| 1. |
- Asgari, Parham, et al.
(författare)
-
Catalytic hydrogen atom transfer from hydrosilanes to vinylarenes for hydrosilylation and polymerization
- 2019
-
Ingår i: Nature Catalysis. - : Nature Publishing Group. - 2520-1158. ; 2:2, s. 164-173
-
Tidskriftsartikel (refereegranskat)abstract
- Because of the importance of hydrogen atom transfer (HAT) in biology and chemistry, there is increased interest in new strategies to perform HAT in a sustainable manner. Here, we describe a sustainable, net redox-neutral HAT process involving hydrosilanes and alkali metal Lewis base catalysts-eliminating the use of transition metal catalysts-and report an associated mechanism concerning Lewis base-catalysed, complexation-induced HAT. The catalytic Lewis base-catalysed, complexation-induced HAT is capable of accessing both branch-specific hydrosilylation and polymerization of vinylarenes in a highly selective fashion, depending on the Lewis base catalyst used. In this process, the Earth-abundant, alkali metal Lewis base catalyst plays a dual role. It first serves as a HAT initiator and subsequently functions as a silyl radical stabilizing group, which is critical to highly selective cross-radical coupling. An electron paramagnetic resonance study identified a potassiated paramagnetic species, and multistate density functional theory revealed a high HAT character, yet multiconfigurational nature in the transition state of the reaction.
|
|
| 2. |
- Das, Susanta, et al.
(författare)
-
Rapid Convergence of Energy and Free Energy Profiles with Quantum Mechanical Size in Quantum Mechanical–Molecular Mechanical Simulations of Proton Transfer in DNA
- 2018
-
Ingår i: Journal of Chemical Theory and Computation. - : American Chemical Society (ACS). - 1549-9618 .- 1549-9626. ; 14:3, s. 1695-1705
-
Tidskriftsartikel (refereegranskat)abstract
- In recent years, a number of quantum mechanical-molecular mechanical (QM/MM) enzyme studies have investigated the dependence of reaction energetics on the size of the QM region using energy and free energy calculations. In this study, we revisit the question of QM region size dependence in QM/MM simulations within the context of energy and free energy calculations using a proton transfer in a DNA base pair as a test case. In the simulations, the QM region was treated with a dispersion-corrected AM1/d-PhoT Hamiltonian, which was developed to accurately describe phosphoryl and proton transfer reactions, in conjunction with an electrostatic embedding scheme using the particle-mesh Ewald summation method. With this rigorous QM/MM potential, we performed rather extensive QM/MM sampling, and found that the free energy reaction profiles converge rapidly with respect to the QM region size within ca. +/- 1 kcal/mol. This finding suggests that the strategy of QM/MM simulations with reasonably sized and selected QM regions, which has been employed for over four decades, is a valid approach for modeling complex biomolecular systems. We point to possible causes for the sensitivity of the energy and free energy calculations to the size of the QM region, and potential implications.
|
|
| 3. |
- Doron, Dvir, et al.
(författare)
-
How Accurate Are Transition States from Simulations of Enzymatic Reactions?
- 2014
-
Ingår i: Journal of Chemical Theory and Computation. - : American Chemical Society (ACS). - 1549-9618 .- 1549-9626. ; 10:5, s. 1863-1871
-
Tidskriftsartikel (refereegranskat)abstract
- The rate expression of traditional transition state theory (TST) assumes no recrossing of the transition state (TS) and thermal quasi-equilibrium between the ground state and the TS. Currently, it is not well understood to what extent these assumptions influence the nature of the activated complex obtained in traditional TST-based simulations of processes in the condensed phase in general and in enzymes in particular. Here we scrutinize these assumptions by characterizing the TSs for hydride transfer catalyzed by the enzyme Escherichia coli dihydrofolate reductase obtained using various simulation approaches. Specifically, we compare the TSs obtained with common TST-based methods and a dynamics-based method. Using a recently developed accurate hybrid quantum mechanics/molecular mechanics potential, we find that the TST-based and dynamics-based methods give considerably different TS ensembles. This discrepancy, which could be due equilibrium solvation effects and the nature of the reaction coordinate employed and its motion, raises major questions about how to interpret the TSs determined by common simulation methods. We conclude that further investigation is needed to characterize the impact of various TST assumptions on the TS phase-space ensemble and on the reaction kinetics.
|
|
| 4. |
- Dulko-Smith, Beata, et al.
(författare)
-
Mechanistic basis for a connection between the catalytic step and slow opening dynamics of adenylate kinase
- 2023
-
Ingår i: Journal of Chemical Information and Modeling. - : American Chemical Society (ACS). - 1549-9596 .- 1549-960X. ; 63:5, s. 1556-1569
-
Tidskriftsartikel (refereegranskat)abstract
- Escherichia coli adenylate kinase (AdK) is a small, monomeric enzyme that synchronizes the catalytic step with the enzyme’s conformational dynamics to optimize a phosphoryl transfer reaction and the subsequent release of the product. Guided by experimental measurements of low catalytic activity in seven single-point mutation AdK variants (K13Q, R36A, R88A, R123A, R156K, R167A, and D158A), we utilized classical mechanical simulations to probe mutant dynamics linked to product release, and quantum mechanical and molecular mechanical calculations to compute a free energy barrier for the catalytic event. The goal was to establish a mechanistic connection between the two activities. Our calculations of the free energy barriers in AdK variants were in line with those from experiments, and conformational dynamics consistently demonstrated an enhanced tendency toward enzyme opening. This indicates that the catalytic residues in the wild-type AdK serve a dual role in this enzyme’s function─one to lower the energy barrier for the phosphoryl transfer reaction and another to delay enzyme opening, maintaining it in a catalytically active, closed conformation for long enough to enable the subsequent chemical step. Our study also discovers that while each catalytic residue individually contributes to facilitating the catalysis, R36, R123, R156, R167, and D158 are organized in a tightly coordinated interaction network and collectively modulate AdK’s conformational transitions. Unlike the existing notion of product release being rate-limiting, our results suggest a mechanistic interconnection between the chemical step and the enzyme’s conformational dynamics acting as the bottleneck of the catalytic process. Our results also suggest that the enzyme’s active site has evolved to optimize the chemical reaction step while slowing down the overall opening dynamics of the enzyme.
|
|
| 5. |
- Huang, Yang, 1985-, et al.
