| 1. |
- Bettiga, Maurizio, 1978, et al.
(författare)
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Plasma membrane as a crucial player in acetic acid effect on yeast
- 2017
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Ingår i: IMYA12- 12th International Meeting on Yeast Apoptosis, Bari, Italy • 14-18 May 2017.
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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. |
- Genheden, Samuel, et al.
(författare)
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All-atom/coarse-grained hybrid predictions of distribution coefficients in SAMPL5
- 2016
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Ingår i: Journal of Computer-Aided Molecular Design. - : Springer Science and Business Media LLC. - 0920-654X .- 1573-4951. ; 30:11, s. 969-976
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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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| 3. |
- Genheden, Samuel, et al.
(författare)
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Binding affinities by alchemical perturbation using QM/MM with a large QM system and polarizable MM model.
- 2015
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Ingår i: Journal of Computational Chemistry. - : Wiley. - 1096-987X .- 0192-8651. ; 36:28, s. 2114-2124
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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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| 4. |
- Genheden, Samuel
(författare)
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Coarse-grained bond and angle distributions from atomistic simulations: On the systematic parameterisation of lipid models
- 2016
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Ingår i: Journal of Molecular Graphics and Modelling. - : Elsevier BV. - 1093-3263. ; 63, s. 57-64
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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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| 5. |
- Genheden, Samuel, et al.
(författare)
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Computational Chemistry and Molecular Modelling Basics
- 2017
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Ingår i: Computational Tools for Chemical Biology. - : The Royal Society of Chemistry. - 9781782627005 - 9781788012560
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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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| 6. |
- Genheden, Samuel
(författare)
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Effect of solvent model when probing protein dynamics with molecular dynamics
- 2017
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Ingår i: Journal of Molecular Graphics and Modelling. - : Elsevier BV. - 1093-3263 .- 1873-4243. ; 71, s. 80-87
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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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| 7. |
- Genheden, Samuel, et al.
(författare)
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Estimation of Liposome Penetration Barriers of Drug Molecules with All-Atom and Coarse-Grained Models
- 2016
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Ingår i: Journal of Chemical Theory and Computation. - : American Chemical Society (ACS). - 1549-9618 .- 1549-9626. ; 12:9, s. 4651-4661
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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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| 8. |
- Genheden, Samuel
(författare)
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Predicting Partition Coefficients with a Simple All-Atom/Coarse-Grained Hybrid Model
- 2016
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Ingår i: Journal of Chemical Theory and Computation. - : American Chemical Society (ACS). - 1549-9618 .- 1549-9626. ; 12:1, s. 297-304
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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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| 9. |
- Genheden, Samuel
(författare)
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Solvation free energies and partition coefficients with the coarse-grained and hybrid all-atom/coarse-grained MARTINI models
- 2017
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Ingår i: Journal of Computer-Aided Molecular Design. - : Springer Science and Business Media LLC. - 0920-654X .- 1573-4951. ; 31:10, s. 867-876
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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.
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| 10. |
- Genheden, Samuel, et al.
(författare)
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The MM/PBSA and MM/GBSA methods to estimate ligand-binding affinities
- 2015
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Ingår i: Expert Opinion on Drug Discovery. - : Informa Healthcare. - 1746-0441 .- 1746-045X. ; 10:5, s. 449-461
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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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