1
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Ilie IM, Bacci M, Vitalis A, Caflisch A. Antibody binding modulates the dynamics of the membrane-bound prion protein. Biophys J 2022; 121:2813-2825. [PMID: 35672948 DOI: 10.1016/j.bpj.2022.06.007] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2022] [Revised: 04/20/2022] [Accepted: 06/01/2022] [Indexed: 11/18/2022] Open
Abstract
Misfolding of the cellular prion protein (PrPC) is associated with lethal neurodegeneration. PrPC consists of a flexible tail (residues 23-123) and a globular domain (residues 124-231) whose C-terminal end is anchored to the cell membrane. The neurotoxic antibody POM1 and the innocuous antibody POM6 recognize the globular domain. Experimental evidence indicates that POM1 binding to PrPC emulates the influence on PrPC of the misfolded prion protein (PrPSc) while the binding of POM6 has the opposite biological response. Little is known about the potential interactions between flexible tail, globular domain, and the membrane. Here, we used atomistic simulations to investigate how these interactions are modulated by the binding of the Fab fragments of POM1 and POM6 to PrPC and by interstitial sequence truncations to the flexible tail. The simulations show that the binding of the antibodies restricts the range of orientations of the globular domain with respect to the membrane and decreases the distance between tail and membrane. Five of the six sequence truncations influence only marginally this distance and the contact patterns between tail and globular domain. The only exception is a truncation coupled to a charge inversion mutation of four N-terminal residues, which increases the distance of the flexible tail from the membrane. The interactions of the flexible tail and globular domain are modulated differently by the two antibodies.
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Affiliation(s)
- Ioana M Ilie
- Department of Biochemistry, University of Zürich, Zürich, Switzerland
| | - Marco Bacci
- Department of Biochemistry, University of Zürich, Zürich, Switzerland
| | - Andreas Vitalis
- Department of Biochemistry, University of Zürich, Zürich, Switzerland
| | - Amedeo Caflisch
- Department of Biochemistry, University of Zürich, Zürich, Switzerland.
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2
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Glielmo A, Husic BE, Rodriguez A, Clementi C, Noé F, Laio A. Unsupervised Learning Methods for Molecular Simulation Data. Chem Rev 2021; 121:9722-9758. [PMID: 33945269 PMCID: PMC8391792 DOI: 10.1021/acs.chemrev.0c01195] [Citation(s) in RCA: 116] [Impact Index Per Article: 38.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2020] [Indexed: 12/21/2022]
Abstract
Unsupervised learning is becoming an essential tool to analyze the increasingly large amounts of data produced by atomistic and molecular simulations, in material science, solid state physics, biophysics, and biochemistry. In this Review, we provide a comprehensive overview of the methods of unsupervised learning that have been most commonly used to investigate simulation data and indicate likely directions for further developments in the field. In particular, we discuss feature representation of molecular systems and present state-of-the-art algorithms of dimensionality reduction, density estimation, and clustering, and kinetic models. We divide our discussion into self-contained sections, each discussing a specific method. In each section, we briefly touch upon the mathematical and algorithmic foundations of the method, highlight its strengths and limitations, and describe the specific ways in which it has been used-or can be used-to analyze molecular simulation data.
