1
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Duan L, Guo X, Cong Y, Feng G, Li Y, Zhang JZH. Accelerated Molecular Dynamics Simulation for Helical Proteins Folding in Explicit Water. Front Chem 2019; 7:540. [PMID: 31448259 PMCID: PMC6691143 DOI: 10.3389/fchem.2019.00540] [Citation(s) in RCA: 45] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2018] [Accepted: 07/15/2019] [Indexed: 12/26/2022] Open
Abstract
In this study, we examined the folding processes of eight helical proteins (2I9M, TC5B, 1WN8, 1V4Z, 1HO2, 1HLL, 2KFE, and 1YYB) at room temperature using the explicit solvent model under the AMBER14SB force field with the accelerated molecular dynamics (AMD) and traditional molecular dynamics (MD), respectively. We analyzed and compared the simulation results obtained by these two methods based on several aspects, such as root mean square deviation (RMSD), native contacts, cluster analysis, folding snapshots, free energy landscape, and the evolution of the radius of gyration, which showed that these eight proteins were successfully and consistently folded into the corresponding native structures by AMD simulations carried out at room temperature. In addition, the folding occurred in the range of 40~180 ns after starting from the linear structures of the eight proteins at 300 K. By contrast, these stable folding structures were not found when the traditional molecular dynamics (MD) simulation was used. At the same time, the influence of high temperatures (350, 400, and 450 K) is also further investigated. Study found that the simulation efficiency of AMD is higher than that of MD simulations, regardless of the temperature. Of these temperatures, 300 K is the most suitable temperature for protein folding for all systems. To further investigate the efficiency of AMD, another trajectory was simulated for eight proteins with the same linear structure but different random seeds at 300 K. Both AMD trajectories reached the correct folded structures. Our result clearly shows that AMD simulation are a highly efficient and reliable method for the study of protein folding.
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Affiliation(s)
- Lili Duan
- School of Physics and Electronics, Shandong Normal University, Jinan, China
| | - Xiaona Guo
- School of Physics and Electronics, Shandong Normal University, Jinan, China
| | - Yalong Cong
- Shanghai Engineering Research Center of Molecular Therapeutics and New Drug Development, School of Chemistry and Molecular Engineering, East China Normal University, Shanghai, China
| | - Guoqiang Feng
- School of Physics and Electronics, Shandong Normal University, Jinan, China
| | - Yuchen Li
- School of Physics and Electronics, Shandong Normal University, Jinan, China
| | - John Z H Zhang
- Shanghai Engineering Research Center of Molecular Therapeutics and New Drug Development, School of Chemistry and Molecular Engineering, East China Normal University, Shanghai, China.,NYU-ECNU Center for Computational Chemistry at NYU Shanghai, Shanghai, China.,Department of Chemistry, New York University, New York, NY, United States
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2
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Zerze GH, Stillinger FH, Debenedetti PG. Effect of heterochiral inversions on the structure of a β-hairpin peptide. Proteins 2019; 87:569-578. [PMID: 30811673 DOI: 10.1002/prot.25680] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2018] [Accepted: 02/24/2019] [Indexed: 01/25/2023]
Abstract
We study computationally a family of β-hairpin peptides with systematically introduced chiral inversions, in explicit water, and we investigate the extent to which the backbone structure is able to fold in the presence of heterochiral perturbations. In contrast to the recently investigated case of a helical peptide, we do not find a monotonic change in secondary structure content as a function of the number of L- to D-inversions. The effects of L- to D-inversions are instead found to be highly position-specific. Additionally, in contrast to the helical peptide, some inversions increase the stability of the folded peptide: in such cases, we compute an increase in β-sheet content in the aqueous solution equilibrium ensemble. However, the tertiary structures of the stable (folded) configurations for peptides for which inversions cause an increase in β-sheet content show differences from one another, as well as from the native fold of the nonchirally perturbed β-hairpin. Our results suggest that although some chiral perturbations can increase folding stability, chirally perturbed proteins may still underperform functionally, given the relationship between structure and function.
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Affiliation(s)
- Gül H Zerze
- Department of Chemical and Biological Engineering, Princeton University, Princeton, New Jersey
| | | | - Pablo G Debenedetti
- Department of Chemical and Biological Engineering, Princeton University, Princeton, New Jersey
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3
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Sugita Y, Kamiya M, Oshima H, Re S. Replica-Exchange Methods for Biomolecular Simulations. Methods Mol Biol 2019; 2022:155-177. [PMID: 31396903 DOI: 10.1007/978-1-4939-9608-7_7] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
In this study, a replica-exchange method was developed to overcome conformational sampling difficulties in computer simulations of spin glass or other systems with rugged free-energy landscapes. This method was then applied to the protein-folding problem in combination with molecular dynamics (MD) simulation. Owing to its simplicity and sampling efficiency, the replica-exchange method has been applied to many other biological problems and has been continuously improved. The method has often been combined with other sampling techniques, such as umbrella sampling, free-energy perturbation, metadynamics, and Gaussian accelerated MD (GaMD). In this chapter, we first summarize the original replica-exchange molecular dynamics (REMD) method and discuss how new algorithms related to the original method are implemented to add new features. Heterogeneous and flexible structures of an N-glycan in a solution are simulated as an example of applications by REMD, replica exchange with solute tempering, and GaMD. The sampling efficiency of these methods on the N-glycan system and the convergence of the free-energy changes are compared. REMD simulation protocols and trajectory analysis using the GENESIS software are provided to facilitate the practical use of advanced simulation methods.
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Affiliation(s)
- Yuji Sugita
- Theoretical Molecular Science Laboratory, RIKEN Cluster for Pioneering Research, Saitama, Japan. .,Computational Biophysics Research Team, RIKEN Center for Computational Science, Kobe, Japan. .,Laboratory for Biomolecular Function Simulation, RIKEN Center for Biosystems Dynamics Research, Kobe, Japan.
