1
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Rapallo A. Fractional Extended Diffusion Theory to capture anomalous relaxation from biased/accelerated molecular simulations. J Chem Phys 2024; 160:084114. [PMID: 38421066 DOI: 10.1063/5.0189518] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2023] [Accepted: 02/06/2024] [Indexed: 03/02/2024] Open
Abstract
Biased and accelerated molecular simulations (BAMS) are widely used tools to observe relevant molecular phenomena occurring on time scales inaccessible to standard molecular dynamics, but evaluation of the physical time scales involved in the processes is not directly possible from them. For this reason, the problem of recovering dynamics from such kinds of simulations is the object of very active research due to the relevant theoretical and practical implications of dynamics on the properties of both natural and synthetic molecular systems. In a recent paper [A. Rapallo et al., J. Comput. Chem. 42, 586-599 (2021)], it has been shown how the coupling of BAMS (which destroys the dynamics but allows to calculate average properties) with Extended Diffusion Theory (EDT) (which requires input appropriate equilibrium averages calculated over the BAMS trajectories) allows to effectively use the Smoluchowski equation to calculate the orientational time correlation function of the head-tail unit vector defined over a peptide in water solution. Orientational relaxation of this vector is the result of the coupling of internal molecular motions with overall molecular rotation, and it was very well described by correlation functions expressed in terms of weighted sums of suitable time-exponentially decaying functions, in agreement with a Brownian diffusive regime. However, situations occur where exponentially decaying functions are no longer appropriate to capture the actual dynamical behavior, which exhibits persistent long time correlations, compatible with the so called subdiffusive regimes. In this paper, a generalization of EDT will be given, exploiting a fractional Smoluchowski equation (FEDT) to capture the non-exponential character observed in the relaxation of intramolecular distances and molecular radius of gyration, whose dynamics depend on internal molecular motions only. The calculation methods, proper to EDT, are adapted to implement the generalization of the theory, and the resulting algorithm confirms FEDT as a tool of practical value in recovering dynamics from BAMS, to be used in general situations, involving both regular and anomalous diffusion regimes.
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Affiliation(s)
- Arnaldo Rapallo
- CNR - Istituto di Scienze e Tecnologie Chimiche "Giulio Natta" (SCITEC), via A. Corti 12, I-20133 Milano, Italy
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2
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Sormani G, Korde A, Rodriguez A, Denecke M, Hassanali A. Zirconium Coordination Chemistry and Its Role in Optimizing Hydroxymate Chelation: Insights from Molecular Dynamics. ACS OMEGA 2023; 8:36032-36042. [PMID: 37810634 PMCID: PMC10552493 DOI: 10.1021/acsomega.3c04083] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/09/2023] [Accepted: 09/04/2023] [Indexed: 10/10/2023]
Abstract
In the past decade, there has been a growth in using Zirconium-89 (89Zr) as a radionuclide in nuclear medicine for cancer diagnostic imaging and drug discovery processes. Although one of the most popular chelators for 89Zr, desferrioxamine (DFO) is typically presented as a hexadentate ligand, our work suggests a different scenario. The coordination structure of the Zr4+-DFO complex has primarily been informed by DFT-based calculations, which typically ignore temperature and therefore entropic and dynamic solvent effects. In this work, free energy calculations using molecular dynamics simulations, where the conformational fluctuations of both the ligand and the solvent are explicitly included, are used to compare the binding of Zr4+ cations with two different chelators, DFO and 4HMS, the latter of which is an octadentate ligand that has been recently proposed as a better chelator due to the presence of four hydroxymate groups. We find that thermally induced disorder leads to an open hexadentate chelate structure of the Zr4+-DFO complex, leaving the Zr4+ metal exposed to the solvent. A stable coordination of Zr4+ with 4HMS, however, is formed by involving both hydroxamate groups and water molecules in a more closely packed structure.
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Affiliation(s)
- Giulia Sormani
- The
“Abdus Salam” International Centre for Theoretical Physics, I-34151 Trieste, Italy
| | - Aruna Korde
- International
Atomic Energy Agency, A-1400 Vienna, Austria
| | - Alex Rodriguez
- Dipartimento
di Matematica e Geoscienze, University of
Trieste, 34127 Trieste, Italy
| | | | - Ali Hassanali
- The
“Abdus Salam” International Centre for Theoretical Physics, I-34151 Trieste, Italy
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3
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Eldrid C, Cragnolini T, Ben-Younis A, Zou J, Raleigh DP, Thalassinos K. Linking Gas-Phase and Solution-Phase Protein Unfolding via Mobile Proton Simulations. Anal Chem 2022; 94:16113-16121. [DOI: 10.1021/acs.analchem.2c03352] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Charles Eldrid
- School of Biological Sciences, University of Southampton, SouthamptonSO16 1BJ, U.K
- Institute of Structural and Molecular Biology, Division of Bioscience, University College London, LondonWC1E 6BT, U.K
| | - Tristan Cragnolini
- Institute of Structural and Molecular Biology, Birkbeck College, University of London, LondonWC1E 7HX, U.K
| | - Aisha Ben-Younis
- Institute of Structural and Molecular Biology, Division of Bioscience, University College London, LondonWC1E 6BT, U.K
| | - Junjie Zou
- Department of Chemistry, Stony Brook University, 100 Nicolls Rd., Stony Brook, New York11794, United States
| | - Daniel P. Raleigh
- Institute of Structural and Molecular Biology, Division of Bioscience, University College London, LondonWC1E 6BT, U.K
- Department of Chemistry, Stony Brook University, 100 Nicolls Rd., Stony Brook, New York11794, United States
| | - Konstantinos Thalassinos
- Institute of Structural and Molecular Biology, Division of Bioscience, University College London, LondonWC1E 6BT, U.K
- Institute of Structural and Molecular Biology, Birkbeck College, University of London, LondonWC1E 7HX, U.K
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4
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Kameda T, Awazu A, Togashi Y. Molecular dynamics analysis of biomolecular systems including nucleic acids. Biophys Physicobiol 2022; 19:e190027. [DOI: 10.2142/biophysico.bppb-v19.0027] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Accepted: 08/18/2022] [Indexed: 12/01/2022] Open
Affiliation(s)
| | - Akinori Awazu
- Graduate School of Integrated Sciences for Life, Hiroshima University
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5
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Energy landscapes of perfect and defective solids: from structure prediction to ion conduction. Theor Chem Acc 2021. [DOI: 10.1007/s00214-021-02834-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
AbstractThe energy landscape concept is increasingly valuable in understanding and unifying the structural, thermodynamic and dynamic properties of inorganic solids. We present a range of examples which include (i) structure prediction of new bulk phases including carbon nitrides, phosphorus carbides, LiMgF3 and low-density, ultra-flexible polymorphs of B2O3, (ii) prediction of graphene and related forms of ZnO, ZnS and other compounds which crystallise in the bulk with the wurtzite structure, (iii) solid solutions, (iv) understanding grossly non-stoichiometric oxides including the superionic phases of δ-Bi2O3 and BIMEVOX and the consequences for the mechanisms of ion transport in these fast ion conductors. In general, examination of the energy landscapes of disordered materials highlights the importance of local structural environments, rather than sole consideration of the average structure.
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6
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Kamenik AS, Handle PH, Hofer F, Kahler U, Kraml J, Liedl KR. Polarizable and non-polarizable force fields: Protein folding, unfolding, and misfolding. J Chem Phys 2021; 153:185102. [PMID: 33187403 DOI: 10.1063/5.0022135] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
Molecular dynamics simulations are an invaluable tool to characterize the dynamic motions of proteins in atomistic detail. However, the accuracy of models derived from simulations inevitably relies on the quality of the underlying force field. Here, we present an evaluation of current non-polarizable and polarizable force fields (AMBER ff14SB, CHARMM 36m, GROMOS 54A7, and Drude 2013) based on the long-standing biophysical challenge of protein folding. We quantify the thermodynamics and kinetics of the β-hairpin formation using Markov state models of the fast-folding mini-protein CLN025. Furthermore, we study the (partial) folding dynamics of two more complex systems, a villin headpiece variant and a WW domain. Surprisingly, the polarizable force field in our set, Drude 2013, consistently leads to destabilization of the native state, regardless of the secondary structure element present. All non-polarizable force fields, on the other hand, stably characterize the native state ensembles in most cases even when starting from a partially unfolded conformation. Focusing on CLN025, we find that the conformational space captured with AMBER ff14SB and CHARMM 36m is comparable, but the ensembles from CHARMM 36m simulations are clearly shifted toward disordered conformations. While the AMBER ff14SB ensemble overstabilizes the native fold, CHARMM 36m and GROMOS 54A7 ensembles both agree remarkably well with experimental state populations. In addition, GROMOS 54A7 also reproduces experimental folding times most accurately. Our results further indicate an over-stabilization of helical structures with AMBER ff14SB. Nevertheless, the presented investigations strongly imply that reliable (un)folding dynamics of small proteins can be captured in feasible computational time with current additive force fields.