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Affiliation(s)
- Aldo Glielmo
- International
School for Advanced Studies (SISSA) 34014 Trieste, Italy
| | - Brooke E. Husic
- Freie
Universität Berlin, Department of Mathematics
and Computer Science, 14195 Berlin, Germany
| | - Alex Rodriguez
- International Centre for Theoretical
Physics (ICTP), Condensed Matter and Statistical
Physics Section, 34100 Trieste, Italy
| | - Cecilia Clementi
- Freie
Universität Berlin, Department for
Physics, 14195 Berlin, Germany
- Rice
University Houston, Department of Chemistry, Houston, Texas 77005, United States
| | - Frank Noé
- Freie
Universität Berlin, Department of Mathematics
and Computer Science, 14195 Berlin, Germany
- Freie
Universität Berlin, Department for
Physics, 14195 Berlin, Germany
- Rice
University Houston, Department of Chemistry, Houston, Texas 77005, United States
| | - Alessandro Laio
- International
School for Advanced Studies (SISSA) 34014 Trieste, Italy
- International Centre for Theoretical
Physics (ICTP), Condensed Matter and Statistical
Physics Section, 34100 Trieste, Italy
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3
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Chatterjee A, Bhattacharya S. Uncertainty in a Markov state model with missing states and rates: Application to a room temperature kinetic model obtained using high temperature molecular dynamics. J Chem Phys 2015; 143:114109. [DOI: 10.1063/1.4930976] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Affiliation(s)
- Abhijit Chatterjee
- Department of Chemical Engineering, Indian Institute of Technology Bombay, Mumbai 400076, India
| | - Swati Bhattacharya
- Department of Physics, Indian Institute of Technology Guwahati, Guwahati 781039, India
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4
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Chekmarev SF. Equilibration of Protein States: A Time Dependent Free-Energy Disconnectivity Graph. J Phys Chem B 2015; 119:8340-8. [PMID: 26068182 DOI: 10.1021/acs.jpcb.5b04336] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The process of equilibration of protein states in a three-stranded antiparallel β-sheet miniprotein is studied using a time-dependent free energy disconnectivity graph. To determine the rates of transitions, the molecular dynamics simulation results of a recent work (Kalgin, I. V.; J. Phys. Chem. B 2013, 117, 6092) are employed. The vertices of the graph are the free energies of characteristic states of the protein, and the edges are the transition state free energies. To determine the latter, the "complete" partition function (Eyring, 1935) is used, which includes the translational partition function corresponding to the ballistic motion of the system along the reaction coordinate. The distance along the reaction coordinate that enters the translational partition function is taken to be proportional to the observation time and thus measures the number of representative points that cross the transition state surface during given time. As the time increases, the free energy barriers between the clusters of characteristic conformations (native-like, helical, and β-sheet conformations of different degree of organization) decrease and (local) equilibrium between the clusters is established. With time, these clusters are grouped into larger clusters, extending the equilibrium to a larger portion of protein states.
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Affiliation(s)
- Sergei F Chekmarev
- †Institute of Thermophysics, SB RAS, 630090 Novosibirsk, Russia.,‡Department of Physics, Novosibirsk State University, 630090 Novosibirsk, Russia
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5
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Kalgin IV, Chekmarev SF. Folding of a β-sheet miniprotein: probability fluxes, streamlines, and the potential for the driving force. J Phys Chem B 2015; 119:1380-7. [PMID: 25544646 DOI: 10.1021/jp5112795] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
In this work we continue the study of the first-passage folding of an antiparallel β-sheet miniprotein (beta3s) that was initiated in the previous work [Kalgin et al. J. Phys. Chem. B, 2014, 118, 4287]. We consider a larger ensemble of folding trajectories, which allows us to gain a closer insight into the folding dynamics. In particular, we calculate the potential for the driving force of folding in a reduced space of collective variables. The potential has two components. One component (Φ) is responsible for the source and sink of the folding flow, which are formed, respectively, in the regions of the unfolded and native states of the protein, and the other (Ψ) accounts for the flow vorticity inherently generated at the sides of the reaction channel and provides the canalization of the folding flow between the source and sink. We show that both components obey Poisson's equations with the corresponding source/sink terms. The resulting components have a very simple form: the Φ-surface consists of two well-defined peaks of different signs, which correspond, respectively, to the source and sink of the folding flow, and the Ψ-surface consists of two ridges of different signs that connect the source and sink of the flow.
