1
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Zheng LE, Barethiya S, Nordquist E, Chen J. Machine Learning Generation of Dynamic Protein Conformational Ensembles. Molecules 2023; 28:4047. [PMID: 37241789 PMCID: PMC10220786 DOI: 10.3390/molecules28104047] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2023] [Revised: 05/04/2023] [Accepted: 05/09/2023] [Indexed: 05/28/2023] Open
Abstract
Machine learning has achieved remarkable success across a broad range of scientific and engineering disciplines, particularly its use for predicting native protein structures from sequence information alone. However, biomolecules are inherently dynamic, and there is a pressing need for accurate predictions of dynamic structural ensembles across multiple functional levels. These problems range from the relatively well-defined task of predicting conformational dynamics around the native state of a protein, which traditional molecular dynamics (MD) simulations are particularly adept at handling, to generating large-scale conformational transitions connecting distinct functional states of structured proteins or numerous marginally stable states within the dynamic ensembles of intrinsically disordered proteins. Machine learning has been increasingly applied to learn low-dimensional representations of protein conformational spaces, which can then be used to drive additional MD sampling or directly generate novel conformations. These methods promise to greatly reduce the computational cost of generating dynamic protein ensembles, compared to traditional MD simulations. In this review, we examine recent progress in machine learning approaches towards generative modeling of dynamic protein ensembles and emphasize the crucial importance of integrating advances in machine learning, structural data, and physical principles to achieve these ambitious goals.
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Affiliation(s)
- Li-E Zheng
- Department of Gynecology, The First Affiliated Hospital of Fujian Medical University, Fuzhou 350005, China;
| | - Shrishti Barethiya
- Department of Chemistry, University of Massachusetts Amherst, Amherst, MA 01003, USA; (S.B.); (E.N.)
| | - Erik Nordquist
- Department of Chemistry, University of Massachusetts Amherst, Amherst, MA 01003, USA; (S.B.); (E.N.)
| | - Jianhan Chen
- Department of Chemistry, University of Massachusetts Amherst, Amherst, MA 01003, USA; (S.B.); (E.N.)
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2
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Zhang Y, Liu X, Chen J. Re-Balancing Replica Exchange with Solute Tempering for Sampling Dynamic Protein Conformations. J Chem Theory Comput 2023; 19:1602-1614. [PMID: 36791464 PMCID: PMC10795075 DOI: 10.1021/acs.jctc.2c01139] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/17/2023]
Abstract
Replica exchange with solute tempering (REST) is a highly effective variant of replica exchange for enhanced sampling in explicit solvent simulations of biomolecules. By scaling the Hamiltonian for a selected "solute" region of the system, REST effectively applies tempering only to the degrees of freedom of interest but not the rest of the system ("solvent"), allowing fewer replicas for covering the same temperature range. A key consideration of REST is how the solute-solvent interactions are scaled together with the solute-solute interactions. Here, we critically evaluate the performance of the latest REST2 protocol for sampling large-scale conformation fluctuations of intrinsically disordered proteins (IDPs). The results show that REST2 promotes artificial protein conformational collapse at high effective temperatures, which seems to be a designed feature originally to promote the sampling of reversible folding of small proteins. The collapse is particularly severe with larger IDPs, leading to replica segregation in the effective temperature space and hindering effective sampling of large-scale conformational changes. We propose that the scaling of the solute-solvent interactions can be treated as free parameters in REST, which can be tuned to control the solute conformational properties (e.g., chain expansion) at different effective temperatures and achieve more effective sampling. To this end, we derive a new REST3 protocol, where the strengths of the solute-solvent van der Waals interactions are recalibrated to reproduce the levels of protein chain expansion at high effective temperatures. The efficiency of REST3 is examined using two IDPs with nontrivial local and long-range structural features, including the p53 N-terminal domain and the kinase inducible transactivation domain of transcription factor CREB. The results suggest that REST3 leads to a much more efficient temperature random walk and improved sampling efficiency, which also further reduces the number of replicas required. Nonetheless, our analysis also reveals significant challenges of relying on tempering alone for sampling large-scale conformational fluctuations of disordered proteins. It is likely that more efficient sampling protocols will require incorporating more sophisticated Hamiltonian replica exchange schemes in addition to tempering.
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Affiliation(s)
- Yumeng Zhang
- Department of Chemistry, University of Massachusetts, Amherst, MA 01003, USA
| | - Xiaorong Liu
- Corresponding Authors: (XL), (JC), Phone: (413) 545-3386 (JC)
| | - Jianhan Chen
- Department of Chemistry, University of Massachusetts, Amherst, MA 01003, USA
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3
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Fukunishi Y, Higo J, Kasahara K. Computer simulation of molecular recognition in biomolecular system: from in silico screening to generalized ensembles. Biophys Rev 2022; 14:1423-1447. [PMID: 36465086 PMCID: PMC9703445 DOI: 10.1007/s12551-022-01015-8] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2022] [Accepted: 11/06/2022] [Indexed: 11/29/2022] Open
Abstract
Prediction of ligand-receptor complex structure is important in both the basic science and the industry such as drug discovery. We report various computation molecular docking methods: fundamental in silico (virtual) screening, ensemble docking, enhanced sampling (generalized ensemble) methods, and other methods to improve the accuracy of the complex structure. We explain not only the merits of these methods but also their limits of application and discuss some interaction terms which are not considered in the in silico methods. In silico screening and ensemble docking are useful when one focuses on obtaining the native complex structure (the most thermodynamically stable complex). Generalized ensemble method provides a free-energy landscape, which shows the distribution of the most stable complex structure and semi-stable ones in a conformational space. Also, barriers separating those stable structures are identified. A researcher should select one of the methods according to the research aim and depending on complexity of the molecular system to be studied.
