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Title: Non-Gaussian behavior of elastic incoherent neutron scattering profiles of proteins studied by molecular dynamics simulation

Abstract

Elastic incoherent neutron scattering (EINS) data can be approximated with a Gaussian function of q in a low q region. However, in a higher q region the deviation from a Gaussian function becomes non-negligible. Protein dynamic properties can be derived from the analyses of the non-Gaussian behavior, which has been experimentally investigated. To evaluate the origins of the non-Gaussian behavior of protein dynamics, we conducted a molecular dynamics (MD) simulation of staphylococcal nuclease. Instead of the ordinary cumulant expansion, we decomposed the non-Gaussian terms into three components: (i) the component originating from the heterogeneity of the mean-square fluctuation (ii) that from the anisotropy, and (iii) that from higher-order terms such as anharmonicity. The MD simulation revealed various dynamics for each atom. The atomic motions are classified into three types: (i) 'harmonic', (ii) 'anisotropic', and (iii) 'anharmonic'. However, each atom has a different degree of anisotropy. The contribution of the anisotropy to the total scattering function averages out due to these differences. Anharmonic motion is described as the jump among multiple minima. The jump distance and the probability of the residence at one site vary from atom to atom. Each anharmonic component oscillates between positive and negative values. Thus, the contributionmore » of the anharmonicity to the total scattering is canceled due to the variations in the anharmonicity. Consequently, the non-Gaussian behavior of the total EINS from a protein can be analyzed by the dynamical heterogeneity.« less

Authors:
 [1];  [2]; ;  [3];  [2];  [4];  [1];  [2]
  1. Graduate School of Materials Science, Nara Institute of Science and Technology, 8916-5 Takayama, Ikoma, Nara 630-0192 (Japan)
  2. (Japan)
  3. Laboratory of Molecular Design, Institute of Molecular and Cellular Biosciences, University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-0032 (Japan)
  4. Neutron Biophysics Group, Neutron Biology Research Center, Quantum Beam Science Direction, Japan Atomic Energy Agency, Tokai, Ibaraki 319-1195 (Japan)
Publication Date:
OSTI Identifier:
21072416
Resource Type:
Journal Article
Resource Relation:
Journal Name: Physical Review. E, Statistical Physics, Plasmas, Fluids, and Related Interdisciplinary Topics; Journal Volume: 75; Journal Issue: 4; Other Information: DOI: 10.1103/PhysRevE.75.041912; (c) 2007 The American Physical Society; Country of input: International Atomic Energy Agency (IAEA)
Country of Publication:
United States
Language:
English
Subject:
71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSICS; 60 APPLIED LIFE SCIENCES; ANISOTROPY; ATOMS; BIOPHYSICS; COMPUTERIZED SIMULATION; DISTANCE; ENZYMES; FLUCTUATIONS; GAUSS FUNCTION; MOLECULAR DYNAMICS METHOD; NEUTRON DIFFRACTION; PROBABILITY

