1
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Kozlowski N, Grubmüller H. Uncertainties in Markov State Models of Small Proteins. J Chem Theory Comput 2023; 19:5516-5524. [PMID: 37540193 PMCID: PMC10448719 DOI: 10.1021/acs.jctc.3c00372] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2023] [Indexed: 08/05/2023]
Abstract
Markov state models are widely used to describe and analyze protein dynamics based on molecular dynamics simulations, specifically to extract functionally relevant characteristic time scales and motions. Particularly for larger biomolecules such as proteins, however, insufficient sampling is a notorious concern and often the source of large uncertainties that are difficult to quantify. Furthermore, there are several other sources of uncertainty, such as choice of the number of Markov states and lag time, choice and parameters of dimension reduction preprocessing step, and uncertainty due to the limited number of observed transitions; the latter is often estimated via a Bayesian approach. Here, we quantified and ranked all of these uncertainties for four small globular test proteins. We found that the largest uncertainty is due to insufficient sampling and initially increases with the total trajectory length T up to a critical tipping point, after which it decreases as 1 / T , thus providing guidelines for how much sampling is required for given accuracy. We also found that single long trajectories yielded better sampling accuracy than many shorter trajectories starting from the same structure. In comparison, the remaining sources of the above uncertainties are generally smaller by a factor of about 5, rendering them less of a concern but certainly not negligible. Importantly, the Bayes uncertainty, commonly used as the only uncertainty estimate, captures only a relatively small part of the true uncertainty, which is thus often drastically underestimated.
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Affiliation(s)
- Nicolai Kozlowski
- Department of Theoretical and Computational
Biophysics, Max-Planck-Institute for Multidisciplinary
Sciences, Göttingen 37077, Germany
| | - Helmut Grubmüller
- Department of Theoretical and Computational
Biophysics, Max-Planck-Institute for Multidisciplinary
Sciences, Göttingen 37077, Germany
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2
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Kuczera K, Szoszkiewicz R, Shaffer CL, Jas GS. GB1 hairpin kinetics: capturing the folding pathway with molecular dynamics, replica exchange and optimal dimensionality reduction. J Biomol Struct Dyn 2023; 41:11671-11680. [PMID: 36591705 DOI: 10.1080/07391102.2022.2163427] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2022] [Accepted: 12/22/2022] [Indexed: 01/03/2023]
Abstract
We have performed molecular dynamics (MD) and replica-exchange (REMD) simulations of folding of the GB1 hairpin peptide in aqueous solution. REMD results were consistent with a cooperative zipper folding model. 120 μ s MD trajectories at 320 K yielded relaxation times of 1.8 μ s and 100 ns, with the slower assigned to global folding. The MD folding/unfolding transitions also followed the cooperative zipper model, specifying nucleation at the central turn followed by consecutive hydrogen bond formation. Formation of hydrogen bonds and hydrophobic contacts were highly correlated. Coarse-grained kinetic models constructed with the Optimal Dimensionality Reduction (ODR) approach found a folding time of 3.3 μ s and unfolding time of 4.0 μ s . Additionally, relaxation times in the 130-170 ns range could be assigned to formation of the transition state and off-path intermediates. The unfolded state was the most highly populated and, significantly, most heterogenous, assembling the largest number of microstates, primarily composed of extended and turn structures. The folded state was also heterogenous, but a to a lesser degree, involving the fully folded and partially folded in-register hairpins at early stages of the zipper pathway. The transition state corresponded to the nucleated hairpin, with central turn and first beta-sheet hydrogen bond, while the off-path intermediates were off-register partial hairpins. Our simulation results were in excellent agreement with experimental data on folded fraction, relaxation time and folding mechanism. The new findings from this work suggest a highly cooperative zipper folding mechanism, nascent hairpin transition state and ∼100 ns relaxation related to intermediate formation.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Krzysztof Kuczera
- Department of Chemistry, The University of Kansas, Lawrence, KS, USA
- Department of Molecular Biosciences, The University of Kansas, Lawrence, KS, USA
| | - Robert Szoszkiewicz
- Faculty of Chemistry, Biological and Chemical Research Centre University of Warsaw, Warsaw, Poland
| | - Christopher L Shaffer
- College of Pharmacy and Pediatric Clinical Pharmacology, University of Nebraska Medical Center, Omaha, NE, USA
| | - Gouri S Jas
- College of Pharmacy and Pediatric Clinical Pharmacology, University of Nebraska Medical Center, Omaha, NE, USA
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3
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Ploetz EA, Karunaweera S, Smith PE. Kirkwood-Buff-Derived Force Field for Peptides and Proteins: Applications of KBFF20. J Chem Theory Comput 2021; 17:2991-3009. [PMID: 33878264 DOI: 10.1021/acs.jctc.1c00076] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Here, we perform structural, thermodynamic, and kinetics tests of the Kirkwood-Buff-derived force field, KBFF20, for peptides and proteins developed in the previous article. The physical/structural tests measure the ability of KBFF20 to capture the experimental J-couplings for small peptides, to keep globular monomeric and oligomeric proteins folded, and to produce the experimentally relevant expanded conformational ensembles of intrinsically disordered proteins. The thermodynamic-based tests probe KBFF20's ability to quantify the preferential interactions of sodium chloride around native β-lactoglobulin and urea around native lysozyme, to reproduce the melting curves for small helix- and sheet-based peptides, and to fold the small proteins Trp-cage and Villin. The kinetics-based tests quantify how well KBFF20 can match the experimental contact formation rates of small, repeat-sequence peptides of variable lengths and the rotational diffusion coefficients of globular proteins. The results suggest that KBFF20 is naturally able to reproduce properties of both folded and disordered proteins, which we attribute to the use of the Kirkwood-Buff theory as the foundation of the force field's development. However, we show that KBFF20 tends to lose some well-defined secondary structural elements and increases the percentage of coil regions, indicating that the perfect balance of all interactions remains elusive. Nevertheless, we argue that KBFF20 is an improvement over recently modified force fields that require ad hoc interventions to prevent the collapse of intrinsically disordered proteins.