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Affiliation(s)
- Anna S Kamenik
- Institute of General, Inorganic and Theoretical Chemistry, University of Innsbruck, Innrain 80/82, A-6020 Innsbruck, Austria
| | - Philip H Handle
- Institute of General, Inorganic and Theoretical Chemistry, University of Innsbruck, Innrain 80/82, A-6020 Innsbruck, Austria
| | - Florian Hofer
- Institute of General, Inorganic and Theoretical Chemistry, University of Innsbruck, Innrain 80/82, A-6020 Innsbruck, Austria
| | - Ursula Kahler
- Institute of General, Inorganic and Theoretical Chemistry, University of Innsbruck, Innrain 80/82, A-6020 Innsbruck, Austria
| | - Johannes Kraml
- Institute of General, Inorganic and Theoretical Chemistry, University of Innsbruck, Innrain 80/82, A-6020 Innsbruck, Austria
| | - Klaus R Liedl
- Institute of General, Inorganic and Theoretical Chemistry, University of Innsbruck, Innrain 80/82, A-6020 Innsbruck, Austria
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7
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Xia C, He X, Wang J, Wang W. Origin of subdiffusions in proteins: Insight from peptide systems. Phys Rev E 2020; 102:062424. [PMID: 33466075 DOI: 10.1103/physreve.102.062424] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2020] [Accepted: 11/30/2020] [Indexed: 11/07/2022]
Abstract
Subdiffusive kinetics are popular in proteins and peptides as observed in experiments and simulations. For protein systems with diverse interactions, are there multiple mechanisms to produce the common subdiffusion behavior? To approach this problem, long trajectories of two model peptides are simulated to study the mechanism of subdiffusion and the relations with their interactions. The free-energy profiles and the subdiffusive kinetics are observed for these two peptides. A hierarchical plateau analysis is employed to extract the features of the landscape from the mean square of displacement. The mechanism of subdiffusions can be postulated by comparing the exponents by simulations with those based on various models. The results indicate that the mechanisms of these two peptides are different and are related to the characteristics of their energy landscapes. The subdiffusion of the flexible peptide is mainly caused by depth distribution of traps on the energy landscape, while the subdiffusion of the helical peptide is attributed to the fractal topology of local minima on the landscape. The emergence of these different mechanisms reflects different kinetic scenarios in peptide systems though the peptides behave in a similar way of diffusion. To confirm these ideas, the transition networks between various conformations of these peptides are generated. Based on the network description, the controlled kinetics based only on the topology of the networks are calculated and compared with the results based on simulations. For the flexible peptide, the feature of controlled diffusion is distinct from that of simulation, and for the helical peptide, two kinds of kinetics have a similar exponent of subdiffusion. These results further exemplify the importance of the landscape topology in the kinetics of structural proteins and the effect of depth distribution of traps for the subdiffusion of disordered peptides.
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Affiliation(s)
- Chenliang Xia
- School of Physics, Nanjing University, Nanjing 210093, People's Republic of China and National Laboratory of Solid State Microstructure, and Collaborative Innovation Center of Advanced Microstructures, Nanjing University, Nanjing 210093, People's Republic of China
| | - Xuefeng He
- School of Physics, Nanjing University, Nanjing 210093, People's Republic of China and National Laboratory of Solid State Microstructure, and Collaborative Innovation Center of Advanced Microstructures, Nanjing University, Nanjing 210093, People's Republic of China
| | - Jun Wang
- School of Physics, Nanjing University, Nanjing 210093, People's Republic of China and National Laboratory of Solid State Microstructure, and Collaborative Innovation Center of Advanced Microstructures, Nanjing University, Nanjing 210093, People's Republic of China
| | - Wei Wang
- School of Physics, Nanjing University, Nanjing 210093, People's Republic of China and National Laboratory of Solid State Microstructure, and Collaborative Innovation Center of Advanced Microstructures, Nanjing University, Nanjing 210093, People's Republic of China
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8
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Wang Z, Zhou X, Zuo G. EspcTM: Kinetic Transition Network Based on Trajectory Mapping in Effective Energy Rescaling Space. Front Mol Biosci 2020; 7:589718. [PMID: 33195438 PMCID: PMC7653181 DOI: 10.3389/fmolb.2020.589718] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2020] [Accepted: 09/24/2020] [Indexed: 11/27/2022] Open
Abstract
The transition network provides a key to reveal the thermodynamic and kinetic properties of biomolecular systems. In this paper, we introduce a new method, named effective energy rescaling space trajectory mapping (EspcTM), to detect metastable states and construct transition networks based on the simulation trajectories of the complex biomolecular system. It mapped simulation trajectories into an orthogonal function space, whose bases were rescaled by effective energy, and clustered the interrelation between these trajectories to locate metastable states. By using the EspcTM method, we identified the metastable states and elucidated interstate transition kinetics of a Brownian particle and a dodecapeptide. It was found that the scaling parameters of effective energy also provided a clue to the dominating factors in dynamics. We believe that the EspcTM method is a useful tool for the studies of dynamics of the complex system and may provide new insight into the understanding of thermodynamics and kinetics of biomolecular systems.
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Affiliation(s)
- Zhenyu Wang
- T-Life Research Center, State Key Laboratory of Surface Physics, Department of Physics, Fudan University, Shanghai, China
| | - Xin Zhou
- School of Physical Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Guanghong Zuo
- T-Life Research Center, State Key Laboratory of Surface Physics, Department of Physics, Fudan University, Shanghai, China
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9
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Sharpe DJ, Wales DJ. Efficient and exact sampling of transition path ensembles on Markovian networks. J Chem Phys 2020; 153:024121. [DOI: 10.1063/5.0012128] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Affiliation(s)
- Daniel J. Sharpe
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, United Kingdom
| | - David J. Wales
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, United Kingdom
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10
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Sharpe DJ, Wales DJ. Identifying mechanistically distinct pathways in kinetic transition networks. J Chem Phys 2019; 151:124101. [DOI: 10.1063/1.5111939] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Daniel J. Sharpe
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, United Kingdom
| | - David J. Wales
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, United Kingdom
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11
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Kang J, Pae C, Park HJ. Graph-theoretical analysis for energy landscape reveals the organization of state transitions in the resting-state human cerebral cortex. PLoS One 2019; 14:e0222161. [PMID: 31498822 PMCID: PMC6733463 DOI: 10.1371/journal.pone.0222161] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2019] [Accepted: 08/22/2019] [Indexed: 11/19/2022] Open
Abstract
The resting-state brain is often considered a nonlinear dynamic system transitioning among multiple coexisting stable states. Despite the increasing number of studies on the multistability of the brain system, the processes of state transitions have rarely been systematically explored. Thus, we investigated the state transition processes of the human cerebral cortex system at rest by introducing a graph-theoretical analysis of the state transition network. The energy landscape analysis of brain state occurrences, estimated using the pairwise maximum entropy model for resting-state fMRI data, identified multiple local minima, some of which mediate multi-step transitions toward the global minimum. The state transition among local minima is clustered into two groups according to state transition rates and most inter-group state transitions were mediated by a hub transition state. The distance to the hub transition state determined the path length of the inter-group transition. The cortical system appeared to have redundancy in inter-group transitions when the hub transition state was removed. Such a hub-like organization of transition processes disappeared when the connectivity of the cortical system was altered from the resting-state configuration. In the state transition, the default mode network acts as a transition hub, while coactivation of the prefrontal cortex and default mode network is captured as the global minimum. In summary, the resting-state cerebral cortex has a well-organized architecture of state transitions among stable states, when evaluated by a graph-theoretical analysis of the nonlinear state transition network of the brain.