| | - Motoshi Kamiya
- Computational Biophysics Research Team, RIKEN Center for Computational Science, Kobe, Japan
| | - Hiraku Oshima
- Laboratory for Biomolecular Function Simulation, RIKEN Center for Biosystems Dynamics Research, Kobe, Japan
| | - Suyong Re
- Laboratory for Biomolecular Function Simulation, RIKEN Center for Biosystems Dynamics Research, Kobe, Japan
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4
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Hazel AJ, Walters ET, Rowley CN, Gumbart JC. Folding free energy landscapes of β-sheets with non-polarizable and polarizable CHARMM force fields. J Chem Phys 2018; 149:072317. [PMID: 30134731 DOI: 10.1063/1.5025951] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
Molecular dynamics (MD) simulations of peptides and proteins offer atomic-level detail into many biological processes, although the degree of insight depends on the accuracy of the force fields used to represent them. Protein folding is a key example in which the accurate reproduction of folded-state conformations of proteins and kinetics of the folding processes in simulation is a longstanding goal. Although there have been a number of recent successes, challenges remain in capturing the full complexity of folding for even secondary-structure elements. In the present work, we have used all-atom MD simulations to study the folding properties of one such element, the C-terminal β-hairpin of the B1 domain of streptococcal protein G (GB1). Using replica-exchange umbrella sampling simulations, we examined the folding free energy of two fixed-charge CHARMM force fields, CHARMM36 and CHARMM22*, as well as a polarizable force field, the CHARMM Drude-2013 model, which has previously been shown to improve the folding properties of α-helical peptides. The CHARMM22* and Drude-2013 models are in rough agreement with experimental studies of GB1 folding, while CHARMM36 overstabilizes the β-hairpin. Additional free-energy calculations show that small adjustments to the atomic polarizabilities in the Drude-2013 model can improve both the backbone solubility and folding properties of GB1 without significantly affecting the model's ability to properly fold α-helices. We also identify a non-native salt bridge in the β-turn region that overstabilizes the β-hairpin in the C36 model. Finally, we demonstrate that tryptophan fluorescence is insufficient for capturing the full β-hairpin folding pathway.
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Affiliation(s)
- Anthony J Hazel
- School of Physics, Georgia Institute of Technology, Atlanta, Georgia 30332, USA
| | - Evan T Walters
- Department of Chemistry, Memorial University of Newfoundland, St. John's, Newfoundland and Labrador A1B3X7, Canada
| | - Christopher N Rowley
- Department of Chemistry, Memorial University of Newfoundland, St. John's, Newfoundland and Labrador A1B3X7, Canada
| | - James C Gumbart
- School of Physics, Georgia Institute of Technology, Atlanta, Georgia 30332, USA
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5
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Kang WB, He C, Liu ZX, Wang J, Wang W. Composition-related structural transition of random peptides: insight into the boundary between intrinsically disordered proteins and folded proteins. J Biomol Struct Dyn 2018; 37:1956-1967. [PMID: 29734867 DOI: 10.1080/07391102.2018.1472669] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Previous studies based on bioinformatics showed that there is a sharp distinction of structural features and residue composition between the intrinsically disordered proteins and the folded proteins. What induces such a composition-related structural transition? How do various kinds of interactions work in such processes? In this work, we investigate these problems based on a survey on peptides randomly composed of charged residues (including glutamic acids and lysines) and the residues with different hydrophobicity, such as alanines, glycines, or phenylalanines. Based on simulations using all-atom model and replica-exchange Monte Carlo method, a coil-globule transition is observed for each peptide. The corresponding transition temperature is found to be dependent on the contents of the hydrophobic and charged residues. For several cases, when the mean hydrophobicity is larger than a certain threshold, the transition temperature is higher than the room temperature, and vise versa. These thresholds of hydrophobicity and net charge are quantitatively consistent with the border line observed from the study of bioinformatics. These results outline the basic physical reasons for the compositional distinction between the intrinsically disordered proteins and the folded proteins. Furthermore, the contributions of various interactions to the structural variation of peptides are analyzed based on the contact statistics and the charge-pattern dependence of the gyration radii of the peptides. Our observations imply that the hydrophobicity contributes essentially to such composition-related transitions. Thus, we achieve a better understanding on composition-structure relation of the natural proteins and the underlying physics.
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Affiliation(s)
- Wen-Bin Kang
- a School of Physics , Nanjing University , Nanjing 210093 , P.R. China.,b School of Public Health and Management , Hubei University of Medicine , Shiyan 442000 , P.R. China
| | - Chuan He
- a School of Physics , Nanjing University , Nanjing 210093 , P.R. China
| | - Zhen-Xing Liu
- c Department of Physics , Beijing Normal University , Beijing 100875 , P.R. China
| | - Jun Wang
- a School of Physics , Nanjing University , Nanjing 210093 , P.R. China.,d National Laboratory of Solid State Microstructure, and Collaborative Innovation Center of Advanced Microstructures , Nanjing University , Nanjing 210093 , P.R. China
| | - Wei Wang
- a School of Physics , Nanjing University , Nanjing 210093 , P.R. China.,d National Laboratory of Solid State Microstructure, and Collaborative Innovation Center of Advanced Microstructures , Nanjing University , Nanjing 210093 , P.R. China
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6
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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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7
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Duan L, Zhu T, Ji C, Zhang Q, Zhang JZH. Direct folding simulation of helical proteins using an effective polarizable bond force field. Phys Chem Chem Phys 2017; 19:15273-15284. [DOI: 10.1039/c7cp02101a] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Snapshots of the intermediate conformation of Trp-cage at various simulation times using AMBER03, EPB03, AMBER12SB, and EPB12SB. Here, the N terminal is always on the top.
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Affiliation(s)
- Lili Duan
- School of Physics and Electronics
- Shandong Normal University
- Jinan 250014
- China
- School of Chemistry and Molecular Engineering
| | - Tong Zhu
- School of Chemistry and Molecular Engineering
- East China Normal University
- Shanghai 200062
- China
| | - Changge Ji
- School of Chemistry and Molecular Engineering
- East China Normal University
- Shanghai 200062
- China
- NYU-ECNU Center for Computational Chemistry at NYU Shanghai
| | - Qinggang Zhang
- School of Physics and Electronics
- Shandong Normal University
- Jinan 250014
- China
| | - John Z. H. Zhang
- School of Chemistry and Molecular Engineering
- East China Normal University
- Shanghai 200062
- China
- NYU-ECNU Center for Computational Chemistry at NYU Shanghai
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8
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Gupta M, Khatua P, Chakravarty C, Bandyopadhyay S. The sensitivity of folding free energy landscapes of trpzips to mutations in the hydrophobic core. Phys Chem Chem Phys 2017; 19:22813-22825. [DOI: 10.1039/c7cp03825a] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The sensitivity of the stability of folded states and free energy landscapes to the differences in the hydrophobic content of the core residues has been studied for the set of 16-residue trpzips, namely, Trpzip4, Trpzip5 and Trpzip6.