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Affiliation(s)
- Elizabeth A Ploetz
- Department of Chemistry, Kansas State University, 213 CBC Building, 1212 Mid-Campus Drive North, Manhattan, Kansas 66506, United States
| | - Sadish Karunaweera
- Department of Chemistry, Kansas State University, 213 CBC Building, 1212 Mid-Campus Drive North, Manhattan, Kansas 66506, United States
| | - Paul E Smith
- Department of Chemistry, Kansas State University, 213 CBC Building, 1212 Mid-Campus Drive North, Manhattan, Kansas 66506, United States
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4
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Bedford JT, Poutsma J, Diawara N, Greene LH. The nature of persistent interactions in two model β-grasp proteins reveals the advantage of symmetry in stability. J Comput Chem 2021; 42:600-607. [PMID: 33534913 DOI: 10.1002/jcc.26477] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2020] [Revised: 10/27/2020] [Accepted: 11/22/2020] [Indexed: 01/25/2023]
Abstract
Two proteins within the β-grasp superfamily, the B1-domain of protein G and the small archaeal modifier protein 1, were investigated to elucidate the key determinants of structural stability at the level of individual interactions. These symmetrical proteins both contain two β-hairpins which form a sheet flanked by a central α-helix. They were subjected to high temperature molecular dynamics simulations and the detailed behavior of each long-range interaction was characterized. The results revealed that in GB1 the most stable region was the C-terminal hairpin and in SAMP1 it was the opposite, the N-terminal hairpin. Experimental results for GB1 support this finding. In conclusion, it appears that the difference in the location and number of hydrophobic interactions dictate the differential stability which is accommodated due to structural symmetry of the β-grasp fold. Thus, the hairpins are interchangeable and in nature this lends itself to adaptability and flexibility.
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5
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de Sancho D, Aguirre A. MasterMSM: A Package for Constructing Master Equation Models of Molecular Dynamics. J Chem Inf Model 2019; 59:3625-3629. [DOI: 10.1021/acs.jcim.9b00468] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- David de Sancho
- University of the Basque Country, Faculty of Chemistry, Paseo Manuel Lardizabal, 3, 20018 Donostia-San Sebastián, Spain
- Donostia International Physics Center, 20018, Donostia-San Sebastián, Spain
| | - Anne Aguirre
- Donostia International Physics Center, 20018, Donostia-San Sebastián, Spain
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6
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Michaelis M, Hildebrand N, Meißner RH, Wurzler N, Li Z, Hirst JD, Micsonai A, Kardos J, Delle Piane M, Colombi Ciacchi L. Impact of the Conformational Variability of Oligopeptides on the Computational Prediction of Their CD Spectra. J Phys Chem B 2019; 123:6694-6704. [DOI: 10.1021/acs.jpcb.9b03932] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Affiliation(s)
- M. Michaelis
- Faculty of Production Engineering, Bremen Center for Computational Materials Science, Center for Environmental Research and Sustainable Technology (UFT), and MAPEX Center for Materials and Processes, Hybrid Materials Interfaces Group, University of Bremen, Am Fallturm 1, Bremen 28359, Germany
- Biomolecular and Materials Interface Research Group, Interdisciplinary Biomedical Research Centre, School of Science and Technology, Nottingham Trent University, Clifton Lane, Nottingham NG11 8NS, United Kingdom
| | - N. Hildebrand
- Faculty of Production Engineering, Bremen Center for Computational Materials Science, Center for Environmental Research and Sustainable Technology (UFT), and MAPEX Center for Materials and Processes, Hybrid Materials Interfaces Group, University of Bremen, Am Fallturm 1, Bremen 28359, Germany
| | - R. H. Meißner
- Faculty of Production Engineering, Bremen Center for Computational Materials Science, Center for Environmental Research and Sustainable Technology (UFT), and MAPEX Center for Materials and Processes, Hybrid Materials Interfaces Group, University of Bremen, Am Fallturm 1, Bremen 28359, Germany
| | - N. Wurzler
- Faculty of Production Engineering, Bremen Center for Computational Materials Science, Center for Environmental Research and Sustainable Technology (UFT), and MAPEX Center for Materials and Processes, Hybrid Materials Interfaces Group, University of Bremen, Am Fallturm 1, Bremen 28359, Germany
| | - Z. Li
- School of Chemistry, University of Nottingham, University Park, Nottingham NG7 2RD, United Kingdom
| | - J. D. Hirst
- School of Chemistry, University of Nottingham, University Park, Nottingham NG7 2RD, United Kingdom
| | - A. Micsonai
- Department of Biochemistry, ELTE Eötvös Loránd University, Pázmány Péter sétány 1/C, Budapest H-1117, Hungary
| | - J. Kardos
- Department of Biochemistry, ELTE Eötvös Loránd University, Pázmány Péter sétány 1/C, Budapest H-1117, Hungary
| | - M. Delle Piane
- Faculty of Production Engineering, Bremen Center for Computational Materials Science, Center for Environmental Research and Sustainable Technology (UFT), and MAPEX Center for Materials and Processes, Hybrid Materials Interfaces Group, University of Bremen, Am Fallturm 1, Bremen 28359, Germany
| | - L. Colombi Ciacchi
- Faculty of Production Engineering, Bremen Center for Computational Materials Science, Center for Environmental Research and Sustainable Technology (UFT), and MAPEX Center for Materials and Processes, Hybrid Materials Interfaces Group, University of Bremen, Am Fallturm 1, Bremen 28359, Germany
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7
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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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8
