membrane lipids that the yeast Zygosaccharomyces bailii, showing extraordinary tolerance to acetic acid, has a plasma membrane which is rich in sphingolipids. Next, we combined membrane molecular dynamics and in vivo measurements to confirm the specific role of sphingolipids in altering the permeability of plasma membrane to acetic acid. Finally, we investigated the effect of alcohols on the acetic acid permeation rate through the membrane. Our ultimate goal is to engineer the membrane composition of an industrial yeast strain towards reduced permeability, in order to obtain higher acetic acid tolerance.
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2.
  • Ciancetta, Antonella, et al. (författare)
  • A QM/MM study of the binding of RAPTA ligands to cathepsin B
  • 2011
  • Ingår i: Journal of Computer-Aided Molecular Design. - : Springer Science and Business Media LLC. - 1573-4951 .- 0920-654X. ; 25:8, s. 729-742
  • Tidskriftsartikel (refereegranskat)abstract
    • We have carried out quantum mechanical (QM) and QM/MM (combined QM and molecular mechanics) calculations, as well as molecular dynamics (MD) simulations to study the binding of a series of six RAPTA (Ru(II)-arene-1,3,5-triaza-7-phosphatricyclo-[3.3.1.1] decane) complexes with different arene substituents to cathepsin B. The recently developed QM/MM-PBSA approach (QM/MM combined with Poisson-Boltzmann solvent-accessible surface area solvation) has been used to estimate binding affinities. The QM calculations reproduce the antitumour activities of the complexes with a correlation coefficient (r(2)) of 0.35-0.86 after a conformational search. The QM/MM-PBSA method gave a better correlation (r(2) = 0.59) when the protein was fixed to the crystal structure, but more reasonable ligand structures and absolute binding energies were obtained if the protein was allowed to relax, indicating that the ligands are strained when the protein is kept fixed. In addition, the best correlation (r(2) = 0.80) was obtained when only the QM energies were used, which suggests that the MM and continuum solvation energies are not accurate enough to predict the binding of a charged metal complex to a charged protein. Taking into account the protein flexibility by means of MD simulations slightly improves the correlation (r(2) = 0.91), but the absolute energies are still too large and the results are sensitive to the details in the calculations, illustrating that it is hard to obtain stable predictions when full flexible protein is included in the calculations.
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3.
  • Diehl, Carl, et al. (författare)
  • Conformational entropy changes upon lactose binding to the carbohydrate recognition domain of galectin-3.
  • 2009
  • Ingår i: Journal of Biomolecular NMR. - : Springer Science and Business Media LLC. - 1573-5001 .- 0925-2738. ; 45:1-2, s. 157-169
  • Tidskriftsartikel (refereegranskat)abstract
    • The conformational entropy of proteins can make significant contributions to the free energy of ligand binding. NMR spin relaxation enables site-specific investigation of conformational entropy, via order parameters that parameterize local reorientational fluctuations of rank-2 tensors. Here we have probed the conformational entropy of lactose binding to the carbohydrate recognition domain of galectin-3 (Gal3), a protein that plays an important role in cell growth, cell differentiation, cell cycle regulation, and apoptosis, making it a potential target for therapeutic intervention in inflammation and cancer. We used (15)N spin relaxation experiments and molecular dynamics simulations to monitor the backbone amides and secondary amines of the tryptophan and arginine side chains in the ligand-free and lactose-bound states of Gal3. Overall, we observe good agreement between the experimental and computed order parameters of the ligand-free and lactose-bound states. Thus, the (15)N spin relaxation data indicate that the molecular dynamics simulations provide reliable information on the conformational entropy of the binding process. The molecular dynamics simulations reveal a correlation between the simulated order parameters and residue-specific backbone entropy, re-emphasizing that order parameters provide useful estimates of local conformational entropy. The present results show that the protein backbone exhibits an increase in conformational entropy upon binding lactose, without any accompanying structural changes.
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4.
  • Diehl, Carl, et al. (författare)
  • Protein Flexibility and Conformational Entropy in Ligand Design Targeting the Carbohydrate Recognition Domain of Galectin-3.
  • 2010
  • Ingår i: Journal of the American Chemical Society. - : American Chemical Society (ACS). - 1520-5126 .- 0002-7863. ; 132, s. 14577-14589
  • Tidskriftsartikel (refereegranskat)abstract
    • Rational drug design is predicated on knowledge of the three-dimensional structure of the protein-ligand complex and the thermodynamics of ligand binding. Despite the fundamental importance of both enthalpy and entropy in driving ligand binding, the role of conformational entropy is rarely addressed in drug design. In this work, we have probed the conformational entropy and its relative contribution to the free energy of ligand binding to the carbohydrate recognition domain of galectin-3. Using a combination of NMR spectroscopy, isothermal titration calorimetry, and X-ray crystallography, we characterized the binding of three ligands with dissociation constants ranging over 2 orders of magnitude. (15)N and (2)H spin relaxation measurements showed that the protein backbone and side chains respond to ligand binding by increased conformational fluctuations, on average, that differ among the three ligand-bound states. Variability in the response to ligand binding is prominent in the hydrophobic core, where a distal cluster of methyl groups becomes more rigid, whereas methyl groups closer to the binding site become more flexible. The results reveal an intricate interplay between structure and conformational fluctuations in the different complexes that fine-tunes the affinity. The estimated change in conformational entropy is comparable in magnitude to the binding enthalpy, demonstrating that it contributes favorably and significantly to ligand binding. We speculate that the relatively weak inherent protein-carbohydrate interactions and limited hydrophobic effect associated with oligosaccharide binding might have exerted evolutionary pressure on carbohydrate-binding proteins to increase the affinity by means of conformational entropy.
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5.
  • Genheden, Samuel, et al. (författare)
  • A comparison of different initialization protocols to obtain statistically independent molecular dynamics simulations.
  • 2011
  • Ingår i: Journal of Computational Chemistry. - : Wiley. - 1096-987X .- 0192-8651. ; 32:2, s. 187-195
  • Tidskriftsartikel (refereegranskat)abstract
    • We study how the results of molecular dynamics (MD) simulations are affected by various choices during the setup, e.g., the starting velocities, the solvation, the location of protons, the conformation of His, Asn, and Gln residues, the protonation and titration of His residues, and the treatment of alternative conformations. We estimate the binding affinity of ligands to four proteins calculated with the MM/GBSA method (molecular mechanics combined with a generalized Born and surface area solvation energy). For avidin and T4 lysozyme, all variations gave similar results within 2 kJ/mol. For factor Xa, differences in the solvation or in the selection of alternative conformations gave results that are significantly different from those of the other approaches by 4-6 kJ/mol, whereas for galectin-3, changes in the conformations, rotations, and protonation gave results that differed by 10 kJ/mol, but only if residues close to the binding site were modified. This shows that the results of MM/GBSA calculations are reasonably reproducible even if the MD simulations are set up with different software. Moreover, we show that the sampling of phase space can be enhanced by solvating the systems with different equilibrated water boxes, in addition to the common use of different starting velocities. If different conformations are available in the crystal structure, they should also be employed to enhance the sampling. Protonation, ionization, and conformations of Asn, Gln, and His may also be used to enhance sampling, but great effort should be spent to obtain as reliable predictions as possible close to the active site.
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6.
  • Genheden, Samuel, et al. (författare)
  • Accurate Predictions of Nonpolar Solvation Free Energies Require Explicit Consideration of Binding-Site Hydration
  • 2011
  • Ingår i: Journal of the American Chemical Society. - : American Chemical Society (ACS). - 1520-5126 .- 0002-7863. ; 133:33, s. 13081-13092
  • Tidskriftsartikel (refereegranskat)abstract
    • Continuum solvation methods are frequently used to increase the efficiency of computational methods to estimate free energies. In this paper, we have evaluated how well such methods estimate the nonpolar solvation free-energy change when a ligand binds to a protein. Three different continuum methods at various levels of approximation were considered, viz., the polarized continuum model (PCM), a method based on cavity and dispersion terms (CD), and a method based on a linear relation to the solvent-accessible surface area (SASA). Formally rigorous double-decoupling thermodynamic integration was used as a benchmark for the continuum methods. We have studied four protein-ligand complexes with binding sites of varying solvent exposure, namely the binding of phenol to ferritin, a biotin analogue to avidin, 2-aminobenzimidazole to trypsin, and a substituted galactoside to galectin-3. For ferritin and avidin, which have relatively hidden binding sites, rather accurate nonpolar solvation free energies could be obtained with the continuum methods if the binding site is prohibited to be filled by continuum water in the unbound state, even though the simulations and experiments show that the ligand replaces several water molecules upon binding. For the more solvent exposed binding sites of trypsin and galectin-3, no accurate continuum estimates could be obtained, even if the binding site was allowed or prohibited to be filled by continuum water. This shows that continuum methods fail to give accurate free energies on a wide range of systems with varying solvent exposure because they lack a microscopic picture of binding-site hydration as well as information about the entropy of water molecules that are in the binding site before the ligand binds. Consequently, binding affinity estimates based upon continuum solvation methods will give absolute binding energies that may differ by up to 200 kJ/mol depending on the method used. Moreover, even relative energies between ligands with the same scaffold may differ by up to 75 kJ/mol. We have tried to improve the continuum solvation methods by adding information about the solvent exposure of the binding site or the hydration of the binding site, and the results are promising at least for this small set of complexes.
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7.