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Affiliation(s)
- Yoshifumi Fukunishi
- Cellular and Molecular Biotechnology Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), 2-3-26, Aomi, Koto-Ku, Tokyo, 135-0064 Japan
| | - Junichi Higo
- Graduate School of Information Science, University of Hyogo, 7-1-28 Minatojima Minamimachi, Chuo-Ku, Kobe, Hyogo 650-0047 Japan ,Research Organization of Science and Technology, Ritsumeikan University, 1-1-1 Noji-Higashi, Kusatsu, Shiga 525-8577 Japan
| | - Kota Kasahara
- College of Life Sciences, Ritsumeikan University, 1-1-1 Noji-Higashi, Kusatsu, Shiga 525-8577 Japan
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Gong X, Zhang Y, Chen J. Advanced Sampling Methods for Multiscale Simulation of Disordered Proteins and Dynamic Interactions. Biomolecules 2021; 11:1416. [PMID: 34680048 PMCID: PMC8533332 DOI: 10.3390/biom11101416] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Revised: 09/22/2021] [Accepted: 09/24/2021] [Indexed: 11/16/2022] Open
Abstract
Intrinsically disordered proteins (IDPs) are highly prevalent and play important roles in biology and human diseases. It is now also recognized that many IDPs remain dynamic even in specific complexes and functional assemblies. Computer simulations are essential for deriving a molecular description of the disordered protein ensembles and dynamic interactions for a mechanistic understanding of IDPs in biology, diseases, and therapeutics. Here, we provide an in-depth review of recent advances in the multi-scale simulation of disordered protein states, with a particular emphasis on the development and application of advanced sampling techniques for studying IDPs. These techniques are critical for adequate sampling of the manifold functionally relevant conformational spaces of IDPs. Together with dramatically improved protein force fields, these advanced simulation approaches have achieved substantial success and demonstrated significant promise towards the quantitative and predictive modeling of IDPs and their dynamic interactions. We will also discuss important challenges remaining in the atomistic simulation of larger systems and how various coarse-grained approaches may help to bridge the remaining gaps in the accessible time- and length-scales of IDP simulations.
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Affiliation(s)
- Xiping Gong
- Department of Chemistry, University of Massachusetts Amherst, Amherst, MA 01003, USA; (X.G.); (Y.Z.)
| | - Yumeng Zhang
- Department of Chemistry, University of Massachusetts Amherst, Amherst, MA 01003, USA; (X.G.); (Y.Z.)
| | - Jianhan Chen
- Department of Chemistry, University of Massachusetts Amherst, Amherst, MA 01003, USA; (X.G.); (Y.Z.)
- Department of Biochemistry and Molecular Biology, University of Massachusetts Amherst, Amherst, MA 01003, USA
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5
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Peter EK, Manstein DJ, Shea JE, Schug A. CORE-MD II: A fast, adaptive, and accurate enhanced sampling method. J Chem Phys 2021; 155:104114. [PMID: 34525829 DOI: 10.1063/5.0063664] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
In this paper, we present a fast and adaptive correlation guided enhanced sampling method (CORE-MD II). The CORE-MD II technique relies, in part, on partitioning of the entire pathway into short trajectories that we refer to as instances. The sampling within each instance is accelerated by adaptive path-dependent metadynamics simulations. The second part of this approach involves kinetic Monte Carlo (kMC) sampling between the different states that have been accessed during each instance. Through the combination of the partition of the total simulation into short non-equilibrium simulations and the kMC sampling, the CORE-MD II method is capable of sampling protein folding without any a priori definitions of reaction pathways and additional parameters. In the validation simulations, we applied the CORE-MD II on the dialanine peptide and the folding of two peptides: TrpCage and TrpZip2. In a comparison with long time equilibrium Molecular Dynamics (MD), 1 µs replica exchange MD (REMD), and CORE-MD I simulations, we find that the level of convergence of the CORE-MD II method is improved by a factor of 8.8, while the CORE-MD II method reaches acceleration factors of ∼120. In the CORE-MD II simulation of TrpZip2, we observe the formation of the native state in contrast to the REMD and the CORE-MD I simulations. The method is broadly applicable for MD simulations and is not restricted to simulations of protein folding or even biomolecules but also applicable to simulations of protein aggregation, protein signaling, or even materials science simulations.
