1
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Galata AA, Kröger M. Globular Proteins and Where to Find Them within a Polymer Brush-A Case Study. Polymers (Basel) 2023; 15:polym15102407. [PMID: 37242983 DOI: 10.3390/polym15102407] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2023] [Revised: 05/15/2023] [Accepted: 05/19/2023] [Indexed: 05/28/2023] Open
Abstract
Protein adsorption by polymerized surfaces is an interdisciplinary topic that has been approached in many ways, leading to a plethora of theoretical, numerical and experimental insight. There is a wide variety of models trying to accurately capture the essence of adsorption and its effect on the conformations of proteins and polymers. However, atomistic simulations are case-specific and computationally demanding. Here, we explore universal aspects of the dynamics of protein adsorption through a coarse-grained (CG) model, that allows us to explore the effects of various design parameters. To this end, we adopt the hydrophobic-polar (HP) model for proteins, place them uniformly at the upper bound of a CG polymer brush whose multibead-spring chains are tethered to a solid implicit wall. We find that the most crucial factor affecting the adsorption efficiency appears to be the polymer grafting density, while the size of the protein and its hydrophobicity ratio come also into play. We discuss the roles of ligands and attractive tethering surfaces to the primary adsorption as well as secondary and ternary adsorption in the presence of attractive (towards the hydrophilic part of the protein) beads along varying spots of the backbone of the polymer chains. The percentage and rate of adsorption, density profiles and the shapes of the proteins, alongside with the respective potential of mean force are recorded to compare the various scenarios during protein adsorption.
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Affiliation(s)
- Aikaterini A Galata
- Magnetism and Interface Physics, Department of Materials, ETH Zurich, CH-8093 Zurich, Switzerland
| | - Martin Kröger
- Magnetism and Interface Physics, Department of Materials, ETH Zurich, CH-8093 Zurich, Switzerland
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2
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Moses K, Van Tassel PR. Polyelectrolyte Influence on Beta-Hairpin Peptide Stability: A Simulation Study. J Phys Chem B 2023; 127:359-370. [PMID: 36574611 DOI: 10.1021/acs.jpcb.2c06641] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Assemblies of proteins and charged macromolecules (polyelectrolytes) find important applications as pharmaceutical formulations, biocatalysts, and cell-contacting substrates. A key question is how the polymer component influences the structure and function of the protein. The present paper addresses the influence of charged polymers on the thermal stability of two model beta-hairpin-forming peptides through an all-atom, replica exchange molecular dynamics simulation. The (negatively charged) peptides consist of the terminal 16 amino acids of the B1 domain of Protein G (GB1) and a variant with three of the GB1 residues substituted with tryptophan (Tryptophan Zipper 4, or TZ4). A (cationic) lysine polymer is seen to thermally stabilize TZ4 and destabilize GB1, while a (also cationic) chitosan polymer slightly stabilizes GB1 but has essentially no effect on TZ4. Free energy profiles reveal folded and unfolded conformations to be separated by kinetic barriers generally acting in the direction of the thermodynamically favored state. Through application of an Ising-like statistical mechanical model, a mechanism is proposed based on competition between (indirect) entropic stabilization of folded versus unfolded states and (direct) competition for hydrogen-bonding and hydrophobic interactions. These findings have important implications to the design of polyelectrolyte-based materials for biomedical and biotechnological applications.
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Affiliation(s)
- Kevin Moses
- Dept. of Chemical and Environmental Engineering, Yale University, New Haven, Connecticut 06520-8286, United States
| | - Paul R Van Tassel
- Dept. of Chemical and Environmental Engineering, Yale University, New Haven, Connecticut 06520-8286, United States
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3
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Govind G, Nayana EC, Anjukandi P. An account on the factors determining the extra stability of the β-hairpin from B1 domain of protein G. J Biomol Struct Dyn 2022; 40:12841-12847. [PMID: 34570679 DOI: 10.1080/07391102.2021.1977706] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
The folding-unfolding of a 16 residue polypeptide, a β-hairpin in B1 domain of protein G is investigated here to account for the factors assisting the extra stability of the polypeptide in the presence of an explicit solvent and even when a denaturant like urea is present in the medium. It is observed here that the backbone H-bond network well defines the folded state and is even capable of forming the folded state, but it is not the only criteria for making a stable β-hairpin fold. Factors such as the side chain H-bonds and the alignment of the certain hydrophobic group side chains play a prominent role in preserving the β-hairpin structure and thus providing an extra stability to the hairpin architecture. It is also affirmed that the mentioned hydrophobic groups side chain interactions are very crucial in holding the β-hairpin together and without which the hairpin collapses completely. We also confirm that the denaturant urea acts on the GB1-hairpin backbone H-bonds and in the presence of strong hydrophobic interactions with a consistent side chain H-bonding network, the denaturation being comparatively a slower process with respect to the protein devoid of the side chain interactions.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Gokul Govind
- Department of Chemistry, Indian Institute of Technology, Palakkad, India
| | - E C Nayana
- Department of Chemistry, Indian Institute of Technology, Palakkad, India
| | - Padmesh Anjukandi
- Department of Chemistry, Indian Institute of Technology, Palakkad, India
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4
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Lei YK, Zhang Z, Han X, Yang YI, Zhang J, Gao YQ. Locating Transition Zone in Phase Space. J Chem Theory Comput 2022; 18:6124-6133. [PMID: 36135927 DOI: 10.1021/acs.jctc.2c00385] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Understanding the reaction mechanism is required for better control of chemical reactions and is usually achieved by locating transition states (TSs) along a proper one-dimensional coordinate called reaction coordinate (RC). The identification of RC can be very difficult for high-dimensional realistic systems. A number of methods have been proposed to tackle this problem. A machine learning method is developed here to incorporate the influence of velocity on the reaction process. The method is also free of the unbalanced label problem resulting from the rather low fraction of configurations near the TS and can be easily extended to large systems. It locates the transition zone in the phase space and defines the dividing surface with a high transmission coefficient. Moreover, considering that the reaction environment can not only change the reaction path but also activate the reactive mode through energy transfer, we devise two measures to quantify the influence of these two factors on the reaction process and find that solvents can assist the reaction by directly doing work along the reactive mode. Not surprisingly, there is a positive correlation between the efficiency of energy transfer into the reactive mode and the reaction rate.
