Premium
Finite‐state and reduced‐parameter representations of protein backbone conformations
Author(s) -
Buturović Ljubomir J.,
Smith Temple F.,
Vajda Sandor
Publication year - 1994
Publication title -
journal of computational chemistry
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.907
H-Index - 188
eISSN - 1096-987X
pISSN - 0192-8651
DOI - 10.1002/jcc.540150305
Subject(s) - dihedral angle , maxima and minima , representation (politics) , dihedral group , state (computer science) , mathematics , globular protein , square (algebra) , finite set , algorithm , chemistry , crystallography , physics , geometry , mathematical analysis , molecule , quantum mechanics , hydrogen bond , politics , political science , law , group (periodic table)
This article studies the representation of protein backbone conformations using a finite number of values for the backbone dihedral angles. We develop a combinatorial search algorithm that guarantees finding the global minima of functions over the configuration space of discrete protein conformations, and use this procedure to fit finite‐state models to the backbones of globular proteins. It is demonstrated that a finite‐state representation with a reasonably small number of states yields either a small root‐mean‐square error or a small dihedral angle deviation from the native structure, but not both at the same time. The problem can be resolved by introducing limited local optimization in each step of the combinatorial search. In addition, it is shown that acceptable approximation is achieved using a single dihedral angle as an independent variable in local optimization. Results for 11 proteins demonstrate the advantages and shortcomings of both the finite‐state and reduced‐parameter approximations of protein backbone conformations. © 1994 by John Wiley & Sons, Inc.