We present a statistical graphical model to infer specific molecular function for unannotated protein sequences using homology. Based on phylogenomic principles, SIFTER (Statistical Inference of Function Through Evolutionary Relationships) accurately predicts molecular function for members of a protein family given a reconciled phylogeny and available function annotations, even when the data are sparse or noisy. Our method produced specific and consistent molecular function predictions across 100 Pfam families in comparison to the Gene Ontology annotation database, BLAST, GOtcha, and Orthostrapper. We performed a more detailed exploration of functional predictions on the adenosine-5′-monophosphate/adenosine deaminase family and the lactate/malate dehydrogenase family, in the former case comparing the predictions against a gold standard set of published functional characterizations. Given function annotations for 3% of the proteins in the deaminase family, SIFTER achieves 96% accuracy in predicting molecular function for experimentally characterized proteins as reported in the literature. The accuracy of SIFTER on this dataset is a significant improvement over other currently available methods such as BLAST (75%), GeneQuiz (64%), GOtcha (89%), and Orthostrapper (11%). We also experimentally characterized the adenosine deaminase from Plasmodium falciparum, confirming SIFTER's prediction. The results illustrate the predictive power of exploiting a statistical model of function evolution in phylogenomic problems. A software implementation of SIFTER is available from the authors.

has replaced its junior-and senior-level laboratory curriculum with two, two-semester long, student-led research projects as part of the department's American Chemical Society-accredited program. In the first semester of each sequence, a faculty instructor leads the students through a set of previously performed experiments and introduces the students to a research project, specific laboratory techniques, and instrumentation. As such, the first (fall) semester takes the form of a control experiment. During the second (spring) semester, students design and carry out experiments of their own choosing that are based on their research interests and that build upon the first semester's work. In the subsequent academic year, the research is continued by a new set of students. The research from the previous academic year's second semester becomes the control experiments of the current academic year's first semester. In this way, the research project continually grows and develops according to student decisions. During these two semesters, students are assessed on their ability to perform experiments, maintain proper record keeping, designing and following safety protocols, proposal writing, and written and oral presentations of their work. This program, which grants ownership, or autonomy, of a research project to our student body, has been well received by the students, helped to meet departmental objectives, and led to a research publication and a funded grant proposal.

Protein tyrosine kinases are critical cell signaling enzymes. These enzymes have a highly conserved Arg residue in their catalytic loop which is present two residues or four residues downstream from an absolutely conserved Asp catalytic base. Prior studies on protein tyrosine kinases Csk and Src revealed the potential for chemical rescue of catalytically-deficient mutant kinases (Arg to Ala mutations) by small diamino compounds, particularly imidazole, however the potency and efficiency of rescue was greater for Src. This current study further examines the structural and kinetic basis of rescue for mutant Src as compared to mutant Abl tyrosine kinase. An X-ray crystal structure of R388A Src revealed the surprising finding that a histidine residue of the N-terminus of a symmetry-related kinase inserts into the active site of the adjacent Src and mimics the hydrogen bonding pattern seen in wild-type protein tyrosine kinases. Abl R367A shows potent and efficient rescue more comparable to Src, even though its catalytic loop is more like that of Csk. Various enzyme redesigns of the active sites indicate that the degree and specificity of rescue is somewhat flexible, but the overall properties of the enzymes and rescue agents play an overarching role. The newly discovered rescue agent 2-aminoimidazole is about as efficient as imidazole in rescuing R/A Src and Abl. Rate vs. pH studies with these imidazole analogs suggest that the protonated imidazolium is the preferred form for chemical rescue, consistent with structural models. The efficient rescue seen with mutant Abl points to the potential of this approach to be used effectively to analyze Abl phosphorylation pathways in cells.Protein tyrosine kinases (PTKs 1 ) are key enzymes in cell signaling and play roles in a wide range of diseases including cancer (1,2). Several PTKs, including Abl, are targeted clinically with therapeutic agents, and others are the subject of pharmaceutical development (3). As members of the protein kinase superfamily, PTKs share conserved sequences and folds (2), and yet they show distinct substrate selectivity (4,5) and modes of regulation (6). Evidence *To whom correspondence should be addressed: P.A.C.: Tel, Fax, suggests that the mechanism of PTK-catalyzed phosphoryl transfer is dissociative, in which the bond to the leaving group ADP is largely broken prior to tyrosine phenol attack on the gamma phosphorus of ATP (7). The alignment, orientation, and spacing of the tyrosine and ATP substrates by key active site residues are believed to be crucial in facilitating catalysis based on structural (8), mutagenic (9), and kinetic (10) studies.The catalytic loop sequence, DLAARN, is conserved throughout the vast majority of the 90 human PTKs, but differs in the nine members of the Src family, which have the sequence DLRAAN ( Figure 1A) (2). This relocation of the Arg from the D+4 position in most PTKs to the D+2 position in the Src family suggests an unusual functional plasticity. A crystal structure of an insulin receptor tyrosine kina...