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Ren W, Li W, Wang J, Zhang J, Wang W. Consequences of Energetic Frustration on the Ligand-Coupled Folding/Dimerization Dynamics of Allosteric Protein S100A12. J Phys Chem B 2017; 121:9799-9806. [DOI: 10.1021/acs.jpcb.7b06919] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Weitong Ren
- National
Laboratory of Solid State Microstructure, Department of Physics, and
Collaborative Innovation Center of Advanced Microstructures, Nanjing University, Nanjing 210093, China
| | - Wenfei Li
- National
Laboratory of Solid State Microstructure, Department of Physics, and
Collaborative Innovation Center of Advanced Microstructures, Nanjing University, Nanjing 210093, China
| | - Jun Wang
- National
Laboratory of Solid State Microstructure, Department of Physics, and
Collaborative Innovation Center of Advanced Microstructures, Nanjing University, Nanjing 210093, China
| | - Jian Zhang
- National
Laboratory of Solid State Microstructure, Department of Physics, and
Collaborative Innovation Center of Advanced Microstructures, Nanjing University, Nanjing 210093, China
| | - Wei Wang
- National
Laboratory of Solid State Microstructure, Department of Physics, and
Collaborative Innovation Center of Advanced Microstructures, Nanjing University, Nanjing 210093, China
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2
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Nymeyer H. How Efficient Is Replica Exchange Molecular Dynamics? An Analytic Approach. J Chem Theory Comput 2015; 4:626-36. [PMID: 26620937 DOI: 10.1021/ct7003337] [Citation(s) in RCA: 72] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Replica exchange molecular dynamics (REMD) has become a standard technique for accelerating relaxation in biosimulations. Despite its widespread use, questions remain about its efficiency compared with conventional, constant temperature molecular dynamics (MD). An analytic approach is taken to describe the relative efficiency of REMD with respect to MD. This is applied to several simple two-state models and to several real proteins-protein L and the B domain of protein A-to predict the relative efficiency of REMD with respect to MD in actual applications. In agreement with others, we find the following: as long as there is a positive activation energy for folding, REMD is more efficient than MD; the effectiveness of REMD is strongly dependent on the activation enthalpy; and the efficiency of REMD for actual proteins is a strong function of the maximum temperature. Choosing the maximum temperature too high can result in REMD becoming significantly less efficient than conventional MD. A good rule of thumb appears to be to choose the maximum temperature of the REMD simulation slightly above the temperature at which the enthalpy for folding vanishes. Additionally, we find that the number of replicas in REMD, while important for simulations shorter than one or two relaxation times, has a minimal effect on the asymptotic efficiency of the method.
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Affiliation(s)
- Hugh Nymeyer
- Department of Chemistry & Biochemistry, The School of Computational Science and The Institute for Molecular Biophysics, Florida State University, Tallahassee, Florida 32306-4380
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3
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Guardiani C, Marino DD, Tramontano A, Chinappi M, Cecconi F. Exploring the Unfolding Pathway of Maltose Binding Proteins: An Integrated Computational Approach. J Chem Theory Comput 2014; 10:3589-97. [DOI: 10.1021/ct500283s] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Affiliation(s)
- Carlo Guardiani
- Dipartimento
di Fisica, Università di Roma “Sapienza”, I-00185, Rome, Italy
| | - Daniele Di Marino
- Dipartimento
di Fisica, Università di Roma “Sapienza”, I-00185, Rome, Italy
| | - Anna Tramontano
- Dipartimento
di Fisica, Università di Roma “Sapienza”, I-00185, Rome, Italy
| | - Mauro Chinappi
- Center
for Life Nano Science, Istituto Italiano di Tecnologia (IIT), I-00185, Rome, Italy
| | - Fabio Cecconi
- CNR−Istituto dei Sistemi Complessi (ISC), Via dei Taurini 19, I-00185, Rome, Italy
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4
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Feig M, Sugita Y. Reaching new levels of realism in modeling biological macromolecules in cellular environments. J Mol Graph Model 2013; 45:144-56. [PMID: 24036504 DOI: 10.1016/j.jmgm.2013.08.017] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2013] [Revised: 08/14/2013] [Accepted: 08/19/2013] [Indexed: 12/21/2022]
Abstract
An increasing number of studies are aimed at modeling cellular environments in a comprehensive and realistic fashion. A major challenge in these efforts is how to bridge spatial and temporal scales over many orders of magnitude. Furthermore, there are additional challenges in integrating different aspects ranging from questions about biomolecular stability in crowded environments to the description of reactive processes on cellular scales. In this review, recent studies with models of biomolecules in cellular environments at different levels of detail are discussed in terms of their strengths and weaknesses. In particular, atomistic models, implicit representations of cellular environments, coarse-grained and spheroidal models of biomolecules, as well as the inclusion of reactive processes via reaction-diffusion models are described. Furthermore, strategies for integrating the different models into a comprehensive description of cellular environments are discussed.