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Affiliation(s)
- Yao-Kun Lei
- Institute of Systems and Physical Biology, Shenzhen Bay Laboratory, 518055 Shenzhen, China.,Beijing National Laboratory for Molecular Sciences, College of Chemistry and Molecular Engineering, Peking University, 100871 Beijing, China
| | - Zhen Zhang
- School of Physics and Technology, Tangshan Normal University, 063000 Tangshan, China
| | - Xu Han
- Institute of Systems and Physical Biology, Shenzhen Bay Laboratory, 518055 Shenzhen, China.,Beijing National Laboratory for Molecular Sciences, College of Chemistry and Molecular Engineering, Peking University, 100871 Beijing, China
| | - Yi Isaac Yang
- Institute of Systems and Physical Biology, Shenzhen Bay Laboratory, 518055 Shenzhen, China
| | - Jun Zhang
- Institute of Systems and Physical Biology, Shenzhen Bay Laboratory, 518055 Shenzhen, China
| | - Yi Qin Gao
- Institute of Systems and Physical Biology, Shenzhen Bay Laboratory, 518055 Shenzhen, China.,Beijing National Laboratory for Molecular Sciences, College of Chemistry and Molecular Engineering, Peking University, 100871 Beijing, China.,Biomedical Pioneering Innovation Center, Peking University, 100871 Beijing, China
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5
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Abstract
Constantly advancing computer simulations of biomolecules provide huge amounts of data that are difficult to interpret. In particular, obtaining insights into functional aspects of macromolecular dynamics, often related to cascades of transient events, calls for methodologies that depart from the well-grounded framework of equilibrium statistical physics. One of the approaches toward the analysis of complex temporal data which has found applications in the fields of neuroscience and econometrics is Granger causality analysis. It allows determining which components of multidimensional time series are most influential for the evolution of the entire system, thus providing insights into causal relations within the dynamic structure of interest. In this work, we apply Granger analysis to a long molecular dynamics trajectory depicting repetitive folding and unfolding of a mini β-hairpin protein, CLN025. We find objective, quantitative evidence indicating that rearrangements within the hairpin turn region are determinant for protein folding and unfolding. On the contrary, interactions between hairpin arms score low on the causality scale. Taken together, these findings clearly favor the concept of zipperlike folding, which is one of two postulated β-hairpin folding mechanisms. More importantly, the results demonstrate the possibility of a conclusive application of Granger causality analysis to a biomolecular system.
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Affiliation(s)
- Marcin Sobieraj
- Faculty of Physics, University of Warsaw, Pasteura 5, 02-093 Warsaw, Poland.,Centre of New Technologies, University of Warsaw, Banacha 2c, 02-097 Warsaw, Poland
| | - Piotr Setny
- Centre of New Technologies, University of Warsaw, Banacha 2c, 02-097 Warsaw, Poland
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6
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Tang WS, Fawzi NL, Mittal J. Refining All-Atom Protein Force Fields for Polar-Rich, Prion-like, Low-Complexity Intrinsically Disordered Proteins. J Phys Chem B 2020; 124:9505-9512. [PMID: 33078950 DOI: 10.1021/acs.jpcb.0c07545] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Significant efforts in the past decade have given us highly accurate all-atom protein force fields for molecular dynamics (MD) simulations of folded and disordered proteins. These simulations, complemented with experimental data, provide new insights into molecular interactions that underlie the physical properties of proteins, especially for intrinsically disordered proteins (IDPs) for which defining the heterogeneous structural ensemble is hugely challenging by experiments alone. Consequently, the accuracy of these protein force fields is of utmost importance to ensure reliable simulated conformational data. Here, we first assess the accuracy of current state-of-the-art force fields for IDPs (ff99SBws and ff03ws) applied to disordered proteins of low amino acid sequence complexity that can undergo liquid-liquid phase separation. On the basis of a detailed comparison of NMR chemical shifts between simulation and experiment on several IDPs, we find that regions surrounding specific polar residues result in simulated ensembles with exaggerated helicity when compared to experiment. To resolve this discrepancy, we introduce residue-specific modifications to the backbone torsion potential of three residues (Ser, Thr, and Gln) in the ff99SBws force field. The modified force field, ff99SBws-STQ, provides a more accurate representation of helical structure propensity in these LC domains without compromising faithful representation of helicity in a region with distinct sequence composition. Our refinement strategy also suggests a path forward for integrating experimental data in the assessment of residue-specific deficiencies in the current physics-based force fields and improves these force fields further for their broader applicability.
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Affiliation(s)
- Wai Shing Tang
- Department of Physics, Brown University, Providence, Rhode Island 02912, United States
| | - Nicolas L Fawzi
- Department of Molecular Pharmacology, Physiology and Biotechnology, Brown University, Providence, Rhode Island 02912, United States
| | - Jeetain Mittal
- Department of Chemical and Biomolecular Engineering, Lehigh University, Bethlehem, Pennsylvania 18015, United States
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7
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Tao P, Xiao Y. Using the generalized Born surface area model to fold proteins yields more effective sampling while qualitatively preserving the folding landscape. Phys Rev E 2020; 101:062417. [PMID: 32688556 DOI: 10.1103/physreve.101.062417] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2020] [Accepted: 06/01/2020] [Indexed: 11/07/2022]
Abstract
Protein folding is a long-standing problem and has been widely investigated using molecular dynamics simulations with both explicit and implicit solvents. However, to what extent the folding mechanisms observed in two water models agree remains an open question. In this study, ab initio folding simulations of ten proteins with different topologies are performed in two combinations of force fields and water models (ff14SB+TIP3P and ff14SBonlysc+GB-Neck2). Interestingly, the latter combination not only folds more proteins but also provides a better balance of different secondary structures than the former in the same number of integration time steps. More importantly, the folding pathways found in the two types of simulations are conserved and they may only differ in their weights. Our results suggest that simulations with an implicit solvent may also be suitable for the investigation of the mechanism of protein folding.
