1
|
Kehrein J, Sotriffer C. Molecular Dynamics Simulations for Rationalizing Polymer Bioconjugation Strategies: Challenges, Recent Developments, and Future Opportunities. ACS Biomater Sci Eng 2024; 10:51-74. [PMID: 37466304 DOI: 10.1021/acsbiomaterials.3c00636] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/20/2023]
Abstract
The covalent modification of proteins with polymers is a well-established method for improving the pharmacokinetic properties of therapeutically valuable biologics. The conjugated polymer chains of the resulting hybrid represent highly flexible macromolecular structures. As the dynamics of such systems remain rather elusive for established experimental techniques from the field of protein structure elucidation, molecular dynamics simulations have proven as a valuable tool for studying such conjugates at an atomistic level, thereby complementing experimental studies. With a focus on new developments, this review aims to provide researchers from the polymer bioconjugation field with a concise and up to date overview of such approaches. After introducing basic principles of molecular dynamics simulations, as well as methods for and potential pitfalls in modeling bioconjugates, the review illustrates how these computational techniques have contributed to the understanding of bioconjugates and bioconjugation strategies in the recent past and how they may lead to a more rational design of novel bioconjugates in the future.
Collapse
Affiliation(s)
- Josef Kehrein
- Institute of Pharmacy and Food Chemistry, University of Würzburg, Würzburg 97074, Germany
| | - Christoph Sotriffer
- Institute of Pharmacy and Food Chemistry, University of Würzburg, Würzburg 97074, Germany
| |
Collapse
|
2
|
Probing conformational transitions of PIN1 from L. major during chemical and thermal denaturation. Int J Biol Macromol 2020; 154:904-915. [PMID: 32209371 DOI: 10.1016/j.ijbiomac.2020.03.166] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2020] [Revised: 03/13/2020] [Accepted: 03/13/2020] [Indexed: 01/03/2023]
Abstract
PIN1 proteins are a class of peptidyl prolyl cis-trans isomerases (PPIases), which have been implicated in numerous cellular functions like cell cycle progression, transcriptional control, signal transduction, promotion of oncogenesis and host-parasite interactions. In this work, the unfolding mechanism of a single domain PIN1 from Leishmania major (LmPIN1) has been characterized during thermal and denaturant-induced unfolding by differential scanning calorimetry (DSC), fluorescence and circular dichroism. Further, MD simulations have been performed to structurally probe the possible stages of its unfolding process. Both the fluorescence and CD data confirm classical two-state unfolding transitions for urea and GdnHCl. The thermal unfolding of LmPIN1, characterized by DSC, could optimally be fitted to a non two-state transition curve exhibiting two Tm's (53 °C and 57 °C) suggesting the possibility of an intermediate. Thermal unfolding of the modeled LmPIN1 by MD simulation shows that the unfolding process is initiated by increased fluctuations (dynamics) spanning residues 70-80, followed by perturbations in the sheet system and disjuncture of helix-sheet packing. Importantly, simulation and fluorescence quenching studies clearly suggest the possibility of the presence of residual structures of LmPIN1 even after complete denaturation.
Collapse
|
3
|
Baweja L, Roche J. Pushing the Limits of Structure-Based Models: Prediction of Nonglobular Protein Folding and Fibrils Formation with Go-Model Simulations. J Phys Chem B 2018; 122:2525-2535. [DOI: 10.1021/acs.jpcb.7b12129] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Lokesh Baweja
- Department of Biochemistry, Molecular Biology and Biophysics, Iowa State University, Ames, Iowa 50011, United States
| | - Julien Roche
- Department of Biochemistry, Molecular Biology and Biophysics, Iowa State University, Ames, Iowa 50011, United States
| |
Collapse
|
4
|
McKiernan KA, Husic BE, Pande VS. Modeling the mechanism of CLN025 beta-hairpin formation. J Chem Phys 2017; 147:104107. [PMID: 28915754 PMCID: PMC5597441 DOI: 10.1063/1.4993207] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2017] [Accepted: 08/24/2017] [Indexed: 01/26/2023] Open
Abstract
Beta-hairpins are substructures found in proteins that can lend insight into more complex systems. Furthermore, the folding of beta-hairpins is a valuable test case for benchmarking experimental and theoretical methods. Here, we simulate the folding of CLN025, a miniprotein with a beta-hairpin structure, at its experimental melting temperature using a range of state-of-the-art protein force fields. We construct Markov state models in order to examine the thermodynamics, kinetics, mechanism, and rate-determining step of folding. Mechanistically, we find the folding process is rate-limited by the formation of the turn region hydrogen bonds, which occurs following the downhill hydrophobic collapse of the extended denatured protein. These results are presented in the context of established and contradictory theories of the beta-hairpin folding process. Furthermore, our analysis suggests that the AMBER-FB15 force field, at this temperature, best describes the characteristics of the full experimental CLN025 conformational ensemble, while the AMBER ff99SB-ILDN and CHARMM22* force fields display a tendency to overstabilize the native state.