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Affiliation(s)
- Emanuel K Peter
- Institute for Biophysical Chemistry, Fritz-Hartmann-Centre for Medical Research, Hannover Medical School, Carl-Neuberg-Str. 1, Hannover 30625, Germany
| | - Dietmar J Manstein
- Institute for Biophysical Chemistry, Fritz-Hartmann-Centre for Medical Research, Hannover Medical School, Carl-Neuberg-Str. 1, Hannover 30625, Germany
| | - Joan-Emma Shea
- Department of Chemistry and Biochemistry, Department of Physics, University of California, Santa Barbara, California 93106, USA
| | - Alexander Schug
- John von Neumann Institute for Computing and Jülich Supercomputing Centre, Institute for Advanced Simulation, Forschungszentrum Jülich, 52425 Jülich, Germany
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6
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Schrag LG, Liu X, Thevarajan I, Prakash O, Zolkiewski M, Chen J. Cancer-Associated Mutations Perturb the Disordered Ensemble and Interactions of the Intrinsically Disordered p53 Transactivation Domain. J Mol Biol 2021; 433:167048. [PMID: 33984364 PMCID: PMC8286338 DOI: 10.1016/j.jmb.2021.167048] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2021] [Revised: 04/30/2021] [Accepted: 05/04/2021] [Indexed: 01/08/2023]
Abstract
Intrinsically disordered proteins (IDPs) are key components of regulatory networks that control crucial aspects of cell decision making. The intrinsically disordered transactivation domain (TAD) of tumor suppressor p53 mediates its interactions with multiple regulatory pathways to control the p53 homeostasis during the cellular response to genotoxic stress. Many cancer-associated mutations have been discovered in p53-TAD, but their structural and functional consequences are poorly understood. Here, by combining atomistic simulations, NMR spectroscopy, and binding assays, we demonstrate that cancer-associated mutations can significantly perturb the balance of p53 interactions with key activation and degradation regulators. Importantly, the four mutations studied in this work do not all directly disrupt the known interaction interfaces. Instead, at least three of these mutations likely modulate the disordered state of p53-TAD to perturb its interactions with regulators. Specifically, NMR and simulation analysis together suggest that these mutations can modulate the level of conformational expansion as well as rigidity of the disordered state. Our work suggests that the disordered conformational ensemble of p53-TAD can serve as a central conduit in regulating the response to various cellular stimuli at the protein-protein interaction level. Understanding how the disordered state of IDPs may be modulated by regulatory signals and/or disease associated perturbations will be essential in the studies on the role of IDPs in biology and diseases.
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Affiliation(s)
- Lynn G Schrag
- Department of Biochemistry and Molecular Biophysics, Kansas State University, Manhattan, KS 66505, USA
| | - Xiaorong Liu
- Department of Chemistry, University of Massachusetts Amherst, Amherst, MA 01003, USA
| | - Indhujah Thevarajan
- Department of Biochemistry and Molecular Biophysics, Kansas State University, Manhattan, KS 66505, USA
| | - Om Prakash
- Department of Biochemistry and Molecular Biophysics, Kansas State University, Manhattan, KS 66505, USA.
| | - Michal Zolkiewski
- Department of Biochemistry and Molecular Biophysics, Kansas State University, Manhattan, KS 66505, USA.
| | - Jianhan Chen
- Department of Chemistry, University of Massachusetts Amherst, Amherst, MA 01003, USA; Department of Biochemistry and Molecular Biology, University of Massachusetts Amherst, Amherst, MA 01003, USA.
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7
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Higo J, Takashima H, Fukunishi Y, Yoshimori A. Generalized-ensemble method study: A helix-mimetic compound inhibits protein-protein interaction by long-range and short-range intermolecular interactions. J Comput Chem 2021; 42:956-969. [PMID: 33755222 DOI: 10.1002/jcc.26516] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2020] [Revised: 02/25/2021] [Accepted: 03/01/2021] [Indexed: 12/30/2022]
Abstract
A heterocyclic compound mS-11 is a helix-mimetic designed to inhibit binding of an intrinsic disordered protein neural restrictive silence factor/repressor element 1 silencing factor (NRSF/REST) to a receptor protein mSin3B. We apply a generalized ensemble method, multi-dimensional virtual-system coupled molecular dynamics developed by ourselves recently, to a system consisting of mS-11 and mSin3B, and obtain a thermally equilibrated distribution, which is comprised of the bound and unbound states extensively. The lowest free-energy position of mS-11 coincides with the NRSF/REST position in the experimentally-determined NRSF/REST-mSin3B complex. Importantly, the molecular orientation of mS-11 is ordering in a wide region around mSin3B. The resultant binding scenario is: When mS-11 is distant from the binding site of mSin3B, mS-11 descends the free-energy slope toward the binding site maintaining the molecular orientation to be advantageous for binding. Then, finally a long and flexible hydrophobic sidechain of mS-11 fits into the binding site, which is the lowest-free-energy complex structure inhibiting NRSF/REST binding to mSin3B.
