UC San Diego

Understanding the factors that govern protein folding and function is of necessary importance in protein design. At the core of this folding regime, position-specific amino acid distribution determines the propensities of the sequence towards particular secondary and tertiary structures. Several attempts have been made in understanding the key contributors that influence or at times dictate this position-specific distribution. To further elucidate these contributors, we have investigated the role of molecular weight in fixed configuration of the PDZ protein domain in position pairs that are within a certain spacial limit of one another. Furthermore, molecular weight-based site-specific distribution of amino acids in one of these pairs of meaningfully correlated positions fits a modified Boltzmann distribution. This tells us that for position pairs that are affected by molecular weight, under certain criteria, predictive models could be developed.