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Manandhar A, Chakraborty K, Tang PK, Kang M, Zhang P, Cui H, Loverde SM. Rational Coarse-Grained Molecular Dynamics Simulations of Supramolecular Anticancer Nanotubes. J Phys Chem B 2019; 123:10582-10593. [DOI: 10.1021/acs.jpcb.9b07417] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Affiliation(s)
- Anjela Manandhar
- Department of Chemistry, College of Staten Island, City University of New York, New York 10314, United States
- Ph.D. Program in Biochemistry, The Graduate Center of the City University of New York, New York 10016, United States
| | - Kaushik Chakraborty
- Ph.D. Program in Biochemistry, The Graduate Center of the City University of New York, New York 10016, United States
| | - Phu K. Tang
- Department of Chemistry, College of Staten Island, City University of New York, New York 10314, United States
- Ph.D. Program in Biochemistry, The Graduate Center of the City University of New York, New York 10016, United States
| | - Myungshim Kang
- Ph.D. Program in Biochemistry, The Graduate Center of the City University of New York, New York 10016, United States
| | - Pengcheng Zhang
- Center of Pharmaceutics, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Honggang Cui
- Department of Chemical and Biomolecular Engineering and Institute for NanoBioTechnology, The Johns Hopkins University, Baltimore, Maryland 21218, United States
- Department of Oncology and Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, United States
| | - Sharon M. Loverde
- Department of Chemistry, College of Staten Island, City University of New York, New York 10314, United States
- Ph.D. Program in Biochemistry, The Graduate Center of the City University of New York, New York 10016, United States
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2
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Sharadadevi A, Nagaraj R. On the intrinsic propensity of the Asn-Gly sequence to fold into type I′ β-turn: molecular dynamics simulations of Asn-Gly β-turn containing peptide sequences. J Biomol Struct Dyn 2017; 36:3916-3925. [DOI: 10.1080/07391102.2017.1403958] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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3
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Tsai MY, Yuan JM, Teranishi Y, Lin SH. Thermodynamics of protein folding using a modified Wako-Saitô-Muñoz-Eaton model. J Biol Phys 2012; 38:543-71. [PMID: 24615219 PMCID: PMC3473134 DOI: 10.1007/s10867-012-9271-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2011] [Accepted: 05/07/2012] [Indexed: 10/28/2022] Open
Abstract
Herein, we propose a modified version of the Wako-Saitô-Muñoz-Eaton (WSME) model. The proposed model introduces an empirical temperature parameter for the hypothetical structural units (i.e., foldons) in proteins to include site-dependent thermodynamic behavior. The thermodynamics for both our proposed model and the original WSME model were investigated. For a system with beta-hairpin topology, a mathematical treatment (contact-pair treatment) to facilitate the calculation of its partition function was developed. The results show that the proposed model provides better insight into the site-dependent thermodynamic behavior of the system, compared with the original WSME model. From this site-dependent point of view, the relationship between probe-dependent experimental results and model's thermodynamic predictions can be explained. The model allows for suggesting a general principle to identify foldon behavior. We also find that the backbone hydrogen bonds may play a role of structural constraints in modulating the cooperative system. Thus, our study may contribute to the understanding of the fundamental principles for the thermodynamics of protein folding.
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Affiliation(s)
- Min-Yeh Tsai
- National Chiao Tung University, 1001 Ta Hsuen Road, Hsinchu, Taiwan, Republic of China,
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4
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Liu Y, Kellogg E, Liang H. Canonical and micro-canonical analysis of folding of trpzip2: An all-atom replica exchange Monte Carlo simulation study. J Chem Phys 2012; 137:045103. [DOI: 10.1063/1.4738760] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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5
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Han M, Hansmann UHE. Replica exchange molecular dynamics of the thermodynamics of fibril growth of Alzheimer's Aβ42 peptide. J Chem Phys 2012; 135:065101. [PMID: 21842950 DOI: 10.1063/1.3617250] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
The growth of amyloid fibrils is studied by replica exchange molecular dynamics in an implicit solvent. Our data indicate that extremely long simulation times (at least a few hundred ns) are necessary to study the thermodynamics of fibril elongation in detail. However some aspects of the aggregation process are already accessible on the time scales available in the present study. A peak in the specific heat indicates a docking temperature of T(dock) ≈ 320 K. Irreversible locking requires lower temperatures with the locking temperature estimated as T(lock) ≈ 280 K. In our simulation the fibril grows from both sides with the C-terminal of the incoming monomer attaching to the C-terminal of the peptides in the fibril forming a β-sheet on the fibril edge. Our simulation indicates that the C-terminal is crucial for aggregation.