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Affiliation(s)
- Igor V Kalgin
- Institute of Thermophysics, Siberian Branch of the Russian Academy of Sciences, 630090 Novosibirsk, Russia
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6
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Bacci M, Vitalis A, Caflisch A. A molecular simulation protocol to avoid sampling redundancy and discover new states. Biochim Biophys Acta Gen Subj 2014; 1850:889-902. [PMID: 25193737 DOI: 10.1016/j.bbagen.2014.08.013] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2014] [Revised: 08/21/2014] [Accepted: 08/25/2014] [Indexed: 10/24/2022]
Abstract
BACKGROUND For biomacromolecules or their assemblies, experimental knowledge is often restricted to specific states. Ambiguity pervades simulations of these complex systems because there is no prior knowledge of relevant phase space domains, and sampling recurrence is difficult to achieve. In molecular dynamics methods, ruggedness of the free energy surface exacerbates this problem by slowing down the unbiased exploration of phase space. Sampling is inefficient if dwell times in metastable states are large. METHODS We suggest a heuristic algorithm to terminate and reseed trajectories run in multiple copies in parallel. It uses a recent method to order snapshots, which provides notions of "interesting" and "unique" for individual simulations. We define criteria to guide the reseeding of runs from more "interesting" points if they sample overlapping regions of phase space. RESULTS Using a pedagogical example and an α-helical peptide, the approach is demonstrated to amplify the rate of exploration of phase space and to discover metastable states not found by conventional sampling schemes. Evidence is provided that accurate kinetics and pathways can be extracted from the simulations. CONCLUSIONS The method, termed PIGS for Progress Index Guided Sampling, proceeds in unsupervised fashion, is scalable, and benefits synergistically from larger numbers of replicas. Results confirm that the underlying ideas are appropriate and sufficient to enhance sampling. GENERAL SIGNIFICANCE In molecular simulations, errors caused by not exploring relevant domains in phase space are always unquantifiable and can be arbitrarily large. Our protocol adds to the toolkit available to researchers in reducing these types of errors. This article is part of a Special Issue entitled "Recent developments of molecular dynamics".
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Affiliation(s)
- Marco Bacci
- University of Zurich, Department of Biochemistry, Winterthurerstrasse 190, CH-8057 Zurich, Switzerland
| | - Andreas Vitalis
- University of Zurich, Department of Biochemistry, Winterthurerstrasse 190, CH-8057 Zurich, Switzerland.
| | - Amedeo Caflisch
- University of Zurich, Department of Biochemistry, Winterthurerstrasse 190, CH-8057 Zurich, Switzerland.
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7
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Sychev SV, Ivanov VT. Large scale conformational transitions in β
-structural motif of gramicidin A: kinetic analysis based on CD and FT-IR data. J Pept Sci 2014; 20:657-67. [DOI: 10.1002/psc.2643] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2014] [Revised: 03/21/2014] [Accepted: 03/28/2014] [Indexed: 01/28/2023]
Affiliation(s)
- Sergei V. Sychev
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences; 16/10 Miklukho-Maklaya Str. Moscow 117997 Russia
| | - Vadim T. Ivanov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences; 16/10 Miklukho-Maklaya Str. Moscow 117997 Russia
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8
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Kalgin IV, Chekmarev SF, Karplus M. First passage analysis of the folding of a β-sheet miniprotein: is it more realistic than the standard equilibrium approach? J Phys Chem B 2014; 118:4287-99. [PMID: 24669953 PMCID: PMC4002127 DOI: 10.1021/jp412729r] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
![]()
Simulations of first-passage folding
of the antiparallel β-sheet
miniprotein beta3s, which has been intensively studied under equilibrium
conditions by A. Caflisch and co-workers, show that the kinetics and
dynamics are significantly different from those for equilibrium folding.
Because the folding of a protein in a living system generally corresponds
to the former (i.e., the folded protein is stable and unfolding is
a rare event), the difference is of interest. In contrast to equilibrium
folding, the Ch-curl conformations become very rare because they contain
unfavorable parallel β-strand arrangements, which are difficult
to form dynamically due to the distant N- and C-terminal strands.
At the same time, the formation of helical conformations becomes much
easier (particularly in the early stage of folding) due to short-range
contacts. The hydrodynamic descriptions of the folding reaction have
also revealed that while the equilibrium flow field presented a collection
of local vortices with closed ”streamlines”, the first-passage
folding is characterized by a pronounced overall flow from the unfolded
states to the native state. The flows through the locally stable structures
Cs-or and Ns-or, which are conformationally close to the native state,
are negligible due to detailed balance established between these structures
and the native state. Although there are significant differences in
the general picture of the folding process from the equilibrium and
first-passage folding simulations, some aspects of the two are in
agreement. The rate of transitions between the clusters of characteristic
protein conformations in both cases decreases approximately exponentially
with the distance between the clusters in the hydrogen bond distance
space of collective variables, and the folding time distribution in
the first-passage segments of the equilibrium trajectory is in good
agreement with that for the first-passage folding simulations.
