Rotational Dynamics of Proteins from Spin Relaxation Times and Molecular Dynamics Simulations

Show full item record



Permalink

http://hdl.handle.net/10138/254922

Citation

Ollila , S , Heikkinen , H A & Iwaï , H 2018 , ' Rotational Dynamics of Proteins from Spin Relaxation Times and Molecular Dynamics Simulations ' , Journal of Physical Chemistry B , vol. 122 , no. 25 , pp. 6559-6569 . https://doi.org/10.1021/acs.jpcb.8b02250

Title: Rotational Dynamics of Proteins from Spin Relaxation Times and Molecular Dynamics Simulations
Author: Ollila, Samuli; Heikkinen, Harri August; Iwaï, Hideo
Contributor: University of Helsinki, Institute of Biotechnology
University of Helsinki, Department of Chemistry
University of Helsinki, Institute of Biotechnology
Date: 2018-06-28
Language: eng
Number of pages: 11
Belongs to series: Journal of Physical Chemistry B
ISSN: 1520-6106
URI: http://hdl.handle.net/10138/254922
Abstract: Conformational fluctuations and rotational tumbling of proteins can be experimentally accessed with nuclear spin relaxation experiments. However, interpretation of molecular dynamics from the experimental data is often complicated, especially for molecules with anisotropic shape. Here, we apply classical molecular dynamics simulations to interpret the conformational fluctuations and rotational tumbling of proteins with arbitrarily anisotropic shape. The direct calculation of spin relaxation times from simulation data did not reproduce the experimental data. This was successfully corrected by scaling the overall rotational diffusion coefficients around the protein inertia axes with a constant factor. The achieved good agreement with experiments allowed the interpretation of the internal and overall dynamics of proteins with significantly anisotropic shape. The overall rotational diffusion was found to be Brownian, having only a short subdiffusive region below 0.12 ns. The presented methodology can be applied to interpret rotational dynamics and conformation fluctuations of proteins with arbitrary anisotropic shape. However, a water model with more realistic dynamical properties is probably required for intrinsically disordered proteins.
Subject: 1182 Biochemistry, cell and molecular biology
MAGNETIC-RESONANCE RELAXATION
NMR ORDER PARAMETERS
PARTICLE MESH EWALD
BACKBONE DYNAMICS
CONFORMATIONAL ENTROPY
FORCE-FIELD
MD SIMULATIONS
FREE-ENERGY
DIFFUSION
SPECTROSCOPY
MAGNETIC-RESONANCE RELAXATION
NMR ORDER PARAMETERS
PARTICLE MESH EWALD
BACKBONE DYNAMICS
CONFORMATIONAL ENTROPY
FORCE-FIELD
MD SIMULATIONS
FREE-ENERGY
DIFFUSION
SPECTROSCOPY
Rights:


Files in this item

Total number of downloads: Loading...

Files Size Format View
acs.jpcb.pdf 4.443Mb PDF View/Open

This item appears in the following Collection(s)

Show full item record