ArticleBiophysical journal2012
Functional domain motions in proteins on the ~1-100 ns timescale: comparison of neutron spin-echo spectroscopy of phosphoglycerate kinase with molecular-dynamics simulation.
Article in Biophysical journal, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 12 papers.
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12 citing papers in PubMed, 44 citations in OpenAlex.
- A Quantum-Classical Analysis of Variability in Peptide Energies and Conformations.The protein journal · 2026Article
- Review
- Metastable States in the Hinge-Bending Landscape of an Enzyme in an Atomistic Cytoplasm Simulation.The journal of physical chemistry letters · 2024Article
- Conformational dynamics of a multidomain protein by neutron scattering and computational analysis.Biophysical journal · 2021Article
- Intermediate scattering functions of a rigid body monoclonal antibody protein in solution studied by dissipative particle dynamic simulation.Structural dynamics (Melville, N.Y.) · 2021Article
- Using molecular dynamics trajectories to predict nuclear spin relaxation behaviour in large spin systems.Journal of magnetic resonance (San Diego, Calif. : 1997) · 2021Article
- Visualizing the nanoscale: protein internal dynamics and neutron spin echo spectroscopy.Current opinion in structural biology · 2017Review
- Thermal activation of 'allosteric-like' large-scale motions in a eukaryotic Lactate Dehydrogenase.Scientific reports · 2017Article
- Conformational state distributions and catalytically relevant dynamics of a hinge-bending enzyme studied by single-molecule FRET and a coarse-grained simulation.Biophysical journal · 2014Article
- Structure and dynamics of a compact state of a multidomain protein, the mercuric ion reductase.Biophysical journal · 2014Article
- Observation of small cluster formation in concentrated monoclonal antibody solutions and its implications to solution viscosity.Biophysical journal · 2014Article
- Coherent neutron scattering and collective dynamics in the protein, GFP.Biophysical journal · 2013Article
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Authors and funding
5 authors at 4 institutions in 3 countries.
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Abstract
Protein function often requires large-scale domain motion. An exciting new development in the experimental characterization of domain motions in proteins is the application of neutron spin-echo spectroscopy (NSE). NSE directly probes coherent (i.e., pair correlated) scattering on the ~1-100 ns timescale. Here, we report on all-atom molecular-dynamics (MD) simulation of a protein, phosphoglycerate kinase, from which we calculate small-angle neutron scattering (SANS) and NSE scattering properties. The simulation-derived and experimental-solution SANS results are in excellent agreement. The contributions of translational and rotational whole-molecule diffusion to the simulation-derived NSE and potential problems in their estimation are examined. Principal component analysis identifies types of domain motion that dominate the internal motion's contribution to the NSE signal, with the largest being classic hinge bending. The associated free-energy profiles are quasiharmonic and the frictional properties correspond to highly overdamped motion. The amplitudes of the motions derived by MD are smaller than those derived from the experimental analysis, and possible reasons for this difference are discussed. The MD results confirm that a significant component of the NSE arises from internal dynamics. They also demonstrate that the combination of NSE with MD is potentially useful for determining the forms, potentials of mean force, and time dependence of functional domain motions in proteins.
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