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Affiliation(s)
- Ming Han
- Department of Physics, Michigan Technological University, Houghton, Michigan 49931, USA.
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6
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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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7
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Anand P, Hansmann UHE. Internal and environmental effects on folding and dimerization of the Alzheimer's β amyloid peptide. MOLECULAR SIMULATION 2011; 37:10.1080/08927022.2011.551879. [PMID: 24353373 PMCID: PMC3864693 DOI: 10.1080/08927022.2011.551879] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
Amyloid deposits are a hallmark of many diseases. In the case of Alzheimer's disease a turn between 21Ala and 30Ala, stabilized by a salt bridge between 22Glu/23Asp and 28Lys, may nucleate folding and aggregation of the Aβ peptide. In the present paper we test this hypothesis by studying how salt bridge and turn formation vary with intrinsic and environmental changes, and how these changes effect folding and aggregation of the Aβ peptide.
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Affiliation(s)
- Priya Anand
- Department of Physics, Michigan Technological University, Houghton, MI 49931, USA
| | - Ulrich H E Hansmann
- Department of Physics, Michigan Technological University, Houghton, MI 49931, USA
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8
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Enciso M, Rey A. A refined hydrogen bond potential for flexible protein models. J Chem Phys 2010; 132:235102. [DOI: 10.1063/1.3436723] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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9
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Kim J, Keiderling TA. All-Atom Molecular Dynamics Simulations of β-Hairpins Stabilized by a Tight Turn: Pronounced Heterogeneous Folding Pathways. J Phys Chem B 2010; 114:8494-504. [DOI: 10.1021/jp912159t] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Joohyun Kim
- Department of Chemistry, University of Illinois at Chicago, 845 West Taylor Street (M/C 111), Chicago, Illinois 60607-7061
| | - Timothy A. Keiderling
- Department of Chemistry, University of Illinois at Chicago, 845 West Taylor Street (M/C 111), Chicago, Illinois 60607-7061
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10
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Xiao Y, Chen C, He Y. Folding mechanism of β-hairpin trpzip2: heterogeneity, transition state and folding pathways. Int J Mol Sci 2009; 10:2838-2848. [PMID: 19582232 PMCID: PMC2705519 DOI: 10.3390/ijms10062838] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2009] [Revised: 06/18/2009] [Accepted: 06/19/2009] [Indexed: 01/30/2023] Open
Abstract
We review the studies on the folding mechanism of the β-hairpin tryptophan zipper 2 (trpzip2) and present some additional computational results to refine the picture of folding heterogeneity and pathways. We show that trpzip2 can have a two-state or a multi-state folding pattern, depending on whether it folds within the native basin or through local state basins on the high-dimensional free energy surface; Trpzip2 can fold along different pathways according to the packing order of tryptophan pairs. We also point out some important problems related to the folding mechanism of trpzip2 that still need clarification, e.g., a wide distribution of the computed conformations for the transition state ensemble.
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Affiliation(s)
- Yi Xiao
- Author to whom correspondence should be addressed; E-Mail:
; Tel. +86-27-87556652
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11
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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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12
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Luo Z, Ding J, Zhou Y. Folding mechanisms of individual beta-hairpins in a Go model of Pin1 WW domain by all-atom molecular dynamics simulations. J Chem Phys 2008; 128:225103. [PMID: 18554060 DOI: 10.1063/1.2936832] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
This paper examines the folding mechanism of an individual beta-hairpin in the presence of other hairpins by using an off-lattice model of a small triple-stranded antiparallel beta-sheet protein, Pin1 WW domain. The turn zipper model and the hydrophobic collapse model originally developed for a single beta-hairpin in literature is confirmed to be useful in describing beta-hairpins in model Pin1 WW domain. We find that the mechanism for folding a specific hairpin is independent of whether it folds first or second, but the formation process are significantly dependent on temperature. More specifically, beta1-beta2 hairpin folds via the turn zipper model at a low temperature and the hydrophobic collapse model at a high temperature, while the folding of beta2-beta3 hairpin follows the turn zipper model at both temperatures. The change in folding mechanisms is interpreted by the interplay between contact stability (enthalpy) and loop lengths (entropy), the effect of which is temperature dependent.