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Affiliation(s)
- Jiyoung Kang
- Center for Systems and Translational Brain Sciences, Institute of Human Complexity and Systems Science, Yonsei University, Seoul, Republic of Korea
- Department of Nuclear Medicine, Yonsei University College of Medicine, Seoul, Republic of Korea
| | - Chongwon Pae
- Department of Nuclear Medicine, Yonsei University College of Medicine, Seoul, Republic of Korea
| | - Hae-Jeong Park
- Center for Systems and Translational Brain Sciences, Institute of Human Complexity and Systems Science, Yonsei University, Seoul, Republic of Korea
- Department of Nuclear Medicine, Yonsei University College of Medicine, Seoul, Republic of Korea
- BK21 PLUS Project for Medical Science, Yonsei University College of Medicine, Seoul, Republic of Korea
- Department of Cognitive Science, Yonsei University, Seoul, Republic of Korea
- * E-mail:
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12
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Nagel D, Weber A, Lickert B, Stock G. Dynamical coring of Markov state models. J Chem Phys 2019; 150:094111. [DOI: 10.1063/1.5081767] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023] Open
Affiliation(s)
- Daniel Nagel
- Biomolecular Dynamics, Institute of Physics, Albert Ludwigs University, 79104 Freiburg, Germany
| | - Anna Weber
- Biomolecular Dynamics, Institute of Physics, Albert Ludwigs University, 79104 Freiburg, Germany
| | - Benjamin Lickert
- Biomolecular Dynamics, Institute of Physics, Albert Ludwigs University, 79104 Freiburg, Germany
| | - Gerhard Stock
- Biomolecular Dynamics, Institute of Physics, Albert Ludwigs University, 79104 Freiburg, Germany
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13
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El Hage K, Mondal P, Meuwly M. Free energy simulations for protein ligand binding and stability. MOLECULAR SIMULATION 2018. [DOI: 10.1080/08927022.2017.1416115] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- Krystel El Hage
- Department of Chemistry, University of Basel , Basel, Switzerland
| | - Padmabati Mondal
- Department of Chemistry, University of Basel , Basel, Switzerland
| | - Markus Meuwly
- Department of Chemistry, University of Basel , Basel, Switzerland
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14
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El Hage K, Brickel S, Hermelin S, Gaulier G, Schmidt C, Bonacina L, van Keulen SC, Bhattacharyya S, Chergui M, Hamm P, Rothlisberger U, Wolf JP, Meuwly M. Implications of short time scale dynamics on long time processes. STRUCTURAL DYNAMICS (MELVILLE, N.Y.) 2017; 4:061507. [PMID: 29308419 PMCID: PMC5741438 DOI: 10.1063/1.4996448] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/17/2017] [Accepted: 09/15/2017] [Indexed: 05/02/2023]
Abstract
This review provides a comprehensive overview of the structural dynamics in topical gas- and condensed-phase systems on multiple length and time scales. Starting from vibrationally induced dissociation of small molecules in the gas phase, the question of vibrational and internal energy redistribution through conformational dynamics is further developed by considering coupled electron/proton transfer in a model peptide over many orders of magnitude. The influence of the surrounding solvent is probed for electron transfer to the solvent in hydrated I-. Next, the dynamics of a modified PDZ domain over many time scales is analyzed following activation of a photoswitch. The hydration dynamics around halogenated amino acid side chains and their structural dynamics in proteins are relevant for iodinated TyrB26 insulin. Binding of nitric oxide to myoglobin is a process for which experimental and computational analyses have converged to a common view which connects rebinding time scales and the underlying dynamics. Finally, rhodopsin is a paradigmatic system for multiple length- and time-scale processes for which experimental and computational methods provide valuable insights into the functional dynamics. The systems discussed here highlight that for a comprehensive understanding of how structure, flexibility, energetics, and dynamics contribute to functional dynamics, experimental studies in multiple wavelength regions and computational studies including quantum, classical, and more coarse grained levels are required.
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Affiliation(s)
- Krystel El Hage
- Department of Chemistry, University of Basel, Klingelbergstrasse 80, 4056 Basel, Switzerland
| | - Sebastian Brickel
- Department of Chemistry, University of Basel, Klingelbergstrasse 80, 4056 Basel, Switzerland
| | - Sylvain Hermelin
- Department of Applied Physics (GAP), University of Geneva, 22 Ch. de Pinchat, 1211 Geneva 4, Switzerland
| | - Geoffrey Gaulier
- Department of Applied Physics (GAP), University of Geneva, 22 Ch. de Pinchat, 1211 Geneva 4, Switzerland
| | - Cédric Schmidt
- Department of Applied Physics (GAP), University of Geneva, 22 Ch. de Pinchat, 1211 Geneva 4, Switzerland
| | - Luigi Bonacina
- Department of Applied Physics (GAP), University of Geneva, 22 Ch. de Pinchat, 1211 Geneva 4, Switzerland
| | - Siri C van Keulen
- Institute of Chemical Sciences and Engineering, EPFL, Lausanne, Switzerland
| | | | - Majed Chergui
- Institute of Chemical Sciences and Engineering, EPFL, Lausanne, Switzerland
| | - Peter Hamm
- Department of Chemistry, University of Zurich, Zurich, Switzerland
| | | | - Jean-Pierre Wolf
- Department of Applied Physics (GAP), University of Geneva, 22 Ch. de Pinchat, 1211 Geneva 4, Switzerland
| | - Markus Meuwly
- Department of Chemistry, University of Basel, Klingelbergstrasse 80, 4056 Basel, Switzerland
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15
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Meroz Y, Ovchinnikov V, Karplus M. Coexisting origins of subdiffusion in internal dynamics of proteins. Phys Rev E 2017; 95:062403. [PMID: 28709262 DOI: 10.1103/physreve.95.062403] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2016] [Indexed: 11/07/2022]
Abstract
Subdiffusion in conformational dynamics of proteins is observed both experimentally and in simulations. Although its origin has been attributed to multiple mechanisms, including trapping on a rugged energy landscape, fractional Brownian noise, or a fractal topology of the energy landscape, it is unclear which of these, if any, is most relevant. To obtain insights into the actual mechanism, we introduce an analytically tractable hierarchical trapping model and apply it to molecular dynamics simulation trajectories of three proteins in solution. The analysis of the simulations introduces a subdiffusive exponent that varies with time and associates plateaus in the mean-squared displacement with traps on the energy landscape. This analysis permits us to separate the component of subdiffusion due to a trapping mechanism from that due to an underlying fluctuating process, such as fractional Brownian motion. The present results thus provide insights concerning the physical origin of subdiffusion in the dynamics of proteins.
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Affiliation(s)
- Yasmine Meroz
- Harvard University, School of Engineering and Applied Sciences, Cambridge, Massachusetts 02138, USA
| | - Victor Ovchinnikov
- Harvard University, Department of Chemistry and Chemical Biology, Cambridge, Massachusetts 02138, USA
| | - Martin Karplus
- Harvard University, Department of Chemistry and Chemical Biology, Cambridge, Massachusetts 02138, USA.,Laboratoire de Chimie Biophysique, ISIS, Université de Strasbourg, 67000 Strasbourg, France
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16
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Zhang C, Yu J, Zhou X. Imaging Metastable States and Transitions in Proteins by Trajectory Map. J Phys Chem B 2017; 121:4678-4686. [PMID: 28425289 DOI: 10.1021/acs.jpcb.7b00664] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
It has been a long-standing and intriguing issue to develop robust methods to identify metastable states and interstate transitions from simulations or experimental data to understand the functional conformational changes of proteins. It is usually hard to define the complicated boundaries of the states in the conformational space using most of the existing methods, and they often lead to parameter-sensitive results. Here, we present a new approach, visualized Trajectory Map (vTM), to identify the metastable states and the rare interstate transitions, by considering both the conformational similarity and the temporal successiveness of conformations. The vTM is able to give a nonambiguous description of slow dynamics. The case study of a β-hairpin peptide shows that the vTM can reveal the states and transitions from all-atom MD trajectory data even when a single observable (i.e, one-dimensional reaction coordinate) is used. We also use the vTM to refine the folding/unfolding mechanism of HP35 in explicit water by analyzing a 125 μs all-atom MD trajectory and obtain folding/unfolding rates of about 1/μs, which are in good agreement with the experimental values.
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Affiliation(s)
- Chuanbiao Zhang
- School of Physical Sciences, University of Chinese Academy of Sciences , Beijing 100049, China
| | - Jin Yu
- Beijing Computer Science Research Center , Beijing 100193, China
| | - Xin Zhou
- School of Physical Sciences, University of Chinese Academy of Sciences , Beijing 100049, China
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17
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Liao Q, Owen MC, Olubiyi OO, Barz B, Strodel B. Conformational Transitions of the Amyloid-β Peptide Upon Copper(II) Binding and pH Changes. Isr J Chem 2017. [DOI: 10.1002/ijch.201600108] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Affiliation(s)
- Qinghua Liao
- Institute of Complex Systems: Structural Biochemistry (ICS-6); Forschungszentrum Jülich GmbH; 52425 Jülich Germany
| | - Michael C. Owen
- Institute of Complex Systems: Structural Biochemistry (ICS-6); Forschungszentrum Jülich GmbH; 52425 Jülich Germany
| | - Olujide O. Olubiyi
- Department of Pharmacology and Therapeutics; College of Medicine and Health Sciences; Afe Babalola University; Nigeria
| | - Bogdan Barz
- Institute of Complex Systems: Structural Biochemistry (ICS-6); Forschungszentrum Jülich GmbH; 52425 Jülich Germany
- Institute of Theoretical and Computational Chemistry; Heinrich Heine University Düsseldorf; 40225 Düsseldorf Germany
| | - Birgit Strodel
- Institute of Complex Systems: Structural Biochemistry (ICS-6); Forschungszentrum Jülich GmbH; 52425 Jülich Germany
- Institute of Theoretical and Computational Chemistry; Heinrich Heine University Düsseldorf; 40225 Düsseldorf Germany
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18
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Taraphder S, Maupin CM, Swanson JJ, Voth GA. Coupling Protein Dynamics with Proton Transport in Human Carbonic Anhydrase II. J Phys Chem B 2016; 120:8389-404. [PMID: 27063577 PMCID: PMC5003118 DOI: 10.1021/acs.jpcb.6b02166] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2016] [Revised: 04/06/2016] [Indexed: 11/28/2022]
Abstract
The role of protein dynamics in enzyme catalysis is one of the most highly debated topics in enzymology. The main controversy centers around what may be defined as functionally significant conformational fluctuations and how, if at all, these fluctuations couple to enzyme catalyzed events. To shed light on this debate, the conformational dynamics along the transition path surmounting the highest free energy barrier have been herein investigated for the rate limiting proton transport event in human carbonic anhydrase (HCA) II. Special attention has been placed on whether the motion of an excess proton is correlated with fluctuations in the surrounding protein and solvent matrix, which may be rare on the picosecond and subpicosecond time scales of molecular motions. It is found that several active site residues, which do not directly participate in the proton transport event, have a significant impact on the dynamics of the excess proton. These secondary participants are shown to strongly influence the active site environment, resulting in the creation of water clusters that are conducive to fast, moderately slow, or slow proton transport events. The identification and characterization of these secondary participants illuminates the role of protein dynamics in the catalytic efficiency of HCA II.