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Affiliation(s)
- Junichi Higo
- Graduate School of Simulation Studies, University of Hyogo, Kobe, Japan
| | - Hajime Takashima
- Department of Research and Development, PRISM BioLab Co., Ltd., Fujisawa, Japan
| | - Yoshifumi Fukunishi
- Cellular and Molecular Biotechnology Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Tokyo, Japan
| | - Atsushi Yoshimori
- Chemoinformatics & AI Research Group, Institute for Theoretical Medicine, Inc., Fujisawa, Japan
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8
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Peter EK, Shea JE, Schug A. CORE-MD, a path correlated molecular dynamics simulation method. J Chem Phys 2020; 153:084114. [DOI: 10.1063/5.0015398] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Emanuel K. Peter
- John von Neumann Institute for Computing and Julich Supercomputing Centre, Institute for Advanced Simulation, Forschungszentrum Jülich, Jülich, Germany
| | - Joan-Emma Shea
- Department of Chemistry and Biochemistry, Department of Physics, University of California, Santa Barbara, Santa Barbara, California 93106, USA
| | - Alexander Schug
- John von Neumann Institute for Computing and Julich Supercomputing Centre, Institute for Advanced Simulation, Forschungszentrum Jülich, Jülich, Germany
- Faculty of Biology, University of Duisburg-Essen, Duisburg, Germany
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9
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Chen J, Liu X, Chen J. Targeting Intrinsically Disordered Proteins through Dynamic Interactions. Biomolecules 2020; 10:E743. [PMID: 32403216 PMCID: PMC7277182 DOI: 10.3390/biom10050743] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2020] [Revised: 05/04/2020] [Accepted: 05/09/2020] [Indexed: 12/18/2022] Open
Abstract
Intrinsically disordered proteins (IDPs) are over-represented in major disease pathways and have attracted significant interest in understanding if and how they may be targeted using small molecules for therapeutic purposes. While most existing studies have focused on extending the traditional structure-centric drug design strategies and emphasized exploring pre-existing structure features of IDPs for specific binding, several examples have also emerged to suggest that small molecules could achieve specificity in binding IDPs and affect their function through dynamic and transient interactions. These dynamic interactions can modulate the disordered conformational ensemble and often lead to modest compaction to shield functionally important interaction sites. Much work remains to be done on further elucidation of the molecular basis of the dynamic small molecule-IDP interaction and determining how it can be exploited for targeting IDPs in practice. These efforts will rely critically on an integrated experimental and computational framework for disordered protein ensemble characterization. In particular, exciting advances have been made in recent years in enhanced sampling techniques, Graphic Processing Unit (GPU)-computing, and protein force field optimization, which have now allowed rigorous physics-based atomistic simulations to generate reliable structure ensembles for nontrivial IDPs of modest sizes. Such de novo atomistic simulations will play crucial roles in exploring the exciting opportunity of targeting IDPs through dynamic interactions.
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Affiliation(s)
- Jianlin Chen
- Department of Hematology, Taizhou Central Hospital (Taizhou University Hospital), Taizhou 318000, Zhejiang, China;
| | - Xiaorong Liu
- Department of Chemistry, University of Massachusetts, Amherst, MA 01003, USA;
| | - Jianhan Chen
- Department of Chemistry, University of Massachusetts, Amherst, MA 01003, USA;
- Department of Biochemistry and Molecular Biology, University of Massachusetts, Amherst, MA 01003, USA
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10
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Dreßler C, Kabbe G, Brehm M, Sebastiani D. Exploring non-equilibrium molecular dynamics of mobile protons in the solid acid CsH2PO4 at the micrometer and microsecond scale. J Chem Phys 2020; 152:164110. [DOI: 10.1063/5.0002167] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Affiliation(s)
- Christian Dreßler
- Institute of Chemistry, Martin Luther University Halle-Wittenberg, Von-Danckelmann-Platz 4, 06120 Halle (Saale), Germany
| | - Gabriel Kabbe
- Institute of Chemistry, Martin Luther University Halle-Wittenberg, Von-Danckelmann-Platz 4, 06120 Halle (Saale), Germany
| | - Martin Brehm
- Institute of Chemistry, Martin Luther University Halle-Wittenberg, Von-Danckelmann-Platz 4, 06120 Halle (Saale), Germany
| | - Daniel Sebastiani
- Institute of Chemistry, Martin Luther University Halle-Wittenberg, Von-Danckelmann-Platz 4, 06120 Halle (Saale), Germany
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11
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Dreßler C, Kabbe G, Brehm M, Sebastiani D. Dynamical matrix propagator scheme for large-scale proton dynamics simulations. J Chem Phys 2020; 152:114114. [PMID: 32199428 DOI: 10.1063/1.5140635] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023] Open
Abstract
We derive a matrix formalism for the simulation of long range proton dynamics for extended systems and timescales. On the basis of an ab initio molecular dynamics simulation, we construct a Markov chain, which allows us to store the entire proton dynamics in an M × M transition matrix (where M is the number of oxygen atoms). In this article, we start from common topology features of the hydrogen bond network of good proton conductors and utilize them as constituent constraints of our dynamic model. We present a thorough mathematical derivation of our approach and verify its uniqueness and correct asymptotic behavior. We propagate the proton distribution by means of transition matrices, which contain kinetic data from both ultra-short (sub-ps) and intermediate (ps) timescales. This concept allows us to keep the most relevant features from the microscopic level while effectively reaching larger time and length scales. We demonstrate the applicability of the transition matrices for the description of proton conduction trends in proton exchange membrane materials.
