The Structural Biology Knowledgebase (SBKB, http://sbkb.org) is a scientific search portal that returns comprehensive biological and methodological information about a protein sequence. Information related to 3D protein structures and the sequences targeted by worldwide structural genomics efforts are combined with links to open biological resources to give an integrated view of a protein. It is made in collaboration with the Protein Structure Initiative and the Nature Publishing Group, and features the latest research and technology advances each month to enable researchers in a broad range of biomedical fields. This presentation will introduce the Web portal and its services, and illustrate common user cases of the SBKB.

The Protein Structure Initiative’s Structural Biology Knowledgebase (SBKB, URL: http://sbkb.org ) is an open web resource designed to turn the products of the structural genomics and structural biology efforts into knowledge that can be used by the biological community to understand living systems and disease. Here we will present examples on how to use the SBKB to enable biological research. For example, a protein sequence or Protein Data Bank (PDB) structure ID search will provide a list of related protein structures in the PDB, associated biological descriptions (annotations), homology models, structural genomics protein target status, experimental protocols, and the ability to order available DNA clones from the PSI:Biology-Materials Repository. A text search will find publication and technology reports resulting from the PSI’s high-throughput research efforts. Web tools that aid in research, including a system that accepts protein structure requests from the community, will also be described. Created in collaboration with the Nature Publishing Group, the Structural Biology Knowledgebase monthly update also provides a research library, editorials about new research advances, news, and an events calendar to present a broader view of structural genomics and structural biology.

Sessions C555Since CpxP has no homologues of known function, we have initially focused on its biophysical and structural characterization.Using multi-angle laser light scattering (MALLS), small-angle Xray scattering (SAXS) analysis, and formaldehyde-mediated crosslinking experiments, we show that full-length E. coli CpxP is a dimer in vivo as well as in pathway inactivating (pH 5.8) and activating (pH 8.0) conditions in vitro.Far-UV circular dichroism (CD) was used to demonstrate that CpxP is mainly α-helical, while near-UV CD and SAXS revealed that the protein may undergo a small structural adjustment in response to a pathway-inducing stimulus (pH 8.0).The crystal structure of CpxP, determined to 2.85 Å resolution, revealed an antiparallel dimer of intertwined α-helices with a highly basic concave surface.Each protomer consists of a long, hooked and bent hairpin fold with conserved LTXXQ motifs forming two diverging turns at one end.Three of six previously characterized cpxP loss-of-function mutations, M 59 T, Q 55 P, and Q 128 H, likely result from a destabilization of the protein fold, whereas the R 60 Q, D 61 E, and D 61 V mutations may alter interactions important for the signalling or proteolytic adaptor functions of CpxP.

A consensus classification and nomenclature are defined for RNA backbone structure using all of the backbone torsion angles. By a consensus of several independent analysis methods, 46 discrete conformers are identified as suitably clustered in a quality-filtered, multidimensional dihedral angle distribution. Most of these conformers represent identifiable features or roles within RNA structures. The conformers are given two-character names that reflect the seven-angle delta epsilon zeta alpha beta gamma delta combinations empirically found favorable for the sugar-to-sugar "suite" unit within which the angle correlations are strongest (e.g., 1a for A-form, 5z for the start of S-motifs). Since the half-nucleotides are specified by a number for delta epsilon zeta and a lowercase letter for alpha beta gamma delta, this modular system can also be parsed to describe traditional nucleotide units (e.g., a1) or the dinucleotides (e.g., a1a1) that are especially useful at the level of crystallographic map fitting. This nomenclature can also be written as a string with two-character suite names between the uppercase letters of the base sequence (N1aG1gN1aR1aA1cN1a for a GNRA tetraloop), facilitating bioinformatic comparisons. Cluster means, standard deviations, coordinates, and examples are made available, as well as the Suitename software that assigns suite conformer names and conformer match quality (suiteness) from atomic coordinates. The RNA Ontology Consortium will combine this new backbone system with others that define base pairs, base-stacking, and hydrogen-bond relationships to provide a full description of RNA structural motifs.

Areas of Specialization struCtural Biology & BioinformatiCs Plant genetiCs Protein BioChemistry DeveloPmental Biology ComPutational BioinformatiCs laBoratory moleCular genetiCs of leaf DeveloPment PlastiD moleCular genetiCs moleCular genetiCs of meiotiC reComBination & Chromosome segregation moleCular Biology of Plant DeveloPment DeveloPmental & moleCular genetiCs segmentation During animal DeveloPment synaPse formation & the Central nervous system meChanisms of transCriPtion in miCroorganisms reProDuCtive Biology, Cell-Cell interaCtions emBryoniC Patterning, hematoPoiesis & ePigenetiC Control of gene exPression in DrosoPhilia outreaCh aCtivities Cell anD Cell ProDuCts fermentation faCility transCriPtional regulation in yeast BeneDiCt miChael fellow Charles anD Johanna BusCh fellow list of PuBliCations Waksman institute faculty DiRectoRy Mission Statement The Waksman Institute's mission is to conduct research in microbial molecular genetics, developmental molecular genetics, plant molecular genetics, and structural and computational biology. The Institute also provides a catalyst for general university initiatives, a life science infrastructure, undergraduate and graduate education, and a public service function for the state. Background The principal mission of the Waksman Institute is research. While the initial emphasis of the institute at its founding was microbiology, its focus soon turned toward molecular genetics, and was later broadened to include organisms other than viruses, bacteria, and fungi. As a reflection of this new, broadened, vision of research at the Institute, under previous directors fruit flies and plants were also studied. Since my assumption of the Institute's directorship, I have strived to expand its investigative horizons to include computational and structural biology, and a further emphasis on the molecular genetics of regulation of gene expression and biomolecular interactions. This new expansion of the Waksman Institute's investigative goals has stimulated the introduction of interdisciplinary programs with chemistry, computer science, and plant science. Indeed, the Institute's research mission has evolved from a diversity of disciplines centered on antibiotics to a unified discipline of molecular genetics with a more diverse set of biological problems. The Institute today employs faculty teams that concentrate on certain classes of organisms amenable to genetic analysis such as bacteria and fungi (Escherichia coli and yeast), animal systems (e.g., Drosophila and C. elegans), and plants (Arabidopsis, tobacco, and maize). Although the Institute focuses on basic academic questions in microbial, animal, and plant research, it continues to seek practical and commercially viable applications of its discoveries. Historically, in fact, the Institute owes its existence to the symbiotic relationship that exists between academic research institutions and the private sector. In 1939 Dr. Selman Waksman, the Institute's founder …