ArticleProceedings of the National Academy of Sciences of the United States of America2010
Protein dynamics investigated by inherent structure analysis.
Article in Proceedings of the National Academy of Sciences of the United States of America, 2010. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 22 papers.
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Who cites it
22 citing papers in PubMed.
- Design of an immunogen containing multidimensionally conserved and immunogenic parts of the HIV proteome.PLoS computational biology · 2026Article
- Zirconium Coordination Chemistry and Its Role in Optimizing Hydroxymate Chelation: Insights from Molecular Dynamics.ACS omega · 2023Article
- Linking Gas-Phase and Solution-Phase Protein Unfolding via Mobile Proton Simulations.Analytical chemistry · 2022Article
- Molecular dynamics analysis of biomolecular systems including nucleic acids.Biophysics and physicobiology · 2022Article
- EspcTM: Kinetic Transition Network Based on Trajectory Mapping in Effective Energy Rescaling Space.Frontiers in molecular biosciences · 2020Article
- Article
- Implications of short time scale dynamics on long time processes.Structural dynamics (Melville, N.Y.) · 2017Review
- Coupling Protein Dynamics with Proton Transport in Human Carbonic Anhydrase II.The journal of physical chemistry. B · 2016Article
- Cluster analysis of molecular simulation trajectories for systems where both conformation and orientation of the sampled states are important.Journal of computational chemistry · 2016Article
- Inherent structure versus geometric metric for state space discretization.Journal of computational chemistry · 2016Article
- Mapping the intrinsically disordered properties of the flexible loop domain of Bcl-2: a molecular dynamics simulation study.Journal of molecular modeling · 2016Article
- Rigid Residue Scan Simulations Systematically Reveal Residue Entropic Roles in Protein Allostery.PLoS computational biology · 2016Article
- Systematically constructing kinetic transition network in polypeptide from top to down: trajectory mapping.PloS one · 2015Article
- Elucidating the role of disulfide bond on amyloid formation and fibril reversibility of somatostatin-14: relevance to its storage and secretion.The Journal of biological chemistry · 2014Article
- A kinetic approach to the sequence-aggregation relationship in disease-related protein assembly.The journal of physical chemistry. B · 2014Article
- Network visualization of conformational sampling during molecular dynamics simulation.Journal of molecular graphics & modelling · 2013Article
- Hidden protein folding pathways in free-energy landscapes uncovered by network analysis.Journal of chemical theory and computation · 2012Article
- Beyond the binding site: the role of the β₂-β₃ loop and extra-domain structures in PDZ domains.PLoS computational biology · 2012Article
- Beyond microscopic reversibility: Are observable non-equilibrium processes precisely reversible?Journal of chemical theory and computation · 2011Article
- Perspectives on: ion selectivity: design principles for K+ selectivity in membrane transport.The Journal of general physiology · 2011Article
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Authors and funding
2 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Molecular dynamics (MD) simulations provide essential information about the thermodynamics and dynamics of proteins. To construct the free-energy surface from equilibrium trajectories, it is necessary to group the individual snapshots in a meaningful way. The inherent structures (IS) are shown to provide an appropriate discretization of the trajectory and to avoid problems that can arise in clustering algorithms that have been employed previously. The IS-based approach is illustrated with a 30-ns room temperature "native" state MD simulation of a 10-residue peptide in a beta-hairpin conformation. The transitions between the IS are used to construct a configuration space network from which a one-dimensional free-energy profile is obtained with the mincut method. The results demonstrate that the IS approach is useful and that even for this simple system, there exists a nontrivial organization of the native state into several valleys separated by barriers as high as 3 kcal/mol. Further, by introducing a coarse-grained network, it is demonstrated that there are multiple pathways connecting the valleys. This scenario is hidden when the snapshots of the trajectory are used directly with rmsd clustering to compute the free-energy profile. Application of the IS approach to the native state of the PDZ2 signaling domain indicates its utility for the study of biologically relevant systems.
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