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

Research output: Contribution to journalArticleScientificpeer-review

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.
Original languageEnglish
JournalJournal of Physical Chemistry B
Volume122
Issue number25
Pages (from-to)6559-6569
Number of pages11
ISSN1520-6106
DOIs
Publication statusPublished - 28 Jun 2018
MoE publication typeA1 Journal article-refereed

Fields of Science

  • 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

Cite this

@article{902e897ef6e44505bd70dc4f5686b06a,
title = "Rotational Dynamics of Proteins from Spin Relaxation Times and Molecular Dynamics Simulations",
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.",
keywords = "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",
author = "Samuli Ollila and Heikkinen, {Harri August} and Hideo Iwa{\"i}",
year = "2018",
month = "6",
day = "28",
doi = "10.1021/acs.jpcb.8b02250",
language = "English",
volume = "122",
pages = "6559--6569",
journal = "Journal of Physical Chemistry B",
issn = "1520-6106",
publisher = "American Chemical Society Journals",
number = "25",

}

Rotational Dynamics of Proteins from Spin Relaxation Times and Molecular Dynamics Simulations. / Ollila, Samuli; Heikkinen, Harri August; Iwaï, Hideo.

In: Journal of Physical Chemistry B, Vol. 122, No. 25, 28.06.2018, p. 6559-6569.

Research output: Contribution to journalArticleScientificpeer-review

TY - JOUR

T1 - Rotational Dynamics of Proteins from Spin Relaxation Times and Molecular Dynamics Simulations

AU - Ollila, Samuli

AU - Heikkinen, Harri August

AU - Iwaï, Hideo

PY - 2018/6/28

Y1 - 2018/6/28

N2 - 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.

AB - 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.

KW - 1182 Biochemistry, cell and molecular biology

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KW - NMR ORDER PARAMETERS

KW - PARTICLE MESH EWALD

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KW - CONFORMATIONAL ENTROPY

KW - FORCE-FIELD

KW - MD SIMULATIONS

KW - FREE-ENERGY

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