1
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Galano‐Frutos JJ, Sancho J. Energy, water, and protein folding: A molecular dynamics-based quantitative inventory of molecular interactions and forces that make proteins stable. Protein Sci 2024; 33:e4905. [PMID: 38284492 PMCID: PMC10804899 DOI: 10.1002/pro.4905] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2023] [Revised: 12/12/2023] [Accepted: 01/05/2024] [Indexed: 01/30/2024]
Abstract
Protein folding energetics can be determined experimentally on a case-by-case basis but it is not understood in sufficient detail to provide deep control in protein design. The fundamentals of protein stability have been outlined by calorimetry, protein engineering, and biophysical modeling, but these approaches still face great difficulty in elucidating the specific contributions of the intervening molecules and physical interactions. Recently, we have shown that the enthalpy and heat capacity changes associated to the protein folding reaction can be calculated within experimental error using molecular dynamics simulations of native protein structures and their corresponding unfolded ensembles. Analyzing in depth molecular dynamics simulations of four model proteins (CI2, barnase, SNase, and apoflavodoxin), we dissect here the energy contributions to ΔH (a key component of protein stability) made by the molecular players (polypeptide and solvent molecules) and physical interactions (electrostatic, van der Waals, and bonded) involved. Although the proteins analyzed differ in length, isoelectric point and fold class, their folding energetics is governed by the same quantitative pattern. Relative to the unfolded ensemble, the native conformations are enthalpically stabilized by comparable contributions from protein-protein and solvent-solvent interactions, and almost equally destabilized by interactions between protein and solvent molecules. The native protein surface seems to interact better with water than the unfolded one, but this is outweighed by the unfolded surface being larger. From the perspective of physical interactions, the native conformations are stabilized by van de Waals and Coulomb interactions and destabilized by conformational strain arising from bonded interactions. Also common to the four proteins, the sign of the heat capacity change is set by interactions between protein and solvent molecules or, from the alternative perspective, by Coulomb interactions.
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Affiliation(s)
- Juan José Galano‐Frutos
- Biocomputation and Complex Systems Physics Institute (BIFI)‐Joint Unit GBsC‐CSICUniversity of ZaragozaZaragozaSpain
- Departamento de Bioquímica y Biología Molecular y Celular, Facultad de CienciasUniversity of ZaragozaZaragozaSpain
| | - Javier Sancho
- Biocomputation and Complex Systems Physics Institute (BIFI)‐Joint Unit GBsC‐CSICUniversity of ZaragozaZaragozaSpain
- Departamento de Bioquímica y Biología Molecular y Celular, Facultad de CienciasUniversity of ZaragozaZaragozaSpain
- Aragon Health Research Institute (IIS Aragón)ZaragozaSpain
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2
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Lazzeri G, Jung H, Bolhuis PG, Covino R. Molecular Free Energies, Rates, and Mechanisms from Data-Efficient Path Sampling Simulations. J Chem Theory Comput 2023; 19:9060-9076. [PMID: 37988412 PMCID: PMC10753783 DOI: 10.1021/acs.jctc.3c00821] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2023] [Revised: 10/24/2023] [Accepted: 10/24/2023] [Indexed: 11/23/2023]
Abstract
Molecular dynamics is a powerful tool for studying the thermodynamics and kinetics of complex molecular events. However, these simulations can rarely sample the required time scales in practice. Transition path sampling overcomes this limitation by collecting unbiased trajectories and capturing the relevant events. Moreover, the integration of machine learning can boost the sampling while simultaneously learning a quantitative representation of the mechanism. Still, the resulting trajectories are by construction non-Boltzmann-distributed, preventing the calculation of free energies and rates. We developed an algorithm to approximate the equilibrium path ensemble from machine-learning-guided path sampling data. At the same time, our algorithm provides efficient sampling, mechanism, free energy, and rates of rare molecular events at a very moderate computational cost. We tested the method on the folding of the mini-protein chignolin. Our algorithm is straightforward and data-efficient, opening the door to applications in many challenging molecular systems.
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Affiliation(s)
- Gianmarco Lazzeri
- Frankfurt
Institute for Advanced Studies, Frankfurt am Main, 60438, Germany
- Goethe
University Frankfurt, Frankfurt
am Main, 60438, Germany
| | - Hendrik Jung
- Goethe
University Frankfurt, Frankfurt
am Main, 60438, Germany
- Department
of Theoretical Biophysics, Max Planck Institute
of Biophysics, Frankfurt
am Main, 60438, Germany
| | - Peter G. Bolhuis
- Van’t
Hoff Institute for Molecular Sciences, University
of Amsterdam, Amsterdam, 1090GD, The Netherlands
| | - Roberto Covino
- Frankfurt
Institute for Advanced Studies, Frankfurt am Main, 60438, Germany
- Goethe
University Frankfurt, Frankfurt
am Main, 60438, Germany
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3
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Galano-Frutos JJ, Nerín-Fonz F, Sancho J. Calculation of Protein Folding Thermodynamics Using Molecular Dynamics Simulations. J Chem Inf Model 2023; 63:7791-7806. [PMID: 37955428 PMCID: PMC10751793 DOI: 10.1021/acs.jcim.3c01107] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2023] [Revised: 10/18/2023] [Accepted: 10/18/2023] [Indexed: 11/14/2023]
Abstract
Despite advances in artificial intelligence methods, protein folding remains in many ways an enigma to be solved. Accurate computation of protein folding energetics could help drive fields such as protein and drug design and genetic interpretation. However, the challenge of calculating the state functions governing protein folding from first-principles remains unaddressed. We present here a simple approach that allows us to accurately calculate the energetics of protein folding. It is based on computing the energy of the folded and unfolded states at different temperatures using molecular dynamics simulations. From this, two essential quantities (ΔH and ΔCp) are obtained and used to calculate the conformational stability of the protein (ΔG). With this approach, we have successfully calculated the energetics of two- and three-state proteins, representatives of the major structural classes, as well as small stability differences (ΔΔG) due to changes in solution conditions or variations in an amino acid residue.
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Affiliation(s)
- Juan J. Galano-Frutos
- Department
of Biochemistry, Molecular and Cell Biology, Faculty of Science, University of Zaragoza, 50009 Zaragoza, Spain
- Biocomputation
and Complex Systems Physics Institute (BIFI), Joint Unit GBs-CSIC, University of Zaragoza, 50018 Zaragoza, Spain
| | - Francho Nerín-Fonz
- Department
of Biochemistry, Molecular and Cell Biology, Faculty of Science, University of Zaragoza, 50009 Zaragoza, Spain
| | - Javier Sancho
- Department
of Biochemistry, Molecular and Cell Biology, Faculty of Science, University of Zaragoza, 50009 Zaragoza, Spain
- Biocomputation
and Complex Systems Physics Institute (BIFI), Joint Unit GBs-CSIC, University of Zaragoza, 50018 Zaragoza, Spain
- Aragon
Health Research Institute (IIS Aragón), 50009 Zaragoza, Spain
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4
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Galata AA, Kröger M. Globular Proteins and Where to Find Them within a Polymer Brush-A Case Study. Polymers (Basel) 2023; 15:polym15102407. [PMID: 37242983 DOI: 10.3390/polym15102407] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2023] [Revised: 05/15/2023] [Accepted: 05/19/2023] [Indexed: 05/28/2023] Open
Abstract
Protein adsorption by polymerized surfaces is an interdisciplinary topic that has been approached in many ways, leading to a plethora of theoretical, numerical and experimental insight. There is a wide variety of models trying to accurately capture the essence of adsorption and its effect on the conformations of proteins and polymers. However, atomistic simulations are case-specific and computationally demanding. Here, we explore universal aspects of the dynamics of protein adsorption through a coarse-grained (CG) model, that allows us to explore the effects of various design parameters. To this end, we adopt the hydrophobic-polar (HP) model for proteins, place them uniformly at the upper bound of a CG polymer brush whose multibead-spring chains are tethered to a solid implicit wall. We find that the most crucial factor affecting the adsorption efficiency appears to be the polymer grafting density, while the size of the protein and its hydrophobicity ratio come also into play. We discuss the roles of ligands and attractive tethering surfaces to the primary adsorption as well as secondary and ternary adsorption in the presence of attractive (towards the hydrophilic part of the protein) beads along varying spots of the backbone of the polymer chains. The percentage and rate of adsorption, density profiles and the shapes of the proteins, alongside with the respective potential of mean force are recorded to compare the various scenarios during protein adsorption.
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Affiliation(s)
- Aikaterini A Galata
- Magnetism and Interface Physics, Department of Materials, ETH Zurich, CH-8093 Zurich, Switzerland
| | - Martin Kröger
- Magnetism and Interface Physics, Department of Materials, ETH Zurich, CH-8093 Zurich, Switzerland
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5
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Pampel B, Holbach S, Hartung L, Valsson O. Sampling rare event energy landscapes via birth-death augmented dynamics. Phys Rev E 2023; 107:024141. [PMID: 36932520 DOI: 10.1103/physreve.107.024141] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2022] [Accepted: 12/21/2022] [Indexed: 06/18/2023]
Abstract
A common problem that affects simulations of complex systems within the computational physics and chemistry communities is the so-called sampling problem or rare event problem where proper sampling of energy landscapes is impeded by the presences of high kinetic barriers that hinder transitions between metastable states on typical simulation time scales. Many enhanced sampling methods have been developed to address this sampling problem and more efficiently sample rare event systems. An interesting idea, coming from the field of statistics, was introduced in a recent work [Lu, Lu, and Nolen, Accelerating Langevin sampling with birth-death, arXiv:1905.09863] in the form of a novel sampling algorithm that augments overdamped Langevin dynamics with a birth-death process. In this work, we expand on this idea and show that this birth-death sampling scheme can efficiently sample prototypical rare event energy landscapes, and that the speed of equilibration is independent of the barrier height. We amend a crucial shortcoming of the original algorithm that leads to incorrect sampling of barrier regions by introducing an alternative approximation of the birth-death term. We establish important theoretical properties of the modified algorithm and prove mathematically that the relevant convergence results still hold. We investigate via numerical simulations the effect of various parameters, and we investigate ways to reduce the computational effort of the sampling scheme. We show that the birth-death mechanism can be used to accelerate sampling in the more general case of underdamped Langevin dynamics that is more commonly used in simulating physical systems. Our results show that this birth-death scheme is a promising method for sampling rare event energy landscapes.
