The use of protein sequence analysis to obtain structural, functional and evolutionary gleanings from biological systems

Protein sequences have long been considered basic purveyors of biological understanding. Unlike previously, the current, concerted sequencing efforts have resulted in an increased availability of sequence data in terms of phyletic range and completeness. This allows the opportunity to understand the evolution of protein sequences and provides means of extracting functional and structural information regarding the protein from their sequence. To this end, I have analyzed protein sequences using local alignment and profile searches, phylogenetic analysis, statistical and structural evaluation of multiple alignments. As a result, I was able extract biologically significant information at a level greater than what has been previously possible. Primary results obtained in this work are: (1) The identification of new protein superfamilies and reconstruction of active sites, catalytic mechanisms and functional features for these proteins. (2) The use of the recently developed profile search method PSI-BLAST to recognize folds of a large number of protein families by establishing statistically significant alignments between a protein of unknown fold and a protein with a determined structure. Subsequently, multiple alignments derived from these searches are used to predict features governing structural and functional properties of these protein families. This includes uncovering of the mechanisms of some basic enzymes, DNA and protein-protein interaction mode of transcription factors and adhesion molecules and a common allosteric regulation of a vast class of enzymes. (3) The dissection of biological functional systems such as the apoptotic machinery and the DNA repair systems. This has led to understanding the basic trends in the evolution of these systems and an improved functional reconstruction based on new findings such as active domains or active sites identified based on sequence analysis. (4) The use of sequence analysis to annotate complete or partial genome sequences and to reconstruct the biology of the organisms from the predicted proteome. One prominent feature of these studies includes the estimation of the level and nature of horizontal transfer in diverse prokaryotic taxa. Another important outcome of this study is the determination of the possible genomic cognates in terms of protein family expansions that accompanied the origin of multicellular animals.