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Affiliation(s)
- Zhonglin Luo
- Key Laboratory of Molecular Engineering of Polymers of Ministry of Education, Department of Macromolecular Science, Laboratory of Advanced Materials, Fudan University, Shanghai 200433, People's Republic of China
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13
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St-Pierre JF, Mousseau N, Derreumaux P. The complex folding pathways of protein A suggest a multiple-funnelled energy landscape. J Chem Phys 2008; 128:045101. [PMID: 18248008 DOI: 10.1063/1.2812562] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023] Open
Abstract
Folding proteins into their native states requires the formation of both secondary and tertiary structures. Many questions remain, however, as to whether these form into a precise order, and various pictures have been proposed that place the emphasis on the first or the second level of structure in describing folding. One of the favorite test models for studying this question is the B domain of protein A, which has been characterized by numerous experiments and simulations. Using the activation-relaxation technique coupled with a generic energy model (optimized potential for efficient peptide structure prediction), we generate more than 50 folding trajectories for this 60-residue protein. While the folding pathways to the native state are fully consistent with the funnel-like description of the free energy landscape, we find a wide range of mechanisms in which secondary and tertiary structures form in various orders. Our nonbiased simulations also reveal the presence of a significant number of non-native beta and alpha conformations both on and off pathway, including the visit, for a non-negligible fraction of trajectories, of fully ordered structures resembling the native state of nonhomologous proteins.
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Affiliation(s)
- Jean-Francois St-Pierre
- Département de Physique, Université de Montréal, C.P. 6128, Succursale Centre-Ville, Montréal, Québec H3C 3J7, Canada
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14
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Chen C, Xiao Y. Observation of multiple folding pathways of -hairpin trpzip2 from independent continuous folding trajectories. Bioinformatics 2008; 24:659-65. [DOI: 10.1093/bioinformatics/btn029] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
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15
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Abstract
We present a minimal model for proteins, which is able to capture the structural conversion between the alpha-helix and beta-hairpin. In most regimes of the parameter space, the model produces a stable structure at a low temperature; in a few limited regimes of the parameter space, the model displays an beta-hairpin transition as the physical conditions vary. These variations include a perturbation on hydrogen bonding propensity at the middle of the modeled chain, or the change of the hydrophobicity of a designated pair along the chain. Using Monte Carlo simulations, we demonstrate the structural conversion by means of state diagrams, heat capacity maps, and free energy maps.
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Affiliation(s)
- Hideo Imamura
- Department of Physics, University of Waterloo, Waterloo, Ontario, Canada, N2L 3G1
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16
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Boucher G, Mousseau N, Derreumaux P. Aggregating the amyloid Abeta(11-25) peptide into a four-stranded beta-sheet structure. Proteins 2007; 65:877-88. [PMID: 17019697 DOI: 10.1002/prot.21134] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
We present a detailed analysis of the structural properties of one monomer of Abeta(11-25) as well as of the aggregation mechanisms for four chains of Abeta(11-25) using the activation-relaxation technique coupled with a generic energy potential. Starting from a random distribution of these four chains, we find that the system assembles rapidly into a random globular state that evolves into three- and four-stranded antiparallel beta-sheets. The aggregation process is considerably accelerated by the presence of preformed dimers. We also find that the reptation mechanism already identified in shorter peptides plays a significant role here in allowing the structure to reorganize without having to fully dissociate.
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Affiliation(s)
- Geneviève Boucher
- Département de Physique and Centre Robert-Cedergren en bioinformatique, Université de Montréal, C.P. 6128, Succursale Centre-ville Montréal, Québec H3C 3J7, Canada
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17
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Abstract
A limiting factor in biological science is the time-scale gap between experimental and computational trajectories. At this point, all-atom explicit solvent molecular dynamics (MD) are clearly too expensive to explore long-range protein motions and extract accurate thermodynamics of proteins in isolated or multimeric forms. To reach the appropriate time scale, we must then resort to coarse graining. Here we couple the coarse-grained OPEP model, which has already been used with activated methods, to MD simulations. Two test cases are studied: the stability of three proteins around their experimental structures and the aggregation mechanisms of the Alzheimer's Abeta16-22 peptides. We find that coarse-grained isolated proteins are stable at room temperature within 50 ns time scale. Based on two 220 ns trajectories starting from disordered chains, we find that four Abeta16-22 peptides can form a three-stranded beta sheet. We also demonstrate that the reptation move of one chain over the others, first observed using the activation-relaxation technique, is a kinetically important mechanism during aggregation. These results show that MD-OPEP is a particularly appropriate tool to study qualitatively the dynamics of long biological processes and the thermodynamics of molecular assemblies.