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Affiliation(s)
- Madhulika Gupta
- Department of Chemistry
- Indian Institute of Technology-Delhi
- New Delhi 110016
- India
| | - Prabir Khatua
- Molecular Modeling Laboratory
- Department of Chemistry
- Indian Institute of Technology
- Kharagpur 721302
- India
| | | | - Sanjoy Bandyopadhyay
- Molecular Modeling Laboratory
- Department of Chemistry
- Indian Institute of Technology
- Kharagpur 721302
- India
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9
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Melnik BS, Nagibina GS, Glukhov AS, Melnik TN, Uversky VN. Substitutions of Amino Acids with Large Number of Contacts in the Native State Have no Effect on the Rates of Protein Folding. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2016; 1864:1809-1817. [PMID: 27639966 DOI: 10.1016/j.bbapap.2016.09.006] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/06/2016] [Revised: 09/09/2016] [Accepted: 09/13/2016] [Indexed: 11/28/2022]
Abstract
Various effects of amino acid substitutions on properties of globular proteins have been described in a large number of research papers. Nevertheless, no definite "rule" has been formulated as of yet that could be used by experimentalists to introduce desirable changes in the properties of proteins. Herein we attempt to establish such a "rule". To this end, a hypothesis is proposed on the effects of substitutions of hydrophobic residues with large number of contacts on free energies of different states of a globular protein. The hypothesis states: Substitutions of hydrophobic residues engaged in a large number of residue-residue contacts would not change the folding rate of a protein but could affect its unfolding rate. This hypothesis was verified by both theoretical and experimental analyses, generating a general rule that can facilitate the work of experimentalists on constructing mutant forms of proteins.
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Affiliation(s)
- Bogdan S Melnik
- Institute of Protein Research, Russian Academy of Sciences, 142290 Pushchino, Moscow, Region, Russia.
| | - Galina S Nagibina
- Institute of Protein Research, Russian Academy of Sciences, 142290 Pushchino, Moscow, Region, Russia
| | - Anatoly S Glukhov
- Institute of Protein Research, Russian Academy of Sciences, 142290 Pushchino, Moscow, Region, Russia
| | - Tatiana N Melnik
- Institute of Protein Research, Russian Academy of Sciences, 142290 Pushchino, Moscow, Region, Russia
| | - Vladimir N Uversky
- Laboratory of Structural Dynamics, Stability and Folding of Proteins, Institute of Cytology, Russian Academy of Sciences, St. Petersburg, Russia; Department of Molecular Medicine and USF Health Byrd Alzheimer's Research Institute, Morsani College of Medicine, University of South Florida, Tampa, FL, USA.
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10
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Narayanan C, Dias CL. Exploring the free energy landscape of a model β-hairpin peptide and its isoform. Proteins 2014; 82:2394-402. [PMID: 24825659 DOI: 10.1002/prot.24601] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2013] [Revised: 03/21/2014] [Accepted: 04/29/2014] [Indexed: 12/16/2022]
Abstract
Secondary structural transitions from α-helix to β-sheet conformations are observed in several misfolding diseases including Alzheimer's and Parkinson's. Determining factors contributing favorably to the formation of each of these secondary structures is therefore essential to better understand these disease states. β-hairpin peptides form basic components of anti-parallel β-sheets and are suitable model systems for characterizing the fundamental forces stabilizing β-sheets in fibrillar structures. In this study, we explore the free energy landscape of the model β-hairpin peptide GB1 and its E2 isoform that preferentially adopts α-helical conformations at ambient conditions. Umbrella sampling simulations using all-atom models and explicit solvent are performed over a large range of end-to-end distances. Our results show the strong preference of GB1 and the E2 isoform for β-hairpin and α-helical conformations, respectively, consistent with previous studies. We show that the unfolded states of GB1 are largely populated by misfolded β-hairpin structures which differ from each other in the position of the β-turn. We discuss the energetic factors contributing favorably to the formation of α-helix and β-hairpin conformations in these peptides and highlight the energetic role of hydrogen bonds and non-bonded interactions.
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Affiliation(s)
- Chitra Narayanan
- Department of Physics, New Jersey Institute of Technology, University Heights, Newark, New Jersey, 07102-1982
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11
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Rabong C, Schuster C, Liptaj T, Prónayová N, Delchev VB, Jordis U, Phopase J. NXO beta structure mimicry: an ultrashort turn/hairpin mimic that folds in water. RSC Adv 2014. [DOI: 10.1039/c4ra01210k] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
An NXO building block derived tetrapeptide mimic emulates a natural proline-glycine β-turn/hairpin in polar media, including water at room temperature.
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Affiliation(s)
- Constantin Rabong
- Institute of Applied Synthetic Chemistry
- Vienna University of Technology
- A-1060 Vienna, Austria
| | - Christoph Schuster
- Department of Environmental Geosciences
- University of Vienna
- A-1090 Vienna, Austria
| | - Tibor Liptaj
- Department of NMR and Mass Spectrometry
- Institute of Analytical Chemistry
- Faculty of Chemical and Food Technology
- Slovak University of Technology
- 81237 Bratislava, Slovak Republic
| | - Nadežda Prónayová
- Department of NMR and Mass Spectrometry
- Institute of Analytical Chemistry
- Faculty of Chemical and Food Technology
- Slovak University of Technology
- 81237 Bratislava, Slovak Republic
| | - Vassil B. Delchev
- Department of Physical Chemistry
- University of Plovdiv
- 4000 Plovdiv, Bulgaria
| | - Ulrich Jordis
- Institute of Applied Synthetic Chemistry
- Vienna University of Technology
- A-1060 Vienna, Austria
| | - Jaywant Phopase
- Integrative Regenerative Medicine Centre (IGEN) & Department of Physics
- Chemistry and Biology (IFM)
- 58183 Linköping, Sweden
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12
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Yoda T, Sugita Y, Okamoto Y. Salt effects on hydrophobic-core formation in folding of a helical miniprotein studied by molecular dynamics simulations. Proteins 2013; 82:933-43. [PMID: 24214490 DOI: 10.1002/prot.24467] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2013] [Revised: 10/26/2013] [Accepted: 10/29/2013] [Indexed: 11/07/2022]
Abstract
We have investigated effects of salt ions on folding events of a helical miniprotein chicken villin headpiece subdomain HP36. Low concentrations of ions alter electrostatic interactions between charged groups of a protein and can change the populations of conformers. Here, we compare two data sets of folding simulations of HP36 in explicit water solvent with or without ions. For efficient sampling of the conformational space of HP36, the multicanonical replica-exchange molecular dynamics method was employed. Our analyses suggest that salt alters salt-bridging nature of the protein at later stages of folding at room temperature. Especially, more nonnative, nonlocal salt bridges are formed at near-native conformations in pure water. Our analyses also show that such salt-bridge formation hinders the fully native hydrophobic-core packing at the final stages of folding.