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Soranno A, Cabassi F, Orselli ME, Cellmer T, Gori A, Longhi R, Buscaglia M. Dynamics of Structural Elements of GB1 β-Hairpin Revealed by Tryptophan-Cysteine Contact Formation Experiments. J Phys Chem B 2018; 122:11468-11477. [PMID: 30215522 DOI: 10.1021/acs.jpcb.8b07399] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Quenching of the triplet state of tryptophan by close contact with cysteine provides a tool for measuring the rate of intramolecular contact formation, one of the most elementary events in the folding process, in peptides and proteins using only natural probes. Here we present a study performed on a stabilized mutant of the second β-hairpin of the GB1 domain, where we combine steady-state fluorescence, laser-induced temperature-jump, and contact formation measurements to unveil the role of elementary structural components on hairpin dynamics and overall stability. In particular, our methodology provides access to the conformational dynamics of both the folded and unfolded state of the hairpin under native conditions, revealing the presence of extremely slow dynamics on the microsecond time scale in the unfolded state and coexistence of structures with partial pairing of the tails in the folded state. Comparing model peptides that mimic the turn sequence, we found that both ion pairing and hydrogen bonding due to the threonine side chain contribute to the propensity of turn formation but not to the much slower dynamics of the hydrophobic core formation. Interestingly, the dynamics of the turn region in isolation are significantly faster than the dynamics measured for the unfolded state of the complete hairpin, suggesting that non-native hydrophobic contacts slow down the reconfiguration dynamics of the unfolded state. Overall, the information extracted from these experiments provides kinetic limits on interconversions among conformational populations, hence enabling a simplified multistate free-energy landscape for the GB1 hairpin to be drawn.
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Affiliation(s)
- Andrea Soranno
- Department of Biochemistry and Molecular Biophysics , Washington University in St. Louis , St. Louis , Missouri 63130 , United States
| | - Francesca Cabassi
- Department of Medical Biotechnology and Translational Medicine , Università degli Studi di Milano , 20122 Milano , Italy
| | - Maria Elena Orselli
- Department of Medical Biotechnology and Translational Medicine , Università degli Studi di Milano , 20122 Milano , Italy
| | - Troy Cellmer
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases , National Institutes of Health , Bethesda , Maryland 20892 , United States
| | - Alessandro Gori
- Istituto di Chimica del Riconoscimento Molecolare , Consiglio Nazionale delle Ricerche , 20131 Milano , Italy
| | - Renato Longhi
- Istituto di Chimica del Riconoscimento Molecolare , Consiglio Nazionale delle Ricerche , 20131 Milano , Italy
| | - Marco Buscaglia
- Department of Medical Biotechnology and Translational Medicine , Università degli Studi di Milano , 20122 Milano , Italy
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9
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Ahalawat N, Mondal J. Assessment and optimization of collective variables for protein conformational landscape: GB1 β-hairpin as a case study. J Chem Phys 2018; 149:094101. [PMID: 30195312 DOI: 10.1063/1.5041073] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Collective variables (CVs), when chosen judiciously, can play an important role in recognizing rate-limiting processes and rare events in any biomolecular systems. However, high dimensionality and inherent complexities associated with such biochemical systems render the identification of an optimal CV a challenging task, which in turn precludes the elucidation of an underlying conformational landscape in sufficient details. In this context, a relevant model system is presented by a 16-residue β-hairpin of GB1 protein. Despite being the target of numerous theoretical and computational studies for understanding the protein folding, the set of CVs optimally characterizing the conformational landscape of the β-hairpin of GB1 protein has remained elusive, resulting in a lack of consensus on its folding mechanism. Here we address this by proposing a pair of optimal CVs which can resolve the underlying free energy landscape of the GB1 hairpin quite efficiently. Expressed as a linear combination of a number of traditional CVs, the optimal CV for this system is derived by employing the recently introduced time-structured independent component analysis approach on a large number of independent unbiased simulations. By projecting the replica-exchange simulated trajectories along these pair of optimized CVs, the resulting free energy landscape of this system is able to resolve four distinct well-separated metastable states encompassing the extensive ensembles of folded, unfolded, and molten globule states. Importantly, the optimized CVs were found to be capable of automatically recovering a novel partial helical state of this protein, without needing to explicitly invoke helicity as a constituent CV. Furthermore, a quantitative sensitivity analysis of each constituent in the optimized CV provided key insights on the relative contributions of the constituent CVs in the overall free energy landscapes. Finally, the kinetic pathways connecting these metastable states, constructed using a Markov state model, provide an optimum description of the underlying folding mechanism of the peptide. Taken together, this work offers a quantitatively robust approach toward comprehensive mapping of the underlying folding landscape of a quintessential model system along its optimized CV.
