Coarse-graining of protein structures for the normal mode studies

Kilho Eom, Seung Chul Baek, Jung H. Ahn, Sung Soo Na

Research output: Contribution to journalArticle

30 Citations (Scopus)

Abstract

The coarse-grained structural model such as Gaussian network has played a vital role in the normal mode studies for understanding protein dynamics related to biological functions. However, for the large proteins, the Gaussian network model is computationally unfavorable for diagonalization of Hessian (stiffness) matrix for the normal mode studies. In this article, we provide the coarse-graining method, referred to as "dynamic model condensation," which enables the further coarse-graining of protein structures consisting of small number of residues. It is shown that the coarser-grained structures reconstructed by dynamic model condensation exhibit the dynamic characteristics, such as low-frequency normal modes, qualitatively comparable to original structures. This sheds light on that dynamic model condensation and may enable one to study the large protein dynamics for gaining insight into biological functions of proteins.

Original languageEnglish
Pages (from-to)1400-1410
Number of pages11
JournalJournal of Computational Chemistry
Volume28
Issue number8
DOIs
Publication statusPublished - 2007 Jun 1

Fingerprint

Coarse-graining
Normal Modes
Protein Structure
Condensation
Proteins
Protein
Dynamic Model
Dynamic models
Hessian matrix
Diagonalization
Structural Model
Gaussian Model
Dynamic Characteristics
Stiffness Matrix
Network Model
Structural Models
Low Frequency
Stiffness matrix

Keywords

  • Coarse-graining
  • Gaussian network model
  • Low-frequency normal modes
  • Normal mode analysis
  • Protein dynamics

ASJC Scopus subject areas

  • Chemistry(all)
  • Safety, Risk, Reliability and Quality

Cite this

Coarse-graining of protein structures for the normal mode studies. / Eom, Kilho; Baek, Seung Chul; Ahn, Jung H.; Na, Sung Soo.

In: Journal of Computational Chemistry, Vol. 28, No. 8, 01.06.2007, p. 1400-1410.

Research output: Contribution to journalArticle

Eom, Kilho ; Baek, Seung Chul ; Ahn, Jung H. ; Na, Sung Soo. / Coarse-graining of protein structures for the normal mode studies. In: Journal of Computational Chemistry. 2007 ; Vol. 28, No. 8. pp. 1400-1410.
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