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Affiliation(s)
- Takao Yoda
- Nagahama Institute of Bio-Science and Technology, Tamura, Nagahama, Shiga, 526-0829, Japan; RIKEN Advanced Institute for Computational Science, Chuo-ku, Kobe, Hyogo, 650-0047, Japan
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13
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Compiani M, Capriotti E. Computational and theoretical methods for protein folding. Biochemistry 2013; 52:8601-24. [PMID: 24187909 DOI: 10.1021/bi4001529] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
A computational approach is essential whenever the complexity of the process under study is such that direct theoretical or experimental approaches are not viable. This is the case for protein folding, for which a significant amount of data are being collected. This paper reports on the essential role of in silico methods and the unprecedented interplay of computational and theoretical approaches, which is a defining point of the interdisciplinary investigations of the protein folding process. Besides giving an overview of the available computational methods and tools, we argue that computation plays not merely an ancillary role but has a more constructive function in that computational work may precede theory and experiments. More precisely, computation can provide the primary conceptual clues to inspire subsequent theoretical and experimental work even in a case where no preexisting evidence or theoretical frameworks are available. This is cogently manifested in the application of machine learning methods to come to grips with the folding dynamics. These close relationships suggested complementing the review of computational methods within the appropriate theoretical context to provide a self-contained outlook of the basic concepts that have converged into a unified description of folding and have grown in a synergic relationship with their computational counterpart. Finally, the advantages and limitations of current computational methodologies are discussed to show how the smart analysis of large amounts of data and the development of more effective algorithms can improve our understanding of protein folding.
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Affiliation(s)
- Mario Compiani
- School of Sciences and Technology, University of Camerino , Camerino, Macerata 62032, Italy
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14
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Hu JP, He HQ, Jiao X, Chang S. Understanding the folding and stability of a designed WW domain protein with replica exchange molecular dynamics simulations. MOLECULAR SIMULATION 2013. [DOI: 10.1080/08927022.2013.773431] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
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15
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Tsai M, Yuan J, Yamaki M, Lin C, Lin SH. Molecular Dynamics Insight into the Diverse Thermodynamic Behavior of a Beta‐Hairpin Peptide. J CHIN CHEM SOC-TAIP 2013. [DOI: 10.1002/jccs.201300173] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Min‐Yeh Tsai
- Department of Applied Chemistry, National Chiao Tung University, Hsinchu, Taiwan 30010, ROC
- Department of Chemistry, National Taiwan University, Taipei, Taiwan 10617, ROC
| | - Jian‐Min Yuan
- Department of Physics, Drexel University, Philadelphia, Pennsylvania 19104, USA
| | - Masahiro Yamaki
- Department of Applied Chemistry, National Chiao Tung University, Hsinchu, Taiwan 30010, ROC
| | - Chih‐Kai Lin
- Department of Applied Chemistry, National Chiao Tung University, Hsinchu, Taiwan 30010, ROC
| | - Sheng Hsien Lin
- Department of Applied Chemistry, National Chiao Tung University, Hsinchu, Taiwan 30010, ROC
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16
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Liu L, Cao Z. Turn-directed α-β conformational transition of α-syn12 peptide at different pH revealed by unbiased molecular dynamics simulations. Int J Mol Sci 2013; 14:10896-907. [PMID: 23708094 PMCID: PMC3709708 DOI: 10.3390/ijms140610896] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2013] [Revised: 04/24/2013] [Accepted: 04/24/2013] [Indexed: 11/16/2022] Open
Abstract
The transition from α-helical to β-hairpin conformations of α-syn12 peptide is characterized here using long timescale, unbiased molecular dynamics (MD) simulations in explicit solvent models at physiological and acidic pH values. Four independent normal MD trajectories, each 2500 ns, are performed at 300 K using the GROMOS 43A1 force field and SPC water model. The most clustered structures at both pH values are β-hairpin but with different turns and hydrogen bonds. Turn9-6 and four hydrogen bonds (HB9-6, HB6-9, HB11-4 and HB4-11) are formed at physiological pH; turn8-5 and five hydrogen bonds (HB8-5, HB5-8, HB10-3, HB3-10 and HB12-1) are formed at acidic pH. A common folding mechanism is observed: the formation of the turn is always before the formation of the hydrogen bonds, which means the turn is always found to be the major determinant in initiating the transition process. Furthermore, two transition paths are observed at physiological pH. One of the transition paths tends to form the most-clustered turn and improper hydrogen bonds at the beginning, and then form the most-clustered hydrogen bonds. Another transition path tends to form the most-clustered turn, and turn5-2 firstly, followed by the formation of part hydrogen bonds, then turn5-2 is extended and more hydrogen bonds are formed. The transition path at acidic pH is as the same as the first path described at physiological pH.
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Affiliation(s)
- Lei Liu
- Department of Computer Science and Technology, Dezhou University, Dezhou 253023, China; E-Mail:
- Shandong Provincial Key Laboratory of Functional Macromolecular Biophysics, Dezhou 253023, China
| | - Zanxia Cao
- Shandong Provincial Key Laboratory of Functional Macromolecular Biophysics, Dezhou 253023, China
- Author to whom correspondence should be addressed; E-Mail: ; Tel.: +86-534-8985879; Fax: +86-534-8985884
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17
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De Sancho D, Mittal J, Best RB. Folding Kinetics and Unfolded State Dynamics of the GB1 Hairpin from Molecular Simulation. J Chem Theory Comput 2013; 9:1743-53. [PMID: 26587632 DOI: 10.1021/ct301033r] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
The C-terminal β-hairpin of protein G is a 16-residue peptide that folds in a two-state fashion akin to many larger proteins. However, with an experimental folding time of ∼6 μs, it remains a challenging system for all-atom, explicitly solvated, molecular dynamics simulations. Here, we use a large simulation data set (0.7 ms total) of the hairpin at 300 and 350 K to interpret its folding via a master equation approach. We find a separation of over an order of magnitude between the longest and second longest relaxation times, with the slowest relaxation corresponding to folding. However, in spite of this apparent two-state dynamics, the folding rate determined based on a first-passage time analysis depends on the initial conditions chosen, with a nonexponential distribution of first passage times being obtained in some cases. Using the master equation model, we are now able to account quantitatively for the observed distribution of first passage times. The deviation from the expected exponential distribution for a two-state system arises from slow dynamics in the unfolded state, associated with formation and melting of helical structures. Our results help to reconcile recent findings of slow dynamics in unfolded proteins with observed two-state folding kinetics. At the same time, they indicate that care is required in estimating folding kinetics from many short folding simulations. Last, we are able to use the master equation model to obtain details of the folding mechanism and folding transition state, which appear consistent with the "zipper" mechanism inferred from the experiment.