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Affiliation(s)
- Philippe Derreumaux
- Laboratoire de Biochimie Théorique, UPR 9080 CNRS, Institut de Biologie Physico, Chimique et Université Paris 7, 13 Rue Pierre et Marie Curie, 75005 Paris, France.
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18
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Abstract
Backbone hydrogen bonds contribute very importantly to the stability of proteins and therefore they must be appropriately represented in protein folding simulations. Simple models are frequently used in theoretical approaches to this process, but their simplifications are often confronted with the need to be true to the physics of the interactions. Here we study the effects of different levels of coarse graining in the modeling of backbone hydrogen bonds. We study three different models taken from the bibliography in a twofold fashion. First, we calculate the hydrogen bonds in 2gb1, an (alpha + beta)-protein, and see how different backbone representations and potentials can mimic the effects of real hydrogen bonds both in helices and sheets. Second, we use an evolutionary method for protein fragment assembly to locate the global energy minimum for a set of small beta-proteins with these models. This way, we assess the effects of coarse graining in hydrogen bonding models and show what can be expected from them when used in simulation experiments.
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Affiliation(s)
- David De Sancho
- Departamento de Química Física I, Universidad Complutense, Madrid, Spain
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19
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Chen C, Xiao Y. Molecular dynamics simulations of folding processes of a β-hairpin in an implicit solvent. Phys Biol 2006; 3:161-71. [PMID: 17021380 DOI: 10.1088/1478-3975/3/3/001] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
Computer simulations of beta-hairpin folding are relatively difficult, especially those based on the explicit water model. This greatly limits the complete analysis and understanding of their folding mechanisms. In this paper, we use the generalized Born/solvent accessible implicit solvent model to simulate the folding processes of a nine-residue beta-hairpin. We find that the beta-hairpin can fold into its native structure very easily, even using the traditional molecular dynamics method. This allows us to extract 21 complete folding events and investigate the folding process sufficiently. Our results show that there exist four most stable states on the free energy landscape of the short peptide, one native state and three intermediates. We find that two of the non-native stable states have almost the same potential energy as the native state but with lower entropy. This suggests that the native state can be stabilized entropically. Furthermore, we find that the folding processes of this peptide have common features: to fold into its native state, the peptide undergoes a continuous collapsing-extending-recollapsing process to adjust the positions of the side chains in order to form the native middle inter-strand hydrogen bonds. The formations of these bonds are the key step of the folding process. Once these bonds are formed, the peptide can fold into the native state quickly.
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Affiliation(s)
- Changjun Chen
- Biomolecular Physics and Modeling Group, Department of Physics, Huazhong University of Science and Technology, Wuhan, Hubei, People's Republic of China
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20
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Hughes RM, Waters ML. Model systems for β-hairpins and β-sheets. Curr Opin Struct Biol 2006; 16:514-24. [PMID: 16837192 DOI: 10.1016/j.sbi.2006.06.008] [Citation(s) in RCA: 163] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2006] [Revised: 05/16/2006] [Accepted: 06/27/2006] [Indexed: 11/18/2022]
Abstract
beta-Sheets and alpha-helices are the two principal secondary structures in proteins. However, our understanding of beta-sheet structure lags behind that of alpha-helices, largely because, until recently, there was no model system to study the beta-sheet secondary structure in isolation. With the development of well-folded beta-hairpins, this is changing rapidly. Recent advances include: increased understanding of the relative contributions of turn, strand and sidechain interactions to beta-hairpin and beta-sheet stability, with the role of aromatic residues as a common subtheme; experimental and theoretical kinetic and thermodynamic studies of beta-hairpin and beta-sheet folding; de novo protein design, including all-beta structures, mixed alpha/beta motifs and switchable systems; and the creation of functional beta-hairpins.
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Affiliation(s)
- Robert M Hughes
- Department of Chemistry, CB 3290, University of North Carolina, Chapel Hill, NC 27599, USA
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