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A method for characterizing transition concertedness from polymer dynamics computer simulations
Author(s) -
Brown Michael L.,
Venable Richard M.,
Pastor Richard W.
Publication year - 1995
Publication title -
biopolymers
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.556
H-Index - 125
eISSN - 1097-0282
pISSN - 0006-3525
DOI - 10.1002/bip.360350105
Subject(s) - chemistry , dynamics (music) , polymer , transition (genetics) , chemical physics , molecular dynamics , statistical physics , nanotechnology , computational chemistry , organic chemistry , physics , biochemistry , materials science , acoustics , gene
Abstract A statistical method based on classifying the transitions among a set of dihedral angles within an “energy transfer window” is developed, and used to analyze Brownian (BD) and molecular dynamics (MD) simulations of the acyl chains in a lipid bilayer, and MD of neat hexadecane. It is shown for the BD simulation that when a transition of the dihedral angle in the center of the chain occurs, a transition of a particular next nearest neighbor (or angle 2‐apart) will follow concertedly with a probability of approximately 0.10 within a lime window of approximately 3 ps. The MD bilayer simulations, which are based on a more flexible model of the hydrocarbon chains, yield corresponding concerted transition probabilities of approximately 0.083 and window sizes of 1–2 ps. An analysis of angles 4‐apart yields concerted transition probabilities of 0.03 and 0.04 for the BD and MD bilayer simulations, respectively, and window sizes close to those of the corresponding 2‐apart cases. Statistical hypothesis testing very strongly rejects the assertion that these follower transitions are occurring at random. Similar analysis reveals marginal or no evidence of concertedness between 1‐apart (nearest neighbor) and between 3‐apart dihedral angle transitions. The pattern of concertedness for hexadecane is qualitatively similar to that of the lipid chains, although concertedness is somewhat stronger for the 3‐apart transitions and somewhat weaker for those 4‐apart. Finally, it is suggested that the diffusion of small solute molecules in membranes is better facilitated by non concerted transitions, which are associated with relatively large displacements of the chains, than by concerted transitions, which do little to change the chain shape. © 1995 John Wiley & Sons, Inc.