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Affiliation(s)
- Navjeet Ahalawat
- Tata Institute of Fundamental Research, Center for Interdisciplinary Sciences, Hyderabad 500107, India
| | - Jagannath Mondal
- Tata Institute of Fundamental Research, Center for Interdisciplinary Sciences, Hyderabad 500107, India
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10
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Arsiccio A, McCarty J, Pisano R, Shea JE. Effect of Surfactants on Surface-Induced Denaturation of Proteins: Evidence of an Orientation-Dependent Mechanism. J Phys Chem B 2018; 122:11390-11399. [DOI: 10.1021/acs.jpcb.8b07368] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Andrea Arsiccio
- Department of Applied Science and Technology, Politecnico di Torino, 24 corso Duca degli Abruzzi, Torino 10129, Italy
| | - James McCarty
- Department of Chemistry and Biochemistry, University of California, Santa Barbara, California 93106, United States
| | - Roberto Pisano
- Department of Applied Science and Technology, Politecnico di Torino, 24 corso Duca degli Abruzzi, Torino 10129, Italy
| | - Joan-Emma Shea
- Department of Chemistry and Biochemistry, University of California, Santa Barbara, California 93106, United States
- Department of Physics, University of California, Santa Barbara, California 93106, United States
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11
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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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12
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Palazzesi F, Salvalaglio M, Barducci A, Parrinello M. Communication: Role of explicit water models in the helix folding/unfolding processes. J Chem Phys 2016; 145:121101. [DOI: 10.1063/1.4963340] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Affiliation(s)
- Ferruccio Palazzesi
- Department of Chemistry and Applied Biosciences, Eidgenössische Technische Hochschule Zürich, 8093 Zurich, Switzerland
- Facoltá di Informatica, Istituto di Scienze Computazionali, Universitá della Svizzera Italiana, 6900 Lugano, Switzerland
| | - Matteo Salvalaglio
- Department of Chemical Engineering, University College London, London WC1E 7JE, United Kingdom
| | - Alessandro Barducci
- Inserm, U1054 Montpellier, France
- Université de Montpellier, CNRS, UMR 5048, Centre de Biochimie Structurale, Montpellier, France
| | - Michele Parrinello
- Department of Chemistry and Applied Biosciences, Eidgenössische Technische Hochschule Zürich, 8093 Zurich, Switzerland
- Facoltá di Informatica, Istituto di Scienze Computazionali, Universitá della Svizzera Italiana, 6900 Lugano, Switzerland
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13
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Microscopic interpretation of folding ϕ-values using the transition path ensemble. Proc Natl Acad Sci U S A 2016; 113:3263-8. [PMID: 26957599 DOI: 10.1073/pnas.1520864113] [Citation(s) in RCA: 44] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
All-atom molecular dynamics simulations now allow us to create movies of proteins folding and unfolding. However, it is difficult to assess the accuracy of the folding mechanisms observed because experiments cannot yet directly resolve events occurring along the transition paths between unfolded and folded states. Protein folding ϕ-values provide residue-resolved information about folding mechanisms by comparing the effects of mutations on folding rates and stability, but determining ϕ-values by separately simulating mutant proteins would be computationally demanding and prone to large statistical errors. Here we use transition path theory to develop a method for computing ϕ-values directly from the transition path ensemble, without the need for additional simulations. This path-based approach uses the full transition path information available from equilibrium folding and unfolding trajectories, or from transition path sampling, and does not require identification of folding transition states. Applying our approach to a set of simulations of 10 small proteins by Shaw and coworkers [Lindorff-Larsen K, Piana S, Dror RO, Shaw DE (2011) Science 334(6055):517-520; Piana S, Lindorff-Larsen K, Shaw DE (2011) Biophys J100(9):L47-L49; and Piana S, Lindorff-Larsen K, Shaw DE (2013) Proc Natl Acad Sci USA 110(15):5915-5920], we find good agreement with experiments in most cases where data are available. We can further resolve the contributions to fractional ϕ-values coming from partial contact formation versus transition path heterogeneity. Although in some cases, there is substantial heterogeneity of folding mechanism, in others, such as Ubiquitin, the mechanism is strongly conserved.
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14
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Computation of Rate Constants for Diffusion of Small Ligands to and from Buried Protein Active Sites. Methods Enzymol 2016; 578:299-326. [DOI: 10.1016/bs.mie.2016.05.039] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/17/2023]
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15
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Peter EK, Shea JE, Pivkin IV. Coarse kMC-based replica exchange algorithms for the accelerated simulation of protein folding in explicit solvent. Phys Chem Chem Phys 2016; 18:13052-65. [DOI: 10.1039/c5cp06867c] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
In this paper, we present a coarse replica exchange molecular dynamics (REMD) approach, based on kinetic Monte Carlo (kMC).
