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

Hiroshi Wako, Shigeru Endo

Research output: Contribution to journalReview article

7 Citations (Scopus)

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.

Original languageEnglish
Pages (from-to)877-893
Number of pages17
JournalBiophysical Reviews
Volume9
Issue number6
DOIs
Publication statusPublished - 2017 Dec 1

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Databases
Proteins
Cyclic AMP Receptor Protein
DNA
DNA-Binding Proteins
Binding Sites
Ligands
Peptides

Keywords

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

ASJC Scopus subject areas

  • Biophysics
  • Structural Biology
  • Molecular Biology

Cite this

Normal mode analysis as a method to derive protein dynamics information from the Protein Data Bank. / Wako, Hiroshi; Endo, Shigeru.

In: Biophysical Reviews, Vol. 9, No. 6, 01.12.2017, p. 877-893.

Research output: Contribution to journalReview article

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