COLLECTIVE VARIABLE DESCRIPTION OF NATIVE PROTEIN DYNAMICS

The importance of collective motions in proteins, such as hinge-bendin g motions or motions involving domains, has been recognized. Occurrenc e of such motions and their experimental and theoretical studies are r eviewed. Normal-mode analysis and principal component analysis are pow erful theoretical tools for studying such motions. The former is based on the assumption of harmonicity of the dynamics, while the latter is valid even when the dynamics is highly anharmonic. The results of the latter analysis indicate that most important conformational events ar e taking place in a conformational subspace spanned by a rather small number of principal modes, and this important subspace is also spanned by a small number of normal modes. The normal-mode refinement method of protein X-ray crystallography, which is developed based on the conc ept of the above important subspace, is discussed.