(författare)
-
The water R1(ω) NMRD profiles of a hydrated protein from molecular dynamics simulation
- 2013
-
Ingår i: Physical Chemistry, Chemical Physics - PCCP. - : RSC Publishing. - 1463-9076 .- 1463-9084. ; 15:33, s. 14089-14097
-
Tidskriftsartikel (refereegranskat)abstract
- The hydration of a protein, peroxiredoxin 5, is obtained from a molecular dynamics simulation and compared with the picture of hydration which is obtained by analysing the water proton R1 NMRD profiles using a generally accepted relaxation model [K. Venu, V.P. Denisov and B. Halle, J. Am. Chem. Soc. 119,3122(1997)]. The discrepancy between the hydration pictures derived from the water R1(ω 0)-NMRD profiles and MD is relevant in a discussion of the factors behind the stretched NMRD profile, the distribution of orientationalorder parameters and residence times of buried water used in the NMRD model.
|
|
| 6. |
- Koag, Myong-Chul, et al.
(författare)
-
The spontaneous replication error and the mismatch discrimination mechanisms of human DNA polymerase beta
- 2014
-
Ingår i: Nucleic Acids Research. - : Oxford University Press (OUP). - 0305-1048 .- 1362-4962. ; 42:17, s. 11233-11245
-
Tidskriftsartikel (refereegranskat)abstract
- To provide molecular-level insights into the spontaneous replication error and the mismatch discrimination mechanisms of human DNA polymerase beta (pol beta), we report four crystal structures of pol beta complexed with dG.dTTP and dA.dCTP mismatches in the presence of Mg2+ or Mn2+. The Mg2+-bound ground-state structures show that the dA.dCTP-Mg2+ complex adopts an 'intermediate' protein conformation while the dG.dTTP-Mg2+ complex adopts an open protein conformation. The Mn2+-bound 'pre-chemistry-state' structures show that the dA.dCTP-Mn2+ complex is structurally very similar to the dA.dCTP-Mg2+ complex, whereas the dG.dTTP-Mn2+ complex undergoes a large-scale conformational change to adopt a Watson-Crick-like dG.dTTP base pair and a closed protein conformation. These structural differences, together with our molecular dynamics simulation studies, suggest that pol beta increases replication fidelity via a two-stage mismatch discrimination mechanism, where one is in the ground state and the other in the closed conformation state. In the closed conformation state, pol beta appears to allow only a Watson-Crick-like conformation for purine.pyrimidine base pairs, thereby discriminating the mismatched base pairs based on their ability to form the Watson-Crick-like conformation. Overall, the present studies provide new insights into the spontaneous replication error and the replication fidelity mechanisms of pol beta.
|
|
| 7. |
- Li, Yaozong, et al.
(författare)
-
Dynamic, structural and thermodynamic basis of insulin-like growth factor 1 kinase allostery mediated by activation loop phosphorylation
- 2017
-
Ingår i: Chemical Science. - : Royal Society of Chemistry (RSC). - 2041-6539 .- 2041-6520. ; 8:5, s. 3453-3464
-
Tidskriftsartikel (refereegranskat)abstract
- Despite the importance of kinases' catalytic activity regulation in cell signaling, detailed mechanisms underlying their activity regulation are poorly understood. Herein, using insulin-like growth factor 1 receptor kinase (IGF-1RK) as a model, the mechanisms of kinase regulation by its activation loop (A-loop) phosphorylation were investigated through molecular dynamics (MD) and alchemical free energy simulations. Analyses of the simulation results and free energy landscapes determined for the entire catalytic cycle of the kinase revealed that A-loop phosphorylation affects each step in the IGF-1RK catalytic cycle, including conformational change, substrate binding/product release and catalytic phosphoryl transfer. Specifically, the conformational equilibrium of the kinase is shifted by 13.2 kcal mol−1 to favor the active conformation after A-loop phosphorylation, which increases substrate binding affinity of the activated kinase. This free energy shift is achieved primarily viadestabilization of the inactive conformation. The free energy of the catalytic reaction is also changed by 3.3 kcal mol−1 after the phosphorylation and in the end, facilitates product release. Analyses of MD simulations showed that A-loop phosphorylation produces these energetic effects by perturbing the side chain interactions around each A-loop tyrosine. These interaction changes are propagated to the remainder of the kinase to modify the orientations and dynamics of the αC-helix and A-loop, and together yield the observed free energy changes. Since many protein kinases share similar interactions identified in this work, the mechanisms of kinase allostery and catalysis unraveled here can be applicable to them.
|
|
| 8. |
|
|
| 9. |
- Li, Yaozong, et al.
(författare)
-
Repulsive Soft-Core Potentials for Efficient Alchemical Free Energy Calculations
- 2020
-
Ingår i: Journal of Chemical Theory and Computation. - : American Chemical Society (ACS). - 1549-9618 .- 1549-9626. ; 16:8, s. 4776-4789
-
Tidskriftsartikel (refereegranskat)abstract
- In alchemical free energy (FE) simulations, annihilation and creation of atoms are generally achieved with the soft-core potential that shifts the interparticle separations. While this soft-core potential eliminates the numerical instability occurring near the two end states of the transformation, it makes the hybrid Hamiltonian vary nonlinearly with respect to the parameter λ, which interpolates between the Hamiltonians representing the two end states. This complicates FE estimation by Bennett acceptance ratio (BAR), free energy perturbation (FEP), and thermodynamic integration (TI) methods, thus reducing their calculation efficiency. In this work, we develop a new type of repulsive soft-core potential, called Gaussian soft-core (GSC) potential, with two parameters controlling its maximum and width. The main advantage of this potential is the linearity of the hybrid Hamiltonian with respect to λ, thus permitting the direct application of BAR, FEP, TI, and other variant FE methods. The accuracy and efficiency of the GSC potential are demonstrated by comparing the free energies of annihilation determined for 13 small molecules and an alchemical mutation of a protein side chain. In addition, in combination with a TI integrand (∂H/∂λ) estimation strategy, we show that GSC can considerably reduce the number of λ simulations compared to the commonly used separation-shifted soft-core potential.