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Affiliation(s)
- Christian Dreßler
- Institute of Chemistry, Martin Luther University Halle-Wittenberg, Von-Danckelmann-Platz 4, 06120 Halle (Saale), Germany
| | - Gabriel Kabbe
- Institute of Chemistry, Martin Luther University Halle-Wittenberg, Von-Danckelmann-Platz 4, 06120 Halle (Saale), Germany
| | - Martin Brehm
- Institute of Chemistry, Martin Luther University Halle-Wittenberg, Von-Danckelmann-Platz 4, 06120 Halle (Saale), Germany
| | - Daniel Sebastiani
- Institute of Chemistry, Martin Luther University Halle-Wittenberg, Von-Danckelmann-Platz 4, 06120 Halle (Saale), Germany
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12
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Peter EK, Černý J. A Hybrid Hamiltonian for the Accelerated Sampling along Experimental Restraints. Int J Mol Sci 2019; 20:E370. [PMID: 30654563 PMCID: PMC6359555 DOI: 10.3390/ijms20020370] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2018] [Revised: 01/07/2019] [Accepted: 01/10/2019] [Indexed: 12/25/2022] Open
Abstract
In this article, we present an enhanced sampling method based on a hybrid Hamiltonian which combines experimental distance restraints with a bias dependent from multiple path-dependent variables. This simulation method determines the bias-coordinates on the fly and does not require a priori knowledge about reaction coordinates. The hybrid Hamiltonian accelerates the sampling of proteins, and, combined with experimental distance information, the technique considers the restraints adaptively and in dependency of the system's intrinsic dynamics. We validate the methodology on the dipole relaxation of two water models and the conformational landscape of dialanine. Using experimental NMR-restraint data, we explore the folding landscape of the TrpCage mini-protein and in a second example apply distance restraints from chemical crosslinking/mass spectrometry experiments for the sampling of the conformation space of the Killer Cell Lectin-like Receptor Subfamily B Member 1A (NKR-P1A). The new methodology has the potential to adaptively introduce experimental restraints without affecting the conformational space of the system along an ergodic trajectory. Since only a limited number of input- and no-order parameters are required for the setup of the simulation, the method is broadly applicable and has the potential to be combined with coarse-graining methods.
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Affiliation(s)
- Emanuel K Peter
- Institute of Biotechnology of the Czech Academy of Sciences, BIOCEV, Průmyslová 595, 252 50 Vestec, Prague West, Czech Republic.
| | - Jiří Černý
- Institute of Biotechnology of the Czech Academy of Sciences, BIOCEV, Průmyslová 595, 252 50 Vestec, Prague West, Czech Republic.
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13
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Peter EK, Cerny J. Enriched Conformational Sampling of DNA and Proteins with a Hybrid Hamiltonian Derived from the Protein Data Bank. Int J Mol Sci 2018; 19:E3405. [PMID: 30380800 PMCID: PMC6274895 DOI: 10.3390/ijms19113405] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2018] [Revised: 10/22/2018] [Accepted: 10/27/2018] [Indexed: 12/26/2022] Open
Abstract
In this article, we present a method for the enhanced molecular dynamics simulation of protein and DNA systems called potential of mean force (PMF)-enriched sampling. The method uses partitions derived from the potentials of mean force, which we determined from DNA and protein structures in the Protein Data Bank (PDB). We define a partition function from a set of PDB-derived PMFs, which efficiently compensates for the error introduced by the assumption of a homogeneous partition function from the PDB datasets. The bias based on the PDB-derived partitions is added in the form of a hybrid Hamiltonian using a renormalization method, which adds the PMF-enriched gradient to the system depending on a linear weighting factor and the underlying force field. We validated the method using simulations of dialanine, the folding of TrpCage, and the conformational sampling of the Dickerson⁻Drew DNA dodecamer. Our results show the potential for the PMF-enriched simulation technique to enrich the conformational space of biomolecules along their order parameters, while we also observe a considerable speed increase in the sampling by factors ranging from 13.1 to 82. The novel method can effectively be combined with enhanced sampling or coarse-graining methods to enrich conformational sampling with a partition derived from the PDB.
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Affiliation(s)
- Emanuel K Peter
- Institute of Biotechnology of the Czech Academy of Sciences, BIOCEV, Průmyslová 595, 252 50 Vestec, Czech Republic.
| | - Jiri Cerny
- Institute of Biotechnology of the Czech Academy of Sciences, BIOCEV, Průmyslová 595, 252 50 Vestec, Czech Republic.