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Affiliation(s)
- Igor V Kalgin
- Department of Physics, Novosibirsk State University , 630090 Novosibirsk, Russia
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9
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Using Agrawal integral equation and thermogravimetric analysis (TGA) to study the pyrolysis kinetics of nanocomposites of polybenzoxazine and exfoliated montmorillonite from a mono-functionalized azide polyhedral oligomeric silsesquioxane and click chemistry. Polym Bull (Berl) 2013. [DOI: 10.1007/s00289-013-1013-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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10
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Kalgin IV, Caflisch A, Chekmarev SF, Karplus M. New insights into the folding of a β-sheet miniprotein in a reduced space of collective hydrogen bond variables: application to a hydrodynamic analysis of the folding flow. J Phys Chem B 2013; 117:6092-105. [PMID: 23621790 DOI: 10.1021/jp401742y] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
A new analysis of the 20 μs equilibrium folding/unfolding molecular dynamics simulations of the three-stranded antiparallel β-sheet miniprotein (beta3s) in implicit solvent is presented. The conformation space is reduced in dimensionality by introduction of linear combinations of hydrogen bond distances as the collective variables making use of a specially adapted principal component analysis (PCA); i.e., to make structured conformations more pronounced, only the formed bonds are included in determining the principal components. It is shown that a three-dimensional (3D) subspace gives a meaningful representation of the folding behavior. The first component, to which eight native hydrogen bonds make the major contribution (four in each beta hairpin), is found to play the role of the reaction coordinate for the overall folding process, while the second and third components distinguish the structured conformations. The representative points of the trajectory in the 3D space are grouped into conformational clusters that correspond to locally stable conformations of beta3s identified in earlier work. A simplified kinetic network based on the three components is constructed, and it is complemented by a hydrodynamic analysis. The latter, making use of "passive tracers" in 3D space, indicates that the folding flow is much more complex than suggested by the kinetic network. A 2D representation of streamlines shows there are vortices which correspond to repeated local rearrangement, not only around minima of the free energy surface but also in flat regions between minima. The vortices revealed by the hydrodynamic analysis are apparently not evident in folding pathways generated by transition-path sampling. Making use of the fact that the values of the collective hydrogen bond variables are linearly related to the Cartesian coordinate space, the RMSD between clusters is determined. Interestingly, the transition rates show an approximate exponential correlation with distance in the hydrogen bond subspace. Comparison with the many published studies shows good agreement with the present analysis for the parts that can be compared, supporting the robust character of our understanding of this "hydrogen atom" of protein folding.
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Affiliation(s)
- Igor V Kalgin
- Department of Physics, Novosibirsk State University, 630090 Novosibirsk, Russia
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11
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Baumketner A. The mechanism of the converter domain rotation in the recovery stroke of myosin motor protein. Proteins 2012; 80:2701-10. [PMID: 22855405 PMCID: PMC3486948 DOI: 10.1002/prot.24155] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2012] [Revised: 07/06/2012] [Accepted: 07/16/2012] [Indexed: 02/04/2023]
Abstract
Upon ATP binding, myosin motor protein is found in two alternative conformations, prerecovery state M* and postrecovery state M**. The transition from one state to the other, known as the recovery stroke, plays a key role in the myosin functional cycle. Despite much recent research, the microscopic details of this transition remain elusive. A critical step in the recovery stroke is the rotation of the converter domain from "up" position in prerecovery state to "down" position in postrecovery state that leads to the swing of the lever arm attached to it. In this work, we demonstrate that the two rotational states of the converter domain are determined by the interactions within a small structural motif in the force-generating region of the protein that can be accurately modeled on computers using atomic representation and explicit solvent. Our simulations show that the transition between the two states is controlled by a small helix (SH1) located next to the relay helix and relay loop. A small translation in the position of SH1 away from the relay helix is seen to trigger the transition from "up" state to "down" state. The transition is driven by a cluster of hydrophobic residues I687, F487, and F506 that make significant contributions to the stability of both states. The proposed mechanism agrees well with the available structural and mutational studies.
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Affiliation(s)
- Andrij Baumketner
- Department of Physics and Optical Science, University of North Carolina Charlotte, Charlotte, NC 28262, USA.