|
|
| 10. |
- Li, Yaozong, 1982-
(författare)
-
Understanding molecular mechanisms of protein tyrosine kinases by molecular dynamics and free energy calculations
- 2017
-
Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- Background: Insulin receptor kinase (IRK) and Insulin-like growth factor 1 receptor kinase (IGF-1RK) are two important members in the large class of tyrosine kinase receptors. They play pivotalroles in the regulation of glucose homeostasis, cell proliferation, differentiation, motility, andtransformation. Their dysfunctions are linked to diabetes, rheumatoid arthritis and many cancers.Although their regulatory mechanisms have been widely studied experimentally, the atomisticdetails are still poorly understood, especially for the influences caused by activation loop (A-loop)phosphorylation.Methods: Molecular dynamics (MD) and alchemical free energy simulations are carried out tounderstand mechanisms underlying the kinase proteins regulation and their thermodynamic basis.To capture a full picture about the entire kinase catalytic cycle, different functional steps areconsidered, i.e., conformational transition, substrate binding, phosphoryl transfer and productrelease. The effects of the A-loop phosphorylation on protein’s dynamics, structure, stability, andfree energy landscape are examined by various analysis methods, including principle componentanalysis (PCA), motion projection, dynamical network analysis and free energy perturbation.Results: The main findings are: 1) A-loop phosphorylation shifts the kinase conformationalpopulation to the active one by changing the electrostatic environments in the kinase apo form, 2)allosterically fine-tunes the orientation of the catalytic residues mediated by the >C-helix in thereactant and product binding states, and 3) thermodynamically favors the kinase catalysis presentedby a catalytic-cycle-mimic free energy landscape. An integrated view on the roles of A-loopphosphorylation in kinase allostery is developed by incorporating kinase’s dynamics, structuralinteractions, thermodynamics and free energy landscape. In addition, new soft-core potentials(Gaussian soft-core) and protocols are developed to conduct accurate and efficient alchemical freeenergy calculations.Conclusions: The entire catalytic cycle is examined by MD and free energy calculations andcomprehensive analyses are conducted. The findings from the studied kinases are general and canbe implemented to the other members in IRK family or even to more non-homologous familiesbecause of the conservation of the characteristic residues between their A-loop and >C-helix. Inaddition, the Gaussian soft-core potentials provide a new tool to perform alchemical free energycalculations in an efficient way.
|
|
| 11. |
|
|
| 12. |
- Liem-Nguyen, Van, et al.
(författare)
-
Thermodynamic stability of mercury(II) complexes formed with environmentally relevant low-molecular-mass thiols studied by competing ligand exchange and density functional theory
- 2017
-
Ingår i: Environmental Chemistry. - : CSIRO PUBLISHING. - 1448-2517 .- 1449-8979. ; 14:4, s. 243-253
-
Tidskriftsartikel (refereegranskat)abstract
- Inorganic divalent mercury (Hg-II) has a very high affinity for reduced sulfur functional groups. Reports from laboratory experiments suggest that Hg-II complexes with specific low-molecular-mass (LMM) thiol (RSH) ligands control rates of Hg-II transformation reactions. Because of methodological limitations for precise determination of the highly stable Hg-II complexes with LMM thiol ligands, constants reported in the literature remain inconsistent. This uncertainty impedes accurate modelling of the chemical speciation of Hg-II and the possibility to elucidate the role of Hg-II complexes with LMM thiols for Hg transformation reactions. Here, we report values of thermodynamic stability constants for 15 monodentate, two-coordinated Hg-II complexes, Hg(SR)(2), formed with biogeochemically relevant LMM thiol ligands. The constants were determined by a two-step ligand-exchange procedure where the specific Hg(SR)(2) complexes were quantified by liquid chromatography-inductively coupled plasma mass spectrometry. Thermodynamic stability constants (log (2)) determined for the Hg(SR)(2) complexes ranged from 34.6, N-cysteinylglycine, to 42.1, 3-mercaptopropionic acid, for the general reaction Hg2++2RS(-) Hg(SR)(2). Density functional theory (DFT) calculations showed that electron-donating carboxyl and carbonyl groups have a stabilising effect on the Hg-II-LMM thiol complexes, whereas electron-withdrawing protonated primary amino groups have a destabilising effect. Experimental results and DFT calculations demonstrated that the presence of such functional groups in the vicinity of the RSH group caused significant differences in the stability of Hg(SR)(2) complexes. These differences are expected to be important for the chemical speciation of Hg-II and its transformation reactions in environments where a multitude of LMM thiol compounds are present.
|
|
| 13. |
- Mishra, Yogesh, et al.
(författare)
-
Active-site plasticity revealed in the asymmetric dimer of AnPrx6 the 1-Cys peroxiredoxin and molecular chaperone from Anabaena sp. PCC 7120
- 2017
-
Ingår i: Scientific Reports. - : Nature Publishing Group. - 2045-2322. ; 7
-
Tidskriftsartikel (refereegranskat)abstract
- Peroxiredoxins (Prxs) are vital regulators of intracellular reactive oxygen species levels in all living organisms. Their activity depends on one or two catalytically active cysteine residues, the peroxidatic Cys (C-P) and, if present, the resolving Cys (C-R). A detailed catalytic cycle has been derived for typical 2-Cys Prxs, however, little is known about the catalytic cycle of 1-Cys Prxs. We have characterized Prx6 from the cyanobacterium Anabaena sp. strain PCC7120 (AnPrx6) and found that in addition to the expected peroxidase activity, AnPrx6 can act as a molecular chaperone in its dimeric state, contrary to other Prxs. The AnPrx6 crystal structure at 2.3 angstrom resolution reveals different active site conformations in each monomer of the asymmetric obligate homo-dimer. Molecular dynamic simulations support the observed structural plasticity. A FSH motif, conserved in 1-Cys Prxs, precedes the active site PxxxTxxCp signature and might contribute to the 1-Cys Prx reaction cycle.