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14
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Peter EK. Adaptive enhanced sampling with a path-variable for the simulation of protein folding and aggregation. J Chem Phys 2018; 147:214902. [PMID: 29221375 DOI: 10.1063/1.5000930] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
In this article, we present a novel adaptive enhanced sampling molecular dynamics (MD) method for the accelerated simulation of protein folding and aggregation. We introduce a path-variable L based on the un-biased momenta p and displacements dq for the definition of the bias s applied to the system and derive 3 algorithms: general adaptive bias MD, adaptive path-sampling, and a hybrid method which combines the first 2 methodologies. Through the analysis of the correlations between the bias and the un-biased gradient in the system, we find that the hybrid methodology leads to an improved force correlation and acceleration in the sampling of the phase space. We apply our method on SPC/E water, where we find a conservation of the average water structure. We then use our method to sample dialanine and the folding of TrpCage, where we find a good agreement with simulation data reported in the literature. Finally, we apply our methodologies on the initial stages of aggregation of a hexamer of Alzheimer's amyloid β fragment 25-35 (Aβ 25-35) and find that transitions within the hexameric aggregate are dominated by entropic barriers, while we speculate that especially the conformation entropy plays a major role in the formation of the fibril as a rate limiting factor.
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Affiliation(s)
- Emanuel K Peter
- Department of Pharmacy and Chemistry, Institute of Physical and Theoretical Chemistry, University of Regensburg, Regensburg, Germany
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15
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Peter EK, Shea JE. An adaptive bias - hybrid MD/kMC algorithm for protein folding and aggregation. Phys Chem Chem Phys 2018. [PMID: 28650060 DOI: 10.1039/c7cp03035e] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
In this paper, we present a novel hybrid Molecular Dynamics/kinetic Monte Carlo (MD/kMC) algorithm and apply it to protein folding and aggregation in explicit solvent. The new algorithm uses a dynamical definition of biases throughout the MD component of the simulation, normalized in relation to the unbiased forces. The algorithm guarantees sampling of the underlying ensemble in dependency of one average linear coupling factor 〈α〉τ. We test the validity of the kinetics in simulations of dialanine and compare dihedral transition kinetics with long-time MD-simulations. We find that for low 〈α〉τ values, kinetics are in good quantitative agreement. In folding simulations of TrpCage and TrpZip4 in explicit solvent, we also find good quantitative agreement with experimental results and prior MD/kMC simulations. Finally, we apply our algorithm to study growth of the Alzheimer Amyloid Aβ 16-22 fibril by monomer addition. We observe two possible binding modes, one at the extremity of the fibril (elongation) and one on the surface of the fibril (lateral growth), on timescales ranging from ns to 8 μs.
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Affiliation(s)
- Emanuel K Peter
- Department of Pharmacy and Chemistry, Institute of Physical and Theoretical Chemistry, University of Regensburg, Germany
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16
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Aussems DUB, Bal KM, Morgan TW, van de Sanden MCM, Neyts EC. Atomistic simulations of graphite etching at realistic time scales. Chem Sci 2017; 8:7160-7168. [PMID: 29081947 PMCID: PMC5635421 DOI: 10.1039/c7sc02763j] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2017] [Accepted: 08/23/2017] [Indexed: 11/21/2022] Open
Abstract
Hydrogen-graphite interactions are relevant to a wide variety of applications, ranging from astrophysics to fusion devices and nano-electronics. In order to shed light on these interactions, atomistic simulation using Molecular Dynamics (MD) has been shown to be an invaluable tool. It suffers, however, from severe time-scale limitations. In this work we apply the recently developed Collective Variable-Driven Hyperdynamics (CVHD) method to hydrogen etching of graphite for varying inter-impact times up to a realistic value of 1 ms, which corresponds to a flux of ∼1020 m-2 s-1. The results show that the erosion yield, hydrogen surface coverage and species distribution are significantly affected by the time between impacts. This can be explained by the higher probability of C-C bond breaking due to the prolonged exposure to thermal stress and the subsequent transition from ion- to thermal-induced etching. This latter regime of thermal-induced etching - chemical erosion - is here accessed for the first time using atomistic simulations. In conclusion, this study demonstrates that accounting for long time-scales significantly affects ion bombardment simulations and should not be neglected in a wide range of conditions, in contrast to what is typically assumed.
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Affiliation(s)
- D U B Aussems
- DIFFER - Dutch Institute for Fundamental Energy Research , De Zaale 20 , 5612 AJ Eindhoven , The Netherlands .
| | - K M Bal
- University of Antwerp , Department of Chemistry , PLASMANT Research Group , Universiteitsplein 1 , 2610 Antwerp , Belgium
| | - T W Morgan
- DIFFER - Dutch Institute for Fundamental Energy Research , De Zaale 20 , 5612 AJ Eindhoven , The Netherlands .
| | - M C M van de Sanden
- DIFFER - Dutch Institute for Fundamental Energy Research , De Zaale 20 , 5612 AJ Eindhoven , The Netherlands .