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Affiliation(s)
- Benjamin Pampel
- Max Planck Institute for Polymer Research, Ackermannweg 10, 55128 Mainz, Germany
| | - Simon Holbach
- Institut für Mathematik, Johannes Gutenberg-Universität Mainz, Staudingerweg 9, 55099 Mainz, Germany
| | - Lisa Hartung
- Institut für Mathematik, Johannes Gutenberg-Universität Mainz, Staudingerweg 9, 55099 Mainz, Germany
| | - Omar Valsson
- Max Planck Institute for Polymer Research, Ackermannweg 10, 55128 Mainz, Germany
- Department of Chemistry, University of North Texas, Denton, Texas, USA
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6
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Yang J, Cheng WX, Zhao XF, Wu G, Sheng ST, Hu Q, Ge H, Qin Q, Jin X, Zhang L, Zhang P. Comprehensive folding variations for protein folding. Proteins 2022; 90:1851-1872. [DOI: 10.1002/prot.26381] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2022] [Revised: 04/12/2022] [Accepted: 04/22/2022] [Indexed: 11/12/2022]
Affiliation(s)
- Jiaan Yang
- Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences Shenzhen Guangdong China
- Micro Biotech, Ltd. Shanghai China
| | - Wen Xiang Cheng
- Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences Shenzhen Guangdong China
| | | | - Gang Wu
- School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology Wuhan China
| | - Shi Tong Sheng
- Shenzhen Hua Ying Kang Gene Technology Co., Ltd Shenzhen Guangdong China
| | - Qiyue Hu
- Shanghai Hengrui Pharmaceutical Co. Ltd. Shanghai China
| | - Hu Ge
- Shanghai Hengrui Pharmaceutical Co. Ltd. Shanghai China
| | - Qianshan Qin
- Shanghai Hengrui Pharmaceutical Co. Ltd. Shanghai China
| | - Xinshen Jin
- Shanghai Hengrui Pharmaceutical Co. Ltd. Shanghai China
| | | | - Peng Zhang
- Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences Shenzhen Guangdong China
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7
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Abstract
Constantly advancing computer simulations of biomolecules provide huge amounts of data that are difficult to interpret. In particular, obtaining insights into functional aspects of macromolecular dynamics, often related to cascades of transient events, calls for methodologies that depart from the well-grounded framework of equilibrium statistical physics. One of the approaches toward the analysis of complex temporal data which has found applications in the fields of neuroscience and econometrics is Granger causality analysis. It allows determining which components of multidimensional time series are most influential for the evolution of the entire system, thus providing insights into causal relations within the dynamic structure of interest. In this work, we apply Granger analysis to a long molecular dynamics trajectory depicting repetitive folding and unfolding of a mini β-hairpin protein, CLN025. We find objective, quantitative evidence indicating that rearrangements within the hairpin turn region are determinant for protein folding and unfolding. On the contrary, interactions between hairpin arms score low on the causality scale. Taken together, these findings clearly favor the concept of zipperlike folding, which is one of two postulated β-hairpin folding mechanisms. More importantly, the results demonstrate the possibility of a conclusive application of Granger causality analysis to a biomolecular system.
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Affiliation(s)
- Marcin Sobieraj
- Faculty of Physics, University of Warsaw, Pasteura 5, 02-093 Warsaw, Poland.,Centre of New Technologies, University of Warsaw, Banacha 2c, 02-097 Warsaw, Poland
| | - Piotr Setny
- Centre of New Technologies, University of Warsaw, Banacha 2c, 02-097 Warsaw, Poland
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8
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Abstract
Unbiased molecular dynamics simulations of proteins can now capture spontaneous folding events. This provides a wealth of data reflecting information on folding mechanism, but raises the challenge of interpreting it in a meaningful way. Here, I describe how such simulations can be used to identify reactive states and reaction coordinates for describing folding, and how folding dynamics can be captured by projection onto those coordinates. Methods are described for quantifying the interactions important for defining the folding mechanism, and for comparison of simulations with experimental mechanistic probes, such as ϕ-values.
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Affiliation(s)
- Robert B Best
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, USA.
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9
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Zhang C, Zhao DX, Feng Y, Wang J, Yang ZZ. Energetics and J-coupling constants for Ala, Gly, and Val peptides demonstrated using ABEEM polarizable force field in vacuo and an aqueous solution. Phys Chem Chem Phys 2022; 24:4232-4250. [DOI: 10.1039/d1cp05676j] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The development of an atom-bond electronegativity equalisation method at the σπ-level (ABEEM) polarisable force field (PFF) for peptides is presented. ABEEM PFF utilises a fluctuating charge model to explicitly describe...
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10
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Mothi N, Muñoz V. Protein Folding Dynamics as Diffusion on a Free Energy Surface: Rate Equation Terms, Transition Paths, and Analysis of Single-Molecule Photon Trajectories. J Phys Chem B 2021; 125:12413-12425. [PMID: 34735144 DOI: 10.1021/acs.jpcb.1c05401] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The rates of protein (un)folding are often described as diffusion on the projection of a hyperdimensional energy landscape onto a few (ideally one) order parameters. Testing such an approximation by experiment requires resolving the reactive transition paths of individual molecules, which is now becoming feasible with advanced single-molecule spectroscopic techniques. This has also sparked the interest of theorists in better understanding reactive transition paths. Here we focus on these issues aiming to establish (i) practical guidelines for the mechanistic interpretation of transition path times (TPT) and (ii) methods to extract the free energy surface and protein dynamics from the maximum likelihood analysis of photon trajectories (MLA-PT). We represent the (un)folding rates as diffusion on a 1D free energy surface with the FRET efficiency as a reaction coordinate proxy. We then perform diffusive kinetic simulations on surfaces with two minima and a barrier, but with different shapes (curvatures, barrier height, and symmetry), coupled to stochastic simulations of photon emissions that reproduce current SM-FRET experiments. From the analysis of transition paths, we find that the TPT is inversely proportional to the barrier height (difference in free energy between minimum and barrier top) for any given surface shape, and that dividing the TPT into climb and descent segments provides key information about the barrier's symmetry. We also find that the original MLA-PT procedure used to determine the TPT from experiments underestimates its value, particularly for the cases with smaller barriers (e.g., fast folders), and we suggest a simple strategy to correct for this bias. Importantly, we also demonstrate that photon trajectories contain enough information to extract the 1D free energy surface's shape and dynamics (if TPT is >4-5-fold longer than the interphoton time) using the MLA-PT directly implemented with a diffusive free energy surface model. When dealing with real (unknown) experimental data, the comparison between the likelihoods of the free energy surface and discrete kinetic three-state models can be used to evaluate the statistical significance of the estimated free energy surface.
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Affiliation(s)
- Nivin Mothi
- NSF-CREST Center for Cellular and Biomolecular Machines (CCBM), University of California, Merced, 95343 California, United States.,Chemistry and Chemical Biology Graduate Program, University of California, Merced, 95343 California, United States
| | - Victor Muñoz
- NSF-CREST Center for Cellular and Biomolecular Machines (CCBM), University of California, Merced, 95343 California, United States.,Chemistry and Chemical Biology Graduate Program, University of California, Merced, 95343 California, United States.,Department of Bioengineering, University of California, Merced, 95343 California, United States
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11
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Dingfelder F, Macocco I, Benke S, Nettels D, Faccioli P, Schuler B. Slow Escape from a Helical Misfolded State of the Pore-Forming Toxin Cytolysin A. JACS AU 2021; 1:1217-1230. [PMID: 34467360 PMCID: PMC8397351 DOI: 10.1021/jacsau.1c00175] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/20/2021] [Indexed: 05/12/2023]
Abstract
The pore-forming toxin cytolysin A (ClyA) is expressed as a large α-helical monomer that, upon interaction with membranes, undergoes a major conformational rearrangement into the protomer conformation, which then assembles into a cytolytic pore. Here, we investigate the folding kinetics of the ClyA monomer with single-molecule Förster resonance energy transfer spectroscopy in combination with microfluidic mixing, stopped-flow circular dichroism experiments, and molecular simulations. The complex folding process occurs over a broad range of time scales, from hundreds of nanoseconds to minutes. The very slow formation of the native state occurs from a rapidly formed and highly collapsed intermediate with large helical content and nonnative topology. Molecular dynamics simulations suggest pronounced non-native interactions as the origin of the slow escape from this deep trap in the free-energy surface, and a variational enhanced path-sampling approach enables a glimpse of the folding process that is supported by the experimental data.
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Affiliation(s)
- Fabian Dingfelder
- Department
of Biochemistry, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
| | - Iuri Macocco
- Department
of Physics, Trento University, Via Sommarive 14, 38123 Povo (Trento), Italy
- SISSA, Via Bonomea 265, 34136 Trieste, Italy
| | - Stephan Benke
- Department
of Biochemistry, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
| | - Daniel Nettels
- Department
of Biochemistry, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
| | - Pietro Faccioli
- Department
of Physics, Trento University, Via Sommarive 14, 38123 Povo (Trento), Italy
- INFN-TIFPA, Via Sommarive 14, 38123 Povo (Trento), Italy
| | - Benjamin Schuler
- Department
of Biochemistry, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
- Department
of Physics, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
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12
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Suay-Corredera C, Pricolo MR, Velázquez-Carreras D, Pathak D, Nandwani N, Pimenta-Lopes C, Sánchez-Ortiz D, Urrutia-Irazabal I, Vilches S, Dominguez F, Frisso G, Monserrat L, García-Pavía P, de Sancho D, Spudich JA, Ruppel KM, Herrero-Galán E, Alegre-Cebollada J. Nanomechanical Phenotypes in Cardiac Myosin-Binding Protein C Mutants That Cause Hypertrophic Cardiomyopathy. ACS NANO 2021; 15:10203-10216. [PMID: 34060810 PMCID: PMC8514129 DOI: 10.1021/acsnano.1c02242] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Hypertrophic cardiomyopathy (HCM) is a disease of the myocardium caused by mutations in sarcomeric proteins with mechanical roles, such as the molecular motor myosin. Around half of the HCM-causing genetic variants target contraction modulator cardiac myosin-binding protein C (cMyBP-C), although the underlying pathogenic mechanisms remain unclear since many of these mutations cause no alterations in protein structure and stability. As an alternative pathomechanism, here we have examined whether pathogenic mutations perturb the nanomechanics of cMyBP-C, which would compromise its modulatory mechanical tethers across sliding actomyosin filaments. Using single-molecule atomic force spectroscopy, we have quantified mechanical folding and unfolding transitions in cMyBP-C domains targeted by HCM mutations that do not induce RNA splicing alterations or protein thermodynamic destabilization. Our results show that domains containing mutation R495W are mechanically weaker than wild-type at forces below 40 pN and that R502Q mutant domains fold faster than wild-type. None of these alterations are found in control, nonpathogenic variants, suggesting that nanomechanical phenotypes induced by pathogenic cMyBP-C mutations contribute to HCM development. We propose that mutation-induced nanomechanical alterations may be common in mechanical proteins involved in human pathologies.