Collapse
Affiliation(s)
- Keri A McKiernan
- Department of Chemistry, Stanford University, Stanford, California 94305, USA
| | - Brooke E Husic
- Department of Chemistry, Stanford University, Stanford, California 94305, USA
| | - Vijay S Pande
- Department of Chemistry, Stanford University, Stanford, California 94305, USA
| |
Collapse
|
5
|
Matsuoka M, Sugita M, Kikuchi T. Implication of the cause of differences in 3D structures of proteins with high sequence identity based on analyses of amino acid sequences and 3D structures. BMC Res Notes 2014; 7:654. [PMID: 25231773 PMCID: PMC4180342 DOI: 10.1186/1756-0500-7-654] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2014] [Accepted: 09/05/2014] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Proteins that share a high sequence homology while exhibiting drastically different 3D structures are investigated in this study. Recently, artificial proteins related to the sequences of the GA and IgG binding GB domains of human serum albumin have been designed. These artificial proteins, referred to as GA and GB, share 98% amino acid sequence identity but exhibit different 3D structures, namely, a 3α bundle versus a 4β + α structure. Discriminating between their 3D structures based on their amino acid sequences is a very difficult problem. In the present work, in addition to using bioinformatics techniques, an analysis based on inter-residue average distance statistics is used to address this problem. RESULTS It was hard to distinguish which structure a given sequence would take only with the results of ordinary analyses like BLAST and conservation analyses. However, in addition to these analyses, with the analysis based on the inter-residue average distance statistics and our sequence tendency analysis, we could infer which part would play an important role in its structural formation. CONCLUSIONS The results suggest possible determinants of the different 3D structures for sequences with high sequence identity. The possibility of discriminating between the 3D structures based on the given sequences is also discussed.
Collapse
Affiliation(s)
| | | | - Takeshi Kikuchi
- Department of Bioinformatics, College of Life Sciences, Ritsumeikan University, 1-1-1 Nojihigashi, Kusatsu, Shiga, Japan.
| |
Collapse
|
6
|
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]
|
7
|
Gubskaya AV, Khan IJ, Valenzuela LM, Lisnyak YV, Kohn J. Investigating the Release of a Hydrophobic Peptide from Matrices of Biodegradable Polymers: An Integrated Method Approach. POLYMER 2013; 54:3806-3820. [PMID: 24039300 DOI: 10.1016/j.polymer.2013.05.038] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
The objectives of this work were: (1) to select suitable compositions of tyrosine-derived polycarbonates for controlled delivery of voclosporin, a potent drug candidate to treat ocular diseases, (2) to establish a structure-function relationship between key molecular characteristics of biodegradable polymer matrices and drug release kinetics, and (3) to identify factors contributing in the rate of drug release. For the first time, the experimental study of polymeric drug release was accompanied by a hierarchical sequence of three computational methods. First, suitable polymer compositions used in subsequent neural network modeling were determined by means of response surface methodology (RSM). Second, accurate artificial neural network (ANN) models were built to predict drug release profiles for fifteen polymers located outside the initial design space. Finally, thermodynamic properties and hydrogen-bonding patterns of model drug-polymer complexes were studied using molecular dynamics (MD) technique to elucidate a role of specific interactions in drug release mechanism. This research presents further development of methodological approaches to meet challenges in the design of polymeric drug delivery systems.