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12
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Zhou T, Caflisch A. Distribution of Reciprocal of Interatomic Distances: A Fast Structural Metric. J Chem Theory Comput 2012; 8:2930-7. [PMID: 26592131 DOI: 10.1021/ct3003145] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
We present a structural metric based on the Distribution of Reciprocal of Interatomic Distances (DRID) for evaluating geometrical similarity between two conformations of a molecule. A molecular conformation is described by a vector of 3N orientation-independent DRID descriptors where N is the number of molecular centroids, for example, the non-hydrogen atoms in all nonsymmetric groups of a peptide. For two real-world applications (pairwise comparison of snapshots from an explicit solvent simulation of a protease/peptide substrate complex and implicit solvent simulations of reversible folding of a 20-residue β-sheet peptide), the DRID-based metric is shown to be about 5 and 15 times faster than coordinate root-mean-square deviation (cRMSD) and distance root-mean-square deviation (dRMSD), respectively. A single core of a mainstream processor can perform about 10(8) DRID comparisons in one-half a minute. Importantly, the DRID metric has closer similarity to kinetic distance than does either cRMSD or dRMSD. Therefore, DRID is suitable for clustering molecular dynamics trajectories for kinetic analysis, for example, by Markov state models. Moreover, conformational space networks and free energy profiles derived by DRID-based clustering preserve the kinetic information.
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Affiliation(s)
- Ting Zhou
- Department of Biochemistry, University of Zurich , CH-8057 Zurich, Switzerland
| | - Amedeo Caflisch
- Department of Biochemistry, University of Zurich , CH-8057 Zurich, Switzerland
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13
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Abstract
A free energy-guided sampling (FEGS) method is proposed for accelerating exploration of conformational space in unbiased molecular dynamics. Using the cut-based free energy profile and Markov state models, FEGS speeds up sampling of the canonical ensemble by iteratively restarting multiple short simulations in parallel from regions of the free energy surface visited rarely. This exploration stage is followed by a refinement stage in which multiple independent runs are initiated from Boltzmann distributed conformations. Notably, FEGS does not require either collective variables or reaction coordinates and can control the kinetic distance from the starting conformation. We applied FEGS to the alanine dipeptide, which has a human-comprehensible two-dimensional free energy landscape, and a three-stranded antiparallel β-sheet peptide of 20 residues whose folding/unfolding process is governed by a delicate interplay of enthalpy and entropy. For these two systems, FEGS speeds up the exploration of conformational space by 1 to 2 orders of magnitude with respect to conventional sampling and preserves the basins and barriers on the free energy profile.
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Affiliation(s)
- Ting Zhou
- Department of Biochemistry, University of Zurich, CH-8057 Zurich, Switzerland
| | - Amedeo Caflisch
- Department of Biochemistry, University of Zurich, CH-8057 Zurich, Switzerland
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14
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Dirks RM, Xu H, Shaw DE. Improving Sampling by Exchanging Hamiltonians with Efficiently Configured Nonequilibrium Simulations. J Chem Theory Comput 2011; 8:162-71. [DOI: 10.1021/ct200464v] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Robert M. Dirks
- D. E. Shaw Research, 120 W. 45th St., 39th Floor, New York, New York 10036, United States
| | - Huafeng Xu
- D. E. Shaw Research, 120 W. 45th St., 39th Floor, New York, New York 10036, United States
| | - David E. Shaw
- D. E. Shaw Research, 120 W. 45th St., 39th Floor, New York, New York 10036, United States
- Center for Computational Biology and Bioinformatics, Columbia University, New York, New York 10032, United States
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15
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Prinz JH, Chodera JD, Pande VS, Swope WC, Smith JC, Noé F. Optimal use of data in parallel tempering simulations for the construction of discrete-state Markov models of biomolecular dynamics. J Chem Phys 2011; 134:244108. [PMID: 21721613 DOI: 10.1063/1.3592153] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Parallel tempering (PT) molecular dynamics simulations have been extensively investigated as a means of efficient sampling of the configurations of biomolecular systems. Recent work has demonstrated how the short physical trajectories generated in PT simulations of biomolecules can be used to construct the Markov models describing biomolecular dynamics at each simulated temperature. While this approach describes the temperature-dependent kinetics, it does not make optimal use of all available PT data, instead estimating the rates at a given temperature using only data from that temperature. This can be problematic, as some relevant transitions or states may not be sufficiently sampled at the temperature of interest, but might be readily sampled at nearby temperatures. Further, the comparison of temperature-dependent properties can suffer from the false assumption that data collected from different temperatures are uncorrelated. We propose here a strategy in which, by a simple modification of the PT protocol, the harvested trajectories can be reweighted, permitting data from all temperatures to contribute to the estimated kinetic model. The method reduces the statistical uncertainty in the kinetic model relative to the single temperature approach and provides estimates of transition probabilities even for transitions not observed at the temperature of interest. Further, the method allows the kinetics to be estimated at temperatures other than those at which simulations were run. We illustrate this method by applying it to the generation of a Markov model of the conformational dynamics of the solvated terminally blocked alanine peptide.