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Affiliation(s)
- Michael Feig
- Department of Biochemistry & Molecular Biology and Department of Chemistry, Michigan State University, 603 Wilson Road, BCH 218, East Lansing, MI 48824, United States; RIKEN Quantitative Biology Center, International Medical Device Alliance (IMDA) 6F, 1-6-5 Minatojima-minamimachi, Chuo-ku, Kobe, Hyogo 650-0047, Japan.
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5
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Saha R, Rakshit S, Verma PK, Mitra RK, Pal SK. Protein-cofactor binding and ultrafast electron transfer in riboflavin binding protein under the spatial confinement of nanoscopic reverse micelles. J Mol Recognit 2013; 26:59-66. [DOI: 10.1002/jmr.2246] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2012] [Accepted: 10/09/2012] [Indexed: 11/10/2022]
Affiliation(s)
- Ranajay Saha
- Department of Chemical, Biological and Macromolecular Sciences, S.N. Bose National Centre for Basic Sciences; Block JD, Sector III Salt Lake; Kolkata 700098; India
| | - Surajit Rakshit
- Department of Chemical, Biological and Macromolecular Sciences, S.N. Bose National Centre for Basic Sciences; Block JD, Sector III Salt Lake; Kolkata 700098; India
| | - Pramod Kumar Verma
- Department of Chemical, Biological and Macromolecular Sciences, S.N. Bose National Centre for Basic Sciences; Block JD, Sector III Salt Lake; Kolkata 700098; India
| | - Rajib Kumar Mitra
- Department of Chemical, Biological and Macromolecular Sciences, S.N. Bose National Centre for Basic Sciences; Block JD, Sector III Salt Lake; Kolkata 700098; India
| | - Samir Kumar Pal
- Department of Chemical, Biological and Macromolecular Sciences, S.N. Bose National Centre for Basic Sciences; Block JD, Sector III Salt Lake; Kolkata 700098; India
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6
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Lewis JI, Moss DJ, Knotts TA. Multiple molecule effects on the cooperativity of protein folding transitions in simulations. J Chem Phys 2012; 136:245101. [DOI: 10.1063/1.4729604] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023] Open
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7
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Aguilar X, F. Weise C, Sparrman T, Wolf-Watz M, Wittung-Stafshede P. Macromolecular Crowding Extended to a Heptameric System: The Co-chaperonin Protein 10. Biochemistry 2011; 50:3034-44. [DOI: 10.1021/bi2002086] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Ximena Aguilar
- Department of Chemistry, Chemical Biological Center, Umeå University, 901 87 Umeå, Sweden
| | - Christoph F. Weise
- Department of Chemistry, Chemical Biological Center, Umeå University, 901 87 Umeå, Sweden
| | - Tobias Sparrman
- Department of Chemistry, Chemical Biological Center, Umeå University, 901 87 Umeå, Sweden
| | - Magnus Wolf-Watz
- Department of Chemistry, Chemical Biological Center, Umeå University, 901 87 Umeå, Sweden
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8
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Christiansen A, Wang Q, Samiotakis A, Cheung MS, Wittung-Stafshede P. Factors Defining Effects of Macromolecular Crowding on Protein Stability: An in Vitro/in Silico Case Study Using Cytochrome c. Biochemistry 2010; 49:6519-30. [DOI: 10.1021/bi100578x] [Citation(s) in RCA: 122] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Alexander Christiansen
- Department of Chemistry, Chemical Biological Center, Umeå University, 901 87 Umeå, Sweden
| | - Qian Wang
- Department of Physics, University of Houston, Houston, Texas 77204
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9
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Hills RD, Brooks CL. Insights from coarse-grained Gō models for protein folding and dynamics. Int J Mol Sci 2009; 10:889-905. [PMID: 19399227 PMCID: PMC2672008 DOI: 10.3390/ijms10030889] [Citation(s) in RCA: 204] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2009] [Revised: 02/23/2009] [Accepted: 02/26/2009] [Indexed: 12/17/2022] Open
Abstract
Exploring the landscape of large scale conformational changes such as protein folding at atomistic detail poses a considerable computational challenge. Coarse-grained representations of the peptide chain have therefore been developed and over the last decade have proved extremely valuable. These include topology-based Gō models, which constitute a smooth and funnel-like approximation to the folding landscape. We review the many variations of the Gō model that have been employed to yield insight into folding mechanisms. Their success has been interpreted as a consequence of the dominant role of the native topology in folding. The role of local contact density in determining protein dynamics is also discussed and is used to explain the ability of Gō-like models to capture sequence effects in folding and elucidate conformational transitions.
