Computer Molecular Dynamics Studies on Protein Structures (Visual Pigment Rhodopsin and Cyclin‐Dependent Kinases) Available to Purchase

Based on the computer molecular dynamics (MD) calculations we have simulated for the visual pigment rhodopsin and cyclin‐dependent kinase proteins the dynamical and structural properties at reliable physiological temperatures and conditions. MD simulations are carried out on the rhodopsin protein to investigate the conformational changes of the protein in relation to the inclusion of the 11‐cis chromophore retinal into consideration. It was demonstrated that the adaptation of the chromophore retinal in the opsin site causes a considerable influence on its protein binding pocket, as well as on conformations of the cytoplasmic part, but the extracelluar part of the protein shows a comparably small changes. On the basis of the simulaton results we discuss some molecular mechanisms for the rhodopsin protein function as a G‐protein‐coupled receptor in the dark state, i.e. for the chromophore retinal as a ligand‐agonist stabilizaing the inactive conformation. The central role that cyclin‐dependent kinases (CDK) play in the timing of cell division and repair and the high incidence of genetic alteration of CDKs or deregulation of CDK inhibitors in a number of cancers make CDC28 of yeast Saccharomyces cerevisiae very attractive model for studies of mechanisms of CDK regulation. The crystal structure of the human CDK2 has served as a model for the catalytic core of other CDKs, including CDC28. Nanoseconds long molecular dynamics trajectories of the CDK2/ATP complex were analyzed. The MD simulations of substitution CDK2‐G16S in conserved G‐loop shows an important of this amino acid and a conformational change of CDK2 structure resulting in the moving of the G‐loop away from ATP and a new rearrangement of amino acids in the T‐loop.