Mapping the Native Conformational Ensemble of Proteins from a Combination of Simulations and Experiments: New Insight into the src-SH3 Domain.

No abstract is available for this paper.

• Publication year

  2013

• Venue

  Journal of Physical Chemistry Letters

• Publication date

  2013-05-24

• Fields of study

  Biology, Medicine, Chemistry

• Identifiers
  DOI 10.1021/jz4007806PMID 26283131
• External record

  Open on Semantic Scholar

• Source metadata

  Semantic Scholar, PubMed

• No claims are published for this paper.

• No concepts are published for this paper.

• Mapping the population of protein conformational energy sub-states from NMR dipolar couplings.

  2013cited by this paper
• METAGUI. A VMD interface for analyzing metadynamics and molecular dynamics simulations

  2012cited by this paper
• Structure of an Intermediate State in Protein Folding and Aggregation

  2012cited by this paper
• Interpreting protein structural dynamics from NMR chemical shifts.

  2012cited by this paper
• Protein Folding and Ligand-Enzyme Binding from Bias-Exchange Metadynamics Simulations

  2012cited by this paper
• A VMD interface for analyzing metadynamics and molecular dynamics simulations ✩

  2011cited by this paper
• Residue-specific description of non-native transient structures in the ensemble of acid-denatured structures of the all-beta protein c-src SH3.

  2010cited by this paper
• SPARTA+: a modest improvement in empirical NMR chemical shift prediction by means of an artificial neural network

  2010cited by this paper
• Certification of Molecular Dynamics Trajectories with NMR Chemical Shifts

  2010cited by this paper
• A Collective Variable for the Efficient Exploration of Protein Beta-Sheet Structures: Application to SH3 and GB1.

  2009cited by this paper
• PLUMED: A portable plugin for free-energy calculations with molecular dynamics

  2009cited by this paper
• Amyloid formation by globular proteins under native conditions.

  2009cited by this paper
• The role of dynamic conformational ensembles in biomolecular recognition.

  2009cited by this paper
• A Kinetic Model of Trp-Cage Folding from Multiple Biased Molecular Dynamics Simulations

  2009cited by this paper
• NMR evidence for forming highly populated helical conformations in the partially folded hNck2 SH3 domain.

  2008cited by this paper
• Material for Recognition Dynamics Up to Microseconds Revealed from an RDC-Derived Ubiquitin Ensemble in Solution

  2008cited by this paper
• Recognition Dynamics Up to Microseconds Revealed from an RDC-Derived Ubiquitin Ensemble in Solution

  2008cited by this paper
• GROMACS 4:  Algorithms for Highly Efficient, Load-Balanced, and Scalable Molecular Simulation.

  2008cited by this paper
• An alpha-helical burst in the src SH3 folding pathway.

  2007cited by this paper
• An α-Helical Burst in the src SH3 Folding Pathway

  2007cited by this paper
• A bias-exchange approach to protein folding.

  2007cited by this paper
• Transient Alpha-helical Structure during Folding of Src SH3 Domain at Subzero Temperatures

  2006cited by this paper
• Water mediation in protein folding and molecular recognition.

  2006cited by this paper
• Partial unfolding of diverse SH3 domains on a wide timescale.

  2006cited by this paper
• Recent progress in the study of biomolecular structure and dynamics in solution from residual dipolar couplings

  2005cited by this paper
• Posttransition state desolvation of the hydrophobic core of the src-SH3 protein domain.

  2003cited by this paper
• Rapid and accurate calculation of protein 1H, 13C and 15N chemical shifts

  2003cited by this paper
• A point‐charge force field for molecular mechanics simulations of proteins based on condensed‐phase quantum mechanical calculations

  2003cited by this paper
• Use of chemical shifts in macromolecular structure determination.

  2002cited by this paper
• Escaping free-energy minima

  2002cited by this paper
• Hydrophobic core packing in the SH3 domain folding transition state

  2002cited by this paper
• SH3 domains: complexity in moderation.

  2001cited by this paper
• The folding transition state between SH3 domains is conformationally restricted and evolutionarily conserved

  1999cited by this paper
• Experiment and theory highlight role of native state topology in SH3 folding

  1999cited by this paper
• Replica-exchange molecular dynamics method for protein folding

  1999cited by this paper
• High populations of non-native structures in the denatured state are compatible with the formation of the native folded state.

  1998cited by this paper
• Heteronuclear NMR studies of the combined Src homology domains 2 and 3 of pp60 c-Src: effects of phosphopeptide binding.

  1997cited by this paper
• Folding dynamics of the src SH3 domain.

  1997cited by this paper
• Protein modules and signalling networks

  1995cited by this paper
• Specific interactions outside the proline-rich core of two classes of Src homology 3 ligands.

  1995cited by this paper
• 1H and 15N assignments and secondary structure of the Src SH3 domain

  1993cited by this paper
• Multicanonical ensemble: A new approach to simulate first-order phase transitions.

  1992cited by this paper
• Protein Folding

  1992cited by this paper
• Protein folding

  1988cited by this paper
• Comparison of simple potential functions for simulating liquid water

  1983cited by this paper
• Dictionary of protein secondary structure: Pattern recognition of hydrogen‐bonded and geometrical features

  1983cited by this paper

• Recognition Mechanisms between a Nanobody and Disordered Epitopes of the Human Prion Protein: An Integrative Molecular Dynamics Study

  2022cites this paper
• Phase space and collective variable based simulation methods for studies of rare events

  2019cites this paper
• Advanced simulation techniques for the thermodynamic and kinetic characterization of biological systems

  2018cites this paper
• Exploring high‐dimensional free energy landscapes of chemical reactions

  2018cites this paper
• Equilibrium Ensembles for Insulin Folding from Bias-Exchange Metadynamics.

  2017cites this paper
• Using simulation to interpret experimental data in terms of protein conformational ensembles.

  2017cites this paper
• Structural and Kinetic Characterization of the Intrinsically Disordered Protein SeV NTAIL through Enhanced Sampling Simulations.

  2017cites this paper
• An Efficient Method for Estimating the Hydrodynamic Radius of Disordered Protein Conformations.

  2017cites this paper
• Strategies for the exploration of free energy landscapes: Unity in diversity and challenges ahead

  2017cites this paper
• Thermodynamics of Protein Folding Studied by Umbrella Sampling along a Reaction Coordinate of Native Contacts.

  2017cites this paper
• Principles and Overview of Sampling Methods for Modeling Macromolecular Structure and Dynamics

  2016cites this paper
• Structural determinants in prion protein folding and stability.

  2014cites this paper
• Statistical mechanics of the denatured state of a protein using replica-averaged metadynamics.

  2014cites this paper
• Thermal Adaptation of Conformational Dynamics in Ribonuclease H

  2013cites this paper