- Eindhoven University of Technology , PO Box 513 , 5600 MB Eindhoven , The Netherlands
| | - E C Neyts
- University of Antwerp , Department of Chemistry , PLASMANT Research Group , Universiteitsplein 1 , 2610 Antwerp , Belgium
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17
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Peter EK, Shea JE, Pivkin IV. Coarse kMC-based replica exchange algorithms for the accelerated simulation of protein folding in explicit solvent. Phys Chem Chem Phys 2016; 18:13052-65. [DOI: 10.1039/c5cp06867c] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
In this paper, we present a coarse replica exchange molecular dynamics (REMD) approach, based on kinetic Monte Carlo (kMC).
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Affiliation(s)
- Emanuel K. Peter
- Institute of Computational Science
- Faculty of Informatics
- University of Lugano
- Switzerland
| | - Joan-Emma Shea
- Department of Chemistry and Biochemistry
- Department of Physics
- University of California
- Santa Barbara
- USA
| | - Igor V. Pivkin
- Institute of Computational Science
- Faculty of Informatics
- University of Lugano
- Switzerland
- Swiss Institute of Bioinformatics
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18
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Bal KM, Neyts EC. Merging Metadynamics into Hyperdynamics: Accelerated Molecular Simulations Reaching Time Scales from Microseconds to Seconds. J Chem Theory Comput 2015; 11:4545-54. [DOI: 10.1021/acs.jctc.5b00597] [Citation(s) in RCA: 66] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Kristof M. Bal
- Department
of Chemistry, University of Antwerp, Universiteitsplein 1, 2610 Wilrijk, Antwerp, Belgium
| | - Erik C. Neyts
- Department
of Chemistry, University of Antwerp, Universiteitsplein 1, 2610 Wilrijk, Antwerp, Belgium
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19
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Affiliation(s)
- Zachary A. Levine
- Department
of Physics, University of California Santa Barbara, Santa Barbara, California 93106, United States
- Department
of Chemistry and Biochemistry, University of California Santa Barbara, Santa
Barbara, California 93106, United States
| | - Sean A. Fischer
- Department
of Chemical Engineering, University of Washington, Seattle, Washington 98105, United States
| | - Joan-Emma Shea
- Department
of Physics, University of California Santa Barbara, Santa Barbara, California 93106, United States
- Department
of Chemistry and Biochemistry, University of California Santa Barbara, Santa
Barbara, California 93106, United States
| | - Jim Pfaendtner
- Department
of Chemical Engineering, University of Washington, Seattle, Washington 98105, United States
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20
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Zhang T, Nguyen PH, Nasica-Labouze J, Mu Y, Derreumaux P. Folding Atomistic Proteins in Explicit Solvent Using Simulated Tempering. J Phys Chem B 2015; 119:6941-51. [PMID: 25985144 DOI: 10.1021/acs.jpcb.5b03381] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Following a previous report on a coarse-grained protein model in implicit solvent, we applied simulated tempering (ST) with on-the-fly Helmholtz free energy (weight factors) determination to the folding or aggregation of seven proteins with the CHARMM, OPLS, and AMBER protein, and the SPC and TIP3P water force fields. For efficiency and reliability, we also performed replica exchange molecular dynamics (REMD) simulations on the alanine di- and deca-peptide, and the dimer of the Aβ16-22 Alzheimer's fragment, and used experimental data and previous simulation results on the chignolin, beta3s, Trp-cage, and WW domain peptides of 10-37 amino acids. The sampling with ST is found to be more efficient than with REMD for a much lower CPU cost. Starting from unfolded or extended conformations, the WW domain and the Trp-cage peptide fold to their NMR structures with a backbone RMSD of 2.0 and 1 Å. Remarkably, the ST simulation explores transient non-native topologies for Trp-cage that have been rarely discussed by other simulations. Our ST simulations also show that the CHARMM22* force field has limitations in describing accurately the beta3s peptide. Taken together, these results open the door to the study of the configurations of single proteins, protein aggregates, and any molecular systems at atomic details in explicit solvent using a single normal CPU. They also demonstrate that our ST scheme can be used with any force field ranging from quantum mechanics to coarse-grain and atomistic.