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Affiliation(s)
- Jan-Hendrik Prinz
- Institute for Scientific Computing (IWR), University of Heidelberg, Heidelberg, Germany.
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16
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Zheng W, Qi B, Rohrdanz MA, Caflisch A, Dinner AR, Clementi C. Delineation of folding pathways of a β-sheet miniprotein. J Phys Chem B 2011; 115:13065-74. [PMID: 21942785 DOI: 10.1021/jp2076935] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Several methods have been developed in the past few years for the analysis of molecular dynamics simulations of biological (macro)molecules whose complexity is difficult to capture by simple projections of the free-energy surface onto one or two geometric variables. The locally scaled diffusion map (LSDMap) method is a nonlinear dimensionality reduction technique for describing the dynamics of complex systems in terms of a few collective coordinates. Here, we compare LSDMap to two previously developed approaches for the characterization of the configurational landscape associated with the folding dynamics of a three-stranded antiparallel β-sheet peptide, termed Beta3s. The analysis is aided by an improved procedure for extracting pathways from the equilibrium transition network, which enables calculation of pathway-specific cut-based free energy profiles. We find that the results from LSDMap are consistent with analysis based on transition networks and allow a coherent interpretation of metastable states and folding pathways in terms of different time scales of transitions between minima on the free energy projections.
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Affiliation(s)
- Wenwei Zheng
- Department of Chemistry, Rice University, Houston, Texas 77005, United States
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17
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Scalco R, Caflisch A. Equilibrium Distribution from Distributed Computing (Simulations of Protein Folding). J Phys Chem B 2011; 115:6358-65. [DOI: 10.1021/jp2014918] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Riccardo Scalco
- Department of Biochemistry, University of Zurich, Winterthurerstrasse 190, CH-8057 Zurich, Switzerland
| | - Amedeo Caflisch
- Department of Biochemistry, University of Zurich, Winterthurerstrasse 190, CH-8057 Zurich, Switzerland
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18
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Keller B, Hünenberger P, van Gunsteren WF. An Analysis of the Validity of Markov State Models for Emulating the Dynamics of Classical Molecular Systems and Ensembles. J Chem Theory Comput 2011; 7:1032-44. [DOI: 10.1021/ct200069c] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Bettina Keller
- Laboratory of Physical Chemistry, Swiss Federal Institute of Technology Zürich, ETH Zürich, CH-8093 Zürich, Switzerland
| | - Philippe Hünenberger
- Laboratory of Physical Chemistry, Swiss Federal Institute of Technology Zürich, ETH Zürich, CH-8093 Zürich, Switzerland
| | - Wilfred F. van Gunsteren
- Laboratory of Physical Chemistry, Swiss Federal Institute of Technology Zürich, ETH Zürich, CH-8093 Zürich, Switzerland
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19
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Schuetz P, Wuttke R, Schuler B, Caflisch A. Free Energy Surfaces from Single-Distance Information. J Phys Chem B 2010; 114:15227-35. [DOI: 10.1021/jp1053698] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Philipp Schuetz
- Department of Biochemistry, University of Zürich, Winterthurerstrasse 190, CH-8057 Zürich, Switzerland
| | - René Wuttke
- Department of Biochemistry, University of Zürich, Winterthurerstrasse 190, CH-8057 Zürich, Switzerland
| | - Benjamin Schuler
- Department of Biochemistry, University of Zürich, Winterthurerstrasse 190, CH-8057 Zürich, Switzerland
| | - Amedeo Caflisch
- Department of Biochemistry, University of Zürich, Winterthurerstrasse 190, CH-8057 Zürich, Switzerland
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20
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Qi B, Muff S, Caflisch A, Dinner AR. Extracting physically intuitive reaction coordinates from transition networks of a beta-sheet miniprotein. J Phys Chem B 2010; 114:6979-89. [PMID: 20438066 DOI: 10.1021/jp101476g] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Simulations are important for understanding complex reactions, but their interpretation is challenging owing to the large number of degrees of freedom typically involved. To address this issue, various means for relating the dynamics of a stochastic system to its structural and energetic features have been introduced. Here, we show how two leading approaches can be combined to advantage. We use the network of transitions observed in a reversible folding/unfolding simulation of a 20-residue three-stranded antiparallel beta-sheet peptide (beta3s) to estimate the probabilities of committing to stable states (the native state and major nonnative states), and these then serve as the basis for an efficient statistical procedure for identifying physical variables that describe the dynamics. We find that a single coordinate that jointly characterizes the formation of the two native turns of beta3s can adequately describe the overall folding process, despite its complex nature. Additional features associated with major pathways leading from individual nonnative states are resolved; indeed, a key result is an improved understanding of the unfolded state. Connections to other methods for analyzing complex reactions are discussed.