Collapse
Affiliation(s)
- Anna V Gubskaya
- New Jersey Center for Biomaterials, Rutgers, The State University of New Jersey, Piscataway, NJ 08854-8087, USA
| | | | | | | | | |
Collapse
|
8
|
Chen Y, Ding J. Construction of an intermediate-resolution lattice model and re-examination of the helix-coil transition: a dynamic Monte Carlo simulation. J Biomol Struct Dyn 2013; 32:792-803. [PMID: 23746129 DOI: 10.1080/07391102.2013.791645] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
In protein modeling, spatial resolution and computational efficiency are always incompatible. As a compromise, an intermediate-resolution lattice model has been constructed in the present work. Each residue is decomposed into four basic units, i.e. the α-carbon group, the carboxyl group, the imino group, and the side-chain group, and each basic coarse-grained unit is represented by a minimum cubic box with eight lattice sites. The spacing of the lattice is about 0.56 Å, holding the highest spatial resolution for the present lattice protein models. As the first report of this new model, the helix-coil transition of a polyalanine chain was examined via dynamic Monte Carlo simulation. The period of formed α-helix was about 3.68 residues, close to that of a natural α-helix. The resultant backbone motion was found to be in the realistic regions of the conformational space in the Ramachandran plot. Helix propagation constant and nucleation constant were further determined through the dynamic hydrogen bonding process and torsional angle variation, and the results were used to make comparison between classical Zimm-Bragg theory and Lifson-Roig theory based on the Qian-Schellman relationship. The simulation results confirmed that our lattice model can reproduce the helix-coil transition of polypeptide and construct a moderately fine α-helix conformation without significantly weakening the priority in efficiency for a lattice model.
Collapse
Affiliation(s)
- Yantao Chen
- a State Key Laboratory of Molecular Engineering of Polymers, Shenzhen Key Laboratory of Functional Polymer , College of Chemistry and Chemical Engineering, Shenzhen University , Shenzhen , 518060 , China
| | | |
Collapse
|
9
|
Sugita M, Kikuchi T. Incorporating into a Cα Go model the effects of geometrical restriction on Cα atoms caused by side chain orientations. Proteins 2013; 81:1434-45. [DOI: 10.1002/prot.24294] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2012] [Revised: 03/13/2013] [Accepted: 03/17/2013] [Indexed: 11/10/2022]
Affiliation(s)
- Masatake Sugita
- Department of Bioinformatics; College of Life Sciences; Ritsumeikan University; Kusatsu; Shiga; Japan
| | - Takeshi Kikuchi
- Department of Bioinformatics; College of Life Sciences; Ritsumeikan University; Kusatsu; Shiga; Japan
| |
Collapse
|
10
|
Davis CM, Xiao S, Raleigh DP, Dyer RB. Raising the speed limit for β-hairpin formation. J Am Chem Soc 2012; 134:14476-82. [PMID: 22873643 DOI: 10.1021/ja3046734] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Understanding the folding of the β-hairpin is a crucial step in studying how β-rich proteins fold. We have studied CLN025, an optimized ten residue synthetic peptide, which adopts a compact, well-structured β-hairpin conformation. Formation of the component β-sheet and β-turn structures of CLN025 was probed independently using a combination of equilibrium Fourier transform infrared spectroscopy and laser-induced temperature jump coupled with time-resolved infrared and fluorescence spectroscopies. We find that CLN025 is an ultrafast folder due to its small free energy barrier to folding and that it exceeds the predicted speed limit for β-hairpin formation by an order of magnitude. We also find that the folding mechanism cannot be described by a simple two-state model, but rather is a heterogeneous process involving two independent parallel processes. Formation of stabilizing cross-strand hydrophobic interactions and turn alignment occur competitively, with relaxation lifetimes of 82 ± 10 and 124 ± 10 ns, respectively, at the highest probed temperature. The ultrafast and heterogeneous folding kinetics observed for CLN025 provide evidence for folding on a nearly barrierless free energy landscape, and recalibrate the speed limit for the formation of a β-hairpin.