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Affiliation(s)
- David De Sancho
- Cambridge University, Department of Chemistry, Lensfield Road Cambridge CB2 1EW, United Kingdom
| | - Jeetain Mittal
- Department of Chemical Engineering, 111 Research Drive, Iacocca Hall, Bethlehem, Pennsylvania 18015, United States
| | - Robert B Best
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892-0520, United States
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18
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Abstract
In biomolecular systems (especially all-atom models) with many degrees of freedom such as proteins and nucleic acids, there exist an astronomically large number of local-minimum-energy states. Conventional simulations in the canonical ensemble are of little use, because they tend to get trapped in states of these energy local minima. Enhanced conformational sampling techniques are thus in great demand. A simulation in generalized ensemble performs a random walk in potential energy space and can overcome this difficulty. From only one simulation run, one can obtain canonical-ensemble averages of physical quantities as functions of temperature by the single-histogram and/or multiple-histogram reweighting techniques. In this article we review uses of the generalized-ensemble algorithms in biomolecular systems. Three well-known methods, namely, multicanonical algorithm, simulated tempering, and replica-exchange method, are described first. Both Monte Carlo and molecular dynamics versions of the algorithms are given. We then present various extensions of these three generalized-ensemble algorithms. The effectiveness of the methods is tested with short peptide and protein systems.
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Affiliation(s)
- Ayori Mitsutake
- Department of Physics, Keio University, Yokohama, Kanagawa, Japan
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19
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Han W, Schulten K. Further optimization of a hybrid united-atom and coarse-grained force field for folding simulations: Improved backbone hydration and interactions between charged side chains. J Chem Theory Comput 2012; 8:4413-4424. [PMID: 23204949 PMCID: PMC3507460 DOI: 10.1021/ct300696c] [Citation(s) in RCA: 99] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
PACE, a hybrid force field which couples united-atom protein models with coarse-grained (CG) solvent, has been further optimized, aiming to improve itse ciency for folding simulations. Backbone hydration parameters have been re-optimized based on hydration free energies of polyalanyl peptides through atomistic simulations. Also, atomistic partial charges from all-atom force fields were combined with PACE in order to provide a more realistic description of interactions between charged groups. Using replica exchange molecular dynamics (REMD), ab initio folding using the new PACE has been achieved for seven small proteins (16 - 23 residues) with different structural motifs. Experimental data about folded states, such as their stability at room temperature, melting point and NMR NOE constraints, were also well reproduced. Moreover, a systematic comparison of folding kinetics at room temperature has been made with experiments, through standard MD simulations, showing that the new PACE may speed up the actual folding kinetics 5-10 times. Together with the computational speedup benefited from coarse-graining, the force field provides opportunities to study folding mechanisms. In particular, we used the new PACE to fold a 73-residue protein, 3D, in multiple 10 - 30 μs simulations, to its native states (C(α) RMSD ~ 0.34 nm). Our results suggest the potential applicability of the new PACE for the study of folding and dynamics of proteins.
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Affiliation(s)
- Wei Han
- Beckman Institute, University of Illinois at Urbana-Champaign, USA
- Center for Biophysics and Computational Biology, University of Illinois at Urbana-Champaign, USA
| | - Klaus Schulten
- Beckman Institute, University of Illinois at Urbana-Champaign, USA
- Center for Biophysics and Computational Biology, University of Illinois at Urbana-Champaign, USA
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20
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Duan LL, Gao Y, Mei Y, Zhang QG, Tang B, Zhang JZH. Folding of a helix is critically stabilized by polarization of backbone hydrogen bonds: study in explicit water. J Phys Chem B 2012; 116:3430-5. [PMID: 22369598 DOI: 10.1021/jp212516g] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Multiple single-trajectory molecular dynamics (MD) simulation at room temperature (300 K) in explicit water was carried out to study the folding dynamics of an α-helix (PDB 2I9M ) using a polarized charge scheme that includes electronic polarization of backbone hydrogen bonds. Starting from an extended conformation, the 17-residue peptide was successfully folded into the native structure (α-helix) between 80 and 130 ns with a root-mean-square deviation of ~1.0 Å. Analysis of the time-dependent trajectories revealed that helix formation of the peptide started at the terminals and progressed toward the center of the peptide. For comparison, MD trajectories generated under various versions of standard AMBER force fields failed to show any significant or stable helix formation in our simulation. Our result shows clear evidence that the electronic polarization of backbone hydrogen bonds energetically stabilizes the helix formation and is critical to the stable folding of the short helix structure.
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Affiliation(s)
- Li L Duan
- State Key Laboratory of Precision Spectroscopy, Department of Physics, and Institute of Theoretical and Computational Science, East China Normal University, Shanghai 200062, China
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21
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Engin O, Sayar M. Adsorption, Folding, and Packing of an Amphiphilic Peptide at the Air/Water Interface. J Phys Chem B 2012; 116:2198-207. [DOI: 10.1021/jp206327y] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Ozge Engin
- College of Engineering, Koç University, 34450, Istanbul,
Turkey
| | - Mehmet Sayar
- College of Engineering, Koç University, 34450, Istanbul,
Turkey
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22
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Shao Q, Yang L, Gao YQ. Structure change of β-hairpin induced by turn optimization: An enhanced sampling molecular dynamics simulation study. J Chem Phys 2011; 135:235104. [DOI: 10.1063/1.3668288] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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23
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Microscopic events in β-hairpin folding from alternative unfolded ensembles. Proc Natl Acad Sci U S A 2011; 108:11087-92. [PMID: 21690352 DOI: 10.1073/pnas.1016685108] [Citation(s) in RCA: 64] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023] Open
Abstract
We have performed the first unbiased folding simulations of the GB1 hairpin in explicit solvent, using hundreds of microsecond-long molecular dynamics simulations (total time: 0.7 ms). Our simulations are initiated from two sets of structures. Starting from an equilibrium unfolded state, we obtain single-exponential folding kinetics with rate coefficients in good agreement (T=350 K) or within an order of magnitude (T=300 K) of the experimental values. However, simulations initiated from unfolded configurations lacking secondary structure result in biexponential kinetics with an additional fast nanosecond kinetic mode. This mode can strongly bias the folding rate estimated from the mean first passage time, when the trials are much shorter than the folding time. We find that the mechanism of the hairpin folding is insensitive to the details of the initial unfolded ensemble and is initiated by correct formation of the turn of the hairpin, followed by the formation of the native hydrogen bonds and hydrophobic contacts, consistent with experimental -value analysis. Subsequent native interactions can be formed either from the turn or from the hairpin termini, helping to explain an apparent discrepancy in experimental results. From our simulations, we also obtain the transition path durations, a critical parameter for single molecule experiments aiming to resolve events along folding pathways. The lengths of transition paths span a wide range, from 50 ps to 140 ns, at 300 K.