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Affiliation(s)
| | - Maria Rosaria Pricolo
- Centro Nacional de Investigaciones Cardiovasculares (CNIC), 28029, Madrid, Spain
- Dipartimento di Medicina Molecolare e Biotecnologie Mediche, Università di Napoli Federico II, 80131, Naples, Italy
| | | | - Divya Pathak
- Department of Biochemistry, Stanford University School of Medicine, Stanford, California 94305, United States
- Stanford Cardiovascular Institute, Stanford University School of Medicine, Stanford, California 94305, United States
| | - Neha Nandwani
- Department of Biochemistry, Stanford University School of Medicine, Stanford, California 94305, United States
- Stanford Cardiovascular Institute, Stanford University School of Medicine, Stanford, California 94305, United States
| | | | - David Sánchez-Ortiz
- Centro Nacional de Investigaciones Cardiovasculares (CNIC), 28029, Madrid, Spain
| | | | - Silvia Vilches
- Heart Failure and Inherited Cardiac Diseases Unit, Department of Cardiology, Hospital Universitario Puerta de Hierro, 28222, Madrid, Spain
- European Reference Network for Rare and Low Prevalence Complex Diseases of the Heart (ERN GUARD-HEART, http://guardheart.ern-net.eu/), 28222, Madrid, Spain
| | - Fernando Dominguez
- Centro Nacional de Investigaciones Cardiovasculares (CNIC), 28029, Madrid, Spain
- Heart Failure and Inherited Cardiac Diseases Unit, Department of Cardiology, Hospital Universitario Puerta de Hierro, 28222, Madrid, Spain
- European Reference Network for Rare and Low Prevalence Complex Diseases of the Heart (ERN GUARD-HEART, http://guardheart.ern-net.eu/), 28222, Madrid, Spain
- Centro de Investigación Biomédica en Red en Enfermedades Cardiovasculares (CIBERCV), 28029, Madrid, Spain
| | - Giulia Frisso
- Dipartimento di Medicina Molecolare e Biotecnologie Mediche, Università di Napoli Federico II, 80131, Naples, Italy
- CEINGE Biotecnologie Avanzate, scarl, 80145, Naples, Italy
| | | | - Pablo García-Pavía
- Heart Failure and Inherited Cardiac Diseases Unit, Department of Cardiology, Hospital Universitario Puerta de Hierro, 28222, Madrid, Spain
- European Reference Network for Rare and Low Prevalence Complex Diseases of the Heart (ERN GUARD-HEART, http://guardheart.ern-net.eu/), 28222, Madrid, Spain
- Centro de Investigación Biomédica en Red en Enfermedades Cardiovasculares (CIBERCV), 28029, Madrid, Spain
- Universidad Francisco de Vitoria (UFV), 28223, Pozuelo de Alarcón, Madrid, Spain
| | - David de Sancho
- Polimero eta Material Aurreratuak: Fisika, Kimika eta Teknologia, Kimika Fakultatea, Euskal Herriko Unibertsitatea UPV/EHU, 20018, Donostia-San Sebastián, Spain
- Donostia International Physics Center (DIPC), 20018, Donostia-San Sebastián, Spain
| | - James A Spudich
- Department of Biochemistry, Stanford University School of Medicine, Stanford, California 94305, United States
- Stanford Cardiovascular Institute, Stanford University School of Medicine, Stanford, California 94305, United States
| | - Kathleen M Ruppel
- Department of Biochemistry, Stanford University School of Medicine, Stanford, California 94305, United States
- Stanford Cardiovascular Institute, Stanford University School of Medicine, Stanford, California 94305, United States
| | - Elías Herrero-Galán
- Centro Nacional de Investigaciones Cardiovasculares (CNIC), 28029, Madrid, Spain
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13
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Fonseca G, Poltavsky I, Vassilev-Galindo V, Tkatchenko A. Improving molecular force fields across configurational space by combining supervised and unsupervised machine learning. J Chem Phys 2021; 154:124102. [DOI: 10.1063/5.0035530] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Affiliation(s)
- Gregory Fonseca
- Department of Physics and Materials Science, University of Luxembourg, L-1511 Luxembourg, Luxembourg
| | - Igor Poltavsky
- Department of Physics and Materials Science, University of Luxembourg, L-1511 Luxembourg, Luxembourg
| | - Valentin Vassilev-Galindo
- Department of Physics and Materials Science, University of Luxembourg, L-1511 Luxembourg, Luxembourg
| | - Alexandre Tkatchenko
- Department of Physics and Materials Science, University of Luxembourg, L-1511 Luxembourg, Luxembourg
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14
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Oliva F, Flores-Canales JC, Pieraccini S, Morelli CF, Sironi M, Schiøtt B. Simulating Multiple Substrate-Binding Events by γ-Glutamyltransferase Using Accelerated Molecular Dynamics. J Phys Chem B 2020; 124:10104-10116. [PMID: 33112625 DOI: 10.1021/acs.jpcb.0c06907] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
γ-Glutamyltransferase (GGT) is an enzyme that uses γ-glutamyl compounds as substrates and catalyzes their transfer to a water molecule or an acceptor substrate with varied physiological function in bacteria, plants, and animals. Crystal structures of GGT are known for different species and in different states of the chemical reaction; however, the structural dynamics of the substrate binding to the catalytic site of GGT are unknown. Here, we modeled Escherichia coli GGT's glutamine binding by using a swarm of accelerated molecular dynamics (aMD) simulations. Characterization of multiple binding events identified three structural binding motifs composed of polar residues in the binding pocket that govern glutamine binding into the active site. Simulated open and closed conformations of a lid-loop protecting the binding cavity suggest its role as a gating element by allowing or blocking substrates entry into the binding pocket. Partially open states of the lid-loop are accessible within thermal fluctuations, while the estimated free energy cost of a complete open state is 2.4 kcal/mol. Our results suggest that both specific electrostatic interactions and GGT conformational dynamics dictate the molecular recognition of substrate-GGT complexes.
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Affiliation(s)
- Francesco Oliva
- Dipartimento di Chimica, Università degli studi di Milano, Via Golgi 19, 20133 Milano, Italy
| | - Jose C Flores-Canales
- Department of Chemistry, Aarhus University, Langelandsgade 140, 8000 Aarhus, Denmark
| | - Stefano Pieraccini
- Dipartimento di Chimica, Università degli studi di Milano, Via Golgi 19, 20133 Milano, Italy
| | - Carlo F Morelli
- Dipartimento di Chimica, Università degli studi di Milano, Via Golgi 19, 20133 Milano, Italy
| | - Maurizio Sironi
- Dipartimento di Chimica, Università degli studi di Milano, Via Golgi 19, 20133 Milano, Italy
| | - Birgit Schiøtt
- Department of Chemistry, Aarhus University, Langelandsgade 140, 8000 Aarhus, Denmark
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15
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Liu N, Guo Y, Ning S, Duan M. Phosphorylation regulates the binding of intrinsically disordered proteins via a flexible conformation selection mechanism. Commun Chem 2020; 3:123. [PMID: 36703366 PMCID: PMC9814494 DOI: 10.1038/s42004-020-00370-5] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2020] [Accepted: 08/11/2020] [Indexed: 01/29/2023] Open
Abstract
Phosphorylation is one of the most common post-translational modifications. The phosphorylation of the kinase-inducible domain (KID), which is an intrinsically disordered protein (IDP), promotes the folding of KID and binding with the KID-interacting domain (KIX). However, the regulation mechanism of the phosphorylation on KID is still elusive. In this study, the structural ensembles and binding process of pKID and KIX are studied by all-atom enhanced sampling technologies. The results show that more hydrophobic interactions are formed in pKID, which promote the formation of the special hydrophobic residue cluster (HRC). The pre-formed HRC promotes binding to the correct sites of KIX and further lead the folding of pKID. Consequently, a flexible conformational selection model is proposed to describe the binding and folding process of intrinsically disordered proteins. The binding mechanism revealed in this work provides new insights into the dynamic interactions and phosphorylation regulation of proteins.
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Affiliation(s)
- Na Liu
- grid.458518.50000 0004 1803 4970Key Laboratory of magnetic Resonance in Biological Systems, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, National Center for Magnetic Resonance in Wuhan, Wuhan Institute of Physics and Mathematics, Chinese Academy of Sciences, Wuhan, 430071 People’s Republic of China ,grid.412969.10000 0004 1798 1968School of biological and pharmaceutical engineering, Wuhan Polytechnic University, Wuhan, 430023 People’s Republic of China
| | - Yue Guo
- grid.458518.50000 0004 1803 4970Key Laboratory of magnetic Resonance in Biological Systems, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, National Center for Magnetic Resonance in Wuhan, Wuhan Institute of Physics and Mathematics, Chinese Academy of Sciences, Wuhan, 430071 People’s Republic of China ,grid.410726.60000 0004 1797 8419University of Chinese Academy of Sciences, Beijing, 100049 People’s Republic of China
| | - Shangbo Ning
- grid.458518.50000 0004 1803 4970Key Laboratory of magnetic Resonance in Biological Systems, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, National Center for Magnetic Resonance in Wuhan, Wuhan Institute of Physics and Mathematics, Chinese Academy of Sciences, Wuhan, 430071 People’s Republic of China ,grid.412969.10000 0004 1798 1968School of biological and pharmaceutical engineering, Wuhan Polytechnic University, Wuhan, 430023 People’s Republic of China
| | - Mojie Duan
- grid.458518.50000 0004 1803 4970Key Laboratory of magnetic Resonance in Biological Systems, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, National Center for Magnetic Resonance in Wuhan, Wuhan Institute of Physics and Mathematics, Chinese Academy of Sciences, Wuhan, 430071 People’s Republic of China
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16
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Jayaraman A. 100th Anniversary of Macromolecular Science Viewpoint: Modeling and Simulation of Macromolecules with Hydrogen Bonds: Challenges, Successes, and Opportunities. ACS Macro Lett 2020; 9:656-665. [PMID: 35648569 DOI: 10.1021/acsmacrolett.0c00134] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Macromolecular materials with directional interactions such as hydrogen bonds exhibit numerous attractive features in terms of structure, thermodynamics, and dynamics. Besides enabling precise tuning of desirable geometries in the assembled state (e.g., programmable coordination numbers depending on the valency of the directional interaction), mixing in a blend/composite through stabilization via hydrogen bonds between the various components, hydrogen bonds can also impart responsiveness to external stimuli (e.g., temperature, pH). In biomacromolecules (e.g., proteins, DNA, polysaccharides), hydrogen bonds play a key role in stabilizing secondary and tertiary structures, which in turn define the function of these macromolecules. In this Viewpoint, I present the challenges, successes, and opportunities for molecular modeling and simulations to conduct fundamental and application-focused research on macromolecular materials with hydrogen bonding interactions. The past successes and limitations of atomistic simulations are discussed first, followed by highlights from recent developments in coarse-grained modeling and their use in studies of (synthetic and biologically relevant) macromolecular materials. Model development focused on polynucleotides (e.g., DNA, RNA, etc.), polypeptides, polysaccharides, and synthetic polymers at experimentally relevant conditions are highlighted. This viewpoint ends with potential future directions for macromolecular modeling and simulations with other types of directional interactions beyond hydrogen bonding.
