Journal ArticleDOI
Dynamical transition of myoglobin revealed by inelastic neutron scattering.
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TLDR
The dynamical behaviour of myoglobin (and other globular proteins) suggests a coupling of fast local motions to slower collective motions, which is a characteristic feature of other dense glass-forming systems.Abstract:
Structural fluctuations in proteins on the picosecond timescale have been studied in considerable detail by theoretical methods such as molecular dynamics simulation1,2, but there exist very few experimental data with which to test the conclusions. We have used the technique of inelastic neutron scattering to investigate atomic motion in hydrated myoglobin over the temperature range 4–350 K and on the molecular dynamics timescale 0.1–100 ps. At temperatures below 180 K myglobin behaves as a harmonic solid, with essentially only vibrational motion. Above 180 K there is a striking dynamic transition arising from the excitation of non-vibrational motion, which we interpret as corresponding to tor-sional jumps between states of different energy, with a mean energy asymmetry of KJ mol −1. This extra mobility is reflected in a strong temperature dependence of the mean-square atomic displacements, a phenomenon previously observed specifically for the heme iron by Mossbauer spectroscopy3–5, but on a much slower timescale (10−7 s). It also correlates with a glass-like transition in the hydration shell of myoglobin6 and with the temperature-dependence of ligand-binding rates at the heme iron, as monitored by flash photolysis7. In contrast, the crystal structure of myoglobin determined down to 80 K shows no significant structural transition8–10. The dynamical behaviour we find for myoglobin (and other globular proteins) suggests a coupling of fast local motions to slower collective motions, which is a characteristic feature of other dense glass-forming systems.read more
Citations
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Journal ArticleDOI
Formation of glasses from liquids and biopolymers.
TL;DR: The onset of a sharp change in ddT( is the Debye-Waller factor and T is temperature) in proteins, which is controversially indentified with the glass transition in liquids, is shown to be general for glass formers and observable in computer simulations of strong and fragile ionic liquids, where it proves to be close to the experimental glass transition temperature.
Journal ArticleDOI
Dynamic personalities of proteins.
TL;DR: The dream is to 'watch' proteins in action in real time at atomic resolution, which requires addition of a fourth dimension, time, to structural biology so that the positions in space and time of all atoms in a protein can be described in detail.
Journal ArticleDOI
New spherical-cutoff methods for long-range forces in macromolecular simulation
TL;DR: Force switching and force shifting are the best atom‐based spherical cutoffs, whereas switched group‐shifting is the preferred group‐based method.
Journal ArticleDOI
Molecular dynamics simulations in biology.
Martin Karplus,Gregory A. Petsko +1 more
TL;DR: Molecular dynamics is also being used to determine protein structures from NMR, to refine protein X-ray crystal structures faster from poorer starting models, and to calculate the free energy changes resulting from mutations in proteins.
Book ChapterDOI
Protein hydration and function.
John A. Rupley,Giorgio Careri +1 more
TL;DR: This chapter summarizes the literature that bears on the protein hydration process and the hydration shell, categorized by type of measurement, and provides picture of the hydrated shell and an assessment of the ways in which thehydration shell may modulate enzyme and other protein functions.
References
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Journal ArticleDOI
Dynamics of ligand binding to myoglobin
TL;DR: The nonexponential rebinding observed at low temperatures and in solid samples implies that the innermost barrier has a spectrum of activation energies, similar to how myoglobin achieves specificity and order.
Journal ArticleDOI
Temperature-dependent X-ray diffraction as a probe of protein structural dynamics
Hans Frauenfelder,Hans Frauenfelder,Gregory A. Petsko,Gregory A. Petsko,Gregory A. Petsko,Demetrius Tsernoglou,Demetrius Tsernoglou +6 more
TL;DR: It is concluded that X-ray diffraction can provide the spatial distribution of the dynamic features of a protein.
Journal ArticleDOI
Multiple Conformational States of Proteins: A Molecular Dynamics Analysis of Myoglobin
Ron Elber,Martin Karplus +1 more
TL;DR: A molecular dynamics simulation of myoglobin provides the first direct demonstration that the potential energy surface of a protein is characterized by a large number of thermally accessible minima in the neighborhood of the native structure.