INTERNAL PACKING CONDITIONS AND FLUCTUATIONS OF AMINO-ACID-RESIDUES IN GLOBULAR-PROTEINS

In order to investigate the environmental conditions of amino acid res idues in protein molecules, four kinds of packing studies (atomic, geo metric, hydrophobic and hydration) were formulated and tested on two p roteins; bovine pancreatic trypsin inhibitor (BPTI) and bovine pancrea tic ribonuclease S (RNase S). The inter-relationship of these packings on the fluctuations of amino acid residues was analysed by comparing the packing results with the dynamical studies, such as the root-mean- square-deviation values of atomic displacements obtained from the traj ectories of molecular dynamics simulation, temperature factor informat ion from crystal structures and residue fluctuations in proteins from continuum model. These analyses yield information about the most fluct uating and most stabilizing residue sites. Comparison of the results o btained by these methods indicate a good agreement, specifying an inve rse correlation between the residue packing and fluctuations. This kin d of study is helpful in identifying the specific residue sites such a s nucleation, receptor binding and antigenic determining sites which i n a way indirectly correlates with the functional residues in protein molecules.