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24
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Pietropaolo A, Branduardi D, Bonomi M, Parrinello M. A chirality-based metrics for free-energy calculations in biomolecular systems. J Comput Chem 2011; 32:2627-37. [PMID: 21656787 DOI: 10.1002/jcc.21842] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2011] [Revised: 03/28/2011] [Accepted: 04/23/2011] [Indexed: 12/21/2022]
Abstract
In this work, we exploit the chirality index introduced in (Pietropaolo et al., Proteins 2008, 70, 667) as an effective descriptor of the secondary structure of proteins to explore their complex free-energy landscape. We use the chirality index as an alternative metrics in the path collective variables (PCVs) framework and we show in the prototypical case of the C-terminal domain of immunoglobulin binding protein GB1 that relevant configurations can be efficiently sampled in combination with well-tempered metadynamics. While the projections of the configurations found onto a variety of different descriptors are fully consistent with previously reported calculations, this approach provides a unifying perspective of the folding mechanism which was not possible using metadynamics with the previous formulation of PCVs.
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25
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Barducci A, Bonomi M, Derreumaux P. Assessing the Quality of the OPEP Coarse-Grained Force Field. J Chem Theory Comput 2011; 7:1928-34. [DOI: 10.1021/ct100646f] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Affiliation(s)
- Alessandro Barducci
- Computational Science, Department of Chemistry and Applied Biosciences, ETH Zurich, c/o USI Campus, via Buffi 13, CH-6900 Lugano, Switzerland
| | - Massimiliano Bonomi
- Computational Science, Department of Chemistry and Applied Biosciences, ETH Zurich, c/o USI Campus, via Buffi 13, CH-6900 Lugano, Switzerland
| | - Philippe Derreumaux
- Laboratoire de Biochimie Théorique, UPR 9080 CNRS, Institut de Biologie Physico-Chimique and Université Paris Diderot, Paris 7, Institut Universitaire de France, 13 rue Pierre et Marie Curie, 75005 Paris, France
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26
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Best RB, Mittal J. Free-energy landscape of the GB1 hairpin in all-atom explicit solvent simulations with different force fields: Similarities and differences. Proteins 2011; 79:1318-28. [PMID: 21322056 DOI: 10.1002/prot.22972] [Citation(s) in RCA: 104] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2010] [Revised: 11/29/2010] [Accepted: 12/07/2010] [Indexed: 11/09/2022]
Abstract
Although it is now possible to fold peptides and miniproteins in molecular dynamics simulations, it is well appreciated that force fields are not all transferable to different proteins. Here, we investigate the influence of the protein force field and the solvent model on the folding energy landscape of a prototypical two-state folder, the GB1 hairpin. We use extensive replica-exchange molecular dynamics simulations to characterize the free-energy surface as a function of temperature. Most of these force fields appear similar at a global level, giving a fraction folded at 300 K between 0.2 and 0.8 in all cases, which is a difference in stability of 2.8 kT, and are generally consistent with experimental data at this temperature. The most significant differences appear in the unfolded state, where there are different residual secondary structures which are populated, and the overall dimensions of the unfolded states, which in most of the force fields are too collapsed relative to experimental Förster Resonance Energy Transfer (FRET) data.
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Affiliation(s)
- Robert B Best
- Department of Chemistry, University of Cambridge, Cambridge UK.
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27
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Yoda T, Sugita Y, Okamoto Y. Hydrophobic core formation and dehydration in protein folding studied by generalized-ensemble simulations. Biophys J 2010; 99:1637-44. [PMID: 20816077 DOI: 10.1016/j.bpj.2010.06.045] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2010] [Revised: 06/05/2010] [Accepted: 06/22/2010] [Indexed: 11/30/2022] Open
Abstract
Despite its small size, chicken villin headpiece subdomain HP36 folds into the native structure with a stable hydrophobic core within several microseconds. How such a small protein keeps up its conformational stability and fast folding in solution is an important issue for understanding molecular mechanisms of protein folding. In this study, we performed multicanonical replica-exchange simulations of HP36 in explicit water, starting from a fully extended conformation. We observed at least five events of HP36 folding into nativelike conformations. The smallest backbone root mean-square deviation from the crystal structure was 1.1 A. In the nativelike conformations, the stably formed hydrophobic core was fully dehydrated. Statistical analyses of the simulation trajectories show the following sequential events in folding of HP36: 1), Helix 3 is formed at the earliest stage; 2), the backbone and the side chains near the loop between Helices 2 and 3 take nativelike conformations; and 3), the side-chain packing at the hydrophobic core and the dehydration of the core side chains take place simultaneously at the later stage of folding. This sequence suggests that the initial folding nucleus is not necessarily the same as the hydrophobic core, consistent with a recent experimental phi-value analysis.
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Affiliation(s)
- Takao Yoda
- Nagahama Institute of Bio-Science and Technology, Tamura, Nagahama, Shiga, Japan.
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28
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Duan LL, Mei Y, Zhang D, Zhang QG, Zhang JZH. Folding of a helix at room temperature is critically aided by electrostatic polarization of intraprotein hydrogen bonds. J Am Chem Soc 2010; 132:11159-64. [PMID: 20698682 DOI: 10.1021/ja102735g] [Citation(s) in RCA: 81] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
We report direct folding of a 17-residue helix protein (pdb:2I9M) by standard molecular dynamics simulation (single trajectory) at room temperature with implicit solvent. Starting from a fully extended structure, 2I9M successfully folds into the native conformation within 16 ns using adaptive hydrogen bond-specific charges to take into account the electrostatic polarization effect. Cluster analysis shows that conformations in the native state cluster have the highest population (78.4%) among all sampled conformations. Folding snapshots and the secondary structure analysis demonstrate that the folding of 2I9M begins at terminals and progresses toward the center. A plot of the free energy landscape indicates that there is no significant free energy barrier during folding, which explains the observed fast folding speed. For comparison, exactly the same molecular dynamics simulation but carried out under existing AMBER charges failed to fold 2I9M into native-like structures. The current study demonstrates that electrostatic polarization of intraprotein hydrogen bonding, which stabilizes the helix, is critical to the successful folding of 2I9m.
