An Efficient Timer and Sizer of Biomacromolecular Motions

Justin Chan; Kazuhiro Takemura; Hong-Rui Lin; Kai-Chun Chang; Yuan-Yu Chang; Yasumasa Joti; Akio Kitao; Lee-Wei Yang

doi:10.1016/j.str.2019.10.020

An Efficient Timer and Sizer of Biomacromolecular Motions

Structure. 2020 Feb 4;28(2):259-269.e8. doi: 10.1016/j.str.2019.10.020. Epub 2019 Nov 25.

Authors

Justin Chan¹, Kazuhiro Takemura², Hong-Rui Lin³, Kai-Chun Chang⁴, Yuan-Yu Chang³, Yasumasa Joti⁵, Akio Kitao⁶, Lee-Wei Yang⁷

Affiliations

¹ Institute of Bioinformatics and Structural Biology, National Tsing Hua Univ., No. 101, Section 2, Kuang-Fu Road, Hsinchu 30013, Taiwan; Bioinformatics Program, Taiwan International Graduate Program, Institute of Information Science, Academia Sinica, Taipei, Taiwan.
² School of Life Science and Technology, Tokyo Institute of Technology, M6-13, 2-12-1 Ookayama, Meguro, Tokyo 152-8550, Japan.
³ Institute of Bioinformatics and Structural Biology, National Tsing Hua Univ., No. 101, Section 2, Kuang-Fu Road, Hsinchu 30013, Taiwan.
⁴ Institute of Molecular and Cellular Biology, National Taiwan University, Taipei, Taiwan.
⁵ XFEL Utilization Division, Japan Synchrotron Radiation Research Institute, 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo 679-5198, Japan.
⁶ School of Life Science and Technology, Tokyo Institute of Technology, M6-13, 2-12-1 Ookayama, Meguro, Tokyo 152-8550, Japan. Electronic address: akitao@bio.titech.ac.jp.
⁷ Institute of Bioinformatics and Structural Biology, National Tsing Hua Univ., No. 101, Section 2, Kuang-Fu Road, Hsinchu 30013, Taiwan; Bioinformatics Program, Taiwan International Graduate Program, Institute of Information Science, Academia Sinica, Taipei, Taiwan; Physics Division, National Center for Theoretical Sciences, Hsinchu, Taiwan. Electronic address: lwyang@mx.nthu.edu.tw.

PMID: 31780433
DOI: 10.1016/j.str.2019.10.020

Abstract

Life ticks as fast as how proteins move. Computationally expensive molecular dynamics simulation has been the only theoretical tool to gauge the time and sizes of these motions, though barely to their slowest ends. Here, we convert a computationally cheap elastic network model (ENM) into a molecular timer and sizer to gauge the slowest functional motions of structured biomolecules. Quasi-harmonic analysis, fluctuation profile matching, and the Wiener-Khintchine theorem are used to define the "time periods," t, for anharmonic principal components (PCs), which are validated by nuclear magnetic resonance (NMR) order parameters. The PCs with their respective "time periods" are mapped to the eigenvalues (λ_ENM) of the corresponding ENM modes. Thus, the power laws t(ns) = 56.1λ_ENM^-1.6 and σ²(Å²) = 32.7λ_ENM^-3.0 can be established allowing the characterization of the timescales of NMR-resolved conformers, crystallographic anisotropic displacement parameters, and important ribosomal motions, as well as motional sizes of the latter.

Keywords: Wiener-Khintchine theorem; anharmonicity; elastic network model (ENM); molecular dynamics simulations; order parameter; power spectrum; principal component analysis (PCA); protein dynamics; ribosome; time-correlation function.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

Computational Biology / methods*
Crystallography, X-Ray
Elastic Modulus
Magnetic Resonance Spectroscopy
Models, Molecular
Molecular Dynamics Simulation
Principal Component Analysis
Protein Conformation
Proteins / chemistry*
Time

Substances

Proteins