Citation Formats

Tokuhisa, Atsushi, Computational Biology Group, Neutron Biology Research Center, Quantum Beam Science Direction, Japan Atomic Energy Agency, 8-1 Umemidai, Kizu-cho, Soraku-gun, Kyoto 619-0215, Joti, Yasumasa, Kitao, Akio, Core Research for Evolutional Science and Technology, Japan Science and Technology Agency, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-0032, Nakagawa, Hiroshi, Kataoka, Mikio, and Neutron Biophysics Group, Neutron Biology Research Center, Quantum Beam Science Direction, Japan Atomic Energy Agency, Tokai, Ibaraki 319-1195. Non-Gaussian behavior of elastic incoherent neutron scattering profiles of proteins studied by molecular dynamics simulation. United States: N. p., 2007. Web. doi:10.1103/PHYSREVE.75.041912.
Tokuhisa, Atsushi, Computational Biology Group, Neutron Biology Research Center, Quantum Beam Science Direction, Japan Atomic Energy Agency, 8-1 Umemidai, Kizu-cho, Soraku-gun, Kyoto 619-0215, Joti, Yasumasa, Kitao, Akio, Core Research for Evolutional Science and Technology, Japan Science and Technology Agency, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-0032, Nakagawa, Hiroshi, Kataoka, Mikio, & Neutron Biophysics Group, Neutron Biology Research Center, Quantum Beam Science Direction, Japan Atomic Energy Agency, Tokai, Ibaraki 319-1195. Non-Gaussian behavior of elastic incoherent neutron scattering profiles of proteins studied by molecular dynamics simulation. United States. doi:10.1103/PHYSREVE.75.041912.
Tokuhisa, Atsushi, Computational Biology Group, Neutron Biology Research Center, Quantum Beam Science Direction, Japan Atomic Energy Agency, 8-1 Umemidai, Kizu-cho, Soraku-gun, Kyoto 619-0215, Joti, Yasumasa, Kitao, Akio, Core Research for Evolutional Science and Technology, Japan Science and Technology Agency, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-0032, Nakagawa, Hiroshi, Kataoka, Mikio, and Neutron Biophysics Group, Neutron Biology Research Center, Quantum Beam Science Direction, Japan Atomic Energy Agency, Tokai, Ibaraki 319-1195. Sun . "Non-Gaussian behavior of elastic incoherent neutron scattering profiles of proteins studied by molecular dynamics simulation". United States. doi:10.1103/PHYSREVE.75.041912.
@article{osti_21072416,
title = {Non-Gaussian behavior of elastic incoherent neutron scattering profiles of proteins studied by molecular dynamics simulation},
author = {Tokuhisa, Atsushi and Computational Biology Group, Neutron Biology Research Center, Quantum Beam Science Direction, Japan Atomic Energy Agency, 8-1 Umemidai, Kizu-cho, Soraku-gun, Kyoto 619-0215 and Joti, Yasumasa and Kitao, Akio and Core Research for Evolutional Science and Technology, Japan Science and Technology Agency, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-0032 and Nakagawa, Hiroshi and Kataoka, Mikio and Neutron Biophysics Group, Neutron Biology Research Center, Quantum Beam Science Direction, Japan Atomic Energy Agency, Tokai, Ibaraki 319-1195},
abstractNote = {Elastic incoherent neutron scattering (EINS) data can be approximated with a Gaussian function of q in a low q region. However, in a higher q region the deviation from a Gaussian function becomes non-negligible. Protein dynamic properties can be derived from the analyses of the non-Gaussian behavior, which has been experimentally investigated. To evaluate the origins of the non-Gaussian behavior of protein dynamics, we conducted a molecular dynamics (MD) simulation of staphylococcal nuclease. Instead of the ordinary cumulant expansion, we decomposed the non-Gaussian terms into three components: (i) the component originating from the heterogeneity of the mean-square fluctuation (ii) that from the anisotropy, and (iii) that from higher-order terms such as anharmonicity. The MD simulation revealed various dynamics for each atom. The atomic motions are classified into three types: (i) 'harmonic', (ii) 'anisotropic', and (iii) 'anharmonic'. However, each atom has a different degree of anisotropy. The contribution of the anisotropy to the total scattering function averages out due to these differences. Anharmonic motion is described as the jump among multiple minima. The jump distance and the probability of the residence at one site vary from atom to atom. Each anharmonic component oscillates between positive and negative values. Thus, the contribution of the anharmonicity to the total scattering is canceled due to the variations in the anharmonicity. Consequently, the non-Gaussian behavior of the total EINS from a protein can be analyzed by the dynamical heterogeneity.},
doi = {10.1103/PHYSREVE.75.041912},
journal = {Physical Review. E, Statistical Physics, Plasmas, Fluids, and Related Interdisciplinary Topics},
number = 4,
volume = 75,
place = {United States},
year = {Sun Apr 15 00:00:00 EDT 2007},
month = {Sun Apr 15 00:00:00 EDT 2007}
}