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Affiliation(s)
- Emanuel K. Peter
- Institute of Computational Science
- Faculty of Informatics
- University of Lugano
- Switzerland
| | - Joan-Emma Shea
- Department of Chemistry and Biochemistry
- Department of Physics
- University of California
- Santa Barbara
- USA
| | - Igor V. Pivkin
- Institute of Computational Science
- Faculty of Informatics
- University of Lugano
- Switzerland
- Swiss Institute of Bioinformatics
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16
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Yu H, Han W, Ma W, Schulten K. Transient β-hairpin formation in α-synuclein monomer revealed by coarse-grained molecular dynamics simulation. J Chem Phys 2015; 143:243142. [PMID: 26723627 PMCID: PMC4684271 DOI: 10.1063/1.4936910] [Citation(s) in RCA: 66] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2015] [Accepted: 11/18/2015] [Indexed: 12/18/2022] Open
Abstract
Parkinson's disease, originating from the intrinsically disordered peptide α-synuclein, is a common neurodegenerative disorder that affects more than 5% of the population above age 85. It remains unclear how α-synuclein monomers undergo conformational changes leading to aggregation and formation of fibrils characteristic for the disease. In the present study, we perform molecular dynamics simulations (over 180 μs in aggregated time) using a hybrid-resolution model, Proteins with Atomic details in Coarse-grained Environment (PACE), to characterize in atomic detail structural ensembles of wild type and mutant monomeric α-synuclein in aqueous solution. The simulations reproduce structural properties of α-synuclein characterized in experiments, such as secondary structure content, long-range contacts, chemical shifts, and (3)J(HNHCα )-coupling constants. Most notably, the simulations reveal that a short fragment encompassing region 38-53, adjacent to the non-amyloid-β component region, exhibits a high probability of forming a β-hairpin; this fragment, when isolated from the remainder of α-synuclein, fluctuates frequently into its β-hairpin conformation. Two disease-prone mutations, namely, A30P and A53T, significantly accelerate the formation of a β-hairpin in the stated fragment. We conclude that the formation of a β-hairpin in region 38-53 is a key event during α-synuclein aggregation. We predict further that the G47V mutation impedes the formation of a turn in the β-hairpin and slows down β-hairpin formation, thereby retarding α-synuclein aggregation.
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Affiliation(s)
- Hang Yu
- Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
| | - Wei Han
- Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
| | - Wen Ma
- Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
| | - Klaus Schulten
- Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
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17
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Naganathan AN, De Sancho D. Bridging Experiments and Native-Centric Simulations of a Downhill Folding Protein. J Phys Chem B 2015; 119:14925-33. [DOI: 10.1021/acs.jpcb.5b09568] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Affiliation(s)
- Athi N. Naganathan
- Department of Biotechnology, Bhupat & Jyoti Mehta School of Biosciences, Indian Institute of Technology Madras, Chennai 600036, India
| | - David De Sancho
- CIC nanoGUNE, Tolosa Hiribidea,
76, E-20018 Donostia-San
Sebastián, Spain
- IKERBASQUE, Basque Foundation for Science, María Díaz de Haro 3, 48013 Bilbao, Spain
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18
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Zerze GH, Uz B, Mittal J. Folding thermodynamics ofβ-hairpins studied by replica-exchange molecular dynamics simulations. Proteins 2015; 83:1307-15. [DOI: 10.1002/prot.24827] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2015] [Revised: 04/24/2015] [Accepted: 04/29/2015] [Indexed: 01/21/2023]
Affiliation(s)
- Gül H. Zerze
- Department of Chemical and Biomolecular Engineering; Lehigh University; Bethlehem Pennsylvania 18015
| | - Bilge Uz
- Department of Chemical and Biomolecular Engineering; Lehigh University; Bethlehem Pennsylvania 18015
| | - Jeetain Mittal
- Department of Chemical and Biomolecular Engineering; Lehigh University; Bethlehem Pennsylvania 18015
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19
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Razavi AM, Voelz VA. Kinetic Network Models of Tryptophan Mutations in β-Hairpins Reveal the Importance of Non-Native Interactions. J Chem Theory Comput 2015; 11:2801-12. [DOI: 10.1021/acs.jctc.5b00088] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Affiliation(s)
- Asghar M. Razavi
- Department
of Chemistry, Temple University, Philadelphia, Pennsylvania 19122, United States
| | - Vincent A. Voelz
- Department
of Chemistry, Temple University, Philadelphia, Pennsylvania 19122, United States
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20
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Peter EK, Pivkin IV, Shea JE. A kMC-MD method with generalized move-sets for the simulation of folding of α-helical and β-stranded peptides. J Chem Phys 2015; 142:144903. [DOI: 10.1063/1.4915919] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Affiliation(s)
- Emanuel K. Peter
- Faculty of Informatics, Institute of Computational Science, University of Lugano, Lugano, Switzerland
| | - Igor V. Pivkin
- Faculty of Informatics, Institute of Computational Science, University of Lugano, Lugano, Switzerland
| | - Joan-Emma Shea
- Department of Chemistry and Biochemistry, and Department of Physics, University of California, Santa Barbara, California 93106, USA
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21
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De Sancho D, Kubas A, Wang PH, Blumberger J, Best RB. Identification of Mutational Hot Spots for Substrate Diffusion: Application to Myoglobin. J Chem Theory Comput 2015; 11:1919-27. [PMID: 26574395 PMCID: PMC6132223 DOI: 10.1021/ct5011455] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The pathways by which small molecules (substrates or inhibitors) access active sites are a key aspect of the function of enzymes and other proteins. A key problem in designing or altering such proteins is to identify sites for mutation that will have the desired effect on the substrate transport properties. While specific access channels have been invoked in the past, molecular simulations suggest that multiple routes are possible, complicating the analysis. This complexity, however, can be captured by a Markov State Model (MSM) of the ligand diffusion process. We have developed a sensitivity analysis of the resulting rate matrix, which identifies the locations where mutations should have the largest effect on the diffusive on rate. We apply this method to myoglobin, which is the best characterized example both from experiment and simulation. We validate the approach by translating the sensitivity parameter obtained from this method into the CO binding rates in myoglobin upon mutation, resulting in a semi-quantitative correlation with experiments. The model is further validated against an explicit simulation for one of the experimental mutants.