  • Genheden, Samuel, et al. (författare)
  • All-atom/coarse-grained hybrid predictions of distribution coefficients in SAMPL5
  • 2016
  • Ingår i: Journal of Computer-Aided Molecular Design. - : Springer Science and Business Media LLC. - 0920-654X .- 1573-4951. ; 30:11, s. 969-976
  • Tidskriftsartikel (refereegranskat)abstract
    • We present blind predictions submitted to the SAMPL5 challenge on calculating distribution coefficients. The predictions were based on estimating the solvation free energies in water and cyclohexane of the 53 compounds in the challenge. These free energies were computed using alchemical free energy simulations based on a hybrid all-atom/coarse-grained model. The compounds were treated with the general Amber force field, whereas the solvent molecules were treated with the Elba coarse-grained model. Considering the simplicity of the solvent model and that we approximate the distribution coefficient with the partition coefficient of the neutral species, the predictions are of good accuracy. The correlation coefficient, R is 0.64, 82 % of the predictions have the correct sign and the mean absolute deviation is 1.8 log units. This is on a par with or better than the other simulation-based predictions in the challenge. We present an analysis of the deviations to experiments and compare the predictions to another submission that used all-atom solvent.
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8.
  • Genheden, Samuel, et al. (författare)
  • An MM/3D-RISM approach for ligand binding affinities.
  • 2010
  • Ingår i: The Journal of Physical Chemistry Part B. - : American Chemical Society (ACS). - 1520-5207 .- 1520-6106. ; 114:25, s. 8505-8516
  • Tidskriftsartikel (refereegranskat)abstract
    • We have modified the popular MM/PBSA or MM/GBSA approaches (molecular mechanics for a biomolecule, combined with a Poisson-Boltzmann or generalized Born electrostatic and surface area nonelectrostatic solvation energy) by employing instead the statistical-mechanical, three-dimensional molecular theory of solvation (also known as 3D reference interaction site model, or 3D-RISM-KH) coupled with molecular mechanics or molecular dynamics ( Blinov , N. ; et al. Biophys. J. 2010 ; Luchko , T. ; et al. J. Chem. Theory Comput. 2010 ). Unlike the PBSA or GBSA semiempirical approaches, the 3D-RISM-KH theory yields a full molecular picture of the solvation structure and thermodynamics from the first principles, with proper account of chemical specificities of both solvent and biomolecules, such as hydrogen bonding, hydrophobic interactions, salt bridges, etc. We test the method on the binding of seven biotin analogues to avidin in aqueous solution and show it to work well in predicting the ligand-binding affinities. We have compared the results of 3D-RISM-KH with four different generalized Born and two Poisson-Boltzmann methods. They give absolute binding energies that differ by up to 208 kJ/mol and mean absolute deviations in the relative affinities of 10-43 kJ/mol.
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9.
  • Genheden, Samuel (författare)
  • Are homology models sufficiently good for free-energy simulations?
  • 2012
  • Ingår i: Journal of Chemical Information and Modeling. - : American Chemical Society (ACS). - 1549-960X .- 1549-9596. ; 52:11, s. 3013-3021
  • Tidskriftsartikel (refereegranskat)abstract
    • In this paper, I evaluate the usefulness of protein homology models in rigorous free-energy simulations to determine ligand affinities. Two templates were used to create models of the factor Xa protein and one template was used for dihydrofolate reductase from Plasmodium falciparum. Then, the relative free energies for several pairs of ligands were estimated using thermodynamic integration with the homology models as starting point of the simulation. These binding affinities were compared to affinities obtained when using published crystal structures as starting point of the simulations. Encouragingly, the differences between the affinities obtained when starting from either homology models or crystal structure were not statistical significant for a majority of the considered pairs of ligands. Differences between 1 and 2 kJ/mol were observed for the dihydrofolate reductase ligands and differences between 0 and 8 kJ/mol were observed for the factor Xa ligands. The largest difference for factor Xa was caused by an erroneous modeling of a loop region close to two of the ligands, and it was only observed when using one of the templates. Therefore, it is advisible to always use more than one template when creating homology models if they should be used in free-energy simulations.
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10.
  • Genheden, Samuel, et al. (författare)
  • Binding affinities by alchemical perturbation using QM/MM with a large QM system and polarizable MM model.
  • 2015
  • Ingår i: Journal of Computational Chemistry. - : Wiley. - 1096-987X .- 0192-8651. ; 36:28, s. 2114-2124
  • Tidskriftsartikel (refereegranskat)abstract
    • The most general way to improve the accuracy of binding-affinity calculations for protein-ligand systems is to use quantum-mechanical (QM) methods together with rigorous alchemical-perturbation (AP) methods. We explore this approach by calculating the relative binding free energy of two synthetic disaccharides binding to galectin-3 at a reasonably high QM level (dispersion-corrected density functional theory with a triple-zeta basis set) and with a sufficiently large QM system to include all short-range interactions with the ligand (744-748 atoms). The rest of the protein is treated as a collection of atomic multipoles (up to quadrupoles) and polarizabilities. Several methods for evaluating the binding free energy from the 3600 QM calculations are investigated in terms of stability and accuracy. In particular, methods using QM calculations only at the endpoints of the transformation are compared with the recently proposed non-Boltzmann Bennett acceptance ratio (NBB) method that uses QM calculations at several stages of the transformation. Unfortunately, none of the rigorous approaches give sufficient statistical precision. However, a novel approximate method, involving the direct use of QM energies in the Bennett acceptance ratio method, gives similar results as NBB but with better precision, ∼3 kJ/mol. The statistical error can be further reduced by performing a greater number of QM calculations. © 2015 Wiley Periodicals, Inc.
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11.
  • Genheden, Samuel, et al. (författare)
  • Binding Affinities of Factor Xa Inhibitors Estimated by Thermodynamic Integration and MM/GBSA.
  • 2011
  • Ingår i: Journal of Chemical Information and Modeling. - : American Chemical Society (ACS). - 1549-960X .- 1549-9596. ; 51:Online March 18, 2011, s. 947-958
  • Tidskriftsartikel (refereegranskat)abstract
    • We present free energy estimates of nine 3-amidinobenzyl-1H-indole-2-carboxamide inhibitors of factor Xa. Using alchemical thermodynamic integration (TI) calculations, we estimate the difference in binding free energies with high accuracy and precision, except for mutations involving one of the amidinobenzyl rings. Crystal studies show that the inhibitors may bind in two distinct conformations, and using TI, we show that the two conformations give a similar binding affinity. Furthermore, we show that we can reduce the computational demand, while still retaining a high accuracy and precision, by using fewer integration points and shorter protein-ligand simulations. Finally, we have compared the TI results to those obtained with the simpler MM/GBSA method (molecular-mechanics with generalized Born surface-area solvation). MM/GBSA gives better results for the mutations that involve a change of net charge, but if a precision similar to that of the TI method is required, the MM/GBSA method is actually slightly more expensive. Thus, we have shown that TI could be a valuable tool in drug design.
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12.
  • Genheden, Samuel (författare)
  • Coarse-grained bond and angle distributions from atomistic simulations: On the systematic parameterisation of lipid models
  • 2016
  • Ingår i: Journal of Molecular Graphics and Modelling. - : Elsevier BV. - 1093-3263. ; 63, s. 57-64
  • Tidskriftsartikel (refereegranskat)abstract
    • Coarse-grained (CG) models are popular alternatives to atomistic (AT) force fields as they enable simulations of larger systems at longer timescales. The bottom-up approach is a systematic parameterisation strategy whereby data from AT simulations are used to determine the CG parameters. This is particular straightforward with the bond and angle parameters as a direct Boltzmann inversion can be used. Still, a reference AT force field has to be chosen. In this study, I compare three common AT force fields (Stockholm lipids, Berger and Gromos) and investigate the sampling of bond and angle distributions in two CG models (Martini and Elba). As a test case, I choose a bilayer of POPC lipids. The AT simulations give distributions that agree to a large extent, especially in the fatty acid tails. However, the AT simulations sample distributions that differ from the distributions observed in CG simulations with respect to both location and width. The bond and angle distributions from the AT simulations are then used to re-parameterise the CG force fields. For the Martini model, this significantly alters the physical behaviour of the membrane, which likely is an effect of the mapping. However, for the Elba model the re-parameterised force field gives a membrane that is in some respects closer to the experimental membrane. Implications for CG parameterisation are discussed.
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13.
  • Genheden, Samuel, et al. (författare)
  • Comparison of end-point continuum-solvation methods for the calculation of protein-ligand binding free energies.
  • 2012
  • Ingår i: Proteins. - : Wiley. - 0887-3585. ; 80:5, s. 1326-1342
  • Tidskriftsartikel (refereegranskat)abstract
    • We have compared the predictions of ligand-binding affinities from several methods based on end-point molecular dynamics simulations and continuum solvation, i.e. methods related to MM/PBSA (molecular mechanics combined with Poisson-Boltzmann and surface area solvation). Two continuum-solvation models were considered, viz. the Poisson-Boltzmann (PB) and generalised Born (GB) approaches. The non-electrostatic energies were also obtained in two different ways, viz. either from the sum of the bonded, van der Waals, non-polar solvation energies, and entropy terms (as in MM/PBSA), or from the scaled protein-ligand van der Waals interaction energy (as in the linear interaction energy approach, LIE). Three different approaches to calculate electrostatic energies were tested, viz. the sum of electrostatic interaction energies and polar solvation energies, obtained either from a single simulation of the complex or from three independent simulations of the complex, the free protein, and the free ligand, or the linear-response approximation (LRA). Moreover, we investigated the effect of scaling the electrostatic interactions by an effective internal dielectric constant of the protein (ε(int) ). All these methods were tested on the binding of seven biotin analogues to avidin and nine 3-amidinobenzyl-1H-indole-2-carboxamide inhibitors to factor Xa. For avidin, the best results were obtained with a combination of the LIE non-electrostatic energies with the MM+GB electrostatic energies from a single simulation, using ε(int) = 4. For fXa, standard MM/GBSA, based on one simulation and using ε(int) = 4-10 gave the best result. The optimum internal dielectric constant seems to be slightly higher with PB than with GB solvation. Proteins 2012. © 2012 Wiley-Liss, Inc.
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14.