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Affiliation(s)
- Arthi Jayaraman
- Department of Chemical and Biomolecular Engineering, University of Delaware, 150 Academy Street, Newark, Delaware 19716, United States
- Department of Materials Science and Engineering, University of Delaware, Newark, Delaware 19716, United States
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17
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Anumalla B, Prabhu NP. Surface hydration and preferential interaction directs the charged amino acids-induced changes in protein stability. J Mol Graph Model 2020; 98:107602. [PMID: 32251994 DOI: 10.1016/j.jmgm.2020.107602] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2019] [Revised: 03/20/2020] [Accepted: 03/23/2020] [Indexed: 01/23/2023]
Abstract
In the present study, we investigate the interaction of amino acid osmolytes, Arg, Lys, Asp and Glu, and a denaturant, guanidinium chloride (Gdm) with proteins. To achieve this, molecular dynamics (MD) simulation of RNase A and α-lactalbumin was performed in the presence of three charged amino acids Arg, Lys, and Asp and the molecular mechanism of amino acid-induced (de)stabilization of the proteins was examined by combining with our earlier report on Glu. As Arg has the side chain similar to that of Gdm and destabilizes the proteins, MD simulation was carried out in the presence of Gdm as well. Radial distribution function and hydration fraction around the protein surface reveals that preferential hydration increases upon the addition of any of the cosolvent; however, the extent of increase is more in the presence of stabilizing cosolvents (stAAs: Lys, Asp and Glu) compared to destabilizing cosolvents (Arg and Gdm). Moreover, the preferential interaction of Arg and Gdm with the proteins is higher than that of stAAs. Residue-level interaction analysis suggests that stAAs preferably interacts with charged amino acids of the proteins whereas Arg and Gdm interactions could be found on almost all the surface exposed residues which might provide higher preferential interaction for these residues. From the results, we propose that the net outcome of preferential hydration versus preferential interaction of the amino acids might determine their effect on the stability of proteins.
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Affiliation(s)
- Bramhini Anumalla
- Department of Biotechnology and Bioinformatics, School of Life Sciences, University of Hyderabad, Hyderabad, 500 046, India
| | - N Prakash Prabhu
- Department of Biotechnology and Bioinformatics, School of Life Sciences, University of Hyderabad, Hyderabad, 500 046, India.
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18
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Bastida A, Zúñiga J, Requena A, Cerezo J. Energetic Self-Folding Mechanism in α-Helices. J Phys Chem B 2019; 123:8186-8194. [PMID: 31498638 DOI: 10.1021/acs.jpcb.9b05860] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
A novel energetic route driving the folding of a polyalanine peptide from an extended conformation to its α-helix native conformation is described, supported by a new method to compute mean potential energy surfaces accurately in terms of the dihedral angles of the peptide chain from extensive molecular dynamics simulations. The energetic self-folding (ESF) route arises specifically from the balance between the intrinsic propensity of alanine residues toward the αR conformation and two, opposite, effects: the destabilizing interaction with neighbor residues and the stabilizing formation of native hydrogen bonds, with the latter being dominant for large peptide lengths. The ESF mechanism provides simple but robust support to the nucleation-elongation or zipper models and offers a quantitative energetic funnel picture of the folding process. The mechanism is validated by the reasonable agreement between the computed folding energies and the experimental values.
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Affiliation(s)
- Adolfo Bastida
- Departamento de Química Física , Universidad de Murcia , 30100 Murcia , Spain
| | - José Zúñiga
- Departamento de Química Física , Universidad de Murcia , 30100 Murcia , Spain
| | - Alberto Requena
- Departamento de Química Física , Universidad de Murcia , 30100 Murcia , Spain
| | - Javier Cerezo
- Departamento de Química Física , Universidad de Murcia , 30100 Murcia , Spain
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19
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de Sancho D, Aguirre A. MasterMSM: A Package for Constructing Master Equation Models of Molecular Dynamics. J Chem Inf Model 2019; 59:3625-3629. [DOI: 10.1021/acs.jcim.9b00468] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- David de Sancho
- University of the Basque Country, Faculty of Chemistry, Paseo Manuel Lardizabal, 3, 20018 Donostia-San Sebastián, Spain
- Donostia International Physics Center, 20018, Donostia-San Sebastián, Spain
| | - Anne Aguirre
- Donostia International Physics Center, 20018, Donostia-San Sebastián, Spain
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20
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Investigating the Formation of Structural Elements in Proteins Using Local Sequence-Dependent Information and a Heuristic Search Algorithm. Molecules 2019; 24:molecules24061150. [PMID: 30909488 PMCID: PMC6471799 DOI: 10.3390/molecules24061150] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2019] [Revised: 03/14/2019] [Accepted: 03/19/2019] [Indexed: 11/22/2022] Open
Abstract
Structural elements inserted in proteins are essential to define folding/unfolding mechanisms and partner recognition events governing signaling processes in living organisms. Here, we present an original approach to model the folding mechanism of these structural elements. Our approach is based on the exploitation of local, sequence-dependent structural information encoded in a database of three-residue fragments extracted from a large set of high-resolution experimentally determined protein structures. The computation of conformational transitions leading to the formation of the structural elements is formulated as a discrete path search problem using this database. To solve this problem, we propose a heuristically-guided depth-first search algorithm. The domain-dependent heuristic function aims at minimizing the length of the path in terms of angular distances, while maximizing the local density of the intermediate states, which is related to their probability of existence. We have applied the strategy to two small synthetic polypeptides mimicking two common structural motifs in proteins. The folding mechanisms extracted are very similar to those obtained when using traditional, computationally expensive approaches. These results show that the proposed approach, thanks to its simplicity and computational efficiency, is a promising research direction.
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21
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Meng F, Bellaiche MMJ, Kim JY, Zerze GH, Best RB, Chung HS. Highly Disordered Amyloid-β Monomer Probed by Single-Molecule FRET and MD Simulation. Biophys J 2019; 114:870-884. [PMID: 29490247 DOI: 10.1016/j.bpj.2017.12.025] [Citation(s) in RCA: 70] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2017] [Revised: 12/12/2017] [Accepted: 12/18/2017] [Indexed: 12/13/2022] Open
Abstract
Monomers of amyloid-β (Aβ) protein are known to be disordered, but there is considerable controversy over the existence of residual or transient conformations that can potentially promote oligomerization and fibril formation. We employed single-molecule Förster resonance energy transfer (FRET) spectroscopy with site-specific dye labeling using an unnatural amino acid and molecular dynamics simulations to investigate conformations and dynamics of Aβ isoforms with 40 (Aβ40) and 42 residues (Aβ42). The FRET efficiency distributions of both proteins measured in phosphate-buffered saline at room temperature show a single peak with very similar FRET efficiencies, indicating there is apparently only one state. 2D FRET efficiency-donor lifetime analysis reveals, however, that there is a broad distribution of rapidly interconverting conformations. Using nanosecond fluorescence correlation spectroscopy, we measured the timescale of the fluctuations between these conformations to be ∼35 ns, similar to that of disordered proteins. These results suggest that both Aβ40 and Aβ42 populate an ensemble of rapidly reconfiguring unfolded states, with no long-lived conformational state distinguishable from that of the disordered ensemble. To gain molecular-level insights into these observations, we performed molecular dynamics simulations with a force field optimized to describe disordered proteins. We find, as in experiments, that both peptides populate configurations consistent with random polymer chains, with the vast majority of conformations lacking significant secondary structure, giving rise to very similar ensemble-averaged FRET efficiencies.
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Affiliation(s)
- Fanjie Meng
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland
| | - Mathias M J Bellaiche
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland; Department of Chemistry, University of Cambridge, Cambridge, United Kingdom
| | - Jae-Yeol Kim
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland
| | - Gül H Zerze
- Department of Chemical and Biomolecular Engineering, Lehigh University, Bethlehem, Pennsylvania
| | - Robert B Best
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland.
| | - Hoi Sung Chung
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland.
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22
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Shao Q, Yang L, Zhu W. Selective enhanced sampling in dihedral energy facilitates overcoming the dihedral energy increase in protein folding and accelerates the searching for protein native structure. Phys Chem Chem Phys 2019; 21:10423-10435. [DOI: 10.1039/c9cp00615j] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A dihedral-energy-based selective enhanced sampling method (D-SITSMD) is presented with improved capabilities for searching a protein's natively folded structure and for providing the underlying folding pathway.
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Affiliation(s)
- Qiang Shao
- Drug Discovery and Design Center
- CAS Key Laboratory of Receptor Research
- Shanghai Institute of Materia Medica
- Chinese Academy of Sciences
- Shanghai
| | - Lijiang Yang
- Beijing National Laboratory for Molecular Sciences
- Beijing
- China
- Institute of Theoretical and Computational Chemistry
- College of Chemistry and Molecular Engineering, and Biodynamic Optical Imaging Center
| | - Weiliang Zhu
- Drug Discovery and Design Center
- CAS Key Laboratory of Receptor Research
- Shanghai Institute of Materia Medica
- Chinese Academy of Sciences
- Shanghai
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23
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Buckle AM, Borg NA. Integrating Experiment and Theory to Understand TCR-pMHC Dynamics. Front Immunol 2018; 9:2898. [PMID: 30581442 PMCID: PMC6293202 DOI: 10.3389/fimmu.2018.02898] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2018] [Accepted: 11/26/2018] [Indexed: 11/13/2022] Open
Abstract
The conformational dynamism of proteins is well established. Rather than having a single structure, proteins are more accurately described as a conformational ensemble that exists across a rugged energy landscape, where different conformational sub-states interconvert. The interaction between αβ T cell receptors (TCR) and cognate peptide-MHC (pMHC) is no exception, and is a dynamic process that involves substantial conformational change. This review focuses on technological advances that have begun to establish the role of conformational dynamics and dynamic allostery in TCR recognition of the pMHC and the early stages of signaling. We discuss how the marriage of molecular dynamics (MD) simulations with experimental techniques provides us with new ways to dissect and interpret the process of TCR ligation. Notably, application of simulation techniques lags behind other fields, but is predicted to make substantial contributions. Finally, we highlight integrated approaches that are being used to shed light on some of the key outstanding questions in the early events leading to TCR signaling.