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Affiliation(s)
- Tong Zhang
- †Laboratoire de Biochimie Théorique, UPR 9080 CNRS, Université Denis Diderot, Sorbonne Paris Cité, IBPC, 13 rue Pierre et Marie Curie, 75005 Paris, France.,‡School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551, Singapore
| | - Phuong H Nguyen
- †Laboratoire de Biochimie Théorique, UPR 9080 CNRS, Université Denis Diderot, Sorbonne Paris Cité, IBPC, 13 rue Pierre et Marie Curie, 75005 Paris, France
| | - Jessica Nasica-Labouze
- †Laboratoire de Biochimie Théorique, UPR 9080 CNRS, Université Denis Diderot, Sorbonne Paris Cité, IBPC, 13 rue Pierre et Marie Curie, 75005 Paris, France.,§International School of Advanced Studies (SISSA), Via Bonomea, 265, 34126 Trieste, Italy
| | - Yuguang Mu
- ‡School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551, Singapore
| | - Philippe Derreumaux
- †Laboratoire de Biochimie Théorique, UPR 9080 CNRS, Université Denis Diderot, Sorbonne Paris Cité, IBPC, 13 rue Pierre et Marie Curie, 75005 Paris, France.,∥Institut Universitaire de France, 103 Boulevard Saint-Michel, 75005 Paris, France
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21
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Peter EK, Pivkin IV, Shea JE. A kMC-MD method with generalized move-sets for the simulation of folding of α-helical and β-stranded peptides. J Chem Phys 2015; 142:144903. [DOI: 10.1063/1.4915919] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Affiliation(s)
- Emanuel K. Peter
- Faculty of Informatics, Institute of Computational Science, University of Lugano, Lugano, Switzerland
| | - Igor V. Pivkin
- Faculty of Informatics, Institute of Computational Science, University of Lugano, Lugano, Switzerland
| | - Joan-Emma Shea
- Department of Chemistry and Biochemistry, and Department of Physics, University of California, Santa Barbara, California 93106, USA
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22
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Kabbe G, Wehmeyer C, Sebastiani D. A Coupled Molecular Dynamics/Kinetic Monte Carlo Approach for Protonation Dynamics in Extended Systems. J Chem Theory Comput 2014; 10:4221-8. [DOI: 10.1021/ct500482k] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Gabriel Kabbe
- Institute
of Chemistry for Physical Chemistry, Martin-Luther-University Halle-Wittenberg, von-Danckelmann-Platz
4, 06120 Halle, Germany
| | - Christoph Wehmeyer
- Institute
of Mathematics, Freie Universität Berlin, Arnimallee 14, 14195 Berlin, Germany
| | - Daniel Sebastiani
- Institute
of Chemistry for Physical Chemistry, Martin-Luther-University Halle-Wittenberg, von-Danckelmann-Platz
4, 06120 Halle, Germany
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23
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Zhong ED, Shirts MR. Thermodynamics of coupled protein adsorption and stability using hybrid Monte Carlo simulations. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2014; 30:4952-4961. [PMID: 24716898 DOI: 10.1021/la500511p] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
A better understanding of changes in protein stability upon adsorption can improve the design of protein separation processes. In this study, we examine the coupling of the folding and the adsorption of a model protein, the B1 domain of streptococcal protein G, as a function of surface attraction using a hybrid Monte Carlo (HMC) approach with temperature replica exchange and umbrella sampling. In our HMC implementation, we are able to use a molecular dynamics (MD) time step that is an order of magnitude larger than in a traditional MD simulation protocol and observe a factor of 2 enhancement in the folding and unfolding rate. To demonstrate the convergence of our systems, we measure the travel of our order parameter the fraction of native contacts between folded and unfolded states throughout the length of our simulations. Thermodynamic quantities are extracted with minimum statistical variance using multistate reweighting between simulations at different temperatures and harmonic distance restraints from the surface. The resultant free energies, enthalpies, and entropies of the coupled unfolding and absorption processes are in qualitative agreement with previous experimental and computational observations, including entropic stabilization of the adsorbed, folded state relative to the bulk on surfaces with low attraction.
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Affiliation(s)
- Ellen D Zhong
- Department of Chemical Engineering, University of Virginia , Charlottesville, Virginia 22904, United States
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24
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Orevi T, Rahamim G, Shemesh S, Ben Ishay E, Amir D, Haas E. Fast closure of long loops at the initiation of the folding transition of globular proteins studied by time-resolved FRET-based methods. BIO-ALGORITHMS AND MED-SYSTEMS 2014. [DOI: 10.1515/bams-2014-0018] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
AbstractThe protein folding problem would be considered “solved” when it will be possible to “read genes”, i.e., to predict the native fold of proteins, their dynamics, and the mechanism of fast folding based solely on sequence data. The long-term goal should be the creation of an algorithm that would simulate the stepwise mechanism of folding, which constrains the conformational space and in which random search for stable interactions is possible. Here, we focus attention on the initial phases of the folding transition starting with the compact disordered collapsed ensemble, in search of the initial sub-domain structural biases that direct the otherwise stochastic dynamics of the backbone. Our studies are designed to test the “loop hypothesis”, which suggests that fast closure of long loop structures by non-local interactions between clusters of mainly non-polar residues is an essential conformational step at the initiation of the folding transition of globular proteins. We developed and applied experimental methods based on time-resolved resonance excitation energy transfer (trFRET) measurements combined with fast mixing methods and studied the initial phases of the folding of
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25
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Mandal M, Mukhopadhyay C. Microsecond molecular dynamics simulation of guanidinium chloride induced unfolding of ubiquitin. Phys Chem Chem Phys 2014; 16:21706-16. [DOI: 10.1039/c4cp01657b] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
All atom molecular dynamics simulations have been used to explore the atomic detail mechanism of guanidinium induced unfolding of the protein ubiquitin.
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Affiliation(s)
- Manoj Mandal
- Department of Chemistry
- University of Calcutta
- Kolkata – 700 009, India
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