|
|
| 14. |
- Nam, Kwangho
(författare)
-
Acceleration of Ab Initio QM/MM Calculations under Periodic Boundary Conditions by Multiscale and Multiple Time Step Approaches
- 2014
-
Ingår i: Journal of Chemical Theory and Computation. - : American Chemical Society (ACS). - 1549-9618 .- 1549-9626. ; 10:10, s. 4175-4183
-
Tidskriftsartikel (refereegranskat)abstract
- Development of multiscale ab initio quantum mechanical and molecular mechanical (AI-QM/MM) method for periodic boundary molecular dynamics (MD) simulations and their acceleration by multiple time step approach are described. The developed method achieves accuracy and efficiency by integrating the AI-QM/MM level of theory and the previously developed semiempirical (SE) QM/MM-Ewald sum method [J. Chem. Theory Comput. 2005, 1, 2] extended to the smooth particle-mesh Ewald (PME) summation method. In the developed methods, the total energy of the simulated system is evaluated at the SE-QM/MM-PME level of theory to include long-range QM/MM electrostatic interactions, which is then corrected on the fly using the AI-QM/MM level of theory within the real space cutoff. The resulting energy expression enables decomposition of total forces applied to each atom into forces determined at the low-level SE-QM/MM method and correction forces at the AI-QM/MM level, to integrate the system using the reversible reference system propagator algorithm. The resulting method achieves a substantial speed-up of the entire calculation by minimizing the number of time-consuming energy and gradient evaluations at the AI-QM/MM level. Test calculations show that the developed multiple time step AI-QM/MM method yields MD trajectories and potential of mean force profiles comparable to single time step QM/MM results. The developed method, together with message passing interface (MPI) parallelization, accelerates the present AI-QM/MM MD simulations about 30-fold relative to the speed of single-core AI-QM/MM simulations for the molecular systems tested in the present work, making the method less than one order slower than the SE-QM/MM methods under periodic boundary conditions.
|
|
| 15. |
- Nam, Kwangho
(författare)
-
Acceleration of Semiempirical Quantum Mechanical Calculations by Extended Lagrangian Molecular Dynamics Approach
- 2013
-
Ingår i: Journal of Chemical Theory and Computation. - : American Chemical Society (ACS). - 1549-9618 .- 1549-9626. ; 9:8, s. 3393-3403
-
Tidskriftsartikel (refereegranskat)abstract
- The implementation and performance of the atom-centered density matrix propagation (ADMP) [J. Chem. Phys. 2001, 114, 9758] and the curvy-steps (CURV) methods [J. Chem. Phys. 2004, 121, 1152] are described. These methods solve the electronic Schrodinger equation approximately by propagating the electronic degrees of freedom using the extended Lagrangian molecular dynamics (ELMD) simulation approach. The ADMP and CURV methods are implemented and parallelized to accelerate semiempirical quantum mechanical (QM) methods (such as the MNDO, AM1, PM3, MNDO/d, and AM1/d methods). Test calculations show that both the ADMP and the CURV methods are 2 similar to 4 times faster than the Born-Oppenheimer molecular dynamics (BOMD) method and conserve the total energy well. The accuracy of the ADMP and CURV simulations is comparable to the BOMD simulations. The parallel implementation accelerates the MD simulation by up to 28 fold for the ADMP method and 25 fold for the CURV method, respectively, relative to the speed of the single core BOMD. In addition, a multiple time scale (MTS) approach is introduced to further speed up the semiempirical QM and QM/MM ELMD simulations. Since a larger integration time step is used for the propagation of the nuclear coordinates than that for the electronic degrees of freedom, the MTS approach allows the ELMD simulation to be carried out with a time step that is larger than the time step accessible by the original ADMP and CURV methods. It renders MD simulation to be carried out about 20 times faster than the BOMD simulation, and yields results that are comparable to the single time scale simulation results. The use of the methods introduced in the present work provides an efficient way to extend the length of the QM and QM/MM molecular dynamics simulations beyond the length accessible by BOMD simulation.
|
|
| 16. |
|
|
| 17. |
- Nam, Kwangho, et al.
(författare)
-
Elucidating dynamics of Adenylate kinase from enzyme opening to ligand release
- 2024
-
Ingår i: Journal of Chemical Information and Modeling. - : American Chemical Society (ACS). - 1549-9596 .- 1549-960X. ; 64:1, s. 150-163
-
Tidskriftsartikel (refereegranskat)abstract
- This study explores ligand-driven conformational changes in adenylate kinase (AK), which is known for its open-to-close conformational transitions upon ligand binding and release. By utilizing string free energy simulations, we determine the free energy profiles for both enzyme opening and ligand release and compare them with profiles from the apoenzyme. Results reveal a three-step ligand release process, which initiates with the opening of the adenosine triphosphate-binding subdomain (ATP lid), followed by ligand release and concomitant opening of the adenosine monophosphate-binding subdomain (AMP lid). The ligands then transition to nonspecific positions before complete dissociation. In these processes, the first step is energetically driven by ATP lid opening, whereas the second step is driven by ATP release. In contrast, the AMP lid opening and its ligand release make minor contributions to the total free energy for enzyme opening. Regarding the ligand binding mechanism, our results suggest that AMP lid closure occurs via an induced-fit mechanism triggered by AMP binding, whereas ATP lid closure follows conformational selection. This difference in the closure mechanisms provides an explanation with implications for the debate on ligand-driven conformational changes of AK. Additionally, we determine an X-ray structure of an AK variant that exhibits significant rearrangements in the stacking of catalytic arginines, explaining its reduced catalytic activity. In the context of apoenzyme opening, the sequence of events is different. Here, the AMP lid opens first while the ATP lid remains closed, and the free energy associated with ATP lid opening varies with orientation, aligning with the reported AK opening and closing rate heterogeneity. Finally, this study, in conjunction with our previous research, provides a comprehensive view of the intricate interplay between various structural elements, ligands, and catalytic residues that collectively contribute to the robust catalytic power of the enzyme.
|
|
| 18. |
- Nam, Kwangho, et al.