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Affiliation(s)
- David De Sancho
- Department of Chemistry, University of Cambridge , Lensfield Road, Cambridge CB2 1EW, United Kingdom
- CIC nanoGUNE , Tolosa Hiribidea 76, 20018 Donostia-San Sebastian, Spain
- IKERBASQUE, Basque Foundation for Science , Maria Diaz de Haro 3, 48013 Bilbao, Spain
| | - Adam Kubas
- Department of Physics and Astronomy, University College London , Gower Street, London WC1E 6BT, United Kingdom
| | - Po-Hung Wang
- Department of Physics and Astronomy, University College London , Gower Street, London WC1E 6BT, United Kingdom
- Theoretical Molecular Science Laboratory , 2-1 Hirosawa, Wako-shi, Saitama 351-0198, Japan
| | - Jochen Blumberger
- Department of Physics and Astronomy, University College London , Gower Street, London WC1E 6BT, United Kingdom
| | - 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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22
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Zheng W, De Sancho D, Hoppe T, Best RB. Dependence of internal friction on folding mechanism. J Am Chem Soc 2015; 137:3283-90. [PMID: 25721133 PMCID: PMC4379956 DOI: 10.1021/ja511609u] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2014] [Indexed: 12/25/2022]
Abstract
An outstanding challenge in protein folding is understanding the origin of "internal friction" in folding dynamics, experimentally identified from the dependence of folding rates on solvent viscosity. A possible origin suggested by simulation is the crossing of local torsion barriers. However, it was unclear why internal friction varied from protein to protein or for different folding barriers of the same protein. Using all-atom simulations with variable solvent viscosity, in conjunction with transition-path sampling to obtain reaction rates and analysis via Markov state models, we are able to determine the internal friction in the folding of several peptides and miniproteins. In agreement with experiment, we find that the folding events with greatest internal friction are those that mainly involve helix formation, while hairpin formation exhibits little or no evidence of friction. Via a careful analysis of folding transition paths, we show that internal friction arises when torsion angle changes are an important part of the folding mechanism near the folding free energy barrier. These results suggest an explanation for the variation of internal friction effects from protein to protein and across the energy landscape of the same protein.
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Affiliation(s)
- Wenwei Zheng
- Laboratory
of Chemical Physics, National Institute of Diabetes and Digestive
and Kidney Diseases, National Institutes
of Health, Bethesda, Maryland 20892, United
States
| | - David De Sancho
- Department
of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, United Kingdom
- CIC
nanoGUNE, 20018 Donostia−San Sebastián, Spain
- IKERBASQUE,
Basque Foundation for Science, Maria Diaz de Haro 3, 48013 Bilbao, Spain
| | - Travis Hoppe
- Laboratory
of Chemical Physics, National Institute of Diabetes and Digestive
and Kidney Diseases, National Institutes
of Health, Bethesda, Maryland 20892, 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, United
States
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23
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Ardevol A, Tribello GA, Ceriotti M, Parrinello M. Probing the Unfolded Configurations of a β-Hairpin Using Sketch-Map. J Chem Theory Comput 2015; 11:1086-93. [DOI: 10.1021/ct500950z] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Affiliation(s)
- Albert Ardevol
- Computational
Science, Department of Chemistry and Applied Biosciences, ETH Zurich, USI-Campus, Via Giuseppe Buffi 13, C-6900 Lugano, Switzerland
| | - Gareth A. Tribello
- Atomistic
Simulation Centre, School of Mathematics and Physics, Queen’s University Belfast, Belfast BT7 1NN, United Kingdom
| | - Michele Ceriotti
- Laboratory
of Computational Science and Modelling, EPFL, CH-1015 Lausanne, Switzerland
| | - Michele Parrinello
- Computational
Science, Department of Chemistry and Applied Biosciences, ETH Zurich, USI-Campus, Via Giuseppe Buffi 13, C-6900 Lugano, Switzerland
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24
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Voelz VA, Elman B, Razavi AM, Zhou G. Surprisal Metrics for Quantifying Perturbed Conformational Dynamics in Markov State Models. J Chem Theory Comput 2014; 10:5716-28. [DOI: 10.1021/ct500827g] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Affiliation(s)
- Vincent A. Voelz
- Department of Chemistry, Temple University, Philadelphia, Pennsylvania 19122, United States
| | - Brandon Elman
- Department of Chemistry, Temple University, Philadelphia, Pennsylvania 19122, United States
| | - Asghar M. Razavi
- Department of Chemistry, Temple University, Philadelphia, Pennsylvania 19122, United States
| | - Guangfeng Zhou
- Department of Chemistry, Temple University, Philadelphia, Pennsylvania 19122, United States
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25
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Best RB, Zheng W, Mittal J. Balanced Protein-Water Interactions Improve Properties of Disordered Proteins and Non-Specific Protein Association. J Chem Theory Comput 2014; 10:5113-5124. [PMID: 25400522 PMCID: PMC4230380 DOI: 10.1021/ct500569b] [Citation(s) in RCA: 476] [Impact Index Per Article: 47.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2014] [Indexed: 12/22/2022]
Abstract