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Affiliation(s)
- Peng Tao
- School of Physics, Huazhong University of Science and Technology, Wuhan 430074, Hubei, China
| | - Yi Xiao
- School of Physics, Huazhong University of Science and Technology, Wuhan 430074, Hubei, China
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8
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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: 8] [Impact Index Per Article: 1.6] [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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9
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Shao Q, Zhu W. Assessing AMBER force fields for protein folding in an implicit solvent. Phys Chem Chem Phys 2018; 20:7206-7216. [PMID: 29480910 DOI: 10.1039/c7cp08010g] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
Molecular dynamics (MD) simulation implemented with a state-of-the-art protein force field and implicit solvent model is an attractive approach to investigate protein folding, one of the most perplexing problems in molecular biology. But how well can force fields developed independently of implicit solvent models work together in reproducing diverse protein native structures and measuring the corresponding folding thermodynamics is not always clear. In this work, we performed enhanced sampling MD simulations to assess the ability of six AMBER force fields (FF99SBildn, FF99SBnmr, FF12SB, FF14ipq, FF14SB, and FF14SBonlysc) as coupled with a recently improved pair-wise GB-Neck2 model in modeling the folding of two helical and two β-sheet peptides. Whilst most of the tested force fields can yield roughly similar features for equilibrium conformational ensembles and detailed folding free-energy profiles for short α-helical TC10b in an implicit solvent, the measured counterparts are significantly discrepant in the cases of larger or β-structured peptides (HP35, 1E0Q, and GTT). Additionally, the calculated folding/unfolding thermodynamic quantities can only partially match the experimental data. Although a combination of the force fields and GB-Neck2 implicit model able to describe all aspects of the folding transitions towards the native structures of all the considered peptides was not identified, we found that FF14SBonlysc coupled with the GB-Neck2 model seems to be a reasonably balanced combination to predict peptide folding preferences.
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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.
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10
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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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11
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Chen J, Liu X, Chen J. Atomistic Peptide Folding Simulations Reveal Interplay of Entropy and Long-Range Interactions in Folding Cooperativity. Sci Rep 2018; 8:13668. [PMID: 30209295 PMCID: PMC6135771 DOI: 10.1038/s41598-018-32028-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2018] [Accepted: 08/30/2018] [Indexed: 11/23/2022] Open
Abstract
Understanding how proteins fold has remained a problem of great interest in biophysical research. Atomistic computer simulations using physics-based force fields can provide important insights on the interplay of different interactions and energetics and their roles in governing the folding thermodynamics and mechanism. In particular, generalized Born (GB)-based implicit solvent force fields can be optimized to provide an appropriate balance between solvation and intramolecular interactions and successfully recapitulate experimental conformational equilibria for a set of helical and β-hairpin peptides. Here, we further demonstrate that key thermodynamic properties and their temperature dependence obtained from replica exchange molecular dynamics simulations of these peptides are in quantitative agreement with experimental results. Useful lessons can be learned on how the interplay of entropy and sequentially long-range interactions governs the mechanism and cooperativity of folding. These results highlight the great potential of high-quality implicit solvent force fields for studying protein folding and large-scale conformational transitions.
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Affiliation(s)
- Jianlin Chen
- Department of Hematology, The Central Hospital of Taizhou, Taizhou, Zhejiang, 318000, P.R. China
| | - Xiaorong Liu
- Department of Chemistry, University of Massachusetts Amherst, Amherst, MA, 01003, USA
| | - Jianhan Chen
- Department of Chemistry, University of Massachusetts Amherst, Amherst, MA, 01003, USA. .,Department of Biochemistry and Molecular Biology, University of Massachusetts Amherst, Amherst, MA, 01003, USA.
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12
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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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13
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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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14
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Hanke CA, Gohlke H. Tertiary Interactions in the Unbound Guanine-Sensing Riboswitch Focus Functional Conformational Variability on the Binding Site. J Chem Inf Model 2017; 57:2822-2832. [DOI: 10.1021/acs.jcim.7b00567] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- Christian A. Hanke
- Mathematisch-Naturwissenschaftliche
Fakultät, Institut für Pharmazeutische und Medizinische
Chemie, Heinrich-Heine-Universität Düsseldorf, 40225 Düsseldorf, Germany
| | - Holger Gohlke
- Mathematisch-Naturwissenschaftliche
Fakultät, Institut für Pharmazeutische und Medizinische
Chemie, Heinrich-Heine-Universität Düsseldorf, 40225 Düsseldorf, Germany
- John von Neumann Institute for Computing (NIC), Jülich Supercomputing Centre (JSC) & Institute for Complex Systems - Structural Biochemistry (ICS 6), Forschungszentrum Jülich GmbH, 52425 Jülich, Germany
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15
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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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16
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Shao Q, Shi J, Zhu W. Determining Protein Folding Pathway and Associated Energetics through Partitioned Integrated-Tempering-Sampling Simulation. J Chem Theory Comput 2017; 13:1229-1243. [DOI: 10.1021/acs.jctc.6b00967] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
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
| | - Jiye Shi
- UCB Biopharma
SPRL, Chemin du Foriest, 1420 Braine-l’Alleud, Belgium
| | - 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
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17
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Straus RN, Jockusch RA. Probing the Gaseous Structure of a β-Hairpin Peptide with H/D Exchange and Electron Capture Dissociation. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2017; 28:358-369. [PMID: 27943124 DOI: 10.1007/s13361-016-1528-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/27/2016] [Revised: 10/05/2016] [Accepted: 10/10/2016] [Indexed: 06/06/2023]
Abstract
An improved understanding of the extent to which native protein structure is retained upon transfer to the gas phase promises to enhance biological mass spectrometry, potentially streamlining workflows and providing fundamental insights into hydration effects. Here, we investigate the gaseous conformation of a model β-hairpin peptide using gas-phase hydrogen-deuterium (H/D) exchange with subsequent electron capture dissociation (ECD). Global gas-phase H/D exchange levels, and residue-specific exchange levels derived from ECD data, are compared among the wild type 16-residue peptide GB1p and several variants. High protection from H/D exchange observed for GB1p, but not for a truncated version, is consistent with the retention of secondary structure of GB1p in the gas phase or its refolding into some other compact structure. Four alanine mutants that destabilize the hairpin in solution show levels of protection similar to that of GB1p, suggesting collapse or (re)folding of these peptides upon transfer to the gas phase. These results offer a starting point from which to understand how a key secondary structural element, the β-hairpin, is affected by transfer to the gas phase. This work also demonstrates the utility of a much-needed addition to the tool set that is currently available for the investigation of the gaseous conformation of biomolecules, which can be employed in the future to better characterize gaseous proteins and protein complexes. Graphical Abstract ᅟ.