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Affiliation(s)
- Srabani Taraphder
- Department
of Chemistry, Indian Institute of Technology, Kharagpur 721302, India
| | - C. Mark Maupin
- Department
of Chemical and Biological Engineering, Colorado School of Mines, 1500 Illinois Street, Golden, Colorado 80401, United
States
| | - Jessica
M. J. Swanson
- Department
of Chemistry, Institute for Biophysical Dynamics, James Frank Institute,
and Computation Institute, University of
Chicago, 5735 South Ellis
Avenue, Chicago, Illinois 60637, United States
| | - Gregory A. Voth
- Department
of Chemistry, Institute for Biophysical Dynamics, James Frank Institute,
and Computation Institute, University of
Chicago, 5735 South Ellis
Avenue, Chicago, Illinois 60637, United States
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19
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Abramyan TM, Snyder JA, Thyparambil AA, Stuart SJ, Latour RA. Cluster analysis of molecular simulation trajectories for systems where both conformation and orientation of the sampled states are important. J Comput Chem 2016; 37:1973-82. [PMID: 27292100 DOI: 10.1002/jcc.24416] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2016] [Accepted: 05/17/2016] [Indexed: 01/28/2023]
Abstract
Clustering methods have been widely used to group together similar conformational states from molecular simulations of biomolecules in solution. For applications such as the interaction of a protein with a surface, the orientation of the protein relative to the surface is also an important clustering parameter because of its potential effect on adsorbed-state bioactivity. This study presents cluster analysis methods that are specifically designed for systems where both molecular orientation and conformation are important, and the methods are demonstrated using test cases of adsorbed proteins for validation. Additionally, because cluster analysis can be a very subjective process, an objective procedure for identifying both the optimal number of clusters and the best clustering algorithm to be applied to analyze a given dataset is presented. The method is demonstrated for several agglomerative hierarchical clustering algorithms used in conjunction with three cluster validation techniques. © 2016 Wiley Periodicals, Inc.
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Affiliation(s)
- Tigran M Abramyan
- Department of Bioengineering, 501 Rhodes Engineering Research Center, Clemson University, Clemson, South Carolina, 29634
| | - James A Snyder
- Department of Bioengineering, 501 Rhodes Engineering Research Center, Clemson University, Clemson, South Carolina, 29634
| | - Aby A Thyparambil
- Department of Bioengineering, 501 Rhodes Engineering Research Center, Clemson University, Clemson, South Carolina, 29634
| | - Steven J Stuart
- Department of Chemistry 369 Hunter Laboratory, Clemson University, Clemson, South Carolina, 29634
| | - Robert A Latour
- Department of Bioengineering, 501 Rhodes Engineering Research Center, Clemson University, Clemson, South Carolina, 29634
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20
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Liu H, Li M, Fan J, Huo S. Inherent structure versus geometric metric for state space discretization. J Comput Chem 2016; 37:1251-8. [PMID: 26915811 DOI: 10.1002/jcc.24315] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2015] [Revised: 11/17/2015] [Accepted: 01/06/2016] [Indexed: 01/13/2023]
Abstract
Inherent structure (IS) and geometry-based clustering methods are commonly used for analyzing molecular dynamics trajectories. ISs are obtained by minimizing the sampled conformations into local minima on potential/effective energy surface. The conformations that are minimized into the same energy basin belong to one cluster. We investigate the influence of the applications of these two methods of trajectory decomposition on our understanding of the thermodynamics and kinetics of alanine tetrapeptide. We find that at the microcluster level, the IS approach and root-mean-square deviation (RMSD)-based clustering method give totally different results. Depending on the local features of energy landscape, the conformations with close RMSDs can be minimized into different minima, while the conformations with large RMSDs could be minimized into the same basin. However, the relaxation timescales calculated based on the transition matrices built from the microclusters are similar. The discrepancy at the microcluster level leads to different macroclusters. Although the dynamic models established through both clustering methods are validated approximately Markovian, the IS approach seems to give a meaningful state space discretization at the macrocluster level in terms of conformational features and kinetics.
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Affiliation(s)
- Hanzhong Liu
- Gustaf H. Carlson School of Chemistry and Biochemistry, Clark University, 950 Main Street, Worcester, Massachusetts, 01610
| | - Minghai Li
- Gustaf H. Carlson School of Chemistry and Biochemistry, Clark University, 950 Main Street, Worcester, Massachusetts, 01610
| | - Jue Fan
- Gustaf H. Carlson School of Chemistry and Biochemistry, Clark University, 950 Main Street, Worcester, Massachusetts, 01610
| | - Shuanghong Huo
- Gustaf H. Carlson School of Chemistry and Biochemistry, Clark University, 950 Main Street, Worcester, Massachusetts, 01610
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21
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Kalescky R, Zhou H, Liu J, Tao P. Rigid Residue Scan Simulations Systematically Reveal Residue Entropic Roles in Protein Allostery. PLoS Comput Biol 2016; 12:e1004893. [PMID: 27115535 PMCID: PMC4846164 DOI: 10.1371/journal.pcbi.1004893] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2015] [Accepted: 04/01/2016] [Indexed: 12/22/2022] Open
Abstract
Intra-protein information is transmitted over distances via allosteric processes. This ubiquitous protein process allows for protein function changes due to ligand binding events. Understanding protein allostery is essential to understanding protein functions. In this study, allostery in the second PDZ domain (PDZ2) in the human PTP1E protein is examined as model system to advance a recently developed rigid residue scan method combining with configurational entropy calculation and principal component analysis. The contributions from individual residues to whole-protein dynamics and allostery were systematically assessed via rigid body simulations of both unbound and ligand-bound states of the protein. The entropic contributions of individual residues to whole-protein dynamics were evaluated based on covariance-based correlation analysis of all simulations. The changes of overall protein entropy when individual residues being held rigid support that the rigidity/flexibility equilibrium in protein structure is governed by the La Châtelier's principle of chemical equilibrium. Key residues of PDZ2 allostery were identified with good agreement with NMR studies of the same protein bound to the same peptide. On the other hand, the change of entropic contribution from each residue upon perturbation revealed intrinsic differences among all the residues. The quasi-harmonic and principal component analyses of simulations without rigid residue perturbation showed a coherent allosteric mode from unbound and bound states, respectively. The projection of simulations with rigid residue perturbation onto coherent allosteric modes demonstrated the intrinsic shifting of ensemble distributions supporting the population-shift theory of protein allostery. Overall, the study presented here provides a robust and systematic approach to estimate the contribution of individual residue internal motion to overall protein dynamics and allostery.
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Affiliation(s)
- Robert Kalescky
- Department of Chemistry, Center for Drug Discovery, Design, and Delivery (CD4), Center for Scientific Computation, Southern Methodist University, Dallas, Texas, United States of America
| | - Hongyu Zhou
- Department of Chemistry, Center for Drug Discovery, Design, and Delivery (CD4), Center for Scientific Computation, Southern Methodist University, Dallas, Texas, United States of America
| | - Jin Liu
- Department of Chemistry, Center for Drug Discovery, Design, and Delivery (CD4), Center for Scientific Computation, Southern Methodist University, Dallas, Texas, United States of America
- Department of Pharmaceutical Sciences, University of North Texas System College of Pharmacy, University of North Texas Health Science Center, Fort Worth, Texas, United States of America
- * E-mail: (JL); (PT)
| | - Peng Tao
- Department of Chemistry, Center for Drug Discovery, Design, and Delivery (CD4), Center for Scientific Computation, Southern Methodist University, Dallas, Texas, United States of America
- * E-mail: (JL); (PT)
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22
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Ilizaliturri-Flores I, Correa-Basurto J, Bello M, Rosas-Trigueros JL, Zamora-López B, Benítez-Cardoza CG, Zamorano-Carrillo A. Mapping the intrinsically disordered properties of the flexible loop domain of Bcl-2: a molecular dynamics simulation study. J Mol Model 2016; 22:98. [PMID: 27037822 DOI: 10.1007/s00894-016-2940-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2015] [Accepted: 02/22/2016] [Indexed: 02/07/2023]
Abstract
Most of the B-cell lymphoma-2 (Bcl-2) protein structure has been elucidated; however, the conformation of its flexible loop domain (FLD) has not yet been experimentally predicted. Its high flexibility under physiological conditions is the reason. FLD behaves as an intrinsically disordered region (IDR) and can adopt regular structures in particular conditions associated with the control of Bcl-2's anti-apoptotic functions. In a previous contribution, we analyzed an engineered Bcl-2 construct (Bcl-2-Δ22Σ3) submitted to 25-ns MD and reported a disordered-to-helix transitions in a region of FLD (rFLD, residues 60-77). However, the conformational preferences in solution of rFLD in the nanosecond to microsecond scale were not analyzed. Herein, an average model was obtained for the native Bcl-2 protein by homology modeling and MD simulation techniques. From this, only the atomic coordinates corresponding to the rFLD were simulated for 1 μs by MD at 310 K. In concordance with previous studies, a disordered-to-helix transitions were exhibited, implying that this "interconversion of folding" in the rFLD suggest a possible set of conformations encoded in its sequence. Principal component analysis (PCA) showed that most of the conformational fluctuation of Bcl-2 is provided by rFLD. Dihedral PCA (dPCA) offered information about all the conformations of rFLD in the μs of the simulation, characterizing a dPCA-based free energy landscape of rFLD, and a conformational ensemble of fast interconverting conformations as other IDRs. Furthermore, despite the conformational heterogeneity of rFLD, the analysis of the dihedral angles (Φ, Ψ) showed that this region does not randomly explore the conformational space in solution.
