Protein displacements under external forces: An atomistic Langevin dynamics approach.
We present a fully atomistic Langevin dynamics approach as a method to simulate biopolymers under external forces. In the harmonic regime, this approach permits the computation of the long-term dynamics using only the eigenvalues and eigenvectors of the Hessian matrix of second derivatives. We apply this scheme to identify polymorphs of model proteins by their mechanical response fingerprint, and we relate the averaged dynamics of proteins to their biological functionality, with the ion channel gramicidin A, a phosphorylase, and neuropeptide Y as examples. In an environment akin to dilute solutions, even small proteins show relaxation times up to 50 ns. Atomically resolved Langevin dynamics computations have been performed for the stretched gramicidin A ion channel.
Gnandt
David
D
Institut fur Physikalische Chemie, Universitat Freiburg, Albertstrasse 23a, D-79104 Freiburg im Breisgau, Germany.
Utz
Nadine
N
Blumen
Alexander
A
Koslowski
Thorsten
T
D001704:Biopolymers / Q000737:chemistry; D006096:Gramicidin / Q000737:chemistry; D007700:Kinetics; D009038:Motion; D009478:Neuropeptide Y / Q000737:chemistry; D006005:Phosphorylases / Q000737:chemistry; D011506:Proteins / Q000737:chemistry*; D011789:Quantum Theory; D012996:Solutions
D001704:Biopolymers; D009478:Neuropeptide Y; D011506:Proteins; D012996:Solutions; D006096:Gramicidin; D006005:Phosphorylases