Article
Brownian Dynamics Simulation of Helix-Capping Motifs
Biopolymers
(2003)
Abstract
Helix-capping motifs are believed to play an important role in stabilizing alpha-helices and defining helix start and stop signals. We performed microsecond scale Brownian dynamics simulations to study ten XAAD sequences, with X = (A,E,I,L,N,Q,S,T,V,Y), to examine their propensity to form helix capping motifs and correlate these results with those obtained from analyzing a structural database of proteins. For the widely studied capping box motif S**D, where the asterisk can be any amino acid residue, the simulations suggested that one of the two hydrogen bonds proposed earlier as a stabilizing factor might not be as important. On the other hand, side-chain interactions between the capping residue and the third residue downstream on the polypeptide chain might also play a role in stabilizing this motif. These results are consistent with explicit-solvent molecular dynamics simulations of two capping box motifs found in the proteins BPTI and alpha-dendrotoxin. Principal component analysis of the SAAD trajectory showed that the first three principal components, after those corresponding to translational-rotational motion were removed, accounted for more than half of the conformational fluctuations. The first component separated the conformational space into two parts with the all-helical conformation and the capping box motif lying largely in one part. The second component, on the other hand, could be used to describe conformational transitions between the all-helical form and the capping box motif.
Disciplines
Publication Date
October 1, 2003
DOI
10.1002/bip.10466
Citation Information
Tongye Shen, Chung F. Wong and J. Andrew McCammon. "Brownian Dynamics Simulation of Helix-Capping Motifs" Biopolymers Vol. 70 Iss. 2 (2003) p. 252 - 259 Available at: http://works.bepress.com/chung-wong/40/