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Affiliation(s)
- Ashley M Buckle
- Infection and Immunity Program, Monash Biomedicine Discovery Institute and Department of Biochemistry and Molecular Biology, Monash University, Clayton, VIC, Australia
| | - Natalie A Borg
- Infection and Immunity Program, Monash Biomedicine Discovery Institute and Department of Biochemistry and Molecular Biology, Monash University, Clayton, VIC, Australia
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24
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Hu G, Yu X, Bian Y, Cao Z, Xu S, Zhao L, Ji B, Wang W, Wang J. Atomistic Analysis of ToxN and ToxI Complex Unbinding Mechanism. Int J Mol Sci 2018; 19:E3524. [PMID: 30423909 PMCID: PMC6275071 DOI: 10.3390/ijms19113524] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2018] [Revised: 10/14/2018] [Accepted: 11/02/2018] [Indexed: 12/14/2022] Open
Abstract
ToxIN is a triangular structure formed by three protein toxins (ToxNs) and three specific noncoding RNA antitoxins (ToxIs). To respond to stimuli, ToxI is preferentially degraded, releasing the ToxN. Thus, the dynamic character is essential in the normal function interactions between ToxN and ToxI. Here, equilibrated molecular dynamics (MD) simulations were performed to study the stability of ToxN and ToxI. The results indicate that ToxI adjusts the conformation of 3' and 5' termini to bind to ToxN. Steered molecular dynamics (SMD) simulations combined with the recently developed thermodynamic integration in 3nD (TI3nD) method were carried out to investigate ToxN unbinding from the ToxIN complex. The potentials of mean force (PMFs) and atomistic pictures suggest the unbinding mechanism as follows: (1) dissociation of the 5' terminus from ToxN, (2) missing the interactions involved in the 3' terminus of ToxI without three nucleotides (G31, A32, and A33), (3) starting to unfold for ToxI, (4) leaving the binding package of ToxN for three nucleotides of ToxI, (5) unfolding of ToxI. This work provides information on the structure-function relationship at the atomistic level, which is helpful for designing new potent antibacterial drugs in the future.
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Affiliation(s)
- Guodong Hu
- Shandong Key Laboratory of Biophysics and Institutes of Biophysics, Dezhou University, Dezhou 253023, China.
| | - Xiu Yu
- Shandong Key Laboratory of Biophysics and Institutes of Biophysics, Dezhou University, Dezhou 253023, China.
| | - Yunqiang Bian
- Shandong Key Laboratory of Biophysics and Institutes of Biophysics, Dezhou University, Dezhou 253023, China.
| | - Zanxia Cao
- Shandong Key Laboratory of Biophysics and Institutes of Biophysics, Dezhou University, Dezhou 253023, China.
| | - Shicai Xu
- Shandong Key Laboratory of Biophysics and Institutes of Biophysics, Dezhou University, Dezhou 253023, China.
| | - Liling Zhao
- Shandong Key Laboratory of Biophysics and Institutes of Biophysics, Dezhou University, Dezhou 253023, China.
| | - Baohua Ji
- Shandong Key Laboratory of Biophysics and Institutes of Biophysics, Dezhou University, Dezhou 253023, China.
| | - Wei Wang
- National Laboratory of Solid State Microstructure and Department of Physics, Nanjing University, Nanjing 210093, China.
| | - Jihua Wang
- Shandong Key Laboratory of Biophysics and Institutes of Biophysics, Dezhou University, Dezhou 253023, China.
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25
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Chen J, Liu X, Chen J. Atomistic Peptide Folding Simulations Reveal Interplay of Entropy and Long-Range Interactions in Folding Cooperativity. Sci Rep 2018; 8:13668. [PMID: 30209295 PMCID: PMC6135771 DOI: 10.1038/s41598-018-32028-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2018] [Accepted: 08/30/2018] [Indexed: 11/23/2022] Open
Abstract
Understanding how proteins fold has remained a problem of great interest in biophysical research. Atomistic computer simulations using physics-based force fields can provide important insights on the interplay of different interactions and energetics and their roles in governing the folding thermodynamics and mechanism. In particular, generalized Born (GB)-based implicit solvent force fields can be optimized to provide an appropriate balance between solvation and intramolecular interactions and successfully recapitulate experimental conformational equilibria for a set of helical and β-hairpin peptides. Here, we further demonstrate that key thermodynamic properties and their temperature dependence obtained from replica exchange molecular dynamics simulations of these peptides are in quantitative agreement with experimental results. Useful lessons can be learned on how the interplay of entropy and sequentially long-range interactions governs the mechanism and cooperativity of folding. These results highlight the great potential of high-quality implicit solvent force fields for studying protein folding and large-scale conformational transitions.
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Affiliation(s)
- Jianlin Chen
- Department of Hematology, The Central Hospital of Taizhou, Taizhou, Zhejiang, 318000, P.R. China
| | - Xiaorong Liu
- Department of Chemistry, University of Massachusetts Amherst, Amherst, MA, 01003, 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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26
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Narayan B, Herbert C, Yuan Y, Rodriguez BJ, Brooks BR, Buchete NV. Conformational analysis of replica exchange MD: Temperature-dependent Markov networks for FF amyloid peptides. J Chem Phys 2018; 149:072323. [PMID: 30134732 DOI: 10.1063/1.5027580] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
Recent molecular modeling methods using Markovian descriptions of conformational states of biomolecular systems have led to powerful analysis frameworks that can accurately describe their complex dynamical behavior. In conjunction with enhanced sampling methods, such as replica exchange molecular dynamics (REMD), these frameworks allow the systematic and accurate extraction of transition probabilities between the corresponding states, in the case of Markov state models, and of statistically-optimized transition rates, in the case of the corresponding coarse master equations. However, applying automatically such methods to large molecular dynamics (MD) simulations, with explicit water molecules, remains limited both by the initial ability to identify good candidates for the underlying Markovian states and by the necessity to do so using good collective variables as reaction coordinates that allow the correct counting of inter-state transitions at various lag times. Here, we show that, in cases when representative molecular conformations can be identified for the corresponding Markovian states, and thus their corresponding collective evolution of atomic positions can be calculated along MD trajectories, one can use them to build a new type of simple collective variable, which can be particularly useful in both the correct state assignment and in the subsequent accurate counting of inter-state transition probabilities. In the case of the ubiquitously used root-mean-square deviation (RMSD) of atomic positions, we introduce the relative RMSD (RelRMSD) measure as a good reaction coordinate candidate. We apply this method to the analysis of REMD trajectories of amyloid-forming diphenylalanine (FF) peptides-a system with important nanotechnology and biomedical applications due to its self-assembling and piezoelectric properties-illustrating the use of RelRMSD in extracting its temperature-dependent intrinsic kinetics, without a priori assumptions on the functional form (e.g., Arrhenius or not) of the underlying conformational transition rates. The RelRMSD analysis enables as well a more objective assessment of the convergence of the REMD simulations. This type of collective variable may be generalized to other observables that could accurately capture conformational differences between the underlying Markov states (e.g., distance RMSD, the fraction of native contacts, etc.).
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Affiliation(s)
- Brajesh Narayan
- School of Physics, University College Dublin, Belfield, Dublin 4, Ireland
| | - Colm Herbert
- School of Physics, University College Dublin, Belfield, Dublin 4, Ireland
| | - Ye Yuan
- School of Physics, University College Dublin, Belfield, Dublin 4, Ireland
| | - Brian J Rodriguez
- School of Physics, University College Dublin, Belfield, Dublin 4, Ireland
| | - Bernard R Brooks
- Laboratory of Computational Biology, NHLBI, National Institutes of Health, Bethesda, Maryland 20892, USA
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27
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Joseph JA, Röder K, Chakraborty D, Mantell RG, Wales DJ. Exploring biomolecular energy landscapes. Chem Commun (Camb) 2018; 53:6974-6988. [PMID: 28489083 DOI: 10.1039/c7cc02413d] [Citation(s) in RCA: 59] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The potential energy landscape perspective provides both a conceptual and a computational framework for predicting, understanding and designing molecular properties. In this Feature Article, we highlight some recent advances that greatly facilitate structure prediction and analysis of global thermodynamics and kinetics in proteins and nucleic acids. The geometry optimisation procedures, on which these calculations are based, can be accelerated significantly using local rigidification of selected degrees of freedom, and through implementations on graphics processing units. Results of progressive local rigidification are first summarised for trpzip1, including a systematic analysis of the heat capacity and rearrangement rates. Benchmarks for all the essential optimisation procedures are then provided for a variety of proteins. Applications are then illustrated from a study of how mutation affects the energy landscape for a coiled-coil protein, and for transitions in helix morphology for a DNA duplex. Both systems exhibit an intrinsically multifunnel landscape, with the potential to act as biomolecular switches.
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Affiliation(s)
- Jerelle A Joseph
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW, UK.
| | - Konstantin Röder
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW, UK.
| | - Debayan Chakraborty
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW, UK. and Department of Chemistry, The University of Texas at Austin, 24th Street Stop A5300, Austin, TX 78712, USA
| | - Rosemary G Mantell
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW, UK.
| | - David J Wales
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW, UK.
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28
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Prakash A, Kumar V, Meena NK, Hassan MI, Lynn AM. Comparative analysis of thermal unfolding simulations of RNA recognition motifs (RRMs) of TAR DNA-binding protein 43 (TDP-43). J Biomol Struct Dyn 2018; 37:178-194. [DOI: 10.1080/07391102.2017.1422026] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Affiliation(s)
- Amresh Prakash
- School of Computational & Integrative Sciences, Jawaharlal Nehru University, New Delhi, India
| | - Vijay Kumar
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, New Delhi, India
| | - Naveen Kumar Meena
- School of Computational & Integrative Sciences, Jawaharlal Nehru University, New Delhi, India
| | - Md. Imtaiyaz Hassan
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, New Delhi, India
| | - Andrew M. Lynn
- School of Computational & Integrative Sciences, Jawaharlal Nehru University, New Delhi, India
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29
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Sala D, Giachetti A, Rosato A. Molecular dynamics simulations of metalloproteins: A folding study of rubredoxin from <em>Pyrococcus furiosus</em>. AIMS BIOPHYSICS 2018. [DOI: 10.3934/biophy.2018.1.77] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
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30
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Liu X, Chen J. HyRes: a coarse-grained model for multi-scale enhanced sampling of disordered protein conformations. Phys Chem Chem Phys 2017; 19:32421-32432. [PMID: 29186229 PMCID: PMC5729119 DOI: 10.1039/c7cp06736d] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Efficient coarse-grained (CG) models can be coupled with atomistic force fields to accelerate the sampling of atomistic energy landscapes in the multi-scale enhanced sampling (MSES) framework. This approach may be particularly suitable for generating atomistic conformational ensembles of intrinsically disordered proteins (IDPs). While MSES is relatively robust to inherent CG artifacts, achieving optimal sampling efficiency requires CG modeling to generate the local and long-range fluctuations that are largely consistent with those at the atomistic level. Here, we describe a new hybrid resolution CG model (HyRes) for MSES simulations of disordered protein states, which is specifically designed to provide semi-quantitative secondary structure propensities together with a qualitative description of long-range nonspecific interactions. The HyRes model contains an atomistic description of the backbone with intermediate resolution side chains. The secondary structure propensities are tuned by adjusting the backbone hydrogen-bonding strength and the ϕ/ψ torsion profile. The sizes and covalent geometries of the side chains are parameterized to reproduce distributions derived from atomistic simulations. Lennard-Jones parameters for sidechain beads are assigned to reproduce statistical potentials derived from the protein structural database, and then globally parameterized with nonspecific electrostatic interactions to reproduce the free energy profiles of pair wise interactions and the key conformational properties of model peptides. Application of HyRes to MSES simulations of small IDPs suggests that it is capable of driving faster structural transitions at the atomistic level and increasing the convergence rate compared to the Cα-only Gō-like models previously utilized. With further optimization, we believe that the new CG model could greatly improve the efficiency of MSES simulations of the larger and more complex IDPs frequently involved in cellular signalling and regulation.
