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Title: Low-Temperature Protein Dynamics: A Simulation Analysis of Interprotein Vibrations and the Boson Peak at 150K

Abstract

An understanding of low-frequency, collective protein dynamics at low temperatures can furnish valuable information on functional protein energy landscapes, on the origins of the protein glass transition and on protein-protein interactions. Here, molecular dynamics (MD) simulations and normal-mode analyses are performed on various models of crystalline myoglobin in order to characterize intra- and interprotein vibrations at 150 K. Principal component analysis of the MD trajectories indicates that the Boson peak, a broad peak in the dynamic structure factor centered at about 2-2.5 meV, originates from 102 collective, harmonic vibrations. An accurate description of the environment is found to be essential in reproducing the experimental Boson peak form and position. At lower energies other strong peaks are found in the calculated dynamic structure factor. Characterization of these peaks shows that they arise from harmonic vibrations of proteins relative to each other. These vibrations are likely to furnish valuable information on the physical nature of protein-protein interactions.

Authors:
 [1];  [2]
  1. University of Heidelberg
  2. ORNL
Publication Date:
Research Org.:
Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States)
Sponsoring Org.:
USDOE Laboratory Directed Research and Development (LDRD) Program
OSTI Identifier:
932176
DOE Contract Number:  
DE-AC05-00OR22725
Resource Type:
Journal Article
Resource Relation:
Journal Name: Journal of the American Chemical Society; Journal Volume: 128; Journal Issue: 7
Country of Publication:
United States
Language:
English
Subject:
59 BASIC BIOLOGICAL SCIENCES; 72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS; BOSONS; FUNCTIONALS; GLASS; HARMONICS; MYOGLOBIN; PROTEINS; SIMULATION; STRUCTURE FACTORS; TRAJECTORIES

Citation Formats

Kurkal-Siebert, V, and Smith, Jeremy C. Low-Temperature Protein Dynamics: A Simulation Analysis of Interprotein Vibrations and the Boson Peak at 150K. United States: N. p., 2006. Web. doi:10.1021/ja055962q.
Kurkal-Siebert, V, & Smith, Jeremy C. Low-Temperature Protein Dynamics: A Simulation Analysis of Interprotein Vibrations and the Boson Peak at 150K. United States. doi:10.1021/ja055962q.
Kurkal-Siebert, V, and Smith, Jeremy C. Wed . "Low-Temperature Protein Dynamics: A Simulation Analysis of Interprotein Vibrations and the Boson Peak at 150K". United States. doi:10.1021/ja055962q.
@article{osti_932176,
title = {Low-Temperature Protein Dynamics: A Simulation Analysis of Interprotein Vibrations and the Boson Peak at 150K},
author = {Kurkal-Siebert, V and Smith, Jeremy C},
abstractNote = {An understanding of low-frequency, collective protein dynamics at low temperatures can furnish valuable information on functional protein energy landscapes, on the origins of the protein glass transition and on protein-protein interactions. Here, molecular dynamics (MD) simulations and normal-mode analyses are performed on various models of crystalline myoglobin in order to characterize intra- and interprotein vibrations at 150 K. Principal component analysis of the MD trajectories indicates that the Boson peak, a broad peak in the dynamic structure factor centered at about 2-2.5 meV, originates from 102 collective, harmonic vibrations. An accurate description of the environment is found to be essential in reproducing the experimental Boson peak form and position. At lower energies other strong peaks are found in the calculated dynamic structure factor. Characterization of these peaks shows that they arise from harmonic vibrations of proteins relative to each other. These vibrations are likely to furnish valuable information on the physical nature of protein-protein interactions.},
doi = {10.1021/ja055962q},
journal = {Journal of the American Chemical Society},
number = 7,
volume = 128,
place = {United States},
year = {Wed Feb 01 00:00:00 EST 2006},
month = {Wed Feb 01 00:00:00 EST 2006}
}