  • Genheden, Samuel, et al. (författare)
  • Comparison of the Efficiency of the LIE and MM/GBSA Methods to Calculate Ligand-Binding Energies
  • 2011
  • Ingår i: Journal of Chemical Theory and Computation. - : American Chemical Society (ACS). - 1549-9618 .- 1549-9626. ; 7:11, s. 3768-3778
  • Tidskriftsartikel (refereegranskat)abstract
    • We have evaluated the efficiency of two popular end-point methods to calculate ligand-binding free energies, LIE (linear interaction energy) and MM/GBSA (molecular mechanics with generalized Born surface-area solvation), i.e. the computational effort needed to obtain estimates of a similar precision. As a test case, we use the binding of seven biotin analogues to avidin. The energy terms used by MM/GBSA and LIE exhibit a similar correlation time (similar to 5 ps), and the equilibration time seems also to be similar, although it varies much between the various ligands. The results show that the LIE method is more effective than MM/GBSA, by a factor of 2-7 for a truncated spherical system with a radius of 26 angstrom and by a factor of 1.0-2.4 for the full avidin tetramer (radius 47 angstrom). The reason for this is the cost for the MM/GBSA entropy calculations, which more than compensates for the extra simulation of the free ligand in LIE. On the other hand, LIE requires that the protein is neutralized, whereas MM/GBSA has no such requirements. Our results indicate that both the truncation and neutralization of the proteins may slow the convergence and emphasize small differences in the calculations, e.g., differences between the four subunits in avidin. Moreover, LIE cannot take advantage of the fact that avidin is a tetramer. For this test case, LIE gives poor results with the standard parametrization, but after optimizing the scaling factor of the van der Waals terms, reasonable binding affinities can be obtained, although MM/GBSA still gives a significantly better predictive index and correlation to the experimental affinities.
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15.
  • Genheden, Samuel, et al. (författare)
  • Computational Chemistry and Molecular Modelling Basics
  • 2017
  • Ingår i: Computational Tools for Chemical Biology. - : The Royal Society of Chemistry. - 9781782627005 - 9781788012560
  • Bokkapitel (refereegranskat)abstract
    • Computational modelling has gained an increasingly important role in biochemical and biomolecular sciences over the past decades. This is related to significant developments in terms of methodology and software, as well as the amazing technological advances in computational hardware, and fruitful connections across different disciplines. Today, we readily screen virtual libraries of several million compounds searching for potential new inhibitors, run simulations of large biomolecular complexes in micro or even millisecond timescales, or predict protein structures with similar accuracy to high-resolution X-ray crystallography. In this introductory chapter, the basics of biomolecular modelling are outlined, to help set the foundation for the subsequent, more specialised chapters. In order for the chapter to be ‘readable’ to interested researchers and PhD students in the biochemical and biomolecular fields our aim has been to do so without weighing down the text with too much detailed mathematics—yet at the same time providing a sufficient level of theory so as to give an understanding of what is implied when talking about molecular dynamic simulations, docking or homology modelling.
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16.
  • Genheden, Samuel, et al. (författare)
  • Conformational Entropies and Order Parameters: Convergence, Reproducibility, and Transferability
  • 2014
  • Ingår i: Journal of Chemical Theory and Computation. - : American Chemical Society (ACS). - 1549-9618 .- 1549-9626. ; 10:1, s. 432-438
  • Tidskriftsartikel (refereegranskat)abstract
    • Conformational entropy provides major contributions to protein folding and functions, such as ligand binding, making it a potentially important driver of biologically relevant processes. NMR spectroscopy is a unique technique to estimate conformational entropy changes at atomic resolution, an approach that can be favorably augmented by comparisons with results from molecular dynamics (MD) simulations, for example, by generating an order-parameter-to-entropy dictionary. Here, we address critical issues pertaining to such an approach, including reproducibility, convergence, and transferability by analyzing long (380 ns -1 ms) MD trajectories obtained for five different proteins. We observe that order parameters and conformational entropies calculated over 10-100 ns windows are typically well converged among individual MD trajectories and reproducible between pairs of independent trajectories, when calculated on a per-residue level. However, significant discrepancies sometimes arise for the total conformational entropy evaluated as the sum of the residue-specific entropies, especially in cases that involve rare transitions to alternative conformational states. Furthermore, we find that the order-parameter-to-entropy dictionary depends strongly on the protein and the sampling frequency, but much less so on the molecular dynamics force field. Thus, the transferability of the dictionary is poor between proteins but relatively good between different states (e.g., different ligand-bound complexes) of the same protein, provided that a protein-specific dictionary has been derived.
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17.
  • Genheden, Samuel (författare)
  • Effect of solvent model when probing protein dynamics with molecular dynamics
  • 2017
  • Ingår i: Journal of Molecular Graphics and Modelling. - : Elsevier BV. - 1093-3263 .- 1873-4243. ; 71, s. 80-87
  • Tidskriftsartikel (refereegranskat)abstract
    • We probe the dynamics of the Bpti and Galectin-3 proteins using molecular dynamics simulations employing three water models at different levels of resolution, viz. the atomistic TIP4P-Ewald, the coarse-grained Elba and an implicit generalised Born model. The dynamics are quantified indirectly by model-free order parameters, S2 of the backbone N-H and selected side-chain bond vectors, which also have been determined experimentally through NMR relaxation measurements. For the backbone, the order parameters produced with the three solvent models agree to a large extent with experiments, giving average unsigned deviations between 0.03 and 0.06. For the side-chains, for which the experimental data is incomplete, the deviations are considerably larger with mean deviations between 0.13 and 0.17. However, for both backbone and side-chains, it is difficult to pick a winner, as all models perform equally well overall. For a more complete set of side-chain vectors, we resort to analysing the variation among the estimates from different solvent models. Unfortunately, the variations are found to be sizeable with mean deviations between 0.11 and 0.15. Implications for computational assessment of protein dynamics are discussed.
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18.
  • Genheden, Samuel, et al. (författare)
  • Estimation of Liposome Penetration Barriers of Drug Molecules with All-Atom and Coarse-Grained Models
  • 2016
  • Ingår i: Journal of Chemical Theory and Computation. - : American Chemical Society (ACS). - 1549-9618 .- 1549-9626. ; 12:9, s. 4651-4661
  • Tidskriftsartikel (refereegranskat)abstract
    • Liposomes are common carriers of drug molecules, providing enhanced delivery and accumulation of hydrophilic agents or larger biomolecules. Molecular simulations, can be used to estimate key features of the drug molecules upon interaction with the liposomes, such as penetration barriers and localization. Herein, we investigate several aspects of the computational estimation of penetration barriers, viz. the potential of Mean force (PMFs) along a vector spanning the membrane. First, we provide an: evaluation of the all-atom (AA) and coarse-grained (CG) parametrization of 5-aminolevulinic acid (5-ALA) and two of its alkyl esters by computing n-octanol/water partition :Coefficients. We find that the CG parametrization of the esters performs significantly better than the CG model of 5-ALA, highlighting the difficulty to coarse-grain small, polar molecules. However; the expected trend in partition coefficients is reproduced also with the CG models. Second, we compare PMFs in a small membrane slab described with either the AA or CG models. Here, we:are able to reproduce the all-atom PMF of 5-ALA with CG. However, for the alkyl esters it is unfortunately not possible to correctly reproduce both the depth and the penetration barrier of the PMF seen in the AA simulations with any of the tested CG models. We argue that it is more important to, choose a CG parametrization that reproduces the depth of the PMF. Third, we compare, using the CG model, PMFs in the membrane slab with PMFs in a large, realistic liposome. We find similar depths but slightly different penetration barriers most likely due to differences in the lipid density along the membrane axis. Finally, we compute PMFs in liposomes with three different lipid compositions. Unfortunately, differences in the PMFs could not be quantified, and it remains to be investigated to, what extent liposome simulations can fully reproduce experimental findings.
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19.
  • Genheden, Samuel, et al. (författare)
  • How to obtain statistically converged MM/GBSA results.
  • 2010
  • Ingår i: Journal of Computational Chemistry. - : Wiley. - 1096-987X .- 0192-8651. ; 31:Online 13 Jul 2009, s. 837-846
  • Tidskriftsartikel (refereegranskat)abstract
    • The molecular mechanics/generalized Born surface area (MM/GBSA) method has been investigated with the aim of achieving a statistical precision of 1 kJ/mol for the results. We studied the binding of seven biotin analogues to avidin, taking advantage of the fact that the protein is a tetramer with four independent binding sites, which should give the same estimated binding affinities. We show that it is not enough to use a single long simulation (10 ns), because the standard error of such a calculation underestimates the difference between the four binding sites. Instead, it is better to run several independent simulations and average the results. With such an approach, we obtain the same results for the four binding sites, and any desired precision can be obtained by running a proper number of simulations. We discuss how the simulations should be performed to optimize the use of computer time. The correlation time between the MM/GBSA energies is approximately 5 ps and an equilibration time of 100 ps is needed. For MM/GBSA, we recommend a sampling time of 20-200 ps for each separate simulation, depending on the protein. With 200 ps production time, 5-50 separate simulations are required to reach a statistical precision of 1 kJ/mol (800-8000 energy calculations or 1.5-15 ns total simulation time per ligand) for the seven avidin ligands. This is an order of magnitude more than what is normally used, but such a number of simulations is needed to obtain statistically valid results for the MM/GBSA method. (c) 2009 Wiley Periodicals, Inc. J Comput Chem 2009.
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20.