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Affiliation(s)
- Bo Qi
- Department of Chemistry, The University of Chicago, Chicago, Illinois 60637, USA
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21
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Bowman GR, Huang X, Pande VS. Network models for molecular kinetics and their initial applications to human health. Cell Res 2010; 20:622-30. [PMID: 20421891 PMCID: PMC4441225 DOI: 10.1038/cr.2010.57] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
Molecular kinetics underlies all biological phenomena and, like many other biological processes, may best be understood in terms of networks. These networks, called Markov state models (MSMs), are typically built from physical simulations. Thus, they are capable of quantitative prediction of experiments and can also provide an intuition for complex conformational changes. Their primary application has been to protein folding; however, these technologies and the insights they yield are transferable. For example, MSMs have already proved useful in understanding human diseases, such as protein misfolding and aggregation in Alzheimer's disease.
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Affiliation(s)
- Gregory R Bowman
- Biophysics Program, Stanford University, Stanford, CA 94305, USA
| | - Xuhui Huang
- Department of Chemistry, The Hong Kong University of Science and Technology, Kowloon, Hong Kong
- Department of Bioengineering, Stanford University, Stanford, CA 94305, USA
| | - Vijay S Pande
- Biophysics Program, Stanford University, Stanford, CA 94305, USA
- Department of Chemistry, Stanford University, Stanford, CA 94305, USA
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Yang J, Chen X, Fu R, Luo WA, Li Y, Zhang M. Kinetics of phase separation in polymer blends revealed by resonance light scattering spectroscopy. Phys Chem Chem Phys 2010; 12:2238-45. [DOI: 10.1039/b918069a] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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23
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Kalgin IV, Karplus M, Chekmarev SF. Folding of a SH3 Domain: Standard and “Hydrodynamic” Analyses. J Phys Chem B 2009; 113:12759-72. [DOI: 10.1021/jp903325z] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Igor V. Kalgin
- Department of Physics, Novosibirsk State University, 630090 Novosibirsk, Russia, Laboratoire de Chimie Biophysique, ISIS Université de Strasbourg, 67000 Strasbourg, France, Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts 02138, and Institute of Thermophysics, SB RAS, 630090 Novosibirsk, Russia
| | - Martin Karplus
- Department of Physics, Novosibirsk State University, 630090 Novosibirsk, Russia, Laboratoire de Chimie Biophysique, ISIS Université de Strasbourg, 67000 Strasbourg, France, Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts 02138, and Institute of Thermophysics, SB RAS, 630090 Novosibirsk, Russia
| | - Sergei F. Chekmarev
- Department of Physics, Novosibirsk State University, 630090 Novosibirsk, Russia, Laboratoire de Chimie Biophysique, ISIS Université de Strasbourg, 67000 Strasbourg, France, Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts 02138, and Institute of Thermophysics, SB RAS, 630090 Novosibirsk, Russia
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Muff S, Caflisch A. Identification of the protein folding transition state from molecular dynamics trajectories. J Chem Phys 2009; 130:125104. [DOI: 10.1063/1.3099705] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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