Computational Studies on Stability of Protein Sequences

The distributions of large hydrophobic residues coded by XTX are important in protein stability and function. Thymine is the only nucleotide got changed (to Uracil) in the base upon transcription. This leaves the mRNA less hydrophobic compared to its DNA counterpart. Large Hydrophobic Residues (LHR) such as phenylalanine, isoleucine, leucine, methionine and valine play an important role in protein folding and binding. We further describe the role of these LHR in proteins after analyzing the complete sets of 15 different species. It is observed that the globular proteins prefer to have 27% of large hydrophobic residues in total and all along the sequence except in active site. The active sites prefers to greater than 27% of LHR. A window analysis on these protein sequences shows that the 27% of LHR is well maintained at window length of 45 amino acids. The influenza virus and P. falciparum show a different LHR distribution profile compared to other model organism.