Biomedical subjects

Ram Samudrala

Publications and source records attributed to Ram Samudrala.

39 records · Page 3Linked to original sources

PubMed2002

Genes for the cytoskeletal protein tubulin in the bacterial genus Prosthecobacter.

Tubulins, the protein constituents of the microtubule cytoskeleton, are present in all known eukaryotes but have never been found in the Bacteria or Archaea. Here we report the presence of two tubulin-like genes [bacterial tubulin a (btuba) and bacterial tubulin b (btubb)] in bacteria of the genus Prosthecobacter (Division Verrucomicrobia). In this study, we investigated the organization and expression of these genes and conducted a comparative analysis of the bacterial and eukaryotic protein sequences, focusing on their phylogeny and 3D structures. The btuba and btubb genes are arranged as adjacent loci within the genome along with a kinesin light chain gene homolog. RT-PCR experiments indicate that these three genes are cotranscribed, and a probable promoter was identified upstream of btuba. On the basis of comparative modeling data, we predict that the Prosthecobacter tubulins are monomeric, unlike eukaryotic alpha and beta tubulins, which form dimers and are therefore unlikely to form microtubule-like structures. Phylogenetic analyses indicate that the Prosthecobacter tubulins are quite divergent and do not support recent horizontal transfer of the genes from a eukaryote. The discovery of genes for tubulin in a bacterial genus may offer new insights into the evolution of the cytoskeleton.

Base Sequence↗

PubMed2002

A comprehensive analysis of 40 blind protein structure predictions.

BACKGROUND: We thoroughly analyse the results of 40 blind predictions for which an experimental answer was made available at the fourth meeting on the critical assessment of protein structure methods (CASP4). Using our comparative modelling and fold recognition methodologies, we made 29 predictions for targets that had sequence identities ranging from 50% to 10% to the nearest related protein with known structure. Using our ab initio methodologies, we made eleven predictions for targets that had no detectable sequence relationships. RESULTS: For 23 of these proteins, we produced models ranging from 1.0 to 6.0 A root mean square deviation (RMSD) for the Calpha atoms between the model and the corresponding experimental structure for all or large parts of the protein, with model accuracies scaling fairly linearly with respect to sequence identity (i.e., the higher the sequence identity, the better the prediction). We produced nine models with accuracies ranging from 4.0 to 6.0 A Calpha RMSD for 60-100 residue proteins (or large fragments of a protein), with a prediction accuracy of 4.0 A Calpha RMSD for residues 1-80 for T110/rbfa. CONCLUSIONS: The areas of protein structure prediction that work well, and areas that need improvement, are discernable by examining how our methods have performed over the past four CASP experiments. These results have implications for modelling the structure of all tractable proteins encoded by the genome of an organism.

Amino Acid Sequence↗

PubMed2002

Identification of amino acids in the Dr adhesin required for binding to decay-accelerating factor.

Members of the Dr family of adhesins of Escherichia coli recognize as a receptor the Dr(a) blood-group antigen present on the complement regulatory and signalling molecule, decay-accelerating factor (DAF). One member of this family, the Dr haemagglutinin, also binds to a second receptor, type IV collagen. Structure/function information regarding these adhesins has been limited and domains directly involved in the interaction with DAF have not been determined. We devised a strategy to identify amino acids in the Dr haemagglutinin that are specifically involved in the interaction with DAF. The gene encoding the adhesive subunit, draE, was subjected to random mutagenesis and used to complement a strain defective for its expression. The resulting mutants were enriched and screened to obtain those that do not bind to DAF, but retain binding to type IV collagen. Individual amino acid changes at positions 10, 63, 65, 75, 77, 79 and 131 of the mature DraE sequence significantly reduced the ability of the DraE adhesin to bind DAF, but not collagen. Over half of the mutants obtained had substitutions within amino acids 63-81. Analysis of predicted structures of DraE suggest that these proximal residues may cluster to form a binding domain for DAF.

Adhesins, Bacterial↗