  • Genheden, Samuel, et al. (författare)
  • Improving the Efficiency of Protein-Ligand Binding Free-Energy Calculations by System Truncation
  • 2012
  • Ingår i: Journal of Chemical Theory and Computation. - : American Chemical Society (ACS). - 1549-9618 .- 1549-9626. ; 8:4, s. 1449-1458
  • Tidskriftsartikel (refereegranskat)abstract
    • We have studied whether the efficiency of alchemical free-energy calculations with the Bennett acceptance ratio method of protein-ligand binding energies can be improved by simulating only part of the protein. To this end, we solvated the full protein in a spherical droplet with a radius of 46 angstrom, surrounded by a vacuum. Then, we systematically reduced the size of the droplet and at the same time ignored protein residues that were outside the droplet. Radii of 40-15 angstrom were tested. Ten inhibitors of the blood clotting factor Xa were studied, and the results were compared to an earlier study in which the protein was solvated in a periodic box, showing complete agreement between the two sets of calculations within statistical uncertainty. We then show that the simulated system can be truncated down to 15 angstrom, without changing the calculated affinities by more than 0.5 kJ/mol on average (maximum difference of 1.4 kJ/mol). Moreover, we show that reducing the number of intermediate states in the calculations from eleven to three gave deviations that, on average, were only 0.5 kJ/mol (maximum of 1.4 kJ/mol). Together, these results show that truncation is an appropriate way to improve the efficiency of free-energy calculations for small mutations that preserve the net charge of the ligand. in fact, each calculation of a relative binding affinity requires only six simulations, each of which takes similar to 15 CPU h of computation on a single processor.
  •  
21.
  • Genheden, Samuel (författare)
  • MM/GBSA and LIE estimates of host-guest affinities: dependence on charges and solvation model.
  • 2011
  • Ingår i: Journal of Computer-Aided Molecular Design. - : Springer Science and Business Media LLC. - 1573-4951 .- 0920-654X. ; 25:11, s. 1085-1093
  • Tidskriftsartikel (refereegranskat)abstract
    • The affinities of two sets of guest-host systems were estimated using the popular end-point methods MM/GBSA (molecular-mechanics with generalised Born and surface-area solvation) and LIE (linear interaction energy). A set of six primary alcohols that bind to α-cyclodextrin (α-CD) and a set of eight guest molecules to cucurbit[8]uril (CB8) were considered. Three different charge schemes were used to obtain charges for the host and guest molecules, viz., AM1-BCC, RESP, and the recently suggested xAvESP (which average ESP charges over a number of molecular dynamics snapshots). Furthermore, both the generalised Born and Poisson-Boltzmann solvation models were used in the MM/GBSA calculations. The two solvation models perform equally well in predicting relative affinities, and hence there is no point in using the more expensive Poisson-Boltzmann model for these systems. Both the LIE and MM/GBSA estimates are shown to be robust with respect to the charge model, and therefore it is recommended to use the cheapest AM1-BCC charges. Using AM1-BCC charges, the MM/GBSA method gave a MADtr (mean absolute deviation after removal of systematic error) of 17 kJ/mol and a correlation coefficient (r (2)) of 0.67 for the CB8 complexes, and a MADtr of 10 kJ/mol and an r (2) of 0.96 for the α-CD complexes. The LIE method gave a MADtr of 20 kJ/mol and an r (2) of 0.10 for the CB8 complexes, after optimisation of the non-polar scaling parameter. For the α-CD complexes, no optimisation was necessary and the method gave a MADtr of 2 kJ/mol and a r (2) of 0.96. These results indicate that both MM/GBSA and LIE are able to estimate host-guest affinities accurately.
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22.
  • Genheden, Samuel, et al. (författare)
  • Nonpolar Solvation Free Energies of Protein-Ligand Complexes
  • 2010
  • Ingår i: Journal of Chemical Theory and Computation. - : American Chemical Society (ACS). - 1549-9618 .- 1549-9626. ; 6:11, s. 3558-3568
  • Tidskriftsartikel (refereegranskat)abstract
    • Recent investigations have indicated that different solvation methods give qualitatively different results for the nonpolar solvation contribution to ligand-binding affinities. Therefore, we have calculated the nonpolar solvation contribution to the free energy of benzene binding to the T4 lysozyme Leu99Ala mutant using thermodynamic integration (TI) and three approximate methods. The total binding free energy was calculated with TI and then decomposed into contributions from the solvent and the solute. The nonpolar contribution from the solute was compared to approximate methods within the framework of the molecular-mechanics and generalized Born with surface area method (MM/GBSA). First, the nonpolar solvation energy was calculated with a linear relation to the solvent-accessible surface area (SASA). Second, a recent approach that divides the nonpolar solvation energy into cavity and dispersion parts was used, and third, the nonpolar solvation energy was calculated with the polarized continuum model (PCM). Surprisingly, the simple SASA estimate reproduces the TI results best. However, the reason for this is that all continuum methods assume that the benzene cavity is filled with water for the free protein, contrary to both experimental and simulation results. We present a method to avoid this assumption and then, PCM provides results that are closest to the results obtained with TI.
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23.
  • Genheden, Samuel, et al. (författare)
  • Of mice and men: Dissecting the interaction between Listeria monocytogenes Internalin A and murine vs human E-Cadherin
  • 2013
  • Ingår i: Computational and Structural Biotechnology Journal. - : Elsevier BV. - 2001-0370. ; 6:7, s. 1-13
  • Tidskriftsartikel (refereegranskat)abstract
    • We report a study of the interaction between internalin A (inlA) and human or murine E-cadherin (Ecad). inlA is used by Listeria monocytogenes to internalize itself into host cell, but the bacterium is unable to invade murine cells, which has been attributed to the difference in sequence between hEcad and mEcad. Using molecular dynamics simulations, MM/GBSA free energy calculations, hydrogen bond analysis, water characterization and umbrella sampling, we provide a complete atomistic picture of the binding between inlA and Ecad. We dissect key residues in the protein–protein interface and analyze the energetics using MM/GBSA. From this analysis it is clear that the binding of inlA–mEcad is weaker than inlA–hEcad, on par with the experimentally observed inability of inlA to bind to mEcad. However, extended MD simulations of 200 ns in length show no destabilization of the inlA–mEcad complex and the estimation of the potential of mean force (PMF) using umbrella sampling corroborates this conclusion. The binding strength computed from the PMFs show no significant difference between the two protein complexes. Hence, our study suggests that the inability of L. monocytogenes to invade murine cells cannot be explained by processes at the nanosecond to sub-microsecond time scale probed by the simulations performed here.
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24.
  • Genheden, Samuel (författare)
  • On the estimation of ligand binding affinities
  • 2012
  • Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
    • A method to accurately estimate the binding affinity of a small molecule to a receptor would be indispensable in numerous fields. For instance, most drugs exert their action by binding to a macromolecule target. Thus, a lot of time and resources could be saved in drug design by predicting affinities by computer programs. In a series of 15 papers, we have tested, compared, and improved the most popular methods to estimate binding affinities. We have used for instance molecular mechanics with generalized Born and surface area solvation (MM/GBSA), linear interaction energy (LIE), and alchemical perturbation methods. Some of the topics covered are: * How the precision of MM/GBSA estimates are affected by the simulation protocol * If semiempirical quantum-mechanical methods can improve affinity estimates * A comparison of different polar solvation methods in MM/GBSA * If non-polar solvation methods can model different degrees of active-site hydration * How to obtain normal-mode entropies accurately and efficiently * What method is more efficient: LIE or MM/GBSA * A comparison of several end-point continuum-solvation methods * What charge model to use in simulations of host–guest complexes * The performance of end-point methods in a binding-affinity blind test * How we can make alchemical methods more useful for drug design * If a single-reference state can be used to simulate several ligands * What properties calculated from molecular dynamics simulations do converge Together, these studies clearly show what methods to use and what methods to avoid. We conclude that approximate methods are not very accurate and the results are highly system dependent. On the other hand, using alchemical methods, affinity differences between similar ligands can be accurately estimated both quickly and with a high precision.
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25.
  • Genheden, Samuel (författare)
  • Predicting Partition Coefficients with a Simple All-Atom/Coarse-Grained Hybrid Model
  • 2016
  • Ingår i: Journal of Chemical Theory and Computation. - : American Chemical Society (ACS). - 1549-9618 .- 1549-9626. ; 12:1, s. 297-304
  • Tidskriftsartikel (refereegranskat)abstract
    • The solvation free energy is an essential quantity in force field development and in numerous applications. Here, we present the estimation of solvation free energies in polar (water, hexanol, octanol, and nonanol) and in apolar (hexane, octane, and nonane) media. The estimates are produced using molecular dynamics simulations employing a simple all-atom/coarse-grained hybrid model (AA/ELBA) and are therefore very efficient. More than 150 solutes were taken from the Minnesota solvation database and represent small, organic molecules. The mean absolute deviation for the different solvents ranges between 2.0 and 4.1 kJ/mol, and the correlation coefficient ranges between 0.78 and 0.99, indicating that the predictions are accurate. Outliers are identified, and potential avenues for improvements are discussed. Furthermore, partition coefficients between water and the organic solvents were estimated, and the percentage of the predictions that has the correct sign ranges between 74% (for octane) and 92% (for octanol and hexanol). Finally, membrane/water partition coefficients are replaced with hexane/water and octanol/water partition coefficients, and the latter is found to be as accurate as the expensive membrane calculations, indicating a wider application area.
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26.
  • Genheden, Samuel, et al. (författare)
  • Prediction of the Chemical Context for Buchwald-Hartwig Coupling Reactions
  • 2022
  • Ingår i: Molecular Informatics. - : Wiley. - 1868-1751 .- 1868-1743. ; 41:8
  • Tidskriftsartikel (refereegranskat)abstract
    • We present machine learning models for predicting the chemical context for Buchwald-Hartwig coupling reactions, i. e., what chemicals to add to the reactants to give a productive reaction. Using reaction data from in-house electronic lab notebooks, we train two models: one based on single-label data and one based on multi-label data. Both models show excellent top-3 accuracy of approximately 90 %, which suggests strong predictivity. Furthermore, there seems to be an advantage of including multi-label data because the multi-label model shows higher accuracy and better sensitivity for the individual contexts than the single-label model. Although the models are performant, we also show that such models need to be re-trained periodically as there is a strong temporal characteristic to the usage of different contexts. Therefore, a model trained on historical data will decrease in usefulness with time as newer and better contexts emerge and replace older ones. We hypothesize that such significant transitions in the context-usage will likely affect any model predicting chemical contexts trained on historical data. Consequently, training context prediction models warrants careful planning of what data is used for training and how often the model needs to be re-trained.