(författare)
-
Insights into the origin of the high energy-conversion efficiency of F-1-ATPase
- 2019
-
Ingår i: Proceedings of the National Academy of Sciences of the United States of America. - : NATL ACAD SCIENCES. - 0027-8424 .- 1091-6490. ; 116:32, s. 15924-15929
-
Tidskriftsartikel (refereegranskat)abstract
- Our understanding of the rotary-coupling mechanism of F-1-ATPase has been greatly enhanced in the last decade by advances in X-ray crystallography, single-molecular imaging, and theoretical models. Recently, Volkan-Kacso and Marcus [S. Volkan-Kacso, R. A. Marcus, Proc. Natl. Acad. Sci. U.S.A. 112, 14230 (2015)] presented an insightful thermodynamic model based on the Marcus reaction theory coupled with an elastic structural deformation term to explain the observed gamma-rotation angle dependence of the adenosine triphosphate (ATP)/ adenosine diphosphate (ADP) exchange rates of F-1-ATPase. Although the model is successful in correlating single-molecule data, it is not in agreement with the available theoretical results. We describe a revision of the model, which leads to consistency with the simulation results and other experimental data on the F-1-ATPase rotor compliance. Although the free energy liberated on ATP hydrolysis by F-1-ATPase is rapidly dissipated as heat and so cannot contribute directly to the rotation, we show how, nevertheless, F-1-ATPase functions near the maximum possible efficiency. This surprising result is a consequence of the differential binding of ATP and its hydrolysis products ADP and P-i along a well-defined pathway.
|
|
| 19. |
|
|
| 20. |
- Nam, Kwangho, et al.
(författare)
-
Perspectives on computational enzyme modeling : from mechanisms to design and drug development
- 2024
-
Ingår i: ACS Omega. - : American Chemical Society (ACS). - 2470-1343. ; 9:7, s. 7393-7412
-
Forskningsöversikt (refereegranskat)abstract
- Understanding enzyme mechanisms is essential for unraveling the complex molecular machinery of life. In this review, we survey the field of computational enzymology, highlighting key principles governing enzyme mechanisms and discussing ongoing challenges and promising advances. Over the years, computer simulations have become indispensable in the study of enzyme mechanisms, with the integration of experimental and computational exploration now established as a holistic approach to gain deep insights into enzymatic catalysis. Numerous studies have demonstrated the power of computer simulations in characterizing reaction pathways, transition states, substrate selectivity, product distribution, and dynamic conformational changes for various enzymes. Nevertheless, significant challenges remain in investigating the mechanisms of complex multistep reactions, large-scale conformational changes, and allosteric regulation. Beyond mechanistic studies, computational enzyme modeling has emerged as an essential tool for computer-aided enzyme design and the rational discovery of covalent drugs for targeted therapies. Overall, enzyme design/engineering and covalent drug development can greatly benefit from our understanding of the detailed mechanisms of enzymes, such as protein dynamics, entropy contributions, and allostery, as revealed by computational studies. Such a convergence of different research approaches is expected to continue, creating synergies in enzyme research. This review, by outlining the ever-expanding field of enzyme research, aims to provide guidance for future research directions and facilitate new developments in this important and evolving field.
|
|
| 21. |
- Nam, Kwangho, et al.
(författare)
-
Protein dynamics : the future is bright and complicated!
- 2023
-
Ingår i: Structural Dynamics. - : American Crystallographic Association. - 2329-7778. ; 10:1
-
Tidskriftsartikel (refereegranskat)abstract
- Biological life depends on motion, and this manifests itself in proteins that display motion over a formidable range of time scales spanning from femtoseconds vibrations of atoms at enzymatic transition states, all the way to slow domain motions occurring on micro to milliseconds. An outstanding challenge in contemporary biophysics and structural biology is a quantitative understanding of the linkages among protein structure, dynamics, and function. These linkages are becoming increasingly explorable due to conceptual and methodological advances. In this Perspective article, we will point toward future directions of the field of protein dynamics with an emphasis on enzymes. Research questions in the field are becoming increasingly complex such as the mechanistic understanding of high-order interaction networks in allosteric signal propagation through a protein matrix, or the connection between local and collective motions. In analogy to the solution to the "protein folding problem,"we argue that the way forward to understanding these and other important questions lies in the successful integration of experiment and computation, while utilizing the present rapid expansion of sequence and structure space. Looking forward, the future is bright, and we are in a period where we are on the doorstep to, at least in part, comprehend the importance of dynamics for biological function.
|
|
| 22. |
- Nam, Kwangho, et al.
(författare)
-
Trapping the ATP binding state leads to a detailed understanding of the F-1-ATPase mechanism
- 2014
-
Ingår i: Proceedings of the National Academy of Sciences of the United States of America. - : Proceedings of the National Academy of Sciences. - 0027-8424 .- 1091-6490. ; 111:50, s. 17851-17856
-
Tidskriftsartikel (refereegranskat)abstract
- The rotary motor enzyme FoF1-ATP synthase uses the protonmotive force across a membrane to synthesize ATP from ADP and P-i (H2PO4-) under cellular conditions that favor the hydrolysis reaction by a factor of 2 x 10(5). This remarkable ability to drive a reaction away from equilibrium by harnessing an external force differentiates it from an ordinary enzyme, which increases the rate of reaction without shifting the equilibrium. Hydrolysis takes place in the neighborhood of one conformation of the catalytic moiety F-1-ATPase, whose structure is known from crystallography. By use of molecular dynamics simulations we trap a second structure, which is rotated by 40 degrees from the catalytic dwell conformation and represents the state associated with ATP binding, in accord with single-molecule experiments. Using the two structures, we show why Pi is not released immediately after ATP hydrolysis, but only after a subsequent 120 degrees rotation, in agreement with experiment. A concerted conformational change of the alpha(3)beta(3) crown is shown to induce the 40 degrees rotation of the gamma-subunit only when the beta(E) subunit is empty, whereas with Pi bound, beta(E) serves as a latch to prevent the rotation of gamma. The present results provide a rationalization of how F-1-ATPase achieves the coupling between the small changes in the active site of beta(DP) and the 40 degrees rotation of gamma.
|
|
| 23. |
- Nestor, Stephen T., et al.