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Affiliation(s)
| | - José Correa-Basurto
- Lab de Modelado Molecular y Diseño de Fármacos. ESM-IPN, Ciudad de México, Mexico
| | - Martiniano Bello
- Lab de Modelado Molecular y Diseño de Fármacos. ESM-IPN, Ciudad de México, Mexico
| | - Jorge L Rosas-Trigueros
- Lab Transdisciplinario de Investigación en Sistemas Evolutivos, ESCOM-IPN, Ciudad de México, Mexico
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23
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Cazade PA, Zheng W, Prada-Gracia D, Berezovska G, Rao F, Clementi C, Meuwly M. A comparative analysis of clustering algorithms: O2 migration in truncated hemoglobin I from transition networks. J Chem Phys 2015; 142:025103. [PMID: 25591387 DOI: 10.1063/1.4904431] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
The ligand migration network for O2-diffusion in truncated Hemoglobin N is analyzed based on three different clustering schemes. For coordinate-based clustering, the conventional k-means and the kinetics-based Markov Clustering (MCL) methods are employed, whereas the locally scaled diffusion map (LSDMap) method is a collective-variable-based approach. It is found that all three methods agree well in their geometrical definition of the most important docking site, and all experimentally known docking sites are recovered by all three methods. Also, for most of the states, their population coincides quite favourably, whereas the kinetics of and between the states differs. One of the major differences between k-means and MCL clustering on the one hand and LSDMap on the other is that the latter finds one large primary cluster containing the Xe1a, IS1, and ENT states. This is related to the fact that the motion within the state occurs on similar time scales, whereas structurally the state is found to be quite diverse. In agreement with previous explicit atomistic simulations, the Xe3 pocket is found to be a highly dynamical site which points to its potential role as a hub in the network. This is also highlighted in the fact that LSDMap cannot identify this state. First passage time distributions from MCL clusterings using a one- (ligand-position) and two-dimensional (ligand-position and protein-structure) descriptor suggest that ligand- and protein-motions are coupled. The benefits and drawbacks of the three methods are discussed in a comparative fashion and highlight that depending on the questions at hand the best-performing method for a particular data set may differ.
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Affiliation(s)
- Pierre-André Cazade
- Department of Chemistry, University of Basel, Klingelbergstrasse 80, CH-4056 Basel, Switzerland
| | - Wenwei Zheng
- Department of Chemistry, Rice University, 6100 Main St., Houston, Texas 77005, USA
| | - Diego Prada-Gracia
- School of Soft Matter Research, Freiburg Institute for Advanced Studies, Albertstrasse 19, 79104 Freiburg im Breisgau, Germany
| | - Ganna Berezovska
- Department of Chemistry, University of Basel, Klingelbergstrasse 80, CH-4056 Basel, Switzerland
| | - Francesco Rao
- School of Soft Matter Research, Freiburg Institute for Advanced Studies, Albertstrasse 19, 79104 Freiburg im Breisgau, Germany
| | - Cecilia Clementi
- Department of Chemistry, Rice University, 6100 Main St., Houston, Texas 77005, USA
| | - Markus Meuwly
- Department of Chemistry, University of Basel, Klingelbergstrasse 80, CH-4056 Basel, Switzerland
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24
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Systematically constructing kinetic transition network in polypeptide from top to down: trajectory mapping. PLoS One 2015; 10:e0125932. [PMID: 25962177 PMCID: PMC4427365 DOI: 10.1371/journal.pone.0125932] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2014] [Accepted: 03/24/2015] [Indexed: 11/23/2022] Open
Abstract
Molecular dynamics (MD) simulation is an important tool for understanding bio-molecules in microscopic temporal/spatial scales. Besides the demand in improving simulation techniques to approach experimental scales, it becomes more and more crucial to develop robust methodology for precisely and objectively interpreting massive MD simulation data. In our previous work [J Phys Chem B 114, 10266 (2010)], the trajectory mapping (TM) method was presented to analyze simulation trajectories then to construct a kinetic transition network of metastable states. In this work, we further present a top-down implementation of TM to systematically detect complicate features of conformational space. We first look at longer MD trajectory pieces to get a coarse picture of transition network at larger time scale, and then we gradually cut the trajectory pieces in shorter for more details. A robust clustering algorithm is designed to more effectively identify the metastable states and transition events. We applied this TM method to detect the hierarchical structure in the conformational space of alanine-dodeca-peptide from microsecond to nanosecond time scales. The results show a downhill folding process of the peptide through multiple pathways. Even in this simple system, we found that single common-used order parameter is not sufficient either in distinguishing the metastable states or predicting the transition kinetics among these states.
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25
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Jacobson D, Stratt RM. The inherent dynamics of a molecular liquid: geodesic pathways through the potential energy landscape of a liquid of linear molecules. J Chem Phys 2015; 140:174503. [PMID: 24811642 DOI: 10.1063/1.4872363] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
Because the geodesic pathways that a liquid follows through its potential energy landscape govern its slow, diffusive motion, we suggest that these pathways are logical candidates for the title of a liquid's "inherent dynamics." Like their namesake "inherent structures," these objects are simply features of the system's potential energy surface and thus provide views of the system's structural evolution unobstructed by thermal kinetic energy. This paper shows how these geodesic pathways can be computed for a liquid of linear molecules, allowing us to see precisely how such molecular liquids mix rotational and translational degrees of freedom into their dynamics. The ratio of translational to rotational components of the geodesic path lengths, for example, is significantly larger than would be expected on equipartition grounds, with a value that scales with the molecular aspect ratio. These and other features of the geodesics are consistent with a picture in which molecular reorientation adiabatically follows translation-molecules largely thread their way through narrow channels available in the potential energy landscape.
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Affiliation(s)
- Daniel Jacobson
- Department of Chemistry, Brown University, Providence, Rhode Island 02912, USA
| | - Richard M Stratt
- Department of Chemistry, Brown University, Providence, Rhode Island 02912, USA
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26
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Lu C, Prada-Gracia D, Rao F. Structure and dynamics of water in crowded environments slows down peptide conformational changes. J Chem Phys 2014; 141:045101. [DOI: 10.1063/1.4891465] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
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27
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Shevchuk R, Agmon N, Rao F. Network analysis of proton transfer in liquid water. J Chem Phys 2014; 140:244502. [DOI: 10.1063/1.4884455] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023] Open
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28
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Anoop A, Ranganathan S, Das Dhaked B, Jha NN, Pratihar S, Ghosh S, Sahay S, Kumar S, Das S, Kombrabail M, Agarwal K, Jacob RS, Singru P, Bhaumik P, Padinhateeri R, Kumar A, Maji SK. Elucidating the role of disulfide bond on amyloid formation and fibril reversibility of somatostatin-14: relevance to its storage and secretion. J Biol Chem 2014; 289:16884-903. [PMID: 24782311 DOI: 10.1074/jbc.m114.548354] [Citation(s) in RCA: 58] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
The storage of protein/peptide hormones within subcellular compartments and subsequent release are crucial for their native function, and hence these processes are intricately regulated in mammalian systems. Several peptide hormones were recently suggested to be stored as amyloids within endocrine secretory granules. This leads to an apparent paradox where storage requires formation of aggregates, and their function requires a supply of non-aggregated peptides on demand. The precise mechanism behind amyloid formation by these hormones and their subsequent release remain an open question. To address this, we examined aggregation and fibril reversibility of a cyclic peptide hormone somatostatin (SST)-14 using various techniques. After proving that SST gets stored as amyloid in vivo, we investigated the role of native structure in modulating its conformational dynamics and self-association by disrupting the disulfide bridge (Cys(3)-Cys(14)) in SST. Using two-dimensional NMR, we resolved the initial structure of somatostatin-14 leading to aggregation and further probed its conformational dynamics in silico. The perturbation in native structure (S-S cleavage) led to a significant increase in conformational flexibility and resulted in rapid amyloid formation. The fibrils formed by disulfide-reduced noncyclic SST possess greater resistance to denaturing conditions with decreased monomer releasing potency. MD simulations reveal marked differences in the intermolecular interactions in SST and noncyclic SST providing plausible explanation for differential aggregation and fibril reversibility observed experimentally in these structural variants. Our findings thus emphasize that subtle changes in the native structure of peptide hormone(s) could alter its conformational dynamics and amyloid formation, which might have significant implications on their reversible storage and secretion.
