Computer-Based Screening of Functional Conformers of Proteins

A long-standing goal in biology is to establish the link between function, structure, and dynamics of proteins. Considering that protein function at the molecular level is understood by the ability of proteins to bind to other molecules, the limited structural data of proteins in association with other bio-molecules represents a major hurdle to understanding protein function at the structural level. Recent reports show that protein function can be linked to protein structure and dynamics through network centrality analysis, suggesting that the structures of proteins bound to natural ligands may be inferred computationally. In the present work, a new method is described to discriminate protein conformations relevant to the specific recognition of a ligand. The method relies on a scoring system that matches critical residues with central residues in different structures of a given protein. Central residues are the most traversed residues with the same frequency in networks derived from protein structures. We tested our method in a set of 24 different proteins and more than 260,000 structures of these in the absence of a ligand or bound to it. To illustrate the usefulness of our method in the study of the structure/dynamics/function relationship of proteins, we analyzed mutants of the yeast TATA-binding protein with impaired DNA binding. Our results indicate that critical residues for an interaction are preferentially found as central residues of protein structures in complex with a ligand. Thus, our scoring system effectively distinguishes protein conformations relevant to the function of interest

Reactivation of the relational interface in M_x001B_p2_x001B_sDBMS and implementation of the EWIR database

The primary Department of Defense source for technical parametric performance data on non-communications emitters is the Electronic Warfare Reprogramming Database (EWIRDB). Data representation in the EWIRDB is via disjointed parametric tree models which are implementation oriented. These parametric trees obscure the intended semantics and representation of the data, making the database difficult to use and understand. The problem addressed by this thesis is to determine if the relational model and the relational interface of the Multimodel and Multilingual Database System (M2DBMS) in the Laboratory for Database Systems Research at the Naval Postgraduate School is capable of supporting a representative subset of the EWIRDB. We implemented a representative portion of the EWIR database on the relational interface of the M2DEMS. In order to accomplish this the relational interface was reactivated and returned to its original operational state and fully tested to determine its capabilities. In addition, the schema and an instance of a relational EWIR data model must be developed for implementation. The relational interface was successfully returned to its original operational state. Significant limitations in the interface's ability to process queries were discovered, however, in that the system can not query schema of greater than four relations.http://archive.org/details/reactivationofre1094532201NAU.S. Navy (U.S.N.) authorsApproved for public release; distribution is unlimited

Ezrin and Moesin Function Together to Promote T Cell Activation

Abstract The highly homologous proteins ezrin, radixin, and moesin link proteins to the actin cytoskeleton. The two family members expressed in T cells, ezrin and moesin, are implicated in promoting T cell activation and polarity. To elucidate the contributions of ezrin and moesin, we conducted a systematic analysis of their function during T cell activation. In response to TCR engagement, ezrin and moesin were phosphorylated in parallel at the regulatory threonine, and both proteins ultimately localized to the distal pole complex (DPC). However, ezrin exhibited unique behaviors, including tyrosine phosphorylation and transient localization to the immunological synapse before movement to the DPC. To ask whether these differences reflect unique requirements for ezrin vs moesin in T cell signaling, we generated mice with conditional deletion of ezrin in mature T cells. Ezrin−/− T cells exhibited normal immunological synapse organization based upon localization of protein kinase C-θ, talin, and phospho-ZAP70. DPC localization of CD43 and RhoGDP dissociation inhibitor, as well as the novel DPC protein Src homology region 2 domain-containing phosphatase-1, was also unaffected. However, recruitment of three novel DPC proteins, ezrin binding protein of 50 kDa, Csk binding protein, and the p85 subunit of PI3K was partially perturbed. Biochemical analysis of ezrin−/− T cells or T cells suppressed for moesin using small interfering RNA showed intact early TCR signaling, but diminished levels of IL-2. The defects in IL-2 production were more pronounced in T cells deficient for both ezrin and moesin. These cells also exhibited diminished phospholipase C-γ1 phosphorylation and calcium flux. We conclude that despite their unique movement and phosphorylation patterns, ezrin and moesin function together to promote T cell activation.</jats:p