(författare)
-
Studies on solubility and S-alkylation of 2-thiouracil in ionic liquids
- 2018
-
Ingår i: Journal of Molecular Liquids. - : Elsevier. - 0167-7322 .- 1873-3166. ; 265, s. 463-467
-
Tidskriftsartikel (refereegranskat)abstract
- Ionic liquids have been exploited to assist dissolution of poorly soluble (and poorly bioavailable) drugs, enhancing permeation through physiological barriers to deliver drugs to target sites. Herein, the solubility of 6-methyl-2-thiouracil - a common antithyroid drug, with low solubility in water and common organic solvents- was studied by employing six different imidazolium-based ionic liquids with variable anions. We demonstrate facile, regiospecific S-alkylation of 2-thiouracil with various lipophilic side chains in high yields (91-94%) and in the absence of catalysts. The reaction yields are correlated with the H-bond formation ability between the ILs' anions and the solute, indicating that the hydrogen bond is perhaps responsible for the high solubility of 2-thiouracil in [C(2)mim][OAc] and [C(2)mim][Cl].
|
|
| 24. |
- Nilsson, Lina, et al.
(författare)
-
Small pH and Salt Variations Radically Alter the Thermal Stability of Metal-Binding Domains in the Copper Transporter, Wilson Disease Protein
- 2013
-
Ingår i: Journal of Physical Chemistry B. - : American Chemical Society (ACS). - 1520-6106 .- 1520-5207. ; 117:42, s. 13038-13050
-
Tidskriftsartikel (refereegranskat)abstract
- Although strictly regulated, pH and solute concentrations in cells may exhibit temporal and spatial fluctuations. Here we study the effect of such changes on the stability, structure, and dynamics in vitro and in silico of a two-domain construct (WD56) of the fifth and sixth metal-binding domains of the copper transport protein, ATP7B (Wilson disease protein). We find that the thermal stability of WD56 is increased by 40 °C when increasing the pH from 5.0 to 7.5. In contrast, addition of salt at pH 7.2 decreases WD56 stability by up to 30 °C. In agreement with domain-domain coupling, fractional copper loading increases the stability of both domains. HSQC chemical shift changes demonstrate that, upon lowering the pH from 7.2 to 6, both His in WD6 as well as the second Cys of the copper site in each domain become protonated. MD simulations reveal increased domain-domain fluctuations at pH 6 and in the presence of high salt concentration, as compared to at pH 7 and low salt concentration. Thus, the surface charge distribution at high pH contributes favorably to overall WD56 stability. By introducing more positive charges by lowering the pH, or by diminishing charge-charge interactions by salt, fluctuations among the domains are increased and thereby overall stability is reduced. Copper transfer activity also depends on pH: delivery of copper from chaperone Atox1 to WD56 is more efficient at pH 7.2 than at pH 6 by a factor of 30. It appears that WD56 is an example where the free energy landscapes for folding and function are linked via structural stability.
|
|
| 25. |
- Ojeda-May, Pedro, et al.
(författare)
-
Acceleration of Semiempirical QM/MM Methods through Message Passage Interface (MPI), Hybrid MPI/Open Multiprocessing, and Self-Consistent Field Accelerator Implementations
- 2017
-
Ingår i: Journal of Chemical Theory and Computation. - : American Chemical Society (ACS). - 1549-9618 .- 1549-9626. ; 13:8, s. 3525-3536
-
Tidskriftsartikel (refereegranskat)abstract
- The strategy and implementation of scalable and efficient semiempirical (SE) QM/MM methods in. CHARMM are described. The serial version of the code was first profiled to identify routines that required parallelization. Afterward, the code was parallelized and accelerated with three approaches. The first approach was the parallelization of the entire QM/MM routines, including the Fock matrix diagonalization routines, using the CHARMM message passage interface (MPI) machinery. In the second approach, two different self-consistent.field (SCF) energy convergence accelerators were implemented using density and Pock matrices as targets for their extrapolations in the SCF procedure. In the third approach, the entire QM/MM and MM energy routines were accelerated by implementing the hybrid MPI/open multiprocessing (OpenMP) model in which both the task- and loop-leveL parallelitation strategies were adopted to balance loads between different OpenMP threads. The present implementation was tested on two solvated enzyme systems (including <100 QM atoms) and an S(N)2 symmetric reaction in water. The-MPI version exceeded existing SE QM methods in CHARMM which include the SCC-DFTB and SQUANTUM methods by at least 4-fold. The use of SCF convergence accelerators further accelerated,the code by similar to 12-35% depending on the size of the QM region and the number of CPU cores used. Although the MPI version displayed good scalability, the performance was diminished for large numbers of MPI processes due to the overhead associated with MPI communications between nodes. This issue was partially overcome by the hybrid MPI/OpenMP approach which displayed a better scalability for a larger number of CPU cores (up to 64 CPUs in the tested systems).
|
|
| 26. |
- Ojeda-May, Pedro, et al.
(författare)
-
Dynamic Connection between Enzymatic Catalysis and Collective Protein Motions
- 2021
-
Ingår i: Biochemistry. - : American Chemical Society (ACS). - 0006-2960 .- 1520-4995. ; 60:28, s. 2246-2258
-
Tidskriftsartikel (refereegranskat)abstract
- Enzymes employ a wide range of protein motions to achieve efficient catalysis of chemical reactions. While the role of collective protein motions in substrate binding, product release, and regulation of enzymatic activity is generally understood, their roles in catalytic steps per se remain uncertain. Here, molecular dynamics simulations, enzyme kinetics, X-ray crystallography, and nuclear magnetic resonance spectroscopy are combined to elucidate the catalytic mechanism of adenylate kinase and to delineate the roles of catalytic residues in catalysis and the conformational change in the enzyme. This study reveals that the motions in the active site, which occur on a time scale of picoseconds to nanoseconds, link the catalytic reaction to the slow conformational dynamics of the enzyme by modulating the free energy landscapes of subdomain motions. In particular, substantial conformational rearrangement occurs in the active site following the catalytic reaction. This rearrangement not only affects the reaction barrier but also promotes a more open conformation of the enzyme after the reaction, which then results in an accelerated opening of the enzyme compared to that of the reactant state. The results illustrate a linkage between enzymatic catalysis and collective protein motions, whereby the disparate time scales between the two processes are bridged by a cascade of intermediate-scale motion of catalytic residues modulating the free energy landscapes of the catalytic and conformational change processes.
|
|
| 27. |
- Ojeda-May, Pedro, et al.