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Affiliation(s)
- Arunagiri Anoop
- From the Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Mumbai 400 076
| | - Srivastav Ranganathan
- From the Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Mumbai 400 076
| | - Bhagwan Das Dhaked
- From the Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Mumbai 400 076
| | - Narendra Nath Jha
- From the Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Mumbai 400 076
| | - Supriya Pratihar
- the Department of Chemical Sciences, Tata Institute of Fundamental Research, Mumbai 400 005
| | - Saikat Ghosh
- From the Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Mumbai 400 076
| | - Shruti Sahay
- From the Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Mumbai 400 076
| | - Santosh Kumar
- the School of Biological Sciences, National Institute of Science Education and Research, Bhubaneswar 751 005, and
| | - Subhadeep Das
- From the Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Mumbai 400 076, the IITB-Monash Research Academy, Indian Institute of Technology Bombay, Mumbai 400 076, India
| | - Mamata Kombrabail
- the Department of Chemical Sciences, Tata Institute of Fundamental Research, Mumbai 400 005
| | - Kumud Agarwal
- From the Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Mumbai 400 076
| | - Reeba S Jacob
- From the Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Mumbai 400 076
| | - Praful Singru
- the School of Biological Sciences, National Institute of Science Education and Research, Bhubaneswar 751 005, and
| | - Prasenjit Bhaumik
- From the Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Mumbai 400 076
| | - Ranjith Padinhateeri
- From the Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Mumbai 400 076
| | - Ashutosh Kumar
- From the Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Mumbai 400 076,
| | - Samir K Maji
- From the Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Mumbai 400 076,
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29
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Berezovska G, Prada-Gracia D, Rao F. Consensus for the Fip35 folding mechanism? J Chem Phys 2014; 139:035102. [PMID: 23883056 DOI: 10.1063/1.4812837] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023] Open
Abstract
Recent advances in computational power and simulation programs finally delivered the first examples of reversible folding for small proteins with an all-atom description. But having at hand the atomistic details of the process did not lead to a straightforward interpretation of the mechanism. For the case of the Fip35 WW-domain where multiple long trajectories of 100 μs are available from D. E. Shaw Research, different interpretations emerged. Some of those are in clear contradiction with each other while others are in qualitative agreement. Here, we present a network-based analysis of the same data by looking at the local fluctuations of conventional order parameters for folding. We found that folding occurs through two major pathways, one almost four times more populated than the other. Each pathway involves the formation of an intermediate with one of the two hairpins in a native configuration. The quantitative agreement of our results with a state-of-the-art reaction coordinate optimization procedure as well as qualitative agreement with other Markov-state-models and different simulation schemes provides strong evidence for a multiple folding pathways scenario with the presence of intermediates.
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Affiliation(s)
- Ganna Berezovska
- Freiburg Institute for Advanced Studies, School of Soft Matter Research, Freiburg im Breisgau, Germany
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30
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Barz B, Wales DJ, Strodel B. A kinetic approach to the sequence-aggregation relationship in disease-related protein assembly. J Phys Chem B 2014; 118:1003-11. [PMID: 24401100 PMCID: PMC3908877 DOI: 10.1021/jp412648u] [Citation(s) in RCA: 55] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
It is generally accepted that oligomers of aggregating proteins play an important role in the onset of neurodegenerative diseases. While in silico aggregation studies of full length amyloidogenic proteins are computationally expensive, the assembly of short protein fragments derived from these proteins with similar aggregating properties has been extensively studied. In the present work, molecular dynamics simulations are performed to follow peptide aggregation on the microsecond time scale. By defining aggregation states, we identify transition networks, disconnectivity graphs, and first passage time distributions to describe the kinetics of the assembly process. This approach unravels differences in the aggregation into hexamers of two peptides with different primary structures. The first is GNNQQNY, a hydrophilic fragment from the prion protein Sup35, and the second is KLVFFAE, a fragment from amyloid-β protein, with a hydrophobic core delimited by two charged amino acids. The assembly of GNNQQNY suggests a mechanism of monomer addition, with a bias toward parallel peptide pairs and a gradual increase in the amount of β-strand content. For KLVFFAE, a mechanism involving dimers rather than monomers is revealed, involving a generally higher β-strand content and a transition toward a larger number of antiparallel peptide pairs during the rearrangement of the hexamer. The differences observed for the aggregation of the two peptides suggests the existence of a sequence-aggregation relationship.
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Affiliation(s)
- Bogdan Barz
- Forschungszentrum Jülich GmbH Institute of Complex Systems: Structural Biochemistry (ICS-6), 52425 Jülich, Germany
| | - David J. Wales
- University Chemical Laboratories, Lensfield Road, Cambridge CB2 1EW, UK
| | - Birgit Strodel
- Forschungszentrum Jülich GmbH Institute of Complex Systems: Structural Biochemistry (ICS-6), 52425 Jülich, Germany
- Institute of Theoretical and Computational Chemistry, Heinrich Heine University Düsseldorf, 40225 Düsseldorf, Germany
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31
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Jain A, Stock G. Hierarchical Folding Free Energy Landscape of HP35 Revealed by Most Probable Path Clustering. J Phys Chem B 2014; 118:7750-60. [DOI: 10.1021/jp410398a] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Abhinav Jain
- Biomolecular
Dynamics, Institute
of Physics and Freiburg Institute for Advanced Studies (FRIAS), Albert Ludwigs University, 79104 Freiburg, Germany
| | - Gerhard Stock
- Biomolecular
Dynamics, Institute
of Physics and Freiburg Institute for Advanced Studies (FRIAS), Albert Ludwigs University, 79104 Freiburg, Germany
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32
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Zalibera M, Stébé PN, Dietliker K, Grützmacher H, Spichty M, Gescheidt G. The Redox Chemistry of Mono- and Bis(acyl)phosphane Oxides. European J Org Chem 2013. [DOI: 10.1002/ejoc.201301214] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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33
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Ahlstrom LS, Baker JL, Ehrlich K, Campbell ZT, Patel S, Vorontsov II, Tama F, Miyashita O. Network visualization of conformational sampling during molecular dynamics simulation. J Mol Graph Model 2013; 46:140-9. [PMID: 24211466 DOI: 10.1016/j.jmgm.2013.10.003] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2013] [Revised: 09/06/2013] [Accepted: 10/03/2013] [Indexed: 02/01/2023]
Abstract
Effective data reduction methods are necessary for uncovering the inherent conformational relationships present in large molecular dynamics (MD) trajectories. Clustering algorithms provide a means to interpret the conformational sampling of molecules during simulation by grouping trajectory snapshots into a few subgroups, or clusters, but the relationships between the individual clusters may not be readily understood. Here we show that network analysis can be used to visualize the dominant conformational states explored during simulation as well as the connectivity between them, providing a more coherent description of conformational space than traditional clustering techniques alone. We compare the results of network visualization against 11 clustering algorithms and principal component conformer plots. Several MD simulations of proteins undergoing different conformational changes demonstrate the effectiveness of networks in reaching functional conclusions.
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Affiliation(s)
- Logan S Ahlstrom
- Department of Chemistry and Biochemistry, University of Arizona, Tucson, AZ 85721, USA
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34
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Berezovska G, Prada-Gracia D, Mostarda S, Rao F. Accounting for the kinetics in order parameter analysis: lessons from theoretical models and a disordered peptide. J Chem Phys 2013. [PMID: 23181288 DOI: 10.1063/1.4764868] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Molecular simulations as well as single molecule experiments have been widely analyzed in terms of order parameters, the latter representing candidate probes for the relevant degrees of freedom. Notwithstanding this approach is very intuitive, mounting evidence showed that such descriptions are inaccurate, leading to ambiguous definitions of states and wrong kinetics. To overcome these limitations a framework making use of order parameter fluctuations in conjunction with complex network analysis is investigated. Derived from recent advances in the analysis of single molecule time traces, this approach takes into account the fluctuations around each time point to distinguish between states that have similar values of the order parameter but different dynamics. Snapshots with similar fluctuations are used as nodes of a transition network, the clusterization of which into states provides accurate Markov-state-models of the system under study. Application of the methodology to theoretical models with a noisy order parameter as well as the dynamics of a disordered peptide illustrates the possibility to build accurate descriptions of molecular processes on the sole basis of order parameter time series without using any supplementary information.
