Open AccessTransmembrane Helix Assembly by Window Exchange Umbrella Sampling
Author(s) -
Soohyung Park,
Taehoon Kim,
Wonpil Im
Publication year - 2012
Publication title -
physical review letters
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 3.688
H-Index - 673
eISSN - 1079-7114
pISSN - 0031-9007
DOI - 10.1103/physrevlett.108.108102
Subject(s) - helix (gastropod) , umbrella sampling , sampling (signal processing) , transmembrane domain , dimer , transmembrane protein , molecular dynamics , set (abstract data type) , window (computing) , range (aeronautics) , computer science , biological system , physics , materials science , chemistry , computational chemistry , membrane , nuclear magnetic resonance , biology , computer vision , programming language , receptor , snail , ecology , composite material , filter (signal processing) , biochemistry , operating system
A method of window exchange umbrella sampling molecular dynamics simulation is employed for transmembrane helix assembly. An analytical expression for the average acceptance probability between neighboring windows is derived and combined with the first passage time optimization method to predetermine a parameter set in an optimal range. With the parameter set, the method provides a substantially more efficient sampling of helix-helix interfaces together with the potential of mean force along the helix-helix distance of a transmembrane helix-dimer model, compared to the umbrella sampling method.
Accelerating Research
Robert Robinson Avenue,
Oxford Science Park, Oxford
OX4 4GP, United Kingdom
Address
John Eccles HouseRobert Robinson Avenue,
Oxford Science Park, Oxford
OX4 4GP, United Kingdom