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Affiliation(s)
- Rita N Straus
- Department of Chemistry, University of Toronto, Toronto, ON, M5S 3H6, Canada
| | - Rebecca A Jockusch
- Department of Chemistry, University of Toronto, Toronto, ON, M5S 3H6, Canada.
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18
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Gupta M, Chakravarty C, Bandyopadhyay S. Sensitivity of Protein Glass Transition to the Choice of Water Model. J Chem Theory Comput 2016; 12:5643-5655. [DOI: 10.1021/acs.jctc.6b00825] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Madhulika Gupta
- Department of Chemistry, Indian Institute of Technology-Delhi, New Delhi 110016, India
| | - Charusita Chakravarty
- Department of Chemistry, Indian Institute of Technology-Delhi, New Delhi 110016, India
| | - Sanjoy Bandyopadhyay
- Molecular Modeling Laboratory, Department
of Chemistry, Indian Institute of Technology-Kharagpur, Kharagpur 721302, India
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19
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Ding B, Hilaire MR, Gai F. Infrared and Fluorescence Assessment of Protein Dynamics: From Folding to Function. J Phys Chem B 2016; 120:5103-13. [PMID: 27183318 DOI: 10.1021/acs.jpcb.6b03199] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
While folding or performing functions, a protein can sample a rich set of conformational space. However, experimentally capturing all of the important motions with sufficient detail to allow a mechanistic description of their dynamics is nontrivial since such conformational events often occur over a wide range of time and length scales. Therefore, many methods have been employed to assess protein conformational dynamics, and depending on the nature of the conformational transition in question, some may be more advantageous than others. Herein, we describe our recent efforts, and also those of others, wherever appropriate, to use infrared- and fluorescence-based techniques to interrogate protein folding and functional dynamics. Specifically, we focus on discussing how to use extrinsic spectroscopic probes to enhance the structural resolution of these techniques and how to exploit various cross-linking strategies to acquire dynamic and mechanistic information that was previously difficult to attain.
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Affiliation(s)
- Bei Ding
- Department of Chemistry and ‡The Ultrafast Optical Processes Laboratory, University of Pennsylvania , Philadelphia, Pennsylvania 19104, United States
| | - Mary Rose Hilaire
- Department of Chemistry and ‡The Ultrafast Optical Processes Laboratory, University of Pennsylvania , Philadelphia, Pennsylvania 19104, United States
| | - Feng Gai
- Department of Chemistry and ‡The Ultrafast Optical Processes Laboratory, University of Pennsylvania , Philadelphia, Pennsylvania 19104, United States
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20
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Chen W, Shi C, Shen J. Nascent β-Hairpin Formation of a Natively Unfolded Peptide Reveals the Role of Hydrophobic Contacts. Biophys J 2016; 109:630-8. [PMID: 26244744 PMCID: PMC4571001 DOI: 10.1016/j.bpj.2015.06.035] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2015] [Revised: 06/16/2015] [Accepted: 06/17/2015] [Indexed: 11/21/2022] Open
Abstract
Despite the important role of the unfolded states in protein stability, folding, and aggregation, they remain poorly understood due to the lack of residue-specific experimental data. Here, we explore features of the unfolded state of the NTL9 protein by applying all-atom replica-exchange simulations to the two fragment peptides NTL9(1–22) and NTL9(6–17). We found that while NTL9(6–17) is unstructured, NTL9(1–22) transiently folds as various β-hairpins, a fraction of which contain a native β-sheet. Interestingly, despite a large number of charged residues, the formation of backbone hydrogen bonds is concomitant with hydrophobic but not electrostatic contacts. Although the fragment peptides lack a proposed specific contact between Asp8 and Lys12, the individually weak, nonspecific interactions with lysines together stabilize the charged Asp8, leading to a pKa shift of nearly 0.5 units, in agreement with the NMR data. Taken together, our data suggest that the unfolded state of NTL9 likely contains a β-hairpin in segment 1–22 with sequence-distant hydrophobic contacts, thus lending support to a long-standing hypothesis that the unfolded states of proteins exhibit native-like topology with hydrophobic clusters.
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Affiliation(s)
- Wei Chen
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Maryland, Baltimore, Maryland
| | - Chuanyin Shi
- Eastern Hepatobiliary Surgery Hospital, Second Military Medical University, Shanghai, China
| | - Jana Shen
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Maryland, Baltimore, Maryland.
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21
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Bureau HR, Hershkovits E, Quirk S, Hernandez R. Determining the Energetics of Small β-Sheet Peptides using Adaptive Steered Molecular Dynamics. J Chem Theory Comput 2016; 12:2028-37. [PMID: 26930270 DOI: 10.1021/acs.jctc.5b01110] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Mechanically driven unfolding is a useful computational tool for extracting the energetics and stretching pathway of peptides. In this work, two representative β-hairpin peptides, chignolin (PDB: 1UAO ) and trpzip1 (PDB: 1LE0 ), were investigated using an adaptive variant of the original steered molecular dynamics method called adaptive steered molecular dynamics (ASMD). The ASMD method makes it possible to perform energetic calculations on increasingly complex biological systems. Although the two peptides are similar in length and have similar secondary structures, their unfolding energetics are quite different. The hydrogen bonding profile and specific residue pair interaction energies provide insight into the differing stabilities of these peptides and reveal which of the pairs provides the most significant stabilization.