(författare)
-
Role of Protein Dynamics in Allosteric Control of the Catalytic Phosphoryl Transfer of Insulin Receptor Kinase
- 2015
-
Ingår i: Journal of the American Chemical Society. - : American Chemical Society (ACS). - 0002-7863 .- 1520-5126. ; 137:39, s. 12454-12457
-
Tidskriftsartikel (refereegranskat)abstract
- The catalytic and allosteric mechanisms of insulin receptor kinase (IRK) are investigated by a combination of ab initio and semiempirical quantum mechanical and molecular mechanical (QM/MM) methods and classical molecular dynamics (MD) simulations. The simulations reveal that the catalytic reaction proceeds in two steps, starting with the transfer of a proton from substrate Tyr to the catalytic Asp1132, followed by the phosphoryl transfer from ATP to substrate Tyr. The enhancement of the catalytic rate of IRK upon phosphorylations in the enzyme's activation loop is found to occur mainly via changes to the free energy landscape of the proton transfer step, favoring the proton transfer in the fully phosphorylated enzyme. In contrast, the effects of the phosphorylations on the phosphoryl transfer are smaller. Equilibrium MD simulations show that IRK phosphorylations affect the protein dynamics of the enzyme before the proton transfer to Asp1132 with only a minor effect after the proton transfer. This finding is consistent with the large change in the proton transfer free energy and the smaller change in the free energy barrier of phosphoryl transfer found by QM/MM simulations. Taken together, the present results provide details on how IRK phosphorylation exerts allosteric control of the catalytic activity via modifications of protein dynamics and free energy landscape of catalytic reaction. The results also highlight the importance of protein dynamics in connecting protein allostery and catalysis to control catalytic activity of enzymes.
|
|
| 28. |
- Ovchinnikov, Victor, et al.
(författare)
-
A Simple and Accurate Method To Calculate Free Energy Profiles and Reaction Rates from Restrained Molecular Simulations of Diffusive Processes
- 2016
-
Ingår i: Journal of Physical Chemistry B. - : American Chemical Society (ACS). - 1520-6106 .- 1520-5207. ; 120:33, s. 8457-8472
-
Tidskriftsartikel (refereegranskat)abstract
- A method is developed to obtain simultaneously free energy profiles and diffusion constants from restrained molecular simulations in diffusive systems. The method is based on low-order expansions of the free energy and diffusivity as functions of the reaction coordinate. These expansions lead to simple analytical relationships between simulation statistics and model parameters. The method is tested on 1D and 2D model systems; its accuracy is found to be comparable to or better than that of the existing alternatives, which are briefly discussed. An important aspect of the method is that the free energy is constructed by integrating its derivatives, which can be computed without need for overlapping sampling windows. The implementation of the method in any molecular simulation program that supports external umbrella potentials (e.g., CHARMM) requires modification of only a few lines of code. As a demonstration of its applicability to realistic biomolecular systems, the method is applied to model the alpha-helix <-> beta-sheet transition in a 16-residue peptide in implicit solvent, with the reaction coordinate provided by the string method. Possible modifications of the method are briefly discussed; they include generalization to multidimensional reaction coordinates [in the spirit of the model of Ermak and McCammon (Ermak, D. L.; McCammon, J. A. J. Chem. Phys. 1978, 69, 1352-1360)], a higher-order expansion of the free energy surface, applicability in nonequilibrium systems, and a simple test for Markovianity. In view of the small overhead of the method relative to standard umbrella sampling, we suggest its routine application in the cases where umbrella potential simulations are appropriate.
|
|
| 29. |
- Rogne, Per, et al.
(författare)
-
Structural Basis for GTP versus ATP Selectivity in the NMP Kinase AK3
- 2020
-
Ingår i: Biochemistry. - : American Chemical Society (ACS). - 0006-2960 .- 1520-4995. ; 59:38, s. 3570-3581
-
Tidskriftsartikel (refereegranskat)abstract
- ATP and GTP are exceptionally important molecules in biology with multiple, and often discrete, functions. Therefore, enzymes that bind to either of them must develop robust mechanisms to selectively utilize one or the other. Here, this specific problem is addressed by molecular studies of the human NMP kinase AK3, which uses GTP to phosphorylate AMP. AK3 plays an important role in the citric acid cycle, where it is responsible for GTP/GDP recycling. By combining a structural biology approach with functional experiments, we present a comprehensive structural and mechanistic understanding of the enzyme. We discovered that AK3 functions by recruitment of GTP to the active site, while ATP is rejected and nonproductively bound to the AMP binding site. Consequently, ATP acts as an inhibitor with respect to GTP and AMP. The overall features with specific recognition of the correct substrate and nonproductive binding by the incorrect substrate bear a strong similarity to previous findings for the ATP specific NMP kinase adenylate kinase. Taken together, we are now able to provide the fundamental principles for GTP and ATP selectivity in the large NMP kinase family. As a side-result originating from nonlinearity of chemical shifts in GTP and ATP titrations, we find that protein surfaces offer a general and weak binding affinity for both GTP and ATP. These nonspecific interactions likely act to lower the available intracellular GTP and ATP concentrations and may have driven evolution of the Michaelis constants of NMP kinases accordingly.
|
|
| 30. |
- Shigdel, Uddhav K., et al.
(författare)
-
The trajectory of intrahelical lesion recognition and extrusion by the human 8-oxoguanine DNA glycosylase
- 2020
-
Ingår i: Nature Communications. - : Nature Publishing Group. - 2041-1723. ; 11:1
-
Tidskriftsartikel (refereegranskat)abstract
- Efficient search for DNA damage embedded in vast expanses of the DNA genome presents one of the greatest challenges to DNA repair enzymes. We report here crystal structures of human 8-oxoguanine (oxoG) DNA glycosylase, hOGG1, that interact with the DNA containing the damaged base oxoG and the normal base G while they are nested in the DNA helical stack. The structures reveal that hOGG1 engages the DNA using different protein-DNA contacts from those observed in the previously determined lesion recognition complex and other hOGG1-DNA complexes. By applying molecular dynamics simulations, we have determined the pathways taken by the lesion and normal bases when extruded from the DNA helix and their associated free energy profiles. These results reveal how the human oxoG DNA glycosylase hOGG1 locates the lesions inside the DNA helix and facilitates their extrusion for repair.
|
|
| 31. |
- Spulber, S., et al.