Collapse
Affiliation(s)
- Caitlin M Davis
- Department of Chemistry, Emory University, Atlanta, Georgia 30322, USA
| | | | | | | |
Collapse
|
11
|
Whitford PC, Sanbonmatsu KY, Onuchic JN. Biomolecular dynamics: order-disorder transitions and energy landscapes. REPORTS ON PROGRESS IN PHYSICS. PHYSICAL SOCIETY (GREAT BRITAIN) 2012; 75:076601. [PMID: 22790780 PMCID: PMC3695400 DOI: 10.1088/0034-4885/75/7/076601] [Citation(s) in RCA: 87] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
While the energy landscape theory of protein folding is now a widely accepted view for understanding how relatively weak molecular interactions lead to rapid and cooperative protein folding, such a framework must be extended to describe the large-scale functional motions observed in molecular machines. In this review, we discuss (1) the development of the energy landscape theory of biomolecular folding, (2) recent advances toward establishing a consistent understanding of folding and function and (3) emerging themes in the functional motions of enzymes, biomolecular motors and other biomolecular machines. Recent theoretical, computational and experimental lines of investigation have provided a very dynamic picture of biomolecular motion. In contrast to earlier ideas, where molecular machines were thought to function similarly to macroscopic machines, with rigid components that move along a few degrees of freedom in a deterministic fashion, biomolecular complexes are only marginally stable. Since the stabilizing contribution of each atomic interaction is on the order of the thermal fluctuations in solution, the rigid body description of molecular function must be revisited. An emerging theme is that functional motions encompass order-disorder transitions and structural flexibility provides significant contributions to the free energy. In this review, we describe the biological importance of order-disorder transitions and discuss the statistical-mechanical foundation of theoretical approaches that can characterize such transitions.
Collapse
Affiliation(s)
- Paul C Whitford
- Center for Theoretical Biological Physics, Department of Physics, Rice University, 6100 Main, Houston, TX 77005-1827, USA
| | | | | |
Collapse
|
12
|
Ceres N, Lavery R. Coarse-grain Protein Models. INNOVATIONS IN BIOMOLECULAR MODELING AND SIMULATIONS 2012. [DOI: 10.1039/9781849735049-00219] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
Coarse-graining is a powerful approach for modeling biomolecules that, over the last few decades, has been extensively applied to proteins. Coarse-grain models offer access to large systems and to slow processes without becoming computationally unmanageable. In addition, they are very versatile, enabling both the protein representation and the energy function to be adapted to the biological problem in hand. This review concentrates on modeling soluble proteins and their assemblies. It presents an overview of the coarse-grain representations, of the associated interaction potentials, and of the optimization procedures used to define them. It then shows how coarse-grain models have been used to understand processes involving proteins, from their initial folding to their functional properties, their binary interactions, and the assembly of large complexes.
Collapse
Affiliation(s)
- N. Ceres
- Bases Moléculaires et Structurales des Systèmes Infectieux Université Lyon1/CNRS UMR 5086, IBCP, 7 Passage du Vercors, 69367, Lyon France
| | - R. Lavery
- Bases Moléculaires et Structurales des Systèmes Infectieux Université Lyon1/CNRS UMR 5086, IBCP, 7 Passage du Vercors, 69367, Lyon France
| |
Collapse
|
13
|
Huang L, Shakhnovich EI. Is there an en route folding intermediate for Cold shock proteins? Protein Sci 2012; 21:677-85. [PMID: 22467601 DOI: 10.1002/pro.2053] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2011] [Revised: 01/30/2012] [Accepted: 02/08/2012] [Indexed: 11/12/2022]
Abstract
Cold shock proteins (Csps) play an important role in cold shock response of a diverse number of organisms ranging from bacteria to humans. Numerous studies of the Csp from various species showed that a two-state folding mechanism is conserved and the transition state (TS) appears to be very compact. However, the atomic details of the folding mechanism of Csp remain unclear. This study presents the folding mechanism of Csp in atomic detail using an all-atom Go model-based simulations. Our simulations predict that there may exist an en route intermediate, in which β strands 1-2-3 are well ordered and the contacts between β1 and β4 are almost developed. Such an intermediate might be too unstable to be detected in the previous fluorescence energy transfer experiments. The transition state ensemble has been determined from the P(fold) analysis and the TS appears even more compact than the intermediate state.