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Affiliation(s)
- Hailey R Bureau
- Center for Computational and Molecular Science and Technology, School of Chemistry and Biochemistry, Georgia Institute of Technology , Atlanta, Georgia 30332-0400, United States
| | - Eli Hershkovits
- Center for Computational and Molecular Science and Technology, School of Chemistry and Biochemistry, Georgia Institute of Technology , Atlanta, Georgia 30332-0400, United States
| | - Stephen Quirk
- Kimberly-Clark Corporation , Atlanta, Georgia 30076-2199, United States
| | - Rigoberto Hernandez
- Center for Computational and Molecular Science and Technology, School of Chemistry and Biochemistry, Georgia Institute of Technology , Atlanta, Georgia 30332-0400, United States
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22
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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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23
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Pandini A, Fornili A. Using Local States To Drive the Sampling of Global Conformations in Proteins. J Chem Theory Comput 2016; 12:1368-79. [PMID: 26808351 PMCID: PMC5356493 DOI: 10.1021/acs.jctc.5b00992] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
![]()
Conformational
changes associated with protein function often occur
beyond the time scale currently accessible to unbiased molecular dynamics
(MD) simulations, so that different approaches have been developed
to accelerate their sampling. Here we investigate how the knowledge
of backbone conformations preferentially adopted by protein fragments,
as contained in precalculated libraries known as structural alphabets
(SA), can be used to explore the landscape of protein conformations
in MD simulations. We find that (a) enhancing the sampling of native
local states in both metadynamics and steered MD simulations allows
the recovery of global folded states in small proteins; (b) folded
states can still be recovered when the amount of information on the
native local states is reduced by using a low-resolution version of
the SA, where states are clustered into macrostates; and (c) sequences
of SA states derived from collections of structural motifs can be
used to sample alternative conformations of preselected protein regions.
The present findings have potential impact on several applications,
ranging from protein model refinement to protein folding and design.
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Affiliation(s)
- Alessandro Pandini
- Department of Computer Science, College of Engineering, Design and Physical Sciences and Synthetic Biology Theme, Institute of Environment, Health and Societies, Brunel University London , Uxbridge UB8 3PH, United Kingdom
| | - Arianna Fornili
- School of Biological and Chemical Sciences, Queen Mary University of London , Mile End Road, London E1 4NS, United Kingdom
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24
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Makwana KM, Mahalakshmi R. Nature of aryl-tyrosine interactions contribute to β-hairpin scaffold stability: NMR evidence for alternate ring geometry. Phys Chem Chem Phys 2016; 17:4220-30. [PMID: 25569770 DOI: 10.1039/c4cp04991h] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
The specific contribution of the acidic-aromatic β-sheet favouring amino acid tyrosine to the stability of short octapeptide β-hairpin structures is presented here. Solution NMR analysis in near-apolar environments suggests the energetically favourable mode of interaction to be T-shaped face-to-edge (FtE) and that a Trp-Tyr interacting pair is the most stabilizing. Alternate aryl geometries also exist in solution, which readily equilibrate between a preferred π···π conformation to an aromatic-amide conformation, without any change in the backbone structure. While the phenolic ring is readily accommodated at the "edge" of FtE aryl interactions, it exhibits an overall lowered contribution to scaffold stability in the "face" orientation. Such differential tyrosine interactions are key to its dual nature in proteins.
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Affiliation(s)
- Kamlesh Madhusudan Makwana
- Molecular Biophysics Laboratory, Department of Biological Sciences, Indian Institute of Science Education and Research, Bhopal-462023, India.
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25
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Gupta M, Nayar D, Chakravarty C, Bandyopadhyay S. Comparison of hydration behavior and conformational preferences of the Trp-cage mini-protein in different rigid-body water models. Phys Chem Chem Phys 2016; 18:32796-32813. [DOI: 10.1039/c6cp04634g] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Trp-cage unfolds at different temperatures in different water models revealing the sensitivity of conformational order metrics to the choice of water models.
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Affiliation(s)
- Madhulika Gupta
- Department of Chemistry
- Indian Institute of Technology-Delhi
- New Delhi 110016
- India
| | - Divya Nayar
- Department of Chemistry
- Indian Institute of Technology-Delhi
- New Delhi 110016
- India
| | | | - Sanjoy Bandyopadhyay
- Molecular Modeling Laboratory
- Department of Chemistry
- Indian Institute of Technology
- Kharagpur 721302
- India
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26
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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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27
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Zerze GH, Mullen RG, Levine ZA, Shea JE, Mittal J. To What Extent Does Surface Hydrophobicity Dictate Peptide Folding and Stability near Surfaces? LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2015; 31:12223-12230. [PMID: 26484800 DOI: 10.1021/acs.langmuir.5b03814] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
Protein-surface interactions are ubiquitous in both the cellular setting and in modern bioengineering devices, but how such interactions impact protein stability is not well understood. We investigate the folding of the GB1 hairpin peptide in the presence of self-assembled monolayers and graphite like surfaces using replica exchange molecular dynamics simulations. By varying surface hydrophobicity, and decoupling direct protein-surface interactions from water-mediated interactions, we show that surface wettability plays a surprisingly minor role in dictating protein stability. For both the β-hairpin GB1 and the helical miniprotein TrpCage, adsorption and stability is largely dictated by the nature of the direct chemical interactions between the protein and the surface. Independent of the surface hydrophobicity profile, strong protein-surface interactions destabilize the folded structure while weak interactions stabilize it.