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Affiliation(s)
- Ganna Berezovska
- Freiburg Institute for Advanced Studies, School of Soft Matter Research, Freiburg im Breisgau, Germany
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35
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Prada-Gracia D, Shevchuk R, Hamm P, Rao F. Towards a microscopic description of the free-energy landscape of water. J Chem Phys 2012; 137:144504. [DOI: 10.1063/1.4755746] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023] Open
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36
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Kellogg EH, Lange OF, Baker D. Evaluation and Optimization of Discrete State Models of Protein Folding. J Phys Chem B 2012; 116:11405-13. [PMID: 22958200 DOI: 10.1021/jp3044303] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Elizabeth H. Kellogg
- Department
of Biochemistry, University of Washington, Seattle, Washington 98105,
United States
| | - Oliver F. Lange
- Biomolecular
NMR and Munich
Center for Integrated Protein Science, Department Chemie, Technische Universität München, 85747
Garching, Germany
- Institute
of Structural Biology, Helmholtz Zentrum München, 85764 Neuherberg,
Germany
| | - David Baker
- Department
of Biochemistry, University of Washington, Seattle, Washington 98105,
United States
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37
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Romanowska J, Nowiński KS, Trylska J. Determining Geometrically Stable Domains in Molecular Conformation Sets. J Chem Theory Comput 2012; 8:2588-99. [DOI: 10.1021/ct300206j] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Affiliation(s)
- Julia Romanowska
- Department of Biophysics,
Faculty of Physics, University of Warsaw, Hoża 69, 00-681 Warsaw, Poland
- Interdisciplinary
Centre for Mathematical and Computational Modelling (ICM), University of Warsaw, Pawińskiego
5a, 02-106 Warsaw, Poland
| | - Krzysztof S. Nowiński
- Interdisciplinary
Centre for Mathematical and Computational Modelling (ICM), University of Warsaw, Pawińskiego
5a, 02-106 Warsaw, Poland
| | - Joanna Trylska
- Centre of New Technologies
(CeNT), University of Warsaw, Żwirki i Wigury 93, 02-089 Warsaw, Poland
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38
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Abstract
Recent molecular dynamics simulations of biopolymers have shown that in many cases the global features of the free energy landscape can be characterized in terms of the metastable conformational states of the system. To identify these states, a conceptionally and computationally simple approach is proposed. It consists of (i) an initial preprocessing via principal component analysis to reduce the dimensionality of the data, followed by k-means clustering to generate up to 10(4) microstates, (ii) the most probable path algorithm to identify the metastable states of the system, and (iii) boundary corrections of these states via the introduction of cluster cores in order to obtain the correct dynamics. By adopting two well-studied model problems, hepta-alanine and the villin headpiece protein, the potential and the performance of the approach are demonstrated.
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Affiliation(s)
- Abhinav Jain
- Biomolecular Dynamics, Institute of Physics, Albert Ludwigs University , 79104 Freiburg, Germany
| | - Gerhard Stock
- Biomolecular Dynamics, Institute of Physics, Albert Ludwigs University , 79104 Freiburg, Germany
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39
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Mostarda S, Gfeller D, Rao F. Beyond the binding site: the role of the β₂-β₃ loop and extra-domain structures in PDZ domains. PLoS Comput Biol 2012; 8:e1002429. [PMID: 22412368 PMCID: PMC3297566 DOI: 10.1371/journal.pcbi.1002429] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2011] [Accepted: 01/30/2012] [Indexed: 12/17/2022] Open
Abstract
A general paradigm to understand protein function is to look at properties of isolated well conserved domains, such as SH3 or PDZ domains. While common features of domain families are well understood, the role of subtle differences among members of these families is less clear. Here, molecular dynamics simulations indicate that the binding mechanism in PSD95-PDZ3 is critically regulated via interactions outside the canonical binding site, involving both the poorly conserved β₂-β₃ loop and an extra-domain helix. Using the CRIPT peptide as a prototypical ligand, our simulations suggest that a network of salt-bridges between the ligand and this loop is necessary for binding. These contacts interconvert between each other on a time scale of a few tens of nanoseconds, making them elusive to X-ray crystallography. The loop is stabilized by an extra-domain helix. The latter influences the global dynamics of the domain, considerably increasing binding affinity. We found that two key contacts between the helix and the domain, one involving the β₂-β₃ loop, provide an atomistic interpretation of the increased affinity. Our analysis indicates that both extra-domain segments and loosely conserved regions play critical roles in PDZ binding affinity and specificity.
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Affiliation(s)
- Stefano Mostarda
- Freiburg Institute for Advanced Studies, School of Soft Matter Research, Freiburg im Breisgau, Germany
| | - David Gfeller
- Molecular Modeling, Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Francesco Rao
- Freiburg Institute for Advanced Studies, School of Soft Matter Research, Freiburg im Breisgau, Germany
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40
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Yin Y, Maisuradze GG, Liwo A, Scheraga HA. Hidden protein folding pathways in free-energy landscapes uncovered by network analysis. J Chem Theory Comput 2012; 8:1176-1189. [PMID: 22715321 DOI: 10.1021/ct200806n] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
A network analysis is used to uncover hidden folding pathways in free-energy landscapes usually defined in terms of such arbitrary order parameters as root-mean-square deviation from the native structure, radius of gyration, etc. The analysis has been applied to molecular dynamics (MD) trajectories of the B-domain of staphylococcal protein A, generated with the coarse-grained united-residue (UNRES) force field in a broad range of temperatures (270K ≤ T ≤ 325K). Thousands of folding pathways have been identified at each temperature. Out of these many folding pathways, several most probable ones were selected for investigation of the conformational transitions during protein folding. Unlike other conformational space network (CSN) methods, a node in the CSN variant implemented in this work is defined according to the nativelikeness class of the structure, which defines the similarity of segments of the compared structures in terms of secondary-structure, contact-pattern, and local geometry, as well as the overall geometric similarity of the conformation under consideration to that of the reference (experimental) structure. Our previous findings, regarding the folding model and conformations found at the folding-transition temperature for protein A (Maisuradze et al., J. Am. Chem. Soc. 132, 9444, 2010), were confirmed by the conformational space network analysis. In the methodology and in the analysis of the results, the shortest path identified by using the shortest-path algorithm corresponds to the most probable folding pathway in the conformational space network.
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Affiliation(s)
- Yanping Yin
- Baker Laboratory of Chemistry and Chemical Biology, Cornell University, Ithaca, New York, 14850-1301
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41
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Thermodynamics and kinetics of large-time-step molecular dynamics. J Comput Chem 2011; 33:475-83. [DOI: 10.1002/jcc.21990] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2011] [Revised: 09/22/2011] [Accepted: 10/08/2011] [Indexed: 11/07/2022]
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42
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Varma S, Rogers DM, Pratt LR, Rempe SB. Perspectives on: ion selectivity: design principles for K+ selectivity in membrane transport. ACTA ACUST UNITED AC 2011; 137:479-88. [PMID: 21624944 PMCID: PMC3105521 DOI: 10.1085/jgp.201010579] [Citation(s) in RCA: 68] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Affiliation(s)
- Sameer Varma
- Department of Biological, Chemical and Physical Sciences, Illinois Institute of Technology, Chicago, USA
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43
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Bhatt D, Zuckerman DM. Beyond microscopic reversibility: Are observable non-equilibrium processes precisely reversible? J Chem Theory Comput 2011; 7:2520-2527. [PMID: 21869866 DOI: 10.1021/ct200086k] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Although the principle of microscopic reversibility has been studied for many decades, there remain ambiguities in its application to non-equilibrium processes of importance to chemistry, physics and biology. Examples include whether protein unfolding should follow the same pathways and in the same proportions as folding, and whether unbinding should likewise mirror binding. Using continuum-space calculations which extend previous kinetic analyses, we demonstrate formally that the precise symmetry of forward and reverse processes is expected only under certain special conditions. Approximate symmetry will be exhibited under a separate set of conditions. Exact, approximate, and broken symmetry scenarios are verified in several ways: using numerical calculations on toy and molecular systems; using exact calculations on kinetic models of induced fit in protein-ligand binding; and based on reported experimental results. The analysis highlights intrinsic challenges and ambiguities in the design and analysis of both experiments and simulations.