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Affiliation(s)
- Li L Duan
- College of Physics and Electronics, Shandong Normal University, Jinan 250014, China
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29
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Shao Q, Gao YQ. Temperature Dependence of Hydrogen-Bond Stability in β-Hairpin Structures. J Chem Theory Comput 2010. [DOI: 10.1021/ct100436r] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Qiang Shao
- College of Chemistry and Molecular Engineering, National Laboratory of Molecular Sciences, Peking University, Beijing, China
| | - Yi Qin Gao
- College of Chemistry and Molecular Engineering, National Laboratory of Molecular Sciences, Peking University, Beijing, China
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30
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Best RB, Mittal J. Balance between alpha and beta structures in ab initio protein folding. J Phys Chem B 2010; 114:8790-8. [PMID: 20536262 DOI: 10.1021/jp102575b] [Citation(s) in RCA: 93] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Despite initial successes in folding of proteins by molecular simulation, it is becoming increasingly evident that current energy functions (force fields) tend to favor either alpha or beta secondary structure, such that the choice of force field is governed by the structural class of the protein. Here, we study the folding of peptides with either predominantly alpha (Trp cage) or beta (GB1 hairpin) structure with a modified version of the Amber ff03 force field, optimized to reproduce structural propensity in a helix-forming peptide. Using extensive replica exchange molecular dynamics simulations starting from completely unfolded configurations, we obtain the correct folded structure for each peptide, in close agreement with the experimental native structure (<1.5 A all-atom root-mean-square deviation). We obtain converged equilibrium distributions, with folded populations at standard conditions (approximately 300 K), in remarkable accord with experiment. Further comparison to experimental data from NMR spectroscopy and FRET suggests that although the folded structures are accurately reproduced, the unfolded state remains too structured and compact. Our results suggest that the backbone correction results in a force field that is transferable to the folding of proteins from different structural classes.
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Affiliation(s)
- Robert B Best
- Department of Chemistry, Cambridge University, Lensfield Road, Cambridge CB2 1EW, UK.
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31
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Effects of Turn Stability and Side-Chain Hydrophobicity on the Folding of β-Structures. J Mol Biol 2010; 402:595-609. [DOI: 10.1016/j.jmb.2010.08.037] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2010] [Revised: 07/10/2010] [Accepted: 08/19/2010] [Indexed: 11/24/2022]
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32
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Cossio P, Marinelli F, Laio A, Pietrucci F. Optimizing the Performance of Bias-Exchange Metadynamics: Folding a 48-Residue LysM Domain Using a Coarse-Grained Model. J Phys Chem B 2010; 114:3259-65. [DOI: 10.1021/jp907464b] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Pilar Cossio
- SISSA- Scuola Internazionale Superiore di Studi Avanzati, and CNR-INFM DEMOCRITOS National Simulation Center, via Beirut 2−4, I-34014 Trieste, Italy
| | - Fabrizio Marinelli
- SISSA- Scuola Internazionale Superiore di Studi Avanzati, and CNR-INFM DEMOCRITOS National Simulation Center, via Beirut 2−4, I-34014 Trieste, Italy
| | - Alessandro Laio
- SISSA- Scuola Internazionale Superiore di Studi Avanzati, and CNR-INFM DEMOCRITOS National Simulation Center, via Beirut 2−4, I-34014 Trieste, Italy
| | - Fabio Pietrucci
- SISSA- Scuola Internazionale Superiore di Studi Avanzati, and CNR-INFM DEMOCRITOS National Simulation Center, via Beirut 2−4, I-34014 Trieste, Italy
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33
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Wei H, Shao Q, Gao YQ. The effects of side chain hydrophobicity on the denaturation of simple β-hairpins. Phys Chem Chem Phys 2010; 12:9292-9. [DOI: 10.1039/b924593f] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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34
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Juraszek J, Bolhuis PG. Effects of a Mutation on the Folding Mechanism of a β-Hairpin. J Phys Chem B 2009; 113:16184-96. [DOI: 10.1021/jp904468q] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Jarek Juraszek
- van’t Hoff Institute for Molecular Sciences, University of Amsterdam, Amsterdam, The Netherlands
| | - Peter G. Bolhuis
- van’t Hoff Institute for Molecular Sciences, University of Amsterdam, Amsterdam, The Netherlands
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35
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Lei H, Wang ZX, Wu C, Duan Y. Dual folding pathways of an alpha/beta protein from all-atom ab initio folding simulations. J Chem Phys 2009; 131:165105. [PMID: 19894980 PMCID: PMC2780466 DOI: 10.1063/1.3238567] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2009] [Accepted: 09/07/2009] [Indexed: 11/14/2022] Open
Abstract
Successful ab initio folding of proteins with both alpha-helix and beta-sheet requires a delicate balance among a variety of forces in the simulation model, which may explain that the successful folding of any alpha/beta proteins to within experimental error has yet to be reported. Here we demonstrate that it is an achievable goal to fold alpha/beta proteins with a force field emphasizing the balance between the two major secondary structures. Using our newly developed force field, we conducted extensive ab initio folding simulations on an alpha/beta protein full sequence design (FSD) employing both conventional molecular dynamics and replica exchange molecular dynamics in combination with a generalized-Born solvation model. In these simulations, the folding of FSD to the native state with high population (>64.2%) and high fidelity (C(alpha)-Root Mean Square Deviation of 1.29 A for the most sampled conformation when compared to the experimental structure) was achieved. The folding of FSD was found to follow two pathways. In the major pathway, the folding started from the formation of the helix. In the minor pathway, however, folding of the beta-hairpin started first. Further examination revealed that the helix initiated from the C-terminus and propagated toward the N-terminus. The formation of the hydrophobic contacts coincided with the global folding. Therefore the hydrophobic force does not appear to be the driving force of the folding of this protein.