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27.
  • Genheden, Samuel (författare)
  • Solvation free energies and partition coefficients with the coarse-grained and hybrid all-atom/coarse-grained MARTINI models
  • 2017
  • Ingår i: Journal of Computer-Aided Molecular Design. - : Springer Science and Business Media LLC. - 0920-654X .- 1573-4951. ; 31:10, s. 867-876
  • Tidskriftsartikel (refereegranskat)abstract
    • We present the estimation of solvation free energies of small solutes in water, n-octanol and hexane using molecular dynamics simulations with two MARTINI models at different resolutions, viz. the coarse-grained (CG) and the hybrid all-atom/coarse-grained (AA/CG) models. From these estimates, we also calculate the water/hexane and water/octanol partition coefficients. More than 150 small, organic molecules were selected from the Minnesota solvation database and parameterized in a semi-automatic fashion. Using either the CG or hybrid AA/CG models, we find considerable deviations between the estimated and experimental solvation free energies in all solvents with mean absolute deviations larger than 10 kJ/mol, although the correlation coefficient is between 0.55 and 0.75 and significant. There is also no difference between the results when using the non-polarizable and polarizable water model, although we identify some improvements when using the polarizable model with the AA/CG solutes. In contrast to the estimated solvation energies, the estimated partition coefficients are generally excellent with both the CG and hybrid AA/CG models, giving mean absolute deviations between 0.67 and 0.90 log units and correlation coefficients larger than 0.85. We analyze the error distribution further and suggest avenues for improvements.
  •  
28.
  • Genheden, Samuel, et al. (författare)
  • Starting-Condition Dependence of Order Parameters Derived from Molecular Dynamics Simulations
  • 2010
  • Ingår i: Journal of Chemical Theory and Computation. - : American Chemical Society (ACS). - 1549-9618 .- 1549-9626. ; 6:7, s. 2176-2190
  • Tidskriftsartikel (refereegranskat)abstract
    • We have studied how backbone N-H S-2 order parameters calculated from molecular dynamics simulations depend on the method used to calculate them, the starting conditions, and the length of the simulations. Using the carbohydrate binding domain of galectin-3 in the free and lactose-bound states as a test case, we compared the calculated order parameters with experimental data from NMR relaxation. The results indicate that the sampling can be improved by using several starting structures, taking into account conformational heterogeneity reported in crystal structures. However, the improvement is rather limited, and for 93% of the dihedrals that have alternative conformations in the crystal structures, the conformational space is well sampled even if a single conformation is used as the starting structure. Moreover, the agreement with experimental data is improved when using several short simulations, rather than a single long simulation. In the present case, we find that similar to 10 independent simulations provide sufficient sampling, and the ideal length of the simulations is similar to 10 ns, which is similar to 25% longer than the global correlation time for rotational diffusion. On the other hand, the equilibration time appears to be less important, and our results suggest that an equilibration time of 0.25 ns is sufficient. We have also compared four different methods to extract the order parameters from the simulations, namely, the autocorrelation function and isotropic reorientational eigenmode dynamics using three different window sizes. Overall, the four methods yield comparable results, but large differences between the methods may serve to pinpoint cases for which the calculated parameters are unreliable.
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29.
  • Genheden, Samuel, et al. (författare)
  • The MM/PBSA and MM/GBSA methods to estimate ligand-binding affinities
  • 2015
  • Ingår i: Expert Opinion on Drug Discovery. - : Informa Healthcare. - 1746-0441 .- 1746-045X. ; 10:5, s. 449-461
  • Forskningsöversikt (refereegranskat)abstract
    • Introduction: The molecular mechanics energies combined with the Poisson-Boltzmann or generalized Born and surface area continuum solvation (MM/PBSA and MM/GBSA) methods are popular approaches to estimate the free energy of the binding of small ligands to biological macromolecules. They are typically based on molecular dynamics simulations of the receptor-ligand complex and are therefore intermediate in both accuracy and computational effort between empirical scoring and strict alchemical perturbation methods. They have been applied to a large number of systems with varying success. Areas covered: The authors review the use of MM/PBSA and MM/GBSA methods to calculate ligand-binding affinities, with an emphasis on calibration, testing and validation, as well as attempts to improve the methods, rather than on specific applications. Expert opinion: MM/PBSA and MM/GBSA are attractive approaches owing to their modular nature and that they do not require calculations on a training set. They have been used successfully to reproduce and rationalize experimental findings and to improve the results of virtual screening and docking. However, they contain several crude and questionable approximations, for example, the lack of conformational entropy and information about the number and free energy of water molecules in the binding site. Moreover, there are many variants of the method and their performance varies strongly with the tested system. Likewise, most attempts to ameliorate the methods with more accurate approaches, for example, quantum-mechanical calculations, polarizable force fields or improved solvation have deteriorated the results.
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30.
  • Genheden, Samuel, et al. (författare)
  • The Normal-Mode Entropy in the MM/GBSA Method: Effect of System Truncation, Buffer Region, and Dielectric Constant
  • 2012
  • Ingår i: Journal of Chemical Information and Modeling. - : American Chemical Society (ACS). - 1549-960X .- 1549-9596. ; 52:8, s. 2079-2088
  • Tidskriftsartikel (refereegranskat)abstract
    • We have performed a systematic study of the entropy term in the MM/GBSA (molecular Mechanics combined with generalized Born and surface area solvation) approach to calculate ligand-binding affinities The entropies are calculated by a normal mode analysis of harmonic frequencies from minimized snapshots of molecular dynamics simulations. For computational reasons, these calculations have normally been performed on truncated systems. We have studied the binding of eight inhibitors of blood clotting factor Xa, nine ligands of ferritin, and two ligands of HIV-1 protease and show that removing protein residues with. distances. larger than 8-16 angstrom to the ligand, including a 4 angstrom shell of fixed protein residues and water molecules, change the absolute entropies by 1-5 kJ/mol on average. However, the change is systematic, so relative entropies for different ligands change by only 0.7-1.6 kJ/mol on average. Consequently, entropies from truncated systems give relative binding affinities that are identical to those obtained for the Whole protein within statistical uncertainty (172 kJ/mol). We have also tested to use a distance dependent dielectric constant in the minimization and. frequency calculation (epsilon = 4r), but it typically gives slightly different entropies and poorer binding, affinities. Therefore, we recommend entropies calculated with the smallest truncation radius (8 angstrom) and epsilon =1 Such an approach also gives an improved precision for the calculated binding free energies.
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31.
  • Genheden, Samuel, et al. (författare)
  • Transferability of conformational dependent charges from protein simulations
  • 2012
  • Ingår i: International Journal of Quantum Chemistry. - : Wiley. - 0020-7608. ; 112:7, s. 1768-1785
  • Tidskriftsartikel (refereegranskat)abstract
    • We have studied the transferability of atomic charges for proteins, fitted to the quantum mechanical electrostatic potential and extensively averaged over a set of structures sampled by molecular dynamics (MD) and over all residues of the same kind in the protein sequence (xAvESP). Previously, such charges were obtained for one single protein (avidin). In this study, we use five additional proteins. The aim of this study is fourfold. First, we provide xAvESP charges for all amino acids, including amino- and carboxy-terminal variants of all, as well as alternative protonation states of His, Asp, Glu, Lys, Arg, Cys, and Tyr. Second, we show that the xAvESP charges averaged over the five new proteins are similar to charges obtained in the same way for avidin, with a correlation coefficient of 0.997. This shows that the charges are transferable and system-independent. Electrostatic proteinligand interaction energies calculated with charges obtained from different proteins differ by only 13 kJ/mol on average. The xAvESP charges correlate rather well with Amber charges (except for the N atom of amino-terminal residues that are erroneous in Amber), although they are obtained in a more general way. Third, the conformational dependence of the charges is significant and gives rise to quite large differences in energies. However, these differences are to a large extent screened by solvation effects. For example, the solvent-screened electrostatic interaction energy between the protein galectin-3 and five different ligands varies with the charge sets by less than 3 kJ/mol on average. Finally, we show that the xAvESP charges give a comparable root-mean-squared deviation as the Amber charges for the MD simulations of 18 proteinligand complexes, they give comparable or slightly worse backbone N?H order parameters for two galectin-3 complexes, but they give a better correlation between calculated and experimental affinities for the binding of seven biotin analogues to avidin and for nine inhibitors of factor Xa. (c) 2011 Wiley Periodicals, Inc. Int J Quantum Chem 112:17681785, 2012
  •  
32.
  • Genheden, Samuel, et al. (författare)
  • Will molecular dynamics simulations of proteins ever reach equilibrium?
  • 2012
  • Ingår i: Physical chemistry chemical physics : PCCP. - : Royal Society of Chemistry (RSC). - 1463-9084 .- 1463-9076. ; 14:24, s. 8662-8677
  • Tidskriftsartikel (refereegranskat)abstract
    • We show that conformational entropies calculated for five proteins and protein-ligand complexes with dihedral-distribution histogramming, the von Mises approach, or quasi-harmonic analysis do not converge to any useful precision even if molecular dynamics (MD) simulations of 380-500 ns length are employed (the uncertainty is 12-89 kJ mol(-1)). To explain this, we suggest a simple protein model involving dihedrals with effective barriers forming a uniform distribution and show that for such a model, the entropy increases logarithmically with time until all significantly populated dihedral states have been sampled, in agreement with the simulations (during the simulations, 52-70% of the available dihedral phase space has been visited). This is also confirmed by the analysis of the trajectories of a 1 ms simulation of bovine pancreatic trypsin inhibitor (31 kJ mol(-1) difference in the entropy between the first and second part of the simulation). Strictly speaking, this means that it is practically impossible to equilibrate MD simulations of proteins. We discuss the implications of such a lack of strict equilibration of protein MD simulations and show that ligand-binding free energies estimated with the MM/GBSA method (molecular mechanics with generalised Born and surface-area solvation) vary by 3-15 kJ mol(-1) during a 500 ns simulation (the higher estimate is caused by rare conformational changes), although they involve a questionable but well-converged normal-mode entropy estimate, whereas free energies estimated by free-energy perturbation vary by less than 0.6 kJ mol(-1) for the same simulation.
