Structural analysis of a set of proteins resulting from a bacterial genomics project

The targets of the Structural GenomiX (SGX) bacterial genomics project were proteins conserved in multiple prokaryotic organisms with no obvious sequence homolog in the Protein Data Bank of known structures. The outcome of this work was 80 structures, covering 60 unique sequences and 49 different genes. Experimental phase determination from proteins incorporating Se-Met was carried out for 45 structures with most of the remainder solved by molecular replacement using members of the experimentally phased set as search models. An automated tool was developed to deposit these structures in the Protein Data Bank, along with the associated X-ray diffraction data (including refined experimental phases) and experimentally confirmed sequences. BLAST comparisons of the SGX structures with structures that had appeared in the Protein Data Bank over the intervening 3.5 years since the SGX target list had been compiled identified homologs for 49 of the 60 unique sequences represented by the SGX structures. This result indicates that, for bacterial structures that are relatively easy to express, purify, and crystallize, the structural coverage of gene space is proceeding rapidly. More distant sequence-structure relationships between the SGX and PDB structures were investigated using PDB-BLAST and Combinatorial Extension (CE). Only one structure, SufD, has a truly unique topology compared to all folds in the PDB.     

Predicting knot or catenane type of site-specific recombination products

Site-specific recombination on supercoiled circular DNA yields a variety of knotted or catenated products. Here, we present a topological model of this process and characterize all possible products of the most common substrates: unknots, unlinks, and torus knots and catenanes. This model tightly prescribes the knot or catenane type of previously uncharacterized data. We also discuss how the model helps to distinguish products of distributive recombination and, in some cases, determine the order of processive recombination products.     

Upper Molar Cusp Dimensions of South African Australopithecines

Recently, a number of articles have been published on the mechanisms of dental development, and in particular on the genetic control of dental formation. As a specific example of the potential of this kind of research for paleoanthropological studies, cusp areas of upper molars of two species of South African Australopithecines (Australopithecus africanus, A. robustus) have been examined. The results suggest notable differences between the two species, possibly related to markedly different developmental pathways that are still far from clear in their details.