Collapse
Affiliation(s)
- Lei Huang
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts 02138, USA.
| | | |
Collapse
|
14
|
Discrete Molecular Dynamics Simulation of Biomolecules. COMPUTATIONAL MODELING OF BIOLOGICAL SYSTEMS 2012. [DOI: 10.1007/978-1-4614-2146-7_3] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/12/2023]
|
15
|
Xu J, Huang L, Shakhnovich EI. The ensemble folding kinetics of the FBP28 WW domain revealed by an all-atom Monte Carlo simulation in a knowledge-based potential. Proteins 2011; 79:1704-14. [PMID: 21365688 DOI: 10.1002/prot.22993] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2010] [Revised: 12/10/2010] [Accepted: 01/04/2011] [Indexed: 11/10/2022]
Abstract
In this work, we apply a detailed all-atom model with a transferable knowledge-based potential to study the folding kinetics of Formin-Binding protein, FBP28, which is a canonical three-stranded β-sheet WW domain. Replica exchange Monte Carlo simulations starting from random coils find native-like (Cα RMSD of 2.68 Å) lowest energy structure. We also study the folding kinetics of FBP28 WW domain by performing a large number of ab initio Monte Carlo folding simulations. Using these trajectories, we examine the order of formation of two β-hairpins, the folding mechanism of each individual β-hairpin, and transition state ensemble (TSE) of FBP28 WW domain and compare our results with experimental data and previous computational studies. To obtain detailed structural information on the folding dynamics viewed as an ensemble process, we perform a clustering analysis procedure based on graph theory. Further, a rigorous P(fold) analysis is used to obtain representative samples of the TSEs showing good quantitative agreement between experimental and simulated Φ values. Our analysis shows that the turn structure between first and second β strands is a partially stable structural motif that gets formed before entering the TSE in FBP28 WW domain and there exist two major pathways for the folding of FBP28 WW domain, which differ in the order and mechanism of hairpin formation.
Collapse
Affiliation(s)
- Jiabin Xu
- Department of Chemistry and Chemical Biology, Harvard University, 12 Oxford Street, Cambridge, Massachusetts 02138, USA
| | | | | |
Collapse
|
16
|
Proctor EA, Ding F, Dokholyan NV. Discrete molecular dynamics. WILEY INTERDISCIPLINARY REVIEWS-COMPUTATIONAL MOLECULAR SCIENCE 2011. [DOI: 10.1002/wcms.4] [Citation(s) in RCA: 74] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Elizabeth A. Proctor
- Department of Biochemistry and Biophysics, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Feng Ding
- Department of Biochemistry and Biophysics, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Nikolay V. Dokholyan
- Department of Biochemistry and Biophysics, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| |
Collapse
|
17
|
Thukral L, Smith JC, Daidone I. Common folding mechanism of a beta-hairpin peptide via non-native turn formation revealed by unbiased molecular dynamics simulations. J Am Chem Soc 2010; 131:18147-52. [PMID: 19919102 DOI: 10.1021/ja9064365] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The folding of a 15-residue beta-hairpin peptide (Peptide 1) is characterized using multiple unbiased, atomistic molecular dynamics (MD) simulations. Fifteen independent MD trajectories, each 2.5 micros-long for a total of 37.5 micros, are performed of the peptide in explicit solvent, at room temperature, and without the use of enhanced sampling techniques. The computed folding time of 1-1.5 micros obtained from the simulations is in good agreement with experiment [Xu, Y.; et al. J. Am. Chem. Soc. 2003, 125, 15388-15394]. A common folding mechanism is observed, in which the turn is always found to be the major determinant in initiating the folding process, followed by cooperative formation of the interstrand hydrogen bonds and the side-chain packing. Furthermore, direct transition to the folded state from fully unstructured conformations does not take place. Instead, the peptide is always observed to form partially structured conformations involving a non-native (ESYI) turn from which the native (NPDG) turn forms, triggering the folding to the beta-hairpin.
Collapse
Affiliation(s)
- Lipi Thukral
- Interdisciplinary Center for Scientific Computing, University of Heidelberg, Im Neuenheimer Feld 368, 69120 Heidelberg, Germany
| | | | | |
Collapse
|
18
|
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.
Collapse
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
| |
Collapse
|