  •  
33.
  • Godschalk, Frithjof, et al. (författare)
  • Comparison of MM/GBSA calculations based on explicit and implicit solvent simulations.
  • 2013
  • Ingår i: Physical Chemistry Chemical Physics. - : Royal Society of Chemistry (RSC). - 1463-9084 .- 1463-9076. ; 15:20, s. 7731-7739
  • Tidskriftsartikel (refereegranskat)abstract
    • Molecular mechanics with generalised Born and surface area solvation (MM/GBSA) is a popular method to calculate the free energy of the binding of ligands to proteins. It involves molecular dynamics (MD) simulations with an explicit solvent of the protein-ligand complex to give a set of snapshots for which energies are calculated with an implicit solvent. This change in the solvation method (explicit → implicit) would strictly require that the energies are reweighted with the implicit-solvent energies, which is normally not done. In this paper we calculate MM/GBSA energies with two generalised Born models for snapshots generated by the same methods or by explicit-solvent simulations for five synthetic N-acetyllactosamine derivatives binding to galectin-3. We show that the resulting energies are very different both in absolute and relative terms, showing that the change in the solvent model is far from innocent and that standard MM/GBSA is not a consistent method. The ensembles generated with the various solvent models are quite different with root-mean-square deviations of 1.2-1.4 Å. The ensembles can be converted to each other by performing short MD simulations with the new method, but the convergence is slow, showing mean absolute differences in the calculated energies of 6-7 kJ mol(-1) after 2 ps simulations. Minimisations show even slower convergence and there are strong indications that the energies obtained from minimised structures are different from those obtained by MD.
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34.
  • Irani, Mehdi, et al. (författare)
  • Amino Acid Oxidation of Candida antarctica Lipase B Studied by Molecular Dynamics Simulations and Site-Directed Mutagenesis
  • 2013
  • Ingår i: Biochemistry. - : American Chemical Society (ACS). - 0006-2960 .- 1520-4995. ; 52:7, s. 1280-1289
  • Tidskriftsartikel (refereegranskat)abstract
    • Molecular dynamics simulations have been performed on lipase B from Candida antarctica (CalB) in its native form and with one or two oxidized residues, either methionine oxidized to methionine sulfoxide, tryptophan oxidized to 5-hydroxytryptophan, or cystine oxidized to a pair of cysteic acid residues. We have analyzed how these oxidations affect the general structure of the protein as well as the local structure around the oxidized amino acid and the active site. The results indicate that the methionine and tryptophan oxidations led to rather restricted changes in the structure, whereas the oxidation of cystines, which also caused cleavage of the cystine S-S linkage, gave rise to larger changes in the protein structure. Only two oxidized residues caused significant changes in the structure of the active site, viz., those of the Cys-22/64 and Cys-216/258 pairs. Site-directed mutagenesis studies were also performed. Two variants showed a behavior similar to that of native CalB,(M83I and M129L), whereas W155Q and M72S had severely decreased specific activity. M83I had a slightly higher thermostability than native CalB. No significant increase in stability toward hydrogen peroxide was observed. The same mutants were also studied by molecular dynamics. Even though no significant increase in stability toward hydrogen peroxide was observed, the results from simulations and site-directed mutagenesis give some clues about the direction of further work on stabilization.
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35.
  • Kadhirvel, Saraboji, et al. (författare)
  • The Carbohydrate-Binding Site in Galectin-3 Is Preorganized To Recognize a Sugarlike Framework of Oxygens: Ultra-High-Resolution Structures and Water Dynamics
  • 2012
  • Ingår i: Biochemistry. - : American Chemical Society (ACS). - 0006-2960 .- 1520-4995. ; 51:1, s. 296-306
  • Tidskriftsartikel (refereegranskat)abstract
    • The recognition of carbohydrates by proteins is a fundamental aspect of communication within and between living cells. Understanding the molecular basis of carbohydrate-protein interactions is a prerequisite for the rational design of synthetic ligands. Here we report the high- to ultrahigh-resolution crystal structures of the carbohydrate recognition domain of galectin-3 (Gal3C) in the ligand-free state (1.08 angstrom at 100 K, 1.25 angstrom at 298 K) and in complex with lactose (0.86 angstrom) or glycerol (0.9 angstrom). These structures reveal striking similarities in the positions of water and carbohydrate oxygen atoms in all three states, indicating that the binding site of Gal3C is preorganized to coordinate oxygen atoms in an arrangement that is nearly optimal for the recognition of beta-galactosides. Deuterium nuclear magnetic resonance (NMR) relaxation dispersion experiments and molecular dynamics simulations demonstrate that all water molecules in the lactose-binding site exchange with bulk water on a time scale of nanoseconds or shorter. Nevertheless, molecular dynamics simulations identify transient water binding at sites that agree well with those observed by crystallography, indicating that the energy landscape of the binding site is maintained in solution. All heavy atoms of glycerol are positioned like the corresponding atoms of lactose in the Gal3C complexes. However, binding of glycerol to Gal3C is insignificant in solution at room temperature, as monitored by NMR spectroscopy or isothermal titration calorimetry under conditions where lactose binding is readily detected. These observations make a case for protein cryo-crystallography as a valuable screening method in fragment-based drug discovery and further suggest that identification of water sites might inform inhibitor design.
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36.
  • Lindahl, Lina, 1984, et al. (författare)
  • Alcohols enhance the rate of acetic acid diffusion in S. cerevisiae: biophysical mechanisms and implications for acetic acid tolerance
  • 2018
  • Ingår i: Microbial Cell. - : Shared Science Publishers OG. - 2311-2638. ; 5:1, s. 42-55
  • Tidskriftsartikel (refereegranskat)abstract
    • Microbial cell factories with the ability to maintain high productivity in the presence of weak organic acids, such as acetic acid, are required in many industrial processes. For example, fermentation media derived from lignocellulosic biomass are rich in acetic acid and other weak acids. The rate of diffusional entry of acetic acid is one parameter determining the ability of microorganisms to tolerance the acid. The present study demonstrates that the rate of acetic acid diffusion in S. cerevisiae is strongly affected by the alcohols ethanol and n-butanol. Ethanol of 40 g/L and n-butanol of 8 g/L both caused a 65% increase in the rate of acetic acid diffusion, and higher alcohol concentrations caused even greater increases. Molecular dynamics simulations of membrane dynamics in the presence of alcohols demonstrated that the partitioning of alcohols to the head group region of the lipid bilayer causes a considerable increase in the membrane area, together with reduced membrane thickness and lipid order. These changes in physiochemical membrane properties lead to an increased number of water molecules in the membrane interior, providing biophysical mechanisms for the alcohol-induced increase in acetic acid diffusion rate. nbutanol affected S. cerevisiae and the cell membrane properties at lower concentrations than ethanol, due to greater and deeper partitioning in the membrane. This study demonstrates that the rate of acetic acid diffusion can be strongly affected by compounds that partition into the cell membrane, and highlights the need for considering interaction effects between compounds in the design of microbial processes.
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37.
  • Lindahl, Lina, 1984, et al. (författare)
  • Membrane engineering for reduced acetic acid stress: insights from Zygosaccharomyces bailii
  • 2015
  • Ingår i: Oral presentation at 12th Yeast Lipid Conference, May 20-22 2015, Ghent, Belgium.
  • Konferensbidrag (övrigt vetenskapligt/konstnärligt)abstract
    • The high concentration of acetic acid released during pretreatment of lignocellulose raw material is a major obstacle to the microbial production of bio-based products. Acetic acid enters the cell mainly by passive diffusion across the plasma membrane and inhibits yeast by mechanisms such as reduction of intracellular pH, accumulation of the acetate anion, and by signaling effects triggering cell death. Through extensive characterization of the acetic acid tolerant yeast Zygosaccharomyces bailii, we have identified the cell membrane as a target for strain engineering with potential to increase acetic acid tolerance in Saccharomyces cerevisiae. We propose membrane permeability as a key component for Z. bailii’s acetic acid tolerance. We have previously shown that Z. bailii has a unique ability to remodel its plasma membrane upon acetic acid stress, to strongly increase its fraction of complex sphingolipids, at the expense of a drastic reduction of glycerophospholipids1. Here we further demonstrate the involvement of complex sphingolipids in acetic acid tolerance by decreasing sphingolipid synthesis using the drug myriocin, and characterize the acetic acid tolerance in terms of growth and intracellular pH. Furthermore we show the impact of complex sphingolipids on membrane physical properties using in silico membrane simulations. Ongoing membrane engineering of S. cerevisiae can potentially give additional strength to our findings. References 1 Lindberg et al. (2013), Lipidomic Profiling of Saccharomyces cerevisiae and Zygosaccharomyces bailii Reveals Critical Changes in Lipid Composition in Response to Acetic Acid Stress, PLoS One 8: e73936.
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38.