(författare)
-
Methylmercury interferes with glucocorticoid receptor : Potential role in the mediation of developmental neurotoxicity
- 2018
-
Ingår i: Toxicology and Applied Pharmacology. - : Academic Press. - 0041-008X .- 1096-0333. ; 354, s. 94-100
-
Tidskriftsartikel (refereegranskat)abstract
- Methylmercury (MeHg) is a widespread environmental contaminant with established developmental neurotoxic effects. Computational models have identified glucocorticoid receptor (GR) signaling to be a key mediator behind the birth defects induced by Hg, but the mechanisms were not elucidated. Using molecular dynamics simulations, we found that MeHg can bind to the GR protein at Cys736 (located close to the ligand binding site) and distort the conformation of the ligand binging site. To assess the functional consequences of MeHg interaction with GR, we used a human cell line expressing a luciferase reporter system (HeLa AZ-GR). We found that 100 nM MeHg does not have any significant effect on GR activity alone, but the transactivation of gene expression by GR upon Dex (a synthetic GR agonist) administration was reduced in cells pre-treated with MeHg. Similar effects were found in transgenic zebrafish larvae expressing a GR reporter system (SR4G). Next we asked whether the effects of developmental exposure to MeHg are mediated by the effects on GR. Using a mutant zebrafish line carrying a loss-of-function mutation in the GR (grs(357)) we could show that the effects of developmental exposure to 2.5 nM MeHg are mitigated in absence of functional GR signaling. Taken together, our data indicate that inhibition of GR signaling may have a role in the developmental neurotoxic effects of MeHg.
|
|
| 32. |
- Verma, Apoorv, et al.
(författare)
-
Insights into the evolution of enzymatic specificity and catalysis : from Asgard archaea to human adenylate kinases
- 2022
-
Ingår i: Science Advances. - : American Association for the Advancement of Science (AAAS). - 2375-2548. ; 8:44
-
Tidskriftsartikel (refereegranskat)abstract
- Enzymatic catalysis is critically dependent on selectivity, active site architecture, and dynamics. To contribute insights into the interplay of these properties, we established an approach with NMR, crystallography, and MD simulations focused on the ubiquitous phosphotransferase adenylate kinase (AK) isolated from Odinarchaeota (OdinAK). Odinarchaeota belongs to the Asgard archaeal phylum that is believed to be the closest known ancestor to eukaryotes. We show that OdinAK is a hyperthermophilic trimer that, contrary to other AK family members, can use all NTPs for its phosphorylation reaction. Crystallographic structures of OdinAK-NTP complexes revealed a universal NTP-binding motif, while 19F NMR experiments uncovered a conserved and rate-limiting dynamic signature. As a consequence of trimerization, the active site of OdinAK was found to be lacking a critical catalytic residue and is therefore considered to be "atypical." On the basis of discovered relationships with human monomeric homologs, our findings are discussed in terms of evolution of enzymatic substrate specificity and cold adaptation.
|
|
| 33. |
- Yeh, Johannes T. -H., et al.
(författare)
-
eUnaG : a new ligand-inducible fluorescent reporter to detect drug transporter activity in live cells
- 2017
-
Ingår i: Scientific Reports. - : Nature Publishing Group. - 2045-2322. ; 7
-
Tidskriftsartikel (refereegranskat)abstract
- The absorption, distribution, metabolism and excretion (ADME) of metabolites and toxic organic solutes are orchestrated by the ATP-binding cassette (ABC) transporters and the organic solute carrier family (SLC) proteins. A large number of ABC and SLC transpoters exist; however, only a small number have been well characterized. To facilitate the analysis of these transporters, which is important for drug safety and physiological studies, we developed a sensitive genetically encoded bilirubin (BR)-inducible fluorescence sensor (eUnaG) to detect transporter-coupled influx/efflux of organic compounds. This sensor can be used in live cells to measure transporter activity, as excretion of BR depends on ABC and SLC transporters. Applying eUnaG in functional RNAi screens, we characterize l(2) 03659 as a Drosophila multidrug resistant-associated ABC transporter.
|
|
| 34. |
- Zhang, Jin, et al.
(författare)
-
Identification and Molecular Interaction Studies of Thyroid Hormone Receptor Disruptors among Household Dust Contaminants
- 2016
-
Ingår i: Chemical Research in Toxicology. - : American Chemical Society (ACS). - 0893-228X .- 1520-5010. ; 29:8, s. 1345-1354
-
Tidskriftsartikel (refereegranskat)abstract
- Thyroid hormone disrupting chemicals (THDCs), often found abundantly in the environment, interfere with normal thyroid hormone signaling and induce physiological malfunctions, possibly by affecting thyroid hormone receptors (THRs). Indoor dust ingestion is a significant human exposure route of THDCs, raising serious concerns for human health. Here, we developed a virtual screening protocol based on an ensemble of X-ray crystallographic structures of human THRβ1 and the generalized Born solvation model to identify potential THDCs targeting the human THRβ1 isoform. The protocol was applied to virtually screen an in-house indoor dust contaminant inventory, yielding 31 dust contaminants as potential THRβ1 binders. Five predicted binders and one negative control were tested using isothermal titration calorimetry, of which four, i.e., 2,4,5-trichlorophenoxyacetic acid (2,4,5-T), bisphenol A (3-chloro-2-hydroxypropyl) (2,3-dihydroxypropyl) ether (BADGE-HCl-H2O), 2,2',4,4'-tetrahydroxybenzophenone (BP2), and 2,4-dichlorophenoxyacetic acid (2,4-D), were identified as THRβ1 binders with binding affinities ranging between 60 μM and 460 μM. Molecular dynamics (MD) simulations were employed to examine potential binding modes of these binders and provided a rationale for explaining their specific recognition by THRβ1. The combination of in vitro binding affinity measurements and MD simulations allowed identification of four new potential THR-targeting THDCs that have been found in household dust. We suggest using the developed structure-based virtual screening protocol to identify and prioritize testing of potential THDCs.
|
|