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Affiliation(s)
- Xiaorong Liu
- Department of Chemistry, University of Massachusetts Amherst, Amherst, MA 01003, USA.
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31
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Goyal S, Chattopadhyay A, Kasavajhala K, Priyakumar UD. Role of Urea–Aromatic Stacking Interactions in Stabilizing the Aromatic Residues of the Protein in Urea-Induced Denatured State. J Am Chem Soc 2017; 139:14931-14946. [DOI: 10.1021/jacs.7b05463] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Affiliation(s)
- Siddharth Goyal
- Center for Computational
Natural Sciences and Bioinformatics, International Institute of Information Technology, Hyderabad 500 032, India
| | - Aditya Chattopadhyay
- Center for Computational
Natural Sciences and Bioinformatics, International Institute of Information Technology, Hyderabad 500 032, India
| | - Koushik Kasavajhala
- Center for Computational
Natural Sciences and Bioinformatics, International Institute of Information Technology, Hyderabad 500 032, India
| | - U. Deva Priyakumar
- Center for Computational
Natural Sciences and Bioinformatics, International Institute of Information Technology, Hyderabad 500 032, India
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32
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Shao Q, Zhu W. Effective Conformational Sampling in Explicit Solvent with Gaussian Biased Accelerated Molecular Dynamics. J Chem Theory Comput 2017; 13:4240-4252. [DOI: 10.1021/acs.jctc.7b00242] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Affiliation(s)
- Qiang Shao
- Drug
Discovery and Design Center, CAS Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi
Road, Shanghai, 201203, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Weiliang Zhu
- Drug
Discovery and Design Center, CAS Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi
Road, Shanghai, 201203, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
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33
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Wu HN, Jiang F, Wu YD. Significantly Improved Protein Folding Thermodynamics Using a Dispersion-Corrected Water Model and a New Residue-Specific Force Field. J Phys Chem Lett 2017; 8:3199-3205. [PMID: 28651056 DOI: 10.1021/acs.jpclett.7b01213] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
An accurate potential energy model is crucial for biomolecular simulations. Despite many recent improvements of classical protein force fields, there are remaining key issues: much weaker temperature dependence of folding/unfolding equilibrium and overly collapsed unfolded or disordered states. For the latter problem, a new water model (TIP4P-D) has been proposed to correct the significantly underestimated water dispersion interactions. Here, using TIP4P-D, we reveal problems in current force fields through failures in folding model systems (a polyalanine peptide, Trp-cage, and the GB1 hairpin). By using residue-specific parameters to achieve better match between amino acid sequences and native structures and adding a small H-bond correction to partially compensate the missing many-body effects in α-helix formation, the new RSFF2+ force field with the TIP4P-D water model can excellently reproduce experimental melting curves of both α-helical and β-hairpin systems. The RSFF2+/TIP4P-D method also gives less collapsed unfolded structures and describes well folded proteins simultaneously.
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Affiliation(s)
- Hao-Nan Wu
- Laboratory of Computational Chemistry and Drug Design, Laboratory of Chemical Genomics, Peking University Shenzhen Graduate School , Shenzhen 518055, China
| | - Fan Jiang
- Laboratory of Computational Chemistry and Drug Design, Laboratory of Chemical Genomics, Peking University Shenzhen Graduate School , Shenzhen 518055, China
| | - Yun-Dong Wu
- Laboratory of Computational Chemistry and Drug Design, Laboratory of Chemical Genomics, Peking University Shenzhen Graduate School , Shenzhen 518055, China
- College of Chemistry and Molecular Engineering, Peking University , Beijing 100871, China
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34
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When fast is better: protein folding fundamentals and mechanisms from ultrafast approaches. Biochem J 2017; 473:2545-59. [PMID: 27574021 PMCID: PMC5003694 DOI: 10.1042/bcj20160107] [Citation(s) in RCA: 62] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2016] [Accepted: 04/18/2016] [Indexed: 11/19/2022]
Abstract
Protein folding research stalled for decades because conventional experiments indicated that proteins fold slowly and in single strokes, whereas theory predicted a complex interplay between dynamics and energetics resulting in myriad microscopic pathways. Ultrafast kinetic methods turned the field upside down by providing the means to probe fundamental aspects of folding, test theoretical predictions and benchmark simulations. Accordingly, experimentalists could measure the timescales for all relevant folding motions, determine the folding speed limit and confirm that folding barriers are entropic bottlenecks. Moreover, a catalogue of proteins that fold extremely fast (microseconds) could be identified. Such fast-folding proteins cross shallow free energy barriers or fold downhill, and thus unfold with minimal co-operativity (gradually). A new generation of thermodynamic methods has exploited this property to map folding landscapes, interaction networks and mechanisms at nearly atomic resolution. In parallel, modern molecular dynamics simulations have finally reached the timescales required to watch fast-folding proteins fold and unfold in silico. All of these findings have buttressed the fundamentals of protein folding predicted by theory, and are now offering the first glimpses at the underlying mechanisms. Fast folding appears to also have functional implications as recent results connect downhill folding with intrinsically disordered proteins, their complex binding modes and ability to moonlight. These connections suggest that the coupling between downhill (un)folding and binding enables such protein domains to operate analogically as conformational rheostats.
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35
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Abaskharon RM, Gai F. Meandering Down the Energy Landscape of Protein Folding: Are We There Yet? Biophys J 2017; 110:1924-32. [PMID: 27166801 DOI: 10.1016/j.bpj.2016.03.030] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2016] [Revised: 03/18/2016] [Accepted: 03/22/2016] [Indexed: 12/11/2022] Open
Abstract
As judged by a single publication metric, the activity in the protein folding field has been declining over the past 5 years, after enjoying a decade-long growth. Does this development indicate that the field is sunsetting or is this decline only temporary? Upon surveying a small territory of its landscape, we find that the protein folding field is still quite active and many important findings have emerged from recent experimental studies. However, it is also clear that only continued development of new techniques and methods, especially those enabling dissection of the fine details and features of the protein folding energy landscape, will fuel this old field to move forward.
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Affiliation(s)
- Rachel M Abaskharon
- Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Feng Gai
- Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania; The Ultrafast Optical Processes Laboratory, University of Pennsylvania, Philadelphia, Pennsylvania.
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36
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Lee KH, Chen J. Optimization of the GBMV2 implicit solvent force field for accurate simulation of protein conformational equilibria. J Comput Chem 2017; 38:1332-1341. [PMID: 28397268 DOI: 10.1002/jcc.24734] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2016] [Revised: 11/16/2016] [Accepted: 12/14/2016] [Indexed: 12/12/2022]
Abstract
Accurate treatment of solvent environment is critical for reliable simulations of protein conformational equilibria. Implicit treatment of solvation, such as using the generalized Born (GB) class of models arguably provides an optimal balance between computational efficiency and physical accuracy. Yet, GB models are frequently plagued by a tendency to generate overly compact structures. The physical origins of this drawback are relatively well understood, and the key to a balanced implicit solvent protein force field is careful optimization of physical parameters to achieve a sufficient level of cancellation of errors. The latter has been hampered by the difficulty of generating converged conformational ensembles of non-trivial model proteins using the popular replica exchange sampling technique. Here, we leverage improved sampling efficiency of a newly developed multi-scale enhanced sampling technique to re-optimize the generalized-Born with molecular volume (GBMV2) implicit solvent model with the CHARMM36 protein force field. Recursive optimization of key GBMV2 parameters (such as input radii) and protein torsion profiles (via the CMAP torsion cross terms) has led to a more balanced GBMV2 protein force field that recapitulates the structures and stabilities of both helical and β-hairpin model peptides. Importantly, this force field appears to be free of the over-compaction bias, and can generate structural ensembles of several intrinsically disordered proteins of various lengths that seem highly consistent with available experimental data. © 2017 Wiley Periodicals, Inc.
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Affiliation(s)
- Kuo Hao Lee
- Department of Biochemistry and Molecular Biophysics, Kansas State University, Manhattan, Kansas, 66506
| | - Jianhan Chen
- Department of Biochemistry and Molecular Biophysics, Kansas State University, Manhattan, Kansas, 66506
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37
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Shao Q, Shi J, Zhu W. Determining Protein Folding Pathway and Associated Energetics through Partitioned Integrated-Tempering-Sampling Simulation. J Chem Theory Comput 2017; 13:1229-1243. [DOI: 10.1021/acs.jctc.6b00967] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Affiliation(s)
- Qiang Shao
- Drug
Discovery and Design Center, CAS Key Laboratory of Receptor Research,
Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai 201203, China
| | - Jiye Shi
- UCB Biopharma
SPRL, Chemin du Foriest, 1420 Braine-l’Alleud, Belgium
| | - Weiliang Zhu
- Drug
Discovery and Design Center, CAS Key Laboratory of Receptor Research,
Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai 201203, China
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38
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Rajasekaran N, Suresh S, Gopi S, Raman K, Naganathan AN. A General Mechanism for the Propagation of Mutational Effects in Proteins. Biochemistry 2016; 56:294-305. [DOI: 10.1021/acs.biochem.6b00798] [Citation(s) in RCA: 42] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Nandakumar Rajasekaran
- Department of Biotechnology, Bhupat & Jyoti Mehta School of Biosciences, Indian Institute of Technology Madras, Chennai 600036, India
| | | | - Soundhararajan Gopi
- Department of Biotechnology, Bhupat & Jyoti Mehta School of Biosciences, Indian Institute of Technology Madras, Chennai 600036, India
| | - Karthik Raman
- Department of Biotechnology, Bhupat & Jyoti Mehta School of Biosciences, Indian Institute of Technology Madras, Chennai 600036, India
| | - Athi N. Naganathan
- Department of Biotechnology, Bhupat & Jyoti Mehta School of Biosciences, Indian Institute of Technology Madras, Chennai 600036, India
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39
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Šponer J, Bussi G, Stadlbauer P, Kührová P, Banáš P, Islam B, Haider S, Neidle S, Otyepka M. Folding of guanine quadruplex molecules-funnel-like mechanism or kinetic partitioning? An overview from MD simulation studies. Biochim Biophys Acta Gen Subj 2016; 1861:1246-1263. [PMID: 27979677 DOI: 10.1016/j.bbagen.2016.12.008] [Citation(s) in RCA: 74] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2016] [Revised: 12/04/2016] [Accepted: 12/11/2016] [Indexed: 01/18/2023]
Abstract
BACKGROUND Guanine quadruplexes (GQs) play vital roles in many cellular processes and are of much interest as drug targets. In contrast to the availability of many structural studies, there is still limited knowledge on GQ folding. SCOPE OF REVIEW We review recent molecular dynamics (MD) simulation studies of the folding of GQs, with an emphasis paid to the human telomeric DNA GQ. We explain the basic principles and limitations of all types of MD methods used to study unfolding and folding in a way accessible to non-specialists. We discuss the potential role of G-hairpin, G-triplex and alternative GQ intermediates in the folding process. We argue that, in general, folding of GQs is fundamentally different from funneled folding of small fast-folding proteins, and can be best described by a kinetic partitioning (KP) mechanism. KP is a competition between at least two (but often many) well-separated and structurally different conformational ensembles. MAJOR CONCLUSIONS The KP mechanism is the only plausible way to explain experiments reporting long time-scales of GQ folding and the existence of long-lived sub-states. A significant part of the natural partitioning of the free energy landscape of GQs comes from the ability of the GQ-forming sequences to populate a large number of syn-anti patterns in their G-tracts. The extreme complexity of the KP of GQs typically prevents an appropriate description of the folding landscape using just a few order parameters or collective variables. GENERAL SIGNIFICANCE We reconcile available computational and experimental studies of GQ folding and formulate basic principles characterizing GQ folding landscapes. This article is part of a Special Issue entitled "G-quadruplex" Guest Editor: Dr. Concetta Giancola and Dr. Daniela Montesarchio.