  • Lindahl, Lina, 1984, et al. (författare)
  • Sphingolipids contribute to acetic acid resistance in Zygosaccharomyces bailii
  • 2016
  • Ingår i: Biotechnology and Bioengineering. - : Wiley. - 0006-3592 .- 1097-0290. ; 113:4, s. 744-753
  • Tidskriftsartikel (refereegranskat)abstract
    • Lignocellulosic raw material plays a crucial role in the development of sustainable processes for the production of fuels and chemicals. Weak acids such as acetic acid and formic acid are troublesome inhibitors restricting efficient microbial conversion of the biomass to desired products. To improve our understanding of weak acid inhibition, and to identify engineering strategies to reduce acetic acid toxicity, the highly acetic-acid-tolerant yeast Zygosaccharomyces bailii was studied. The impact of acetic acid membrane permeability on acetic acid tolerance in Z. bailii was investigated with particular focus on how the previously demonstrated high sphingolipid content in the plasma membrane influences acetic acid tolerance and membrane permeability. Through molecular dynamics simulations we concluded that membranes with a high content of sphingolipids are thicker and more dense, increasing the free energy barrier for the permeation of acetic acid through the membrane. Z. bailii cultured with the drug myriocin, known to decrease cellular sphingolipid levels, exhibited significant growth inhibition in the presence of acetic acid, while growth in medium without acetic acid was unaffected by the myriocin addition. Furthermore, following an acetic acid pulse, the intracellular pH decreased more in myriocin-treated cells than in control cells. This indicates a higher inflow rate of acetic acid, and confirms that the reduction in growth of cells cultured with myriocin in the medium with acetic acid, was due to an increase in membrane permeability, thereby demonstrating the importance of a high fraction of sphingolipids in the membrane of Z. bailii to facilitate acetic acid resistance; a property potentially transferable to desired production organisms suffering from weak acid stress
  •  
39.
  • Lindahl, Lina, 1984, et al. (författare)
  • THE INFLUENCE OF MEMBRANE COMPOSTION ON ACETIC ACID PERMEABILITY AND POTENTIALLY ACETIC ACID TOLERANCE
  • 2014
  • Ingår i: ISSY31: 31st International Specialised Symposium on Yeast.
  • Annan publikation (övrigt vetenskapligt/konstnärligt)abstract
    • Compounds entering the cell do so either by passive diffusion over the plasma membrane or through transporters in the membrane. The specific lipid composition of the plasma membrane influences both the passive diffusion rate but also the activity of membrane proteins. Acetic acid, a major hurdle in fermentation processes using lignocellulosic material, is believed to pass through the membrane in its protonated from mainly by passive diffusion [1]. Sterols and sphingolipids are lipid classes thought to contribute to membrane rigidity. Sterols are often found to be involved in stress resistance [2, 3] and in our previous work sphingolipids were pointed at as an important constituent of the plasma membrane of the yeast Zygosaccharomyces bailii, known to be very tolerant to acetic acid, suggesting a possible link between acetic acid tolerance and sphingolipid relative abundance in the membrane [4]. Here we will provide supporting evidence of the importance of sphingolipids and sterols in acetic acid membrane permeability. We have combined biochemistry techniques with in silico membrane modeling to answer the question how membrane engineering can be used to decrease acetic acid membrane permeability. [1] Verduyn et al. Yeast (1992) 501-517. [2] Alexandre et al. FEMS Microbiology Letters (1994) 124:17-22. [3] Liu et al. Journal of Applied Microbiology (2013) 114:482-491. [4] Lindberg et al. PlosONE (2003) 8(9): e73936.
  •  
40.
  • Maertens, Jeroen, 1990, et al. (författare)
  • Molecular-dynamics-simulation-guided membrane engineering allows the increase of membrane fatty acid chain length in Saccharomyces cerevisiae
  • 2021
  • Ingår i: Scientific Reports. - : Springer Science and Business Media LLC. - 2045-2322. ; 11:1
  • Tidskriftsartikel (refereegranskat)abstract
    • The use of lignocellulosic-based fermentation media will be a necessary part of the transition to a circular bio-economy. These media contain many inhibitors to microbial growth, including acetic acid. Under industrially relevant conditions, acetic acid enters the cell predominantly through passive diffusion across the plasma membrane. The lipid composition of the membrane determines the rate of uptake of acetic acid, and thicker, more rigid membranes impede passive diffusion. We hypothesized that the elongation of glycerophospholipid fatty acids would lead to thicker and more rigid membranes, reducing the influx of acetic acid. Molecular dynamics simulations were used to predict the changes in membrane properties. Heterologous expression of Arabidopsis thaliana genes fatty acid elongase 1 (FAE1) and glycerol-3-phosphate acyltransferase 5 (GPAT5) increased the average fatty acid chain length. However, this did not lead to a reduction in the net uptake rate of acetic acid. Despite successful strain engineering, the net uptake rate of acetic acid did not decrease. We suggest that changes in the relative abundance of certain membrane lipid headgroups could mitigate the effect of longer fatty acid chains, resulting in a higher net uptake rate of acetic acid.
  •  
41.
  • Manzoni, Francesco, et al. (författare)
  • Can System Truncation Speed up Ligand-Binding Calculations with Periodic Free-Energy Simulations?
  • 2017
  • Ingår i: Journal of Chemical Information and Modeling. - : American Chemical Society (ACS). - 1549-9596 .- 1520-5142 .- 1549-960X. ; 57, s. 2865-2873
  • Tidskriftsartikel (refereegranskat)abstract
    • We have investigated whether alchemical free-energy perturbation calculations of relative binding energies can be sped up by simulating a truncated protein. Previous studies with spherical nonperiodic systems showed that the number of simulated atoms could be reduced by a factor of 26 without affecting the calculated binding free energies by more than 0.5 kJ/mol on average (Genheden, S.; Ryde, U. J. Chem. Theory Comput. 2012, 8, 1449), leading to a 63-fold decrease in the time consumption. However, such simulations are rather slow, owing to the need of a large cutoff radius for the nonbonded interactions. Periodic simulations with the electrostatics treated by Ewald summation are much faster. Therefore, we have investigated if a similar speed-up can be obtained also for periodic simulations. Unfortunately, our results show that it is harder to truncate periodic systems and that the truncation errors are larger for these systems. In particular, residues need to be removed from the calculations, which means that atoms have to be restrained to avoid that they move in an unrealistic manner. The results strongly depend on the strength on this restraint. For the binding of seven ligands to dihydrofolate reductase and ten inhibitors of blood-clotting factor Xa, the best results are obtained with a small restraining force constant. However, the truncation errors were still significant (e.g., 1.5-2.9 kJ/mol at a truncation radius of 10 Å). Moreover, the gain in computer time was only modest. On the other hand, if the snapshots are truncated after the MD simulations, the truncation errors are small (below 0.9 kJ/mol even for a truncation radius of 10 Å). This indicates that postprocessing with a more accurate energy function (e.g., with quantum chemistry) on truncated snapshots may be a viable approach.
  •  
42.
  • Mikulskis, Paulius, et al. (författare)
  • A Large-Scale Test of Free-Energy Simulation Estimates of Protein-Ligand Binding Affinities.
  • 2014
  • Ingår i: Journal of Chemical Information and Modeling. - : American Chemical Society (ACS). - 1549-960X .- 1549-9596. ; 54:10, s. 2794-2806
  • Tidskriftsartikel (refereegranskat)abstract
    • We have performed a large-scale test of alchemical perturbation calculations with the Bennett acceptance-ratio (BAR) approach to estimate relative affinities for the binding of 107 ligands to 10 different proteins. Employing 20-Å truncated spherical systems and only one intermediate state in the perturbations, we obtain an error of less than 4 kJ/mol for 54% of the studied relative affinities and a precision of 0.5 kJ/mol on average. However, only four of the proteins gave acceptable errors, correlations, and rankings. The results could be improved by using nine intermediate states in the simulations or including the entire protein in the simulations using periodic boundary conditions. However, 27 of the calculated affinities still gave errors of more than 4 kJ/mol, and for three of the proteins the results were not satisfactory. This shows that the performance of BAR calculations depends on the target protein and that several transformations gave poor results owing to limitations in the molecular-mechanics force field or the restricted sampling possible within a reasonable simulation time. Still, the BAR results are better than docking calculations for most of the proteins.
  •  
43.
  • Mikulskis, Paulius, et al. (författare)
  • A semiempirical approach to ligand-binding affinities: Dependence on the Hamiltonian and corrections.
  • 2012
  • Ingår i: Journal of Computational Chemistry. - : Wiley. - 1096-987X .- 0192-8651. ; 33:12, s. 1179-1189
  • Tidskriftsartikel (refereegranskat)abstract
    • We present a combination of semiempirical quantum-mechanical (SQM) calculations in the conductor-like screening model with the MM/GBSA (molecular-mechanics with generalized Born and surface-area solvation) method for ligand-binding affinity calculations. We test three SQM Hamiltonians, AM1, RM1, and PM6, as well as hydrogen-bond corrections and two different dispersion corrections. As test cases, we use the binding of seven biotin analogues to avidin, nine inhibitors to factor Xa, and nine phenol-derivatives to ferritin. The results vary somewhat for the three test cases, but a dispersion correction is mandatory to reproduce experimental estimates. On average, AM1 with the DH2 hydrogen-bond and dispersion corrections gives the best results, which are similar to those of standard MM/GBSA calculations for the same systems. The total time consumption is only 1.3-1.6 times larger than for MM/GBSA. © 2012 Wiley Periodicals, Inc.
  •  
44.
  • Mikulskis, Paulius, et al. (författare)
  • Binding affinities in the SAMPL3 trypsin and host-guest blind tests estimated with the MM/PBSA and LIE methods.
  • 2012
  • Ingår i: Journal of Computer-Aided Molecular Design. - : Springer Science and Business Media LLC. - 1573-4951 .- 0920-654X. ; 26:5, s. 527-541
  • Tidskriftsartikel (refereegranskat)abstract
    • We have estimated affinities for the binding of 34 ligands to trypsin and nine guest molecules to three different hosts in the SAMPL3 blind challenge, using the MM/PBSA, MM/GBSA, LIE, continuum LIE, and Glide score methods. For the trypsin challenge, none of the methods were able to accurately predict the experimental results. For the MM/GB(PB)SA and LIE methods, the rankings were essentially random and the mean absolute deviations were much worse than a null hypothesis giving the same affinity to all ligand. Glide scoring gave a Kendall's τ index better than random, but the ranking is still only mediocre, τ = 0.2. However, the range of affinities is small and most of the pairs of ligands have an experimental affinity difference that is not statistically significant. Removing those pairs improves the ranking metric to 0.4-1.0 for all methods except CLIE. Half of the trypsin ligands were non-binders according to the binding assay. The LIE methods could not separate the inactive ligands from the active ones better than a random guess, whereas MM/GBSA and MM/PBSA were slightly better than random (area under the receiver-operating-characteristic curve, AUC = 0.65-0.68), and Glide scoring was even better (AUC = 0.79). For the first host, MM/GBSA and MM/PBSA reproduce the experimental ranking fairly good, with τ = 0.6 and 0.5, respectively, whereas the Glide scoring was considerably worse, with a τ = 0.4, highlighting that the success of the methods is system-dependent.