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Affiliation(s)
- Ronald D. Hills
- Department of Molecular Biology and Kellogg School of Science and Technology, The Scripps Research Institute, 10550 N. Torrey Pines Rd. TPC6 La Jolla, CA 92037, USA
| | - Charles L. Brooks
- Department of Molecular Biology and Kellogg School of Science and Technology, The Scripps Research Institute, 10550 N. Torrey Pines Rd. TPC6 La Jolla, CA 92037, USA
- Department of Chemistry and Biophysics Program, University of Michigan, 930 N. University Ave, Ann Arbor, MI 48109, USA
- Author to whom correspondence should be addressed; E-Mail:
; Tel. +1-734-647-6682; Fax: +1-734-647-1604
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Kim J, Keyes T. Influence of Go-Like Interactions on Global Shapes of Energy Landscapes in β-Barrel Forming Model Proteins: Inherent Structure Analysis and Statistical Temperature Molecular Dynamics Simulation. J Phys Chem B 2007; 112:954-66. [DOI: 10.1021/jp072872u] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Jaegil Kim
- Department of Chemistry, Boston University, Boston, Massachusetts 02215
| | - Thomas Keyes
- Department of Chemistry, Boston University, Boston, Massachusetts 02215
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11
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Bellesia G, Shea JE. Self-assembly of β-sheet forming peptides into chiral fibrillar aggregates. J Chem Phys 2007; 126:245104. [PMID: 17614592 DOI: 10.1063/1.2739547] [Citation(s) in RCA: 83] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
The authors introduce a novel mid-resolution off-lattice coarse-grained model to investigate the self-assembly of beta-sheet forming peptides. The model retains most of the peptide backbone degrees of freedom as well as one interaction center describing the side chains. The peptide consists of a core of alternating hydrophobic and hydrophilic residues, capped by two oppositely charged residues. Nonbonded interactions are described by Lennard-Jones and Coulombic terms. The influence of different levels of "hydrophobic" and "steric" forces between the side chains of the peptides on the thermodynamics and kinetics of aggregation was investigated using Langevin dynamics. The model is simple enough to allow the simulation of systems consisting of hundreds of peptides, while remaining realistic enough to successfully lead to the formation of chiral, ordered beta tapes, ribbons, as well as higher order fibrillar aggregates.
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Affiliation(s)
- Giovanni Bellesia
- Department of Chemistry and Biochemistry, University of California, Santa Barbara, California 93106, USA.
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12
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Guo W, Shea JE, Berry RS. The Physics of the Interactions Governing Folding and Association of Proteins. Ann N Y Acad Sci 2005; 1066:34-53. [PMID: 16533917 DOI: 10.1196/annals.1363.025] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
The review discusses the molecular origins of the forces and free energies that determine several things about proteins, and how experiment and theory reveal this information. The first subject is the stability of the folded, native structures. The second is the range of molecular mechanisms by which proteins find their way to those folded structures in laboratory environments. The third is the much more complex problem of how folding occurs in the cellular environment. This topic includes a discussion of crowding and of the roles of chaperone molecules. The review concludes with a discussion of protein aggregation and fibril formation and of misfolding and therapies associated with it.
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Affiliation(s)
- Weihua Guo
- Department of Chemistry, The University of Chicago, Chicago, IL 60637, USA
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