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Affiliation(s)
- Jiří Šponer
- Institute of Biophysics, Academy of Sciences of the Czech Republic, Kralovopolska 135, 612 65 Brno, Czech Republic; Regional Centre of Advanced Technologies and Materials, Department of Physical Chemistry, Faculty of Science, Palacky University Olomouc, 17. listopadu 12, 771 46 Olomouc, Czech Republic.
| | - Giovanni Bussi
- Scuola Internazionale Superiore di Studi Avanzati, Via Bonomea 265, 34136 Trieste, Italy
| | - Petr Stadlbauer
- Institute of Biophysics, Academy of Sciences of the Czech Republic, Kralovopolska 135, 612 65 Brno, Czech Republic; Regional Centre of Advanced Technologies and Materials, Department of Physical Chemistry, Faculty of Science, Palacky University Olomouc, 17. listopadu 12, 771 46 Olomouc, Czech Republic
| | - Petra Kührová
- Regional Centre of Advanced Technologies and Materials, Department of Physical Chemistry, Faculty of Science, Palacky University Olomouc, 17. listopadu 12, 771 46 Olomouc, Czech Republic
| | - Pavel Banáš
- Regional Centre of Advanced Technologies and Materials, Department of Physical Chemistry, Faculty of Science, Palacky University Olomouc, 17. listopadu 12, 771 46 Olomouc, Czech Republic
| | - Barira Islam
- Institute of Biophysics, Academy of Sciences of the Czech Republic, Kralovopolska 135, 612 65 Brno, Czech Republic
| | - Shozeb Haider
- UCL School of Pharmacy, 29-39 Brunswick Square, London WC1N 1AX, UK
| | - Stephen Neidle
- UCL School of Pharmacy, 29-39 Brunswick Square, London WC1N 1AX, UK
| | - Michal Otyepka
- Regional Centre of Advanced Technologies and Materials, Department of Physical Chemistry, Faculty of Science, Palacky University Olomouc, 17. listopadu 12, 771 46 Olomouc, Czech Republic
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40
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Joseph JA, Whittleston CS, Wales DJ. Structure, Thermodynamics, and Folding Pathways for a Tryptophan Zipper as a Function of Local Rigidification. J Chem Theory Comput 2016; 12:6109-6117. [DOI: 10.1021/acs.jctc.6b00734] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Affiliation(s)
- Jerelle A. Joseph
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, United Kingdom
| | - Chris S. Whittleston
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, United Kingdom
| | - David J. Wales
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, United Kingdom
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41
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Stadlbauer P, Mazzanti L, Cragnolini T, Wales DJ, Derreumaux P, Pasquali S, Šponer J. Coarse-Grained Simulations Complemented by Atomistic Molecular Dynamics Provide New Insights into Folding and Unfolding of Human Telomeric G-Quadruplexes. J Chem Theory Comput 2016; 12:6077-6097. [DOI: 10.1021/acs.jctc.6b00667] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Affiliation(s)
- Petr Stadlbauer
- Institute
of Biophysics, Academy of Sciences of the Czech Republic, Královopolská
135, 612 65 Brno, Czech Republic
- Regional
Centre of Advanced Technologies and Materials, Departments of Physical
Chemistry, Faculty of Science, Palacký University, 17. listopadu
1192/12, 771 46 Olomouc, Czech Republic
| | - Liuba Mazzanti
- Laboratoire
de Biochimie Théorique, IBPC, CNRS UPR9080, Université Sorbonne Paris Cite, Paris Diderot, 13 rue Pierre et Marie Curie, 75005 Paris, France
| | - Tristan Cragnolini
- Department
of Chemistry, Cambridge University, Lensfield Road, Cambridge CB2 1EW, U.K
| | - David J. Wales
- Department
of Chemistry, Cambridge University, Lensfield Road, Cambridge CB2 1EW, U.K
| | - Philippe Derreumaux
- Laboratoire
de Biochimie Théorique, IBPC, CNRS UPR9080, Université Sorbonne Paris Cite, Paris Diderot, 13 rue Pierre et Marie Curie, 75005 Paris, France
| | - Samuela Pasquali
- Laboratoire
de Biochimie Théorique, IBPC, CNRS UPR9080, Université Sorbonne Paris Cite, Paris Diderot, 13 rue Pierre et Marie Curie, 75005 Paris, France
| | - Jiří Šponer
- Institute
of Biophysics, Academy of Sciences of the Czech Republic, Královopolská
135, 612 65 Brno, Czech Republic
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42
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Malhotra P, Udgaonkar JB. How cooperative are protein folding and unfolding transitions? Protein Sci 2016; 25:1924-1941. [PMID: 27522064 PMCID: PMC5079258 DOI: 10.1002/pro.3015] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2016] [Revised: 08/09/2016] [Accepted: 08/09/2016] [Indexed: 11/12/2022]
Abstract
A thermodynamically and kinetically simple picture of protein folding envisages only two states, native (N) and unfolded (U), separated by a single activation free energy barrier, and interconverting by cooperative two-state transitions. The folding/unfolding transitions of many proteins occur, however, in multiple discrete steps associated with the formation of intermediates, which is indicative of reduced cooperativity. Furthermore, much advancement in experimental and computational approaches has demonstrated entirely non-cooperative (gradual) transitions via a continuum of states and a multitude of small energetic barriers between the N and U states of some proteins. These findings have been instrumental towards providing a structural rationale for cooperative versus noncooperative transitions, based on the coupling between interaction networks in proteins. The cooperativity inherent in a folding/unfolding reaction appears to be context dependent, and can be tuned via experimental conditions which change the stabilities of N and U. The evolution of cooperativity in protein folding transitions is linked closely to the evolution of function as well as the aggregation propensity of the protein. A large activation energy barrier in a fully cooperative transition can provide the kinetic control required to prevent the accumulation of partially unfolded forms, which may promote aggregation. Nevertheless, increasing evidence for barrier-less "downhill" folding, as well as for continuous "uphill" unfolding transitions, indicate that gradual non-cooperative processes may be ubiquitous features on the free energy landscape of protein folding.
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Affiliation(s)
- Pooja Malhotra
- National Centre for Biological Sciences, Tata Institute of Fundamental Research, Bengaluru, 560065, India
| | - Jayant B Udgaonkar
- National Centre for Biological Sciences, Tata Institute of Fundamental Research, Bengaluru, 560065, India.
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43
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Serafeim AP, Salamanos G, Patapati KK, Glykos NM. Sensitivity of Folding Molecular Dynamics Simulations to Even Minor Force Field Changes. J Chem Inf Model 2016; 56:2035-2041. [PMID: 27681090 DOI: 10.1021/acs.jcim.6b00493] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
We examine the sensitivity of folding molecular dynamics simulations on the choice between three variants of the same force field (the AMBER99SB force field and its ILDN, NMR-ILDN, and STAR-ILDN variants). Using two different peptide systems (a marginally stable helical peptide and a β-hairpin) and a grand total of more than 20 μs of simulation time we show that even relatively minor force field changes can lead to appreciable differences in the peptide folding behavior.
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Affiliation(s)
- Athanasia-Panagiota Serafeim
- Department of Molecular Biology and Genetics, Democritus University of Thrace , University campus, 68100 Alexandroupolis, Greece
| | - Georgios Salamanos
- Department of Molecular Biology and Genetics, Democritus University of Thrace , University campus, 68100 Alexandroupolis, Greece
| | - Kalliopi K Patapati
- Department of Molecular Biology and Genetics, Democritus University of Thrace , University campus, 68100 Alexandroupolis, Greece
| | - Nicholas M Glykos
- Department of Molecular Biology and Genetics, Democritus University of Thrace , University campus, 68100 Alexandroupolis, Greece
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44
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The Power of Force: Insights into the Protein Folding Process Using Single-Molecule Force Spectroscopy. J Mol Biol 2016; 428:4245-4257. [PMID: 27639437 DOI: 10.1016/j.jmb.2016.09.006] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2016] [Revised: 09/07/2016] [Accepted: 09/07/2016] [Indexed: 01/03/2023]
Abstract
One of the major challenges in modern biophysics is observing and understanding conformational changes during complex molecular processes, from the fundamental protein folding to the function of molecular machines. Single-molecule techniques have been one of the major driving forces of the huge progress attained in the last few years. Recent advances in resolution of the experimental setups, aided by theoretical developments and molecular dynamics simulations, have revealed a much higher degree of complexity inside these molecular processes than previously reported using traditional ensemble measurements. This review sums up the evolution of these developments and gives an outlook on prospective discoveries.
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45
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Kührová P, Best RB, Bottaro S, Bussi G, Šponer J, Otyepka M, Banáš P. Computer Folding of RNA Tetraloops: Identification of Key Force Field Deficiencies. J Chem Theory Comput 2016; 12:4534-48. [PMID: 27438572 PMCID: PMC6169534 DOI: 10.1021/acs.jctc.6b00300] [Citation(s) in RCA: 91] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
The computer-aided folding of biomolecules, particularly RNAs, is one of the most difficult challenges in computational structural biology. RNA tetraloops are fundamental RNA motifs playing key roles in RNA folding and RNA-RNA and RNA-protein interactions. Although state-of-the-art Molecular Dynamics (MD) force fields correctly describe the native state of these tetraloops as a stable free-energy basin on the microsecond time scale, enhanced sampling techniques reveal that the native state is not the global free energy minimum, suggesting yet unidentified significant imbalances in the force fields. Here, we tested our ability to fold the RNA tetraloops in various force fields and simulation settings. We employed three different enhanced sampling techniques, namely, temperature replica exchange MD (T-REMD), replica exchange with solute tempering (REST2), and well-tempered metadynamics (WT-MetaD). We aimed to separate problems caused by limited sampling from those due to force-field inaccuracies. We found that none of the contemporary force fields is able to correctly describe folding of the 5'-GAGA-3' tetraloop over a range of simulation conditions. We thus aimed to identify which terms of the force field are responsible for this poor description of TL folding. We showed that at least two different imbalances contribute to this behavior, namely, overstabilization of base-phosphate and/or sugar-phosphate interactions and underestimated stability of the hydrogen bonding interaction in base pairing. The first artifact stabilizes the unfolded ensemble, while the second one destabilizes the folded state. The former problem might be partially alleviated by reparametrization of the van der Waals parameters of the phosphate oxygens suggested by Case et al., while in order to overcome the latter effect we suggest local potentials to better capture hydrogen bonding interactions.