  •  
45.
  • Mikulskis, Paulius, et al. (författare)
  • Effect of explicit water molecules on ligand-binding affinities calculated with the MM/GBSA approach.
  • 2014
  • Ingår i: Journal of Molecular Modeling. - : Springer Science and Business Media LLC. - 1610-2940 .- 0948-5023. ; 20:6, s. 2273-2273
  • Tidskriftsartikel (refereegranskat)abstract
    • We tested different approaches to including the effect of binding-site water molecules for ligand-binding affinities within the MM/GBSA approach (molecular mechanics combined with generalised Born and surface-area solvation). As a test case, we studied the binding of nine phenol analogues to ferritin. The effect of water molecules mediating the interaction between the receptor and the ligand can be studied by considering a few water molecules as a part of the receptor. We extended previous methods by allowing for a variable number of water molecules in the binding site. The effect of displaced water molecules can also be considered within the MM/GBSA philosophy by calculating the affinities of binding-site water molecules, both before and after binding of the ligand. To obtain proper energies, both the water molecules and the ligand need then to be converted to non-interacting ghost molecules and a single-average approach (i.e., the same structures are used for bound and unbound states) based on the simulations of both the complex and the free receptor can be used to improve the precision. The only problem is to estimate the free energy of an unbound water molecule. With an experimental estimate of this parameter, promising results were obtained for our test case.
  •  
46.
  • Mikulskis, Paulius, et al. (författare)
  • Free-energy perturbation and quantum mechanical study of SAMPL4 octa-acid host-guest binding energies.
  • 2014
  • Ingår i: Journal of Computer-Aided Molecular Design. - : Springer Science and Business Media LLC. - 1573-4951 .- 0920-654X. ; 28:4, s. 375-400
  • Tidskriftsartikel (refereegranskat)abstract
    • We have estimated free energies for the binding of nine cyclic carboxylate guest molecules to the octa-acid host in the SAMPL4 blind-test challenge with four different approaches. First, we used standard free-energy perturbation calculations of relative binding affinities, performed at the molecular-mechanics (MM) level with TIP3P waters, the GAFF force field, and two different sets of charges for the host and the guest, obtained either with the restrained electrostatic potential or AM1-BCC methods. Both charge sets give good and nearly identical results, with a mean absolute deviation (MAD) of 4 kJ/mol and a correlation coefficient (R (2)) of 0.8 compared to experimental results. Second, we tried to improve these predictions with 28,800 density-functional theory (DFT) calculations for selected snapshots and the non-Boltzmann Bennett acceptance-ratio method, but this led to much worse results, probably because of a too large difference between the MM and DFT potential-energy functions. Third, we tried to calculate absolute affinities using minimised DFT structures. This gave intermediate-quality results with MADs of 5-9 kJ/mol and R (2) = 0.6-0.8, depending on how the structures were obtained. Finally, we tried to improve these results using local coupled-cluster calculations with single and double excitations, and non-iterative perturbative treatment of triple excitations (LCCSD(T0)), employing the polarisable multipole interactions with supermolecular pairs approach. Unfortunately, this only degraded the predictions, probably because of a mismatch between the solvation energies obtained at the DFT and LCCSD(T0) levels.
  •  
47.
  • Olsson, Christoffer, 1987, et al. (författare)
  • Mechanism of Trehalose-Induced Protein Stabilization from Neutron Scattering and Modeling
  • 2019
  • Ingår i: Journal of Physical Chemistry B. - : American Chemical Society (ACS). - 1520-5207 .- 1520-6106. ; 123:17, s. 3679-3687
  • Tidskriftsartikel (refereegranskat)abstract
    • The sugar molecule trehalose has been proven to be an excellent stabilizing cosolute for the preservation of biological materials. However, the stabilizing mechanism of trehalose has been much debated during the previous decades, and it is still not fully understood, partly because it has not been completely established how trehalose molecules structure around proteins. Here, we present a molecular model of a protein-water-trehalose system, based on neutron scattering results obtained from neutron diffraction, quasielastic neutron scattering, and different computer modeling techniques. The structural data clearly show how the proteins are preferentially hydrated, and analysis of the dynamical properties show that the protein residues are slowed down because of reduced dynamics of the protein hydration shell, rather than because of direct trehalose-protein interactions. These findings, thereby, strongly support previous models related to the preferential hydration model and contradict other models based on water replacement at the protein surface. Furthermore, the results are important for understanding the specific role of trehalose in biological stabilization and, more generally, for providing a likely mechanism of how cosolutes affect the dynamics of proteins.
  •  
48.
  • Söderhjelm, Pär, et al. (författare)
  • Estimates of ligand-binding affinities supported by quantum mechanical methods.
  • 2010
  • Ingår i: Interdisciplinary sciences, computational life sciences. - : Springer Science and Business Media LLC. - 1913-2751 .- 1867-1462. ; 2:1, s. 21-37
  • Tidskriftsartikel (refereegranskat)abstract
    • In this paper, we review our efforts to use quantum mechanical (QM) methods to improve free-energy estimates of the binding of drug candidates to their receptor proteins. First, we have tested the influence of various implicit solvation models on predictions of the ligand-binding affinity. The accuracy of implicit solvation models strongly depend on the parameterisation, but also on the magnitude of the solvation energy (i.e. their accuracy should be discussed in relative terms). However, if only relative solvation energies within a series of similar drug molecules with the same net charge are considered, nearly all methods tested give a comparable accuracy of 2-5 kJ/mol. Second, we have studied the conformational dependence of QM charges and their influence on ligand-binding affinities. The conformational dependence is significant, but it is to a large extent cancelled by solvation energies. Third, we have estimated the effect and range of electrostatic interactions beyond a point-charge model. The results show that multipoles up to octupoles and anisotropic polarisabilities have a significant influence on energies for residues up to 10-15 A from the ligand and that different sets of point-charge models may give strongly varying results. However, if only relative energies are considered, the effect is to a large extent cancelled. Fourth, we have tried to develop an accurate QM-based molecular mechanics potential, in which not only the electrostatic terms are improved, but also the dispersion and repulsion. However, even with quite sophisticated expressions, it seems difficult to reduce the average error below 2-3 kJ/mol per interaction (e.g. a hydrogen bond), compared to the full QM treatment. Finally, we have developed a new method, PMISP (polarised multipole interaction with supermolecular pairs), for the calculation of accurate interaction energies. It employs an accurate force field for electrostatics and induction, including multipoles up to octupoles and anisotropic polarisabilities calculated by QM methods on amino-acid fragments of the protein in each conformation observed in snapshots from a molecular dynamics simulation, whereas short-range interactions are estimated by high-level QM calculations for all pairs of the ligand with near-by residues. We show that this approach allows us to go far beyond the current accuracy of molecular mechanics methods, down to an error of 5-10 kJ/mol for a full protein-ligand complex. It can be combined with estimates of solvation, entropy, and dynamic effects to give estimates of binding affinities. However, several problems remain to be solved before any significant improvement in the accuracy can be seen.
  •  
49.
  • Söderhjelm, Pär, et al. (författare)
  • Quantum mechanics in structure-based ligand design
  • 2012
  • Ingår i: Protein-ligand interactions. - Weinheim, Germany : Wiley-VCH Verlag GmbH & Co. KGaA. - 9783527329663 - 9783527645947 ; 53, s. 121-143
  • Bokkapitel (refereegranskat)
  •  
50.
  • Uranga, Jon, et al. (författare)
  • Can the protonation state of histidine residues be determined from molecular dynamics simulations?
  • 2012
  • Ingår i: Computational and Theoretical Chemistry. - : Elsevier BV. - 2210-2728 .- 2210-271X. ; 1000, s. 75-84
  • Tidskriftsartikel (refereegranskat)abstract
    • Histidine (His) residues in proteins can attain three different protonation states at normal pH. This constitutes a prominent problem when adding protons to a protein crystal structure, e.g. in order to perform molecular simulations. Typically, the His protonation is deduced from the hydrogen-bond pattern in crystal structures. Here, we study whether it is possible to detect erroneous His protonation state by analysing short molecular dynamics (MD) trajectories. We systematically vary the His protonation state and measure the root-mean-squared deviation (RMSD) of the His residues and nearby residues relative to the starting structure, as well as the distribution of the dihedral angle that determines the rotation of the His side chain. We study three proteins, hisactophilin with 31 solvent-exposed His residues, galectin-3, for which an experimental assignment is available for two of the His residues, and trypsin, for which the hydrogen-bond analysis is quite conclusive. The results show that improper protonation states have larger RMSD values and larger widths of the dihedral distribution, compared to the correct protonation states. Unfortunately, the variation among different His residues in the same and different proteins is so large that it is hard to define unambiguous thresholds between proper and improper protonation states. Therefore, simulations of all three protonation states are needed for conclusive results. For trypsin, we could obtain a conclusive assignment for all three His residues, which was better than the simple hydrogen-bond analysis. For galectin-3, the MD trajectories confirmed the results of hydrogen-bond analysis and experiments. They also gave additional, more uncertain information for some of the residues. However, for the solvent-exposed His residues in hisactophilin, no unambiguous conclusions regarding the protonation states could be reached. On the other hand, this indicates that protein structures are quite insensitive to the protonation state of the His residues, besides those that involve direct hydrogen bonds to the His side chain. (C) 2012 Elsevier B.V. All rights reserved.
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