New methodology for computer-aided modelling of biomolecular structure and dynamics. 1. Non-cyclic structures.
A general methodology is proposed for the conformational modelling of biomolecular systems. The approach allows one: (i) to describe the system under investigation by an arbitrary set of internal variables, i.e., torsion angles, bond angles, and bond lengths; it offers a possibility to pass from the free structure to a completely fixed one with the number of variables from 3N to zero, respectively, where N is the number of atoms; (ii) to consider both, a single molecule and a complex of many molecules, (e.g., proteins, water, ligands, etc.) in terms of one universal model; (iii) to study the dynamics of the system using explicit analytical Lagrangian equations of motion, thus opening up possibilities for investigations of slow concerted motions such as domain oscillations in proteins etc.; (iv) to calculate the partial derivatives of various functions of conformation, e.g., the conformational energy or external constraints imposed, using a standard efficient procedure regardless of the variables and the structure of the system. The approach is meant to be used in various investigations concerning the conformations and dynamics of biomacromolecules.
Mazur
A K
AK
Pacific Institute of Bioorganic Chemistry, USSR Academy of Sciences, Vladivostok.
Abagyan
R A
RA
D003198:Computer Simulation; D008958:Models, Molecular; D008968:Molecular Conformation; D013816:Thermodynamics