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Affiliation(s)
- Gül H Zerze
- Department of Chemical and Biomolecular Engineering, Lehigh University , Bethlehem, Pennsylvania 18015, United States
| | - Ryan G Mullen
- Department of Chemical Engineering, University of California , Santa Barbara, California 93106, United States
| | - Zachary A Levine
- Department of Chemistry and Biochemistry, University of California , Santa Barbara, California 93106, United States
- Department of Physics, University of California , Santa Barbara, California 93106
| | - 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
| | - Jeetain Mittal
- Department of Chemical and Biomolecular Engineering, Lehigh University , Bethlehem, Pennsylvania 18015, United States
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28
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Nayar D, Chakravarty C. Free Energy Landscapes of Alanine Oligopeptides in Rigid-Body and Hybrid Water Models. J Phys Chem B 2015; 119:11106-20. [PMID: 26132437 DOI: 10.1021/acs.jpcb.5b02937] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Replica exchange molecular dynamics is used to study the effect of different rigid-body (mTIP3P, TIP4P, SPC/E) and hybrid (H1.56, H3.00) water models on the conformational free energy landscape of the alanine oligopeptides (acAnme and acA5nme), in conjunction with the CHARMM22 force field. The free energy landscape is mapped out as a function of the Ramachandran angles. In addition, various secondary structure metrics, solvation shell properties, and the number of peptide-solvent hydrogen bonds are monitored. Alanine dipeptide is found to have similar free energy landscapes in different solvent models, an insensitivity which may be due to the absence of possibilities for forming i-(i + 4) or i-(i + 3) intrapeptide hydrogen bonds. The pentapeptide, acA5nme, where there are three intrapeptide backbone hydrogen bonds, shows a conformational free energy landscape with a much greater degree of sensitivity to the choice of solvent model, though the three rigid-body water models differ only quantitatively. The pentapeptide prefers nonhelical, non-native PPII and β-sheet populations as the solvent is changed from SPC/E to the less tetrahedral liquid (H1.56) to an LJ-like liquid (H3.00). The pentapeptide conformational order metrics indicate a preference for open, solvent-exposed, non-native structures in hybrid solvent models at all temperatures of study. The possible correlations between the properties of solvent models and secondary structure preferences of alanine oligopeptides are discussed, and the competition between intrapeptide, peptide-solvent, and solvent-solvent hydrogen bonding is shown to be crucial in the relative free energies of different conformers.
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Affiliation(s)
- Divya Nayar
- Department of Chemistry, Indian Institute of Technology-Delhi , New Delhi 110016, India
| | - Charusita Chakravarty
- Department of Chemistry, Indian Institute of Technology-Delhi , New Delhi 110016, India
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29
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Hierarchical Conformational Analysis of Native Lysozyme Based on Sub-Millisecond Molecular Dynamics Simulations. PLoS One 2015; 10:e0129846. [PMID: 26057625 PMCID: PMC4461368 DOI: 10.1371/journal.pone.0129846] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2015] [Accepted: 05/12/2015] [Indexed: 11/19/2022] Open
Abstract
Hierarchical organization of free energy landscape (FEL) for native globular proteins has been widely accepted by the biophysics community. However, FEL of native proteins is usually projected onto one or a few dimensions. Here we generated collectively 0.2 milli-second molecular dynamics simulation trajectories in explicit solvent for hen egg white lysozyme (HEWL), and carried out detailed conformational analysis based on backbone torsional degrees of freedom (DOF). Our results demonstrated that at micro-second and coarser temporal resolutions, FEL of HEWL exhibits hub-like topology with crystal structures occupying the dominant structural ensemble that serves as the hub of conformational transitions. However, at 100ns and finer temporal resolutions, conformational substates of HEWL exhibit network-like topology, crystal structures are associated with kinetic traps that are important but not dominant ensembles. Backbone torsional state transitions on time scales ranging from nanoseconds to beyond microseconds were found to be associated with various types of molecular interactions. Even at nanoseconds temporal resolution, the number of conformational substates that are of statistical significance is quite limited. These observations suggest that detailed analysis of conformational substates at multiple temporal resolutions is both important and feasible. Transition state ensembles among various conformational substates at microsecond temporal resolution were observed to be considerably disordered. Life times of these transition state ensembles are found to be nearly independent of the time scales of the participating torsional DOFs.
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30
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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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31
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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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32
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Huang J, MacKerell AD. Induction of peptide bond dipoles drives cooperative helix formation in the (AAQAA)3 peptide. Biophys J 2015; 107:991-7. [PMID: 25140435 DOI: 10.1016/j.bpj.2014.06.038] [Citation(s) in RCA: 70] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2014] [Revised: 06/19/2014] [Accepted: 06/24/2014] [Indexed: 11/27/2022] Open
Abstract
Cooperativity is a central feature in the formation of secondary structures in proteins. However, the driving forces behind this cooperativity are poorly understood. The present work shows that the cooperativity of helix formation in the acetyl-(AAQAA)3-NH2 peptide is significantly enhanced using an empirical force field that explicitly includes the treatment of electronic polarizability. Polarizable simulations yield helical content consistent with experimental measurements and indicate that the dependence of helical content on temperature is improved over additive models, though further sampling is required to fully validate this conclusion. Cooperativity is indicated by the peptide sampling either the coiled state or long helices with relatively low populations of short helices. The cooperativity is shown to be associated with enhanced dipole moments of the peptide backbone upon helix formation. These results indicate the polarizable force field to more accurately model peptide-folding cooperativity based on its physically realistic treatment of electronic polarizability.
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Affiliation(s)
- Jing Huang
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Maryland, Baltimore, Maryland
| | - Alexander D MacKerell
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Maryland, Baltimore, Maryland.
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33
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Schulz JCF, Miettinen MS, Netz RR. Unfolding and folding internal friction of β-hairpins is smaller than that of α-helices. J Phys Chem B 2015; 119:4565-74. [PMID: 25741584 DOI: 10.1021/jp512056k] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
By the forced unfolding of polyglutamine and polyalanine homopeptides in competing α-helix and β-hairpin secondary structures, we disentangle equilibrium free energetics from nonequilibrium dissipative effects. We find that α-helices are characterized by larger friction or dissipation upon unfolding, regardless of whether they are free energetically preferred over β-hairpins or not. Our analysis, based on MD simulations for atomistic peptide models with explicit water, suggests that this difference is related to the internal friction and mostly caused by the different number of intrapeptide hydrogen bonds in the α-helix and β-hairpin states.
