Effects of Physicochemical and Functional Constraints on the Sequence and Structure of Proteins
2013-06-28T00:00:00Z (GMT) by
Proteins carry out essential functions in living organisms. The sequence and structure of proteins are constrained by numerous factors. In this thesis, we use computational methods to examine the effects of some physicochemical and functional constraints at different levels of the sequence and structure of proteins. First, we studied how the hydrophobic environment of cellular membranes directs the evolution of beta-barrel membrane proteins. These proteins play important roles in the outer membrane of gram-negative bacteria, mitochondria, and chloroplasts. We quantified the substitution rates of residues in the transmembrane region. We used the estimated substitution rates to derive scoring matrices that allow a more accurate detection of homologs of beta-barrel membrane proteins through database searches. We also used the substitution rates to engineer a beta-barrel membrane protein with a different oligomerization state, which has important implications for the use of these proteins as nano-devices. Second, we studied functional cavities on enzymes. We propose charge density as a measurement defining these spaces. We found that the catalytic active site, with large values of charge density, is an unusual electrostatic and steric environment in which side chains and reactants are crowded together in a mixture more like an ionic liquid than an ideal infinitely dilute solution. We also found enormous values of charge density in other functional cavities and suggest that this may be one of the forces responsible for dynamic fluctuations on protein enzymes and essential for function. Finally, we investigated lysine carboxylation, a post-translational modification that occurs spontaneously under certain physicochemical conditions, with a critical role in the catalytic mechanism of several important enzymes. We characterized the signature microenvironment of lysine carboxylation sites, and developed a computational method for their detection, which achieves excellent performance. Our results suggest that approximately 2% of large proteins in both prokaryotes and eukaryotes may contain a carboxylated lysine residue, a three-fold increase from what it is currently known. Our results also suggest that spontaneous post-translational modifications, by switching enzymes on and off under appropriate physicochemical conditions, may frequently serve as an efficient biological machinery of regulation.