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Affiliation(s)
- Petra Kührová
- Regional Centre of Advanced Technologies and Materials, Department of Physical Chemistry, Faculty of Science, Palacky University Olomouc, 17. listopadu 12, 771 46 Olomouc, Czech Republic,
| | - Robert B. Best
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892-0520
| | - Sandro Bottaro
- Scuola Internazionale Superiore di Studi Avanzati, Via Bonomea 265, 34136 Trieste, Italy
| | - Giovanni Bussi
- Scuola Internazionale Superiore di Studi Avanzati, Via Bonomea 265, 34136 Trieste, Italy
| | - Jiří Šponer
- Regional Centre of Advanced Technologies and Materials, Department of Physical Chemistry, Faculty of Science, Palacky University Olomouc, 17. listopadu 12, 771 46 Olomouc, Czech Republic,
- Institute of Biophysics, Academy of Sciences of the Czech Republic, Kralovopolska 135, 612 65 Brno, Czech Republic
| | - Michal Otyepka
- Regional Centre of Advanced Technologies and Materials, Department of Physical Chemistry, Faculty of Science, Palacky University Olomouc, 17. listopadu 12, 771 46 Olomouc, Czech Republic,
- Institute of Biophysics, Academy of Sciences of the Czech Republic, Kralovopolska 135, 612 65 Brno, Czech Republic
| | - Pavel Banáš
- Regional Centre of Advanced Technologies and Materials, Department of Physical Chemistry, Faculty of Science, Palacky University Olomouc, 17. listopadu 12, 771 46 Olomouc, Czech Republic,
- Institute of Biophysics, Academy of Sciences of the Czech Republic, Kralovopolska 135, 612 65 Brno, Czech Republic
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46
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Daidone I, Zanetti-Polzi L, Thukral L, Alekozai EM, Amadei A. Theoretical-computational characterization of the temperature-dependent folding thermodynamics of a β-hairpin peptide. Chem Phys Lett 2016. [DOI: 10.1016/j.cplett.2016.07.041] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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47
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Leahy CT, Murphy RD, Hummer G, Rosta E, Buchete NV. Coarse Master Equations for Binding Kinetics of Amyloid Peptide Dimers. J Phys Chem Lett 2016; 7:2676-2682. [PMID: 27323250 DOI: 10.1021/acs.jpclett.6b00518] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
We characterize the kinetics of dimer formation of the short amyloid microcrystal-forming tetrapeptides NNQQ by constructing coarse master equations for the conformational dynamics of the system, using temperature replica-exchange molecular dynamics (REMD) simulations. We minimize the effects of Kramers-type recrossings by assigning conformational states based on their sequential time evolution. Transition rates are further estimated from short-time state propagators by maximizing the likelihood that the extracted rates agree with the observed atomistic trajectories without any a priori assumptions about their temperature dependence. Here, we evaluate the rates for both continuous replica trajectories that visit different temperatures and for discontinuous data corresponding to each REMD temperature. While the binding-unbinding kinetic process is clearly Markovian, the conformational dynamics of the bound NNQQ dimer has a complex character. Our kinetic analysis allows us to discriminate between short-lived encounter pairs and strongly bound conformational states. The conformational dynamics of NNQQ dimers supports a kinetically driven aggregation mechanism, in agreement with the polymorphic character reported for amyloid aggregates such as microcrystals and fibrils.
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Affiliation(s)
- Cathal T Leahy
- School of Physics, University College Dublin , Belfield, Dublin 4, Ireland
- Complex and Adaptive Systems Laboratory, University College Dublin , Belfield, Dublin 4, Ireland
| | - Ronan D Murphy
- School of Physics, University College Dublin , Belfield, Dublin 4, Ireland
- Complex and Adaptive Systems Laboratory, University College Dublin , Belfield, Dublin 4, Ireland
| | - Gerhard Hummer
- Department of Theoretical Biophysics, Max Planck Institute of Biophysics , Max-von-Laue-Straße 3, D-60438 Frankfurt am Main, Germany
| | - Edina Rosta
- Department of Chemistry, King's College London , London SE1 1DB, United Kingdom
| | - Nicolae-Viorel Buchete
- School of Physics, University College Dublin , Belfield, Dublin 4, Ireland
- Complex and Adaptive Systems Laboratory, University College Dublin , Belfield, Dublin 4, Ireland
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Lamiable A, Thevenet P, Tufféry P. A critical assessment of hidden markov model sub-optimal sampling strategies applied to the generation of peptide 3D models. J Comput Chem 2016; 37:2006-16. [PMID: 27317417 DOI: 10.1002/jcc.24422] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2016] [Revised: 05/03/2016] [Accepted: 05/17/2016] [Indexed: 12/23/2022]
Abstract
Hidden Markov Model derived structural alphabets are a probabilistic framework in which the complete conformational space of a peptidic chain is described in terms of probability distributions that can be sampled to identify conformations of largest probabilities. Here, we assess how three strategies to sample sub-optimal conformations-Viterbi k-best, forward backtrack and a taboo sampling approach-can lead to the efficient generation of peptide conformations. We show that the diversity of sampling is essential to compensate biases introduced in the estimates of the probabilities, and we find that only the forward backtrack and a taboo sampling strategies can efficiently generate native or near-native models. Finally, we also find such approaches are as efficient as former protocols, while being one order of magnitude faster, opening the door to the large scale de novo modeling of peptides and mini-proteins. © 2016 Wiley Periodicals, Inc.
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Affiliation(s)
- A Lamiable
- INSERM UMR-S 973, Université Paris Diderot, Sorbonne Paris Cité
| | - P Thevenet
- INSERM UMR-S 973, Université Paris Diderot, Sorbonne Paris Cité
| | - P Tufféry
- INSERM UMR-S 973, Université Paris Diderot, Sorbonne Paris Cité
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Petrov D, Daura X, Zagrovic B. Effect of Oxidative Damage on the Stability and Dimerization of Superoxide Dismutase 1. Biophys J 2016; 110:1499-1509. [PMID: 27074676 PMCID: PMC4833831 DOI: 10.1016/j.bpj.2016.02.037] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2015] [Revised: 02/07/2016] [Accepted: 02/10/2016] [Indexed: 12/13/2022] Open
Abstract
During their life cycle, proteins are subject to different modifications involving reactive oxygen species. Such oxidative damage to proteins may lead to the formation of insoluble aggregates and cytotoxicity and is associated with age-related disorders including neurodegenerative diseases, cancer, and diabetes. Superoxide dismutase 1 (SOD1), a key antioxidant enzyme in human cells, is particularly susceptible to such modifications. Moreover, this homodimeric metalloenzyme has been directly linked to both familial and sporadic amyotrophic lateral sclerosis (ALS), a devastating, late-onset motor neuronal disease, with more than 150 ALS-related mutations in the SOD1 gene. Importantly, oxidatively damaged SOD1 aggregates have been observed in both familial and sporadic forms of the disease. However, the molecular mechanisms as well as potential implications of oxidative stress in SOD1-induced cytotoxicity remain elusive. In this study, we examine the effects of oxidative modification on SOD1 monomer and homodimer stability, the key molecular properties related to SOD1 aggregation. We use molecular dynamics simulations in combination with thermodynamic integration to study microscopic-level site-specific effects of oxidative "mutations" at the dimer interface, including lysine, arginine, proline and threonine carbonylation, and cysteine oxidation. Our results show that oxidative damage of even single residues at the interface may drastically destabilize the SOD1 homodimer, with several modifications exhibiting a comparable effect to that of the most drastic ALS-causing mutations known. Additionally, we show that the SOD1 monomer stability decreases upon oxidative stress, which may lead to partial local unfolding and consequently to increased aggregation propensity. Importantly, these results suggest that oxidative stress may play a key role in development of ALS, with the mutations in the SOD1 gene being an additional factor.
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Affiliation(s)
- Drazen Petrov
- Department of Structural and Computational Biology, Max F. Perutz Laboratories, University of Vienna, Vienna, Austria
| | - Xavier Daura
- Institute of Biotechnology and Biomedicine, Universitat Autònoma de Barcelona, Bellaterra, Spain; Catalan Institution for Research and Advanced Studies (ICREA), Barcelona, Spain
| | - Bojan Zagrovic
- Department of Structural and Computational Biology, Max F. Perutz Laboratories, University of Vienna, Vienna, Austria.
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Maximova T, Moffatt R, Ma B, Nussinov R, Shehu A. Principles and Overview of Sampling Methods for Modeling Macromolecular Structure and Dynamics. PLoS Comput Biol 2016; 12:e1004619. [PMID: 27124275 PMCID: PMC4849799 DOI: 10.1371/journal.pcbi.1004619] [Citation(s) in RCA: 132] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
Investigation of macromolecular structure and dynamics is fundamental to understanding how macromolecules carry out their functions in the cell. Significant advances have been made toward this end in silico, with a growing number of computational methods proposed yearly to study and simulate various aspects of macromolecular structure and dynamics. This review aims to provide an overview of recent advances, focusing primarily on methods proposed for exploring the structure space of macromolecules in isolation and in assemblies for the purpose of characterizing equilibrium structure and dynamics. In addition to surveying recent applications that showcase current capabilities of computational methods, this review highlights state-of-the-art algorithmic techniques proposed to overcome challenges posed in silico by the disparate spatial and time scales accessed by dynamic macromolecules. This review is not meant to be exhaustive, as such an endeavor is impossible, but rather aims to balance breadth and depth of strategies for modeling macromolecular structure and dynamics for a broad audience of novices and experts.
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Affiliation(s)
- Tatiana Maximova
- Department of Computer Science, George Mason University, Fairfax, Virginia, United States of America
| | - Ryan Moffatt
- Department of Computer Science, George Mason University, Fairfax, Virginia, United States of America
| | - Buyong Ma
- Basic Science Program, Leidos Biomedical Research, Inc. Cancer and Inflammation Program, National Cancer Institute, Frederick, Maryland, United States of America
| | - Ruth Nussinov
- Basic Science Program, Leidos Biomedical Research, Inc. Cancer and Inflammation Program, National Cancer Institute, Frederick, Maryland, United States of America
- Sackler Institute of Molecular Medicine, Department of Human Genetics and Molecular Medicine, Sackler School of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Amarda Shehu
- Department of Computer Science, George Mason University, Fairfax, Virginia, United States of America
- Department of Biongineering, George Mason University, Fairfax, Virginia, United States of America
- School of Systems Biology, George Mason University, Manassas, Virginia, United States of America
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