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Affiliation(s)
- Hongxing Lei
- Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100029, China
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36
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Pietrucci F, Laio A. A Collective Variable for the Efficient Exploration of Protein Beta-Sheet Structures: Application to SH3 and GB1. J Chem Theory Comput 2009; 5:2197-201. [DOI: 10.1021/ct900202f] [Citation(s) in RCA: 121] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Fabio Pietrucci
- International School for Advanced Studies (SISSA-ISAS), via Beirut 2-4, I-34014 Trieste, Italy
| | - Alessandro Laio
- International School for Advanced Studies (SISSA-ISAS), via Beirut 2-4, I-34014 Trieste, Italy
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37
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Conformational Studies of the 313-320 and 313-332 Peptide Fragments Derived from the αIIb Subunit of Integrin Receptor with Molecular Dynamics Simulations. Int J Pept Res Ther 2009. [DOI: 10.1007/s10989-009-9187-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
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38
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Shao Q, Yang L, Gao YQ. A test of implicit solvent models on the folding simulation of the GB1 peptide. J Chem Phys 2009; 130:195104. [DOI: 10.1063/1.3132850] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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39
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Chebaro Y, Dong X, Laghaei R, Derreumaux P, Mousseau N. Replica exchange molecular dynamics simulations of coarse-grained proteins in implicit solvent. J Phys Chem B 2009; 113:267-74. [PMID: 19067549 DOI: 10.1021/jp805309e] [Citation(s) in RCA: 66] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Current approaches aimed at determining the free energy surface of all-atom medium-size proteins in explicit solvent are slow and are not sufficient to converge to equilibrium properties. To ensure a proper sampling of the configurational space, it is preferable to use reduced representations such as implicit solvent and/or coarse-grained protein models, which are much lighter computationally. Each model must be verified, however, to ensure that it can recover experimental structures and thermodynamics. Here we test the coarse-grained implicit solvent OPEP model with replica exchange molecular dynamics (REMD) on six peptides ranging in length from 10 to 28 residues: two alanine-based peptides, the second beta-hairpin from protein G, the Trp-cage and zinc-finger motif, and a dimer of a coiled coil peptide. We show that REMD-OPEP recovers the proper thermodynamics of the systems studied, with accurate structural description of the beta-hairpin and Trp-cage peptides (within 1-2 A from experiments). The light computational burden of REMD-OPEP, which enables us to generate many hundred nanoseconds at each temperature and fully assess convergence to equilibrium ensemble, opens the door to the determination of the free energy surface of larger proteins and assemblies.
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Affiliation(s)
- Yassmine Chebaro
- Institut de Biologie Physico-Chimique et Universite Paris 7 Denis Diderot, 75005 Paris, France
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40
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Carr JM, Wales DJ. Refined kinetic transition networks for the GB1 hairpin peptide. Phys Chem Chem Phys 2009; 11:3341-54. [DOI: 10.1039/b820649j] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
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41
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Molecular dynamics simulation of antimicrobial peptide arenicin-2: β-Hairpin stabilization by noncovalent interactions. Biopolymers 2009; 92:143-55. [DOI: 10.1002/bip.21149] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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42
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43
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Bonomi M, Branduardi D, Gervasio FL, Parrinello M. The unfolded ensemble and folding mechanism of the C-terminal GB1 beta-hairpin. J Am Chem Soc 2008; 130:13938-44. [PMID: 18811160 DOI: 10.1021/ja803652f] [Citation(s) in RCA: 90] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
In this work, we shed new light on a much-studied case of beta-hairpin folding by means of advanced molecular dynamics simulations. A fully atomistic description of the protein and the solvent molecule is used, together with metadynamics, to accelerate the sampling and estimate free-energy landscapes. This is achieved using the path collective variables approach, which provides an adaptive description of the mechanism under study. We discover that the folding mechanism is a multiscale process where the turn region conformation leads to two different energy pathways that are connected by elongated structures. The former displays a stable 2:4 native-like structure in which an optimal hydrophobic packing and hydrogen bond pattern leads to 8 kcal/mol of stabilization. The latter shows a less-structured 3:5 beta-sheet, where hydrogen bonds and hydrophobic packing provide only 2.5 kcal/mol of stability. This perspective is fully consistent with experimental evidence that shows this to be a prototypical two-state folder, while it redefines the nature of the unfolded state.
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Affiliation(s)
- Massimiliano Bonomi
- Computational Science, Department of Chemistry and Applied Biosciences, ETH Zürich, USI Campus, Via Giuseppe Buffi 13, CH-6900 Lugano, Switzerland
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Patel S, Sasidhar YU. A shorter peptide model from staphylococcal nuclease for the folding-unfolding equilibrium of a beta-hairpin shows that unfolded state has significant contribution from compact conformational states. J Struct Biol 2008; 164:60-74. [PMID: 18602478 DOI: 10.1016/j.jsb.2008.06.003] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2008] [Revised: 05/26/2008] [Accepted: 06/05/2008] [Indexed: 10/21/2022]
Abstract
It is important to understand the conformational features of the unfolded state in equilibrium with folded state under physiological conditions. In this paper, we consider a short peptide model LMYKGQPM from staphylococcal nuclease to model the conformational equilibrium between a hairpin conformation and its unfolded state using molecular dynamics simulation under NVT conditions at 300K using GROMOS96 force field. The free energy landscape has overall funnel-like shape with hairpin conformations sampling the minima. The "unfolded" state has a higher free energy of approximately 12kJ/mol with respect to native hairpin minimum and occupies a plateau region. We find that the unfolded state has significant contributions from compact conformations. Many of these conformations have hairpin-like topology. Further, these compact conformational forms are stabilized by hydrophobic interactions. Conversion between native and non-native hairpins occurs via unfolded states. Frequent conversions between folded and unfolded hairpins are observed with single exponential kinetics. We compare our results with the emerging picture of unfolded state from both experimental and theoretical studies.
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Affiliation(s)
- Sunita Patel
- Department of Chemistry, Indian Institute of Technology Bombay, Mumbai, Maharashtra, India
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Understanding the roles of amino acid residues in tertiary structure formation of chignolin by using molecular dynamics simulation. Proteins 2008; 73:621-31. [DOI: 10.1002/prot.22100] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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Protein Folding Stability - I. Biophys J 2008. [DOI: 10.1016/s0006-3495(08)79167-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
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Shao J, Tanner SW, Thompson N, Cheatham TE. Clustering Molecular Dynamics Trajectories: 1. Characterizing the Performance of Different Clustering Algorithms. J Chem Theory Comput 2007; 3:2312-34. [DOI: 10.1021/ct700119m] [Citation(s) in RCA: 614] [Impact Index Per Article: 36.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Jianyin Shao
- Departments of Medicinal Chemistry, Pharmaceutics and Pharmaceutical Chemistry, and Bioengineering, College of Pharmacy, University of Utah, 2000 East 30 South, Skaggs Hall 201, Salt Lake City, Utah 84112
| | - Stephen W. Tanner
- Departments of Medicinal Chemistry, Pharmaceutics and Pharmaceutical Chemistry, and Bioengineering, College of Pharmacy, University of Utah, 2000 East 30 South, Skaggs Hall 201, Salt Lake City, Utah 84112
| | - Nephi Thompson
- Departments of Medicinal Chemistry, Pharmaceutics and Pharmaceutical Chemistry, and Bioengineering, College of Pharmacy, University of Utah, 2000 East 30 South, Skaggs Hall 201, Salt Lake City, Utah 84112
| | - Thomas E. Cheatham
- Departments of Medicinal Chemistry, Pharmaceutics and Pharmaceutical Chemistry, and Bioengineering, College of Pharmacy, University of Utah, 2000 East 30 South, Skaggs Hall 201, Salt Lake City, Utah 84112
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