Some frequently encountered deficiencies in all-atom molecular simulations, such as nonspecific protein-protein interactions being too strong, and unfolded or disordered states being too collapsed, suggest that proteins are insufficiently well solvated in simulations using current state-of-the-art force fields. To address these issues, we make the simplest possible change, by modifying the short-range protein-water pair interactions, and leaving all the water-water and protein-protein parameters unchanged. We find that a modest strengthening of protein-water interactions is sufficient to recover the correct dimensions of intrinsically disordered or unfolded proteins, as determined by direct comparison with small-angle X-ray scattering (SAXS) and Förster resonance energy transfer (FRET) data. The modification also results in more realistic protein-protein affinities, and average solvation free energies of model compounds which are more consistent with experiment. Most importantly, we show that this scaling is small enough not to affect adversely the stability of the folded state, with only a modest effect on the stability of model peptides forming α-helix and β-sheet structures. The proposed adjustment opens the way to more accurate atomistic simulations of proteins, particularly for intrinsically disordered proteins, protein-protein association, and crowded cellular environments.
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Affiliation(s)
- Robert B. Best
- Laboratory
of Chemical Physics, National Institute of Diabetes and Digestive
and Kidney Diseases, National Institutes
of Health, Bethesda, Maryland 20892, United
States
| | - Wenwei Zheng
- Laboratory
of Chemical Physics, National Institute of Diabetes and Digestive
and Kidney Diseases, National Institutes
of Health, Bethesda, Maryland 20892, United
States
| | - Jeetain Mittal
- Department
of Chemical and Biomolecular Engineering, Lehigh University, Bethlehem, Pennsylvania 18015, United States
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26
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Jas GS, Hegefeld WA, Middaugh CR, Johnson CK, Kuczera K. Detailed microscopic unfolding pathways of an α-helix and a β-hairpin: direct observation and molecular dynamics. J Phys Chem B 2014; 118:7233-46. [PMID: 24897620 DOI: 10.1021/jp500955z] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
We present a combined experimental and computational study of unfolding pathways of a model 21-residue α-helical heteropeptide (W1H5-21) and a 16-residue β-hairpin (GB41-56). Experimentally, we measured fluorescence energy transfer efficiency as a function of temperature, employing natural tryptophans as donors and dansylated lysines as acceptors. Secondary structural analysis was performed with circular dichroism and Fourier transform infrared spectroscopy. Our studies present markedly different unfolding pathways of the two elementary secondary structural elements. During thermal denaturation, the helical peptide exhibits an initial decrease in length, followed by an increase, while the hairpin undergoes a systematic increase in length. In the complementary computational part of the project, we performed microsecond length replica-exchange molecular dynamics simulations of the peptides in explicit solvent, yielding a detailed microscopic picture of the unfolding processes. For the α-helical peptide, we found a large heterogeneous population of intermediates that are primarily frayed single helices or helix-turn-helix motifs. Unfolding starts at the termini and proceeds through a stable helical region in the interior of the peptide but shifted off-center toward the C-terminus. The simulations explain the experimentally observed non-monotonic variation of helix length with temperature as due primarily to the presence of frayed-end single-helix intermediate structures. For the β-hairpin peptide, our simulations indicate that folding is initiated at the turn, followed by formation of the hairpin in zipper-like fashion, with Cα···Cα contacts propagating from the turn to termini and hairpin hydrogen bonds forming in parallel with these contacts. In the early stages of hairpin formation, the hydrophobic side-chain contacts are only partly populated. Intermediate structures with low numbers of β-hairpin hydrogen bonds have very low populations. This is in accord with the "broken zipper" model of Scheraga. The monotonic increase in length with temperature may be explained by the zipper-like breaking of the hairpin hydrogen bonds and backbone contacts.
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Affiliation(s)
- Gouri S Jas
- Department of Pharmaceutical Chemistry, University of Kansas , Lawrence, Kansas 66047, United States
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27
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Chodera JD, Noé F. Markov state models of biomolecular conformational dynamics. Curr Opin Struct Biol 2014; 25:135-44. [PMID: 24836551 DOI: 10.1016/j.sbi.2014.04.002] [Citation(s) in RCA: 493] [Impact Index Per Article: 49.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2014] [Revised: 04/08/2014] [Accepted: 04/12/2014] [Indexed: 10/25/2022]
Abstract
It has recently become practical to construct Markov state models (MSMs) that reproduce the long-time statistical conformational dynamics of biomolecules using data from molecular dynamics simulations. MSMs can predict both stationary and kinetic quantities on long timescales (e.g. milliseconds) using a set of atomistic molecular dynamics simulations that are individually much shorter, thus addressing the well-known sampling problem in molecular dynamics simulation. In addition to providing predictive quantitative models, MSMs greatly facilitate both the extraction of insight into biomolecular mechanism (such as folding and functional dynamics) and quantitative comparison with single-molecule and ensemble kinetics experiments. A variety of methodological advances and software packages now bring the construction of these models closer to routine practice. Here, we review recent progress in this field, considering theoretical and methodological advances, new software tools, and recent applications of these approaches in several domains of biochemistry and biophysics, commenting on remaining challenges.
