Normal Mode Analysis of G-actin

doi:10.1006/jmbi.1993.1135

Journal of Molecular Biology

Volume 230, Issue 1, 5 March 1993, Pages 186-195

https://doi.org/10.1006/jmbi.1993.1135 Get rights and content

Abstract

We undertook a normal mode analysis of the G-actin monomer bound with ADP and Ca²⁺, in order to better understand the internal modes of this protein. The internal co-ordinates consisted of 1373 single bond torsions, plus an additional 11 torsions to parameterize the motion of the nucleotide and cation with respect to the protein. A generalized eigenvalue problem was solved to yield a complete description of the motion in the 0·1 to 17·0 picosecond time range. The modes were visualized using an interactive graphics routine. The softest, slowest modes include a propeller-like twisting of the large and small domain about the phosphate binding loops, a rolling of subdomain 4 about an α-helix axis and a scissor-type opening and closing of the ADP-binding cleft. The computed temperature factors agree well with experimental ones. A comparable analysis done on G-actin-ATP shows that the softest modes are almost identical.

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Journal of Molecular Biology

Regular ArticleNormal Mode Analysis of G-actin

Abstract

Regular Article
Normal Mode Analysis of G-actin