TY - JOUR
T1 - Evolution of conformational changes in the dynamics of small biological molecules
T2 - A hybrid MD/RRK approach
AU - Segev, Elad
AU - Grumbach, Mikael
AU - Gerber, Robert Benny
PY - 2006
Y1 - 2006
N2 - The dynamics of long timescale evolution of conformational changes in small biological molecules is described by a hybrid molecular dynamics/RRK algorithm. The approach employs classical trajectories for transitions between adjacent structures separated by a low barrier, and the classical statistical RRK approximation when the barrier involved is high. In determining the long-time dynamics from an initial structure to a final structure of interest, an algorithm is introduced for determining the most efficient pathways (sequence of the intermediate conformers). This method uses the Dijkstra algorithm for finding optimal paths on networks. Three applications of the method using an AMBER force field are presented: a detailed study of conformational transitions in a blocked valine dipeptide; a multiple reaction path study of the blocked valine tripeptide; and the evolution in time from the β hairpin to α helix structure of a blocked alanine hexapeptide. Advantages and limitations of the method are discussed in light of the results.
AB - The dynamics of long timescale evolution of conformational changes in small biological molecules is described by a hybrid molecular dynamics/RRK algorithm. The approach employs classical trajectories for transitions between adjacent structures separated by a low barrier, and the classical statistical RRK approximation when the barrier involved is high. In determining the long-time dynamics from an initial structure to a final structure of interest, an algorithm is introduced for determining the most efficient pathways (sequence of the intermediate conformers). This method uses the Dijkstra algorithm for finding optimal paths on networks. Three applications of the method using an AMBER force field are presented: a detailed study of conformational transitions in a blocked valine dipeptide; a multiple reaction path study of the blocked valine tripeptide; and the evolution in time from the β hairpin to α helix structure of a blocked alanine hexapeptide. Advantages and limitations of the method are discussed in light of the results.
UR - http://www.scopus.com/inward/record.url?scp=33750482945&partnerID=8YFLogxK
U2 - 10.1039/b610872e
DO - 10.1039/b610872e
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C2 - 17066182
AN - SCOPUS:33750482945
SN - 1463-9076
VL - 8
SP - 4915
EP - 4923
JO - Physical Chemistry Chemical Physics
JF - Physical Chemistry Chemical Physics
IS - 42
ER -