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Affiliation(s)
| | | | - R R Netz
- Fachbereich Physik, Freie Universität Berlin, 14195 Berlin, Germany
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34
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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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35
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Affiliation(s)
- Qiang Shao
- Drug Discovery and Design
Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai, 201203, China
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36
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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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37
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Shao Q. Important roles of hydrophobic interactions in folding and charge interactions in misfolding of α-helix bundle protein. RSC Adv 2015. [DOI: 10.1039/c4ra14265a] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Abstract
An enhanced-sampling molecular dynamics simulation is presented to quantitatively demonstrate the important roles of hydrophobic and charge interactions in the folding and misfolding of α-helix bundle protein, respectively.
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Affiliation(s)
- Qiang Shao
- Drug Discovery and Design Center
- Shanghai Institute of Materia Medica
- Chinese Academy of Sciences
- Shanghai
- China
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38
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Nissley DA, O'Brien EP. Timing is everything: unifying codon translation rates and nascent proteome behavior. J Am Chem Soc 2014; 136:17892-8. [PMID: 25486504 DOI: 10.1021/ja510082j] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Experiments have demonstrated that changing the rate at which the ribosome translates a codon position in an mRNA molecule's open reading frame can alter the behavior of the newly synthesized protein. That is, codon translation rates can govern nascent proteome behavior. We emphasize that this phenomenon is a manifestation of the nonequilibrium nature of cotranslational processes, and as such, there exist theoretical tools that offer a potential means to quantitatively predict the influence of codon translation rates on the broad spectrum of nascent protein behaviors including cotranslational folding, aggregation, and translocation. We provide a review of the experimental evidence for the impact that codon translation rates can have, followed by a discussion of theoretical methods that can describe this phenomenon. The development and application of these tools are likely to provide fundamental insights into protein maturation and homeostasis, codon usage bias in organisms, the origins of translation related diseases, and new rational design methods for biotechnology and biopharmaceutical applications.
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Affiliation(s)
- Daniel A Nissley
- Department of Chemistry, Pennsylvania State University , University Park, Pennsylvania 16802, United States
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39
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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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40
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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: 483] [Impact Index Per Article: 48.3] [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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41
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42
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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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43
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Narayanan C, Dias CL. Exploring the free energy landscape of a model β-hairpin peptide and its isoform. Proteins 2014; 82:2394-402. [PMID: 24825659 DOI: 10.1002/prot.24601] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2013] [Revised: 03/21/2014] [Accepted: 04/29/2014] [Indexed: 12/16/2022]
Abstract
Secondary structural transitions from α-helix to β-sheet conformations are observed in several misfolding diseases including Alzheimer's and Parkinson's. Determining factors contributing favorably to the formation of each of these secondary structures is therefore essential to better understand these disease states. β-hairpin peptides form basic components of anti-parallel β-sheets and are suitable model systems for characterizing the fundamental forces stabilizing β-sheets in fibrillar structures. In this study, we explore the free energy landscape of the model β-hairpin peptide GB1 and its E2 isoform that preferentially adopts α-helical conformations at ambient conditions. Umbrella sampling simulations using all-atom models and explicit solvent are performed over a large range of end-to-end distances. Our results show the strong preference of GB1 and the E2 isoform for β-hairpin and α-helical conformations, respectively, consistent with previous studies. We show that the unfolded states of GB1 are largely populated by misfolded β-hairpin structures which differ from each other in the position of the β-turn. We discuss the energetic factors contributing favorably to the formation of α-helix and β-hairpin conformations in these peptides and highlight the energetic role of hydrogen bonds and non-bonded interactions.
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Affiliation(s)
- Chitra Narayanan
- Department of Physics, New Jersey Institute of Technology, University Heights, Newark, New Jersey, 07102-1982
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44
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Doshi U, Hamelberg D. Achieving Rigorous Accelerated Conformational Sampling in Explicit Solvent. J Phys Chem Lett 2014; 5:1217-1224. [PMID: 26274474 DOI: 10.1021/jz500179a] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Molecular dynamics simulations can provide valuable atomistic insights into biomolecular function. However, the accuracy of molecular simulations on general-purpose computers depends on the time scale of the events of interest. Advanced simulation methods, such as accelerated molecular dynamics, have shown tremendous promise in sampling the conformational dynamics of biomolecules, where standard molecular dynamics simulations are nonergodic. Here we present a sampling method based on accelerated molecular dynamics in which rotatable dihedral angles and nonbonded interactions are boosted separately. This method (RaMD-db) is a different implementation of the dual-boost accelerated molecular dynamics, introduced earlier. The advantage is that this method speeds up sampling of the conformational space of biomolecules in explicit solvent, as the degrees of freedom most relevant for conformational transitions are accelerated. We tested RaMD-db on one of the most difficult sampling problems - protein folding. Starting from fully extended polypeptide chains, two fast folding α-helical proteins (Trpcage and the double mutant of C-terminal fragment of Villin headpiece) and a designed β-hairpin (Chignolin) were completely folded to their native structures in very short simulation time. Multiple folding/unfolding transitions could be observed in a single trajectory. Our results show that RaMD-db is a promisingly fast and efficient sampling method for conformational transitions in explicit solvent. RaMD-db thus opens new avenues for understanding biomolecular self-assembly and functional dynamics occurring on long time and length scales.
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Affiliation(s)
- Urmi Doshi
- Department of Chemistry and the Center for Biotechnology and Drug Design, Georgia State University, P.O. Box 3965, Atlanta, Georgia 30302-3965, United States
| | - Donald Hamelberg
- Department of Chemistry and the Center for Biotechnology and Drug Design, Georgia State University, P.O. Box 3965, Atlanta, Georgia 30302-3965, United States
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45
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Markiewicz BN, Yang L, Culik RM, Gao YQ, Gai F. How quickly can a β-hairpin fold from its transition state? J Phys Chem B 2014; 118:3317-25. [PMID: 24611730 PMCID: PMC3969101 DOI: 10.1021/jp500774q] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
![]()
Understanding the structural nature
of the free energy bottleneck(s)
encountered in protein folding is essential to elucidating the underlying
dynamics and mechanism. For this reason, several techniques, including
Φ-value analysis, have previously been developed to infer the
structural characteristics of such high free-energy or transition
states. Herein we propose that one (or few) appropriately placed backbone
and/or side chain cross-linkers, such as disulfides, could be used
to populate a thermodynamically accessible conformational state that
mimics the folding transition state. Specifically, we test this hypothesis
on a model β-hairpin, Trpzip4, as its folding mechanism has
been extensively studied and is well understood. Our results show
that cross-linking the two β-strands near the turn region increases
the folding rate by an order of magnitude, to about (500 ns)−1, whereas cross-linking the termini results in a hyperstable β-hairpin
that has essentially the same folding rate as the uncross-linked peptide.
