Application of the Gaussian theory of elastomeric networks to native proteins: analysis of fluctuations and the dynamic scattering function

摘要

The junctions of an elastomeric network fluctuate about well-defined mean positions under the effects of covalently-bonded chains attached to the junctions. The residues of native proteins fluctuate about well-defined mean positions under the Lennard-Jones, dipole moment, hydrogen bond and electrostatic forces exerted by spatially neighbouring residues. Both an elastomer and a native protein are elastic bodies in this respect, and therefore share many structural features. The magnitude of fluctuations of the junctions in networks is significant, leading to their well-known interesting features. The ratio of root-mean-square fluctuations of the distance between two spatially neighbouring residues to the distance between them is of the same order of magnitude as that between two network junctions joined by a network chain. Based on the analogy of the network and protein structure, the method of evaluating the fluctuations of residues and the dynamic coherent and incoherent scattering functions is described and sample calculations for two model proteins are presented.