Structural, Conformational and Interactional Investigation of Proteins with Related Sequences and Multiple Structures

Abstract

Homologous proteins are special macromolecules with related primary sequences and multiple native structures and together with sequence-unrelated nonhomologous ones both constitute the protein amazing universe. Here is made a thorough sample selection, and employed quantitative predictions to analyze structures, conformations, steric and hydrophobic interactions and underlying molecular mechanisms in proteins via two coarse-grained (hydrophobic-polar, large-small) models. First, five empirical relations from nonhomologous samples are determined correlating large and hydrophobic residue sequences from primary to helix and β-sheet structures of functional conformations. When applied to homologous proteins, such empirical relations allow precisely surveying the interaction performance, identifying four types of molecular mechanisms, and computing the stability level in conformation ensembles. 1764 structural inspections capture essential features and furnish structural-interactional insights for homologous proteins, as well as suggest a fruitful way for better understanding conformational variability in biomolecular processes such as protein evolution, dynamics, folding and design.