Computational Structural Analysis of C-Terminal Residues of Proteins Containing Transmembrane Regions
For the past few years, the numbers of transmembrane protein structures in Protein Data Bank have been increased substantially. It is of interest to analyze the terminal residues of transmembrane proteins by using computational approaches. Also, up to our knowledge, no analysis was reported in the literature on the study of terminal residues in transmembrane proteins. While the N-terminal position of alpha and beta transmembrane proteins are composed of signal peptides, in the present work, a careful, in-depth, computational analysis such as residue preference, stability upon mutation, solvent accessibility, hydrogen bonding and carboxy terminal pentapeptide pattern search respectively has been done on C-terminal residues. Alanine in alpha transmembrane proteins and phenylalanine in beta transmembrane proteins are highly preferred. Glutamic acid and glycine residues can be substituted at the terminal sites of alpha and beta transmembrane proteins without affecting the protein's overall stability. Hydrogen bonding of terminal residues is studied in detail. Pattern search of carboxy pentapeptides shows that identical pentapeptides with reference to the position can adopt a different secondary structure. The results discussed in this paper may help to understand the role of carboxy terminal residues in alpha and beta transmembrane proteins. From our analysis, we insist that the preferences and structural analysis of carboxy terminal residues in alpha and beta transmembrane proteins, can help to model and design novel transmembrane proteins.
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