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Affiliation(s)
- John D Chodera
- Computational Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA.
| | - Frank Noé
- Department of Mathematics and Computer Science, Freie Universität Berlin, Arnimallee 6, 14195 Berlin, Germany.
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28
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Cieplak M, Banavar JR. Energy landscape and dynamics of proteins: an exact analysis of a simplified lattice model. PHYSICAL REVIEW. E, STATISTICAL, NONLINEAR, AND SOFT MATTER PHYSICS 2013; 88:040702. [PMID: 24229101 DOI: 10.1103/physreve.88.040702] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/09/2013] [Indexed: 06/02/2023]
Abstract
We present the results of exact numerical studies of the energy landscape and the dynamics of a 12-monomer chain with contact interactions encoding the ground state on a square lattice. In spite of its simplicity, the model is shown to exhibit behavior at odds with the standard picture of proteins.
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Affiliation(s)
- Marek Cieplak
- Institute of Physics, Polish Academy of Sciences, 02-668 Warsaw, Poland
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29
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Levy RM, Dai W, Deng NJ, Makarov DE. How long does it take to equilibrate the unfolded state of a protein? Protein Sci 2013; 22:1459-65. [PMID: 23963761 DOI: 10.1002/pro.2335] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2013] [Revised: 08/09/2013] [Accepted: 08/12/2013] [Indexed: 01/18/2023]
Abstract
How long does it take to equilibrate the unfolded state of a protein? The answer to this question has important implications for our understanding of why many small proteins fold with two state kinetics. When the equilibration within the unfolded state U is much faster than the folding, the folding kinetics will be two state even if there are many folding pathways with different barriers. Yet the mean first passage times (MFPTs) between different regions of the unfolded state can be much longer than the folding time. This seems to imply that the equilibration within U is much slower than the folding. In this communication we resolve this paradox. We present a formula for estimating the time to equilibrate the unfolded state of a protein. We also present a formula for the MFPT to any state within U, which is proportional to the average lifetime of that state divided by the state population. This relation is valid when the equilibration within U is very fast as compared with folding as it often is for small proteins. To illustrate the concepts, we apply the formulas to estimate the time to equilibrate the unfolded state of Trp-cage and MFPTs within the unfolded state based on a Markov State Model using an ultra-long 208 microsecond trajectory of the miniprotein to parameterize the model. The time to equilibrate the unfolded state of Trp-cage is ∼100 ns while the typical MFPTs within U are tens of microseconds or longer.
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Affiliation(s)
- Ronald M Levy
- Department of Chemistry and Chemical Biology, Rutgers, the State University of New Jersey, Piscataway, New Jersey, 08854
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30
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Sterpone F, Nguyen PH, Kalimeri M, Derreumaux P. Importance of the ion-pair interactions in the OPEP coarse-grained force field: parametrization and validation. J Chem Theory Comput 2013; 9:4574-4584. [PMID: 25419192 DOI: 10.1021/ct4003493] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
We have derived new effective interactions that improve the description of ion-pairs in the OPEP coarse-grained force field without introducing explicit electrostatic terms. The iterative Boltzmann inversion method was used to extract these potentials from all atom simulations by targeting the radial distribution function of the distance between the center of mass of the side-chains. The new potentials have been tested on several systems that differ in structural properties, thermodynamic stabilities and number of ion-pairs. Our modeling, by refining the packing of the charged amino-acids, impacts the stability of secondary structure motifs and the population of intermediate states during temperature folding/unfolding; it also improves the aggregation propensity of peptides. The new version of the OPEP force field has the potentiality to describe more realistically a large spectrum of situations where salt-bridges are key interactions.
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Affiliation(s)
- Fabio Sterpone
- Laboratoire de Biochimie Théorique, IBPC, CNRS, UPR9080, Univ. Paris Diderot, Sorbonne Paris Cité, 13 rue Pierre et Marie Curie, 75005, Paris, France
| | - Phuong H Nguyen
- Laboratoire de Biochimie Théorique, IBPC, CNRS, UPR9080, Univ. Paris Diderot, Sorbonne Paris Cité, 13 rue Pierre et Marie Curie, 75005, Paris, France
| | - Maria Kalimeri
- Laboratoire de Biochimie Théorique, IBPC, CNRS, UPR9080, Univ. Paris Diderot, Sorbonne Paris Cité, 13 rue Pierre et Marie Curie, 75005, Paris, France
| | - Philippe Derreumaux
- Laboratoire de Biochimie Théorique, IBPC, CNRS, UPR9080, Univ. Paris Diderot, Sorbonne Paris Cité, 13 rue Pierre et Marie Curie, 75005, Paris, France ; Institut Universitaire de France, Bvd St Michel, 75005, Paris, France
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