A mass weighted chemical elastic network model elucidates closed form domain motions in proteins

Min Hyeok Kim, Sangjae Seo, Jay Il Jeong, Bum Joon Kim, Wing Kam Liu, Byeong Soo Lim, Jae Boong Choi, Moon Ki Kim*

*Corresponding author for this work

Research output: Contribution to journalArticlepeer-review

17 Scopus citations

Abstract

An elastic network model (ENM), usually Cα coarse-grained one, has been widely used to study protein dynamics as an alternative to classical molecular dynamics simulation. This simple approach dramatically saves the computational cost, but sometimes fails to describe a feasible conformational change due to unrealistically excessive spring connections. To overcome this limitation, we propose a mass-weighted chemical elastic network model (MWCENM) in which the total mass of each residue is assumed to be concentrated on the representative alpha carbon atom and various stiffness values are precisely assigned according to the types of chemical interactions. We test MWCENM on several well-known proteins of which both closed and open conformations are available as well as three α-helix rich proteins. Their normal mode analysis reveals that MWCENM not only generates more plausible conformational changes, especially for closed forms of proteins, but also preserves protein secondary structures thus distinguishing MWCENM from traditional ENMs. In addition, MWCENM also reduces computational burden by using a more sparse stiffness matrix.

Original languageEnglish (US)
Pages (from-to)605-613
Number of pages9
JournalProtein Science
Volume22
Issue number5
DOIs
StatePublished - May 2013

Keywords

  • Closed protein conformation
  • Elastic network model
  • Normal mode analysis
  • Protein dynamics

ASJC Scopus subject areas

  • Biochemistry
  • Molecular Biology

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