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Affiliation(s)
- Divesh Bhatt
- Department of Computational and Systems Biology, University of Pittsburgh, 3501 Fifth Ave, Biomedical Sciences Tower 3, Pittsburgh, PA 15260
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44
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Bhattacharyya M, Vishveshwara S. Quantum clustering and network analysis of MD simulation trajectories to probe the conformational ensembles of protein-ligand interactions. MOLECULAR BIOSYSTEMS 2011; 7:2320-30. [PMID: 21617814 DOI: 10.1039/c1mb05038a] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
In this article, we present a novel application of a quantum clustering (QC) technique to objectively cluster the conformations, sampled by molecular dynamics simulations performed on different ligand bound structures of the protein. We further portray each conformational population in terms of dynamically stable network parameters which beautifully capture the ligand induced variations in the ensemble in atomistic detail. The conformational populations thus identified by the QC method and verified by network parameters are evaluated for different ligand bound states of the protein pyrrolysyl-tRNA synthetase (DhPylRS) from D. hafniense. The ligand/environment induced re-distribution of protein conformational ensembles forms the basis for understanding several important biological phenomena such as allostery and enzyme catalysis. The atomistic level characterization of each population in the conformational ensemble in terms of the re-orchestrated networks of amino acids is a challenging problem, especially when the changes are minimal at the backbone level. Here we demonstrate that the QC method is sensitive to such subtle changes and is able to cluster MD snapshots which are similar at the side-chain interaction level. Although we have applied these methods on simulation trajectories of a modest time scale (20 ns each), we emphasize that our methodology provides a general approach towards an objective clustering of large-scale MD simulation data and may be applied to probe multistate equilibria at higher time scales, and to problems related to protein folding for any protein or protein-protein/RNA/DNA complex of interest with a known structure.
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45
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Zhang J, Sapienza PJ, Ke H, Chang A, Hengel SR, Wang H, Phillips GN, Lee AL. Crystallographic and nuclear magnetic resonance evaluation of the impact of peptide binding to the second PDZ domain of protein tyrosine phosphatase 1E. Biochemistry 2010; 49:9280-91. [PMID: 20839809 DOI: 10.1021/bi101131f] [Citation(s) in RCA: 61] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
PDZ (PSD95/Discs large/ZO-1) domains are ubiquitous protein interaction motifs found in scaffolding proteins involved in signal transduction. Despite the fact that many PDZ domains show a limited tendency to undergo structural change, the PDZ family has been associated with long-range communication and allostery. One of the PDZ domains studied most in terms of structure and biophysical properties is the second PDZ ("PDZ2") domain from protein tyrosine phosphatase 1E (PTP1E, also known as PTPL1). Previously, we showed through NMR relaxation studies that binding of the RA-GEF2 C-terminal peptide substrate results in long-range propagation of side-chain dynamic changes in human PDZ2 [Fuentes, E. J., et al. (2004) J. Mol. Biol. 335, 1105-1115]. Here, we present the first X-ray crystal structures of PDZ2 in the absence and presence of RA-GEF2 ligand, determined to resolutions of 1.65 and 1.3 Å, respectively. These structures deviate somewhat from previously determined NMR structures and indicate that very minor structural changes in PDZ2 accompany peptide binding. NMR residual dipolar couplings confirm the crystal structures to be accurate models of the time-averaged atomic coordinates of PDZ2. The impact on side-chain dynamics was further tested with a C-terminal peptide from APC, which showed results nearly identical to those of RA-GEF2. Thus, allosteric transmission in PDZ2 induced by peptide binding is conveyed purely and robustly by dynamics. (15)N relaxation dispersion measurements did not detect appreciable populations of a kinetic structural intermediate. Collectively, for ligand binding to PDZ2, these data support a lock-and-key binding model from a structural perspective and an allosteric model from a dynamical perspective, which together suggest a complex energy landscape for functional transitions within the ensemble.
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Affiliation(s)
- Jun Zhang
- Department of Biochemistry and Biophysics, School of Medicine, University of North Carolina, Chapel Hill, NC 27599, USA
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46
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Rao F. Protein inherent structures by different minimization strategies. J Comput Chem 2010; 32:1113-6. [PMID: 21387337 DOI: 10.1002/jcc.21691] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2010] [Accepted: 09/06/2010] [Indexed: 11/09/2022]
Abstract
Network-based methods provide an accurate description of the free-energy landscape of peptides and proteins sampled by molecular dynamics simulations. To that end, it is necessary to group the individual snapshots in a meaningful way. The inherent structures (ISs) provide an appropriate discretization of the trajectory into microstates, avoiding problems that can arise in clustering algorithms that have been used previously. In this work, different minimization protocols to obtain the IS of a peptide are investigated on the basis of cut-based free-energy profiles. It is found that a computationally more efficient quasi-Newtonian algorithm provides quantitative agreement to the classical conjugate gradient method in terms of the population of the peptide substates and the energy barriers separating them. That is, despite the fact that the two algorithms can occasionally quench a given peptide snapshot in different potential energy minima, the overall properties of the system are not affected. As reported by others, atom permutations affect the calculation of the IS, requiring an improved implementation of current potential energy functions.
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Affiliation(s)
- Francesco Rao
- Freiburg Institute for Advanced Studies (FRIAS), University of Freiburg, Albertstr. 19, 79104 Freiburg, Germany.
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47
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Kalstein A, Fernández-Alberti S, Bastida A, Soler MA, Farag MH, Zúñiga J, Requena A. Vibrational dynamics of polyatomic molecules in solution: assignment, time evolution and mixing of instantaneous normal modes. Theor Chem Acc 2010. [DOI: 10.1007/s00214-010-0832-5] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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48
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Buchner GS, Murphy RD, Buchete NV, Kubelka J. Dynamics of protein folding: probing the kinetic network of folding-unfolding transitions with experiment and theory. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2010; 1814:1001-20. [PMID: 20883829 DOI: 10.1016/j.bbapap.2010.09.013] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/30/2010] [Revised: 09/14/2010] [Accepted: 09/16/2010] [Indexed: 10/19/2022]
Abstract
The problem of spontaneous folding of amino acid chains into highly organized, biologically functional three-dimensional protein structures continues to challenge the modern science. Understanding how proteins fold requires characterization of the underlying energy landscapes as well as the dynamics of the polypeptide chains in all stages of the folding process. In recent years, important advances toward these goals have been achieved owing to the rapidly growing interdisciplinary interest and significant progress in both experimental techniques and theoretical methods. Improvements in the experimental time resolution led to determination of the timescales of the important elementary events in folding, such as formation of secondary structure and tertiary contacts. Sensitive single molecule methods made possible probing the distributions of the unfolded and folded states and following the folding reaction of individual protein molecules. Discovery of proteins that fold in microseconds opened the possibility of atomic-level theoretical simulations of folding and their direct comparisons with experimental data, as well as of direct experimental observation of the barrier-less folding transition. The ultra-fast folding also brought new questions, concerning the intrinsic limits of the folding rates and experimental signatures of barrier-less "downhill" folding. These problems will require novel approaches for even more detailed experimental investigations of the folding dynamics as well as for the analysis of the folding kinetic data. For theoretical simulations of folding, a main challenge is how to extract the relevant information from overwhelmingly detailed atomistic trajectories. New theoretical methods have been devised to allow a systematic approach towards a quantitative analysis of the kinetic network of folding-unfolding transitions between various configuration states of a protein, revealing the transition states and the associated folding pathways at multiple levels, from atomistic to coarse-grained representations. This article is part of a Special Issue entitled: Protein Dynamics: Experimental and Computational Approaches.
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Affiliation(s)
- Ginka S Buchner
- Department of Chemistry, University of Wyoming, Laramie, WY 82071, USA; Universität Würzbug, Würzburg, Germany
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49
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Rao F, Garrett-Roe S, Hamm P. Structural Inhomogeneity of Water by Complex Network Analysis. J Phys Chem B 2010; 114:15598-604. [DOI: 10.1021/jp1060792] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Francesco Rao
- Freiburg Institute for Advanced Studies (FRIAS), University of Freiburg, Freiburg, Germany, Laboratoire de Chimie Biophysique/ISIS, Université de Strasbourg, Strasbourg, France, and Physikalisch-Chemisches Institut, Universität Zürich, Zürich, Switzerland
| | - Sean Garrett-Roe
- Freiburg Institute for Advanced Studies (FRIAS), University of Freiburg, Freiburg, Germany, Laboratoire de Chimie Biophysique/ISIS, Université de Strasbourg, Strasbourg, France, and Physikalisch-Chemisches Institut, Universität Zürich, Zürich, Switzerland
| | - Peter Hamm
- Freiburg Institute for Advanced Studies (FRIAS), University of Freiburg, Freiburg, Germany, Laboratoire de Chimie Biophysique/ISIS, Université de Strasbourg, Strasbourg, France, and Physikalisch-Chemisches Institut, Universität Zürich, Zürich, Switzerland
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50
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Gong L, Zhou X. Kinetic Transition Network Based on Trajectory Mapping. J Phys Chem B 2010; 114:10266-76. [DOI: 10.1021/jp100737g] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Linchen Gong
- Asia Pacific Center for Theoretical Physics, Pohang, Gyeongbuk 790-784, Korea, Institute for Advanced Study, Tsinghua University, Beijing 100080, China, and Department of Physics, Pohang University of Science and Technology, Pohang, Gyeongbuk 790-784, Korea
| | - Xin Zhou
- Asia Pacific Center for Theoretical Physics, Pohang, Gyeongbuk 790-784, Korea, Institute for Advanced Study, Tsinghua University, Beijing 100080, China, and Department of Physics, Pohang University of Science and Technology, Pohang, Gyeongbuk 790-784, Korea
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