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Biophysical Reviews

, Volume 9, Issue 6, pp 877–893 | Cite as

Normal mode analysis as a method to derive protein dynamics information from the Protein Data Bank

  • Hiroshi WakoEmail author
  • Shigeru Endo
Review

Abstract

Normal mode analysis (NMA) can facilitate quick and systematic investigation of protein dynamics using data from the Protein Data Bank (PDB). We developed an elastic network model-based NMA program using dihedral angles as independent variables. Compared to the NMA programs that use Cartesian coordinates as independent variables, key attributes of the proposed program are as follows: (1) chain connectivity related to the folding pattern of a polypeptide chain is naturally embedded in the model; (2) the full-atom system is acceptable, and owing to a considerably smaller number of independent variables, the PDB data can be used without further manipulation; (3) the number of variables can be easily reduced by some of the rotatable dihedral angles; (4) the PDB data for any molecule besides proteins can be considered without coarse-graining; and (5) individual motions of constituent subunits and ligand molecules can be easily decomposed into external and internal motions to examine their mutual and intrinsic motions. Its performance is illustrated with an example of a DNA-binding allosteric protein, a catabolite activator protein. In particular, the focus is on the conformational change upon cAMP and DNA binding, and on the communication between their binding sites remotely located from each other. In this illustration, NMA creates a vivid picture of the protein dynamics at various levels of the structures, i.e., atoms, residues, secondary structures, domains, subunits, and the complete system, including DNA and cAMP. Comparative studies of the specific protein in different states, e.g., apo- and holo-conformations, and free and complexed configurations, provide useful information for studying structurally and functionally important aspects of the protein.

Keywords

Elastic network model Protein structure network Catabolite activator protein Full-atom system Decomposition into internal and external motions 

Notes

Acknowledgements

This work was supported by a JSPS Grant-in-Aid for Scientific Research (C) (grant no. 16K00407).

Compliance with ethical standards

Conflict of interest

Hiroshi Wako declares that he has no conflict of interest. Shigeru Endo declares that he has no conflict of interest.

Ethical approval

This article does not contain any studies with human participants or animals performed by any of the authors.

Supplementary material

12551_2017_330_MOESM1_ESM.docx (503 kb)
ESM 1 (DOCX 503 kb)

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Copyright information

© International Union for Pure and Applied Biophysics (IUPAB) and Springer-Verlag GmbH Germany 2017

Authors and Affiliations

  1. 1.School of Social SciencesWaseda UniversityTokyoJapan
  2. 2.Department of Physics, School of ScienceKitasato UniversitySagamiharaJapan

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