Taken together, these findings suggest that cross-linking is not only
a useful strategy to manipulate folding free energy barriers, as shown
in other studies, but also, in some cases, it can be used to stabilize
a folding transition state analogue and allow for direct assessment
of the folding process on the downhill side of the free energy barrier.
The calculated free energy landscape of the cross-linked Trpzip4 also
supports this picture. An empirical analysis further suggests, when
folding of β-hairpins does not involve a significant free energy
barrier, the folding time (τ) follows a power law dependence
on the number of hydrogen bonds to be formed (nH), namely, τ = τ0nHα, with
τ0 = 20 ns and α = 2.3.
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Affiliation(s)
- Beatrice N Markiewicz
- Department of Chemistry and ‡Department of Biochemistry and Biophysics, University of Pennsylvania , Philadelphia, Pennsylvania 19104, United States
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46
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Nayar D, Chakravarty C. Sensitivity of local hydration behaviour and conformational preferences of peptides to choice of water model. Phys Chem Chem Phys 2014; 16:10199-213. [DOI: 10.1039/c3cp55147d] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Secondary structural preferences of the beta-hairpin of the 2GB1 protein in the folded and unfolded ensembles are shown to be sensitive to the choice of water model.
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Affiliation(s)
- Divya Nayar
- Department of Chemistry
- Indian Institute of Technology-Delhi
- New Delhi: 110016, India
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47
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Shao Q, Wang J, Shi J, Zhu W. The universality of β-hairpin misfolding indicated by molecular dynamics simulations. J Chem Phys 2013; 139:165103. [DOI: 10.1063/1.4826461] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
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48
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Pincus DL, Thirumalai D. Force-induced unzipping transitions in an athermal crowded environment. J Phys Chem B 2013; 117:13107-14. [PMID: 23789729 DOI: 10.1021/jp402922q] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Using theoretical arguments and extensive Monte Carlo (MC) simulations of a coarse-grained three-dimensional off-lattice model of a β-hairpin, we demonstrate that the equilibrium critical force, Fc, needed to unfold the biopolymer increases nonlinearly with increasing volume fraction occupied by the spherical macromolecular crowding agent. Both scaling arguments and MC simulations show that the critical force increases as Fc ≈ φc(α). The exponent α is linked to the Flory exponent relating the size of the unfolded state of the biopolymer and the number of amino acids. The predicted power law dependence is confirmed in simulations of the dependence of the isothermal extensibility and the fraction of native contacts on φc. We also show using MC simulations that Fc is linearly dependent on the average osmotic pressure (P) exerted by the crowding agents on the β-hairpin. The highly significant linear correlation coefficient of 0.99657 between Fc and P makes it straightforward to predict the dependence of the critical force on the density of crowders. Our predictions are amenable to experimental verification using laser optical tweezers.
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Affiliation(s)
- David L Pincus
- Institute for Physical Science and Technology, University of Maryland , College Park, Maryland 20742, United States
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49
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Lee J. Exact partition function zeros of the Wako-Saitô-Muñoz-Eaton β hairpin model. PHYSICAL REVIEW. E, STATISTICAL, NONLINEAR, AND SOFT MATTER PHYSICS 2013; 88:022710. [PMID: 24032867 DOI: 10.1103/physreve.88.022710] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/01/2013] [Indexed: 06/02/2023]
Abstract
I compute exact partition function zeros of β hairpins, using both analytic and numerical methods, extending previous work [J. Lee, Phys. Rev. Lett. 110, 248101 (2013)] where only a restricted class of hairpins was considered. The zeros of β hairpins with an odd number of peptide bonds are computed and the difference of the distribution of zeros from those for an even number of peptide bonds is explained in terms of additional entropy of liberating the extra bond at the turn region. Upon the introduction of a hydrophobic core in the central region of the hairpin, the zeros are distributed uniformly on two concentric circles corresponding to the hydrophobic collapse and the transition to the fully folded conformation. One of the circles dissolves as the core moves toward the turn or the tip region, which is explained in terms of the similarity of the intermediate state with the folded or unfolded states. The exact partition function zeros for a hairpin with a more complex structure of native contacts, the 16 C-terminal residues of streptococcal protein G B1, are numerically computed and their loci are closely approximated by concentric circles.
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Affiliation(s)
- Julian Lee
- Department of Bioinformatics and Life Science, Soongsil University, Seoul 156-743, Korea
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50
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Nayar D, Chakravarty C. Water and water-like liquids: relationships between structure, entropy and mobility. Phys Chem Chem Phys 2013; 15:14162-77. [PMID: 23892732 DOI: 10.1039/c3cp51114f] [Citation(s) in RCA: 61] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Liquids with very diverse underlying interactions share the thermodynamic and transport anomalies of water, including metalloids, ionic melts and mesoscopic fluids. The generic feature that characterises such water-like liquids is a density-driven shift in the nature of local order in the condensed phases. The key semiquantitative relationships between structural order, thermodynamics and transport that are necessary in order to map out the consequences of this common qualitative feature for liquid-state properties and phase transformations of such systems are reviewed here. The application of these ideas to understand and model tetrahedral liquids, especially water, is discussed and possible extensions to other complex fluids are considered.
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Affiliation(s)
- Divya Nayar
- Department of Chemistry, Indian Institute of Technology-Delhi, New Delhi, 110016, India
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