Structure of the SH3 domain of human osteoclast-stimulating factor at atomic resolution.

Osteoclast-stimulating factor (OSF) is an intracellular signaling protein, produced by osteoclasts themselves, that enhances osteoclast formation and bone resorption. It is thought to act via an Src-related signaling pathway and contains SH3 and ankyrin-repeat domains which are involved in protein-protein interactions. As part of a structure-based anti-bone-loss drug-design program, the atomic resolution X-ray structure of the recombinant human OSF SH3 domain (hOSF-SH3) has been determined. The domain, residues 12-72, yielded crystals that diffracted to the ultrahigh resolution of 1.07 A. The overall structure shows a characteristic SH3 fold consisting of two perpendicular beta-sheets that form a beta-barrel. Structure-based sequence alignment reveals that the putative proline-rich peptide-binding site of hOSF-SH3 consists of (i) residues that are highly conserved in the SH3-domain family, including residues Tyr21, Phe23, Trp49, Pro62, Asn64 and Tyr65, and (ii) residues that are less conserved and/or even specific to hOSF, including Thr22, Arg26, Thr27, Glu30, Asp46, Thr47, Asn48 and Leu60, which might be key to designing specific inhibitors for hOSF to fight osteoporosis and related bone-loss diseases. There are a total of 13 well defined water molecules forming hydrogen bonds with the above residues in and around the peptide-binding pocket. Some of those water molecules might be important for drug-design approaches. The hOSF-SH3 structure at atomic resolution provides an accurate framework for structure-based design of its inhibitors.

High resolution crystal structure of human Rab9 GTPase: a novel antiviral drug target.

Rab GTPases and their effectors facilitate vesicular transport by tethering donor vesicles to their respective target membranes. Rab9 mediates late endosome to trans-Golgi transport and has recently been found to be a key cellular component for human immunodeficiency virus-1, Ebola, Marburg, and measles virus replication, suggesting that it may be a novel target in the development of broad spectrum antiviral drugs. As part of our structure-based drug design program, we have determined the crystal structure of a C-terminally truncated human Rab9 (residues 1-177) to 1.25-A resolution. The overall structure shows a characteristic nucleotide binding fold consisting of a six-stranded beta-sheet surrounded by five alpha-helices with a tightly bound GDP molecule in the active site. Structure-based sequence alignment of Rab9 with other Rab proteins reveals that its active site consists of residues highly conserved in the Rab GTPase family, implying a common catalytic mechanism. However, Rab9 contains seven regions that are significantly different in conformation from other Rab proteins. Some of those regions coincide with putative effector-binding sites and switch I and switch II regions identified by structure/sequence alignments. The Rab9 structure at near atomic resolution provides an excellent model for structure-based antiviral drug design.

Purification, crystallization and preliminary X-ray analysis of Caenorhabditis elegans ubiquitin-conjugation enzyme M7.1.

M7.1 is a class IV ubiquitin-conjugation enzyme (UBC) that belongs to the ubiquitination cascade in Caenorhabditis elegans. The clone for this UBC has been overexpressed in Escherichia coli and the 16.7 kDa protein was purified from the soluble fraction. M7.1 was crystallized by sitting-drop vapor diffusion in 10% ethanol, 1.5 M NaCl at 277.5 K. Crystals diffracted to 1.75 A and belong to the orthorhombic space group P2(1)2(1)2(1), with unit-cell parameters a = 44.3, b = 54.3, c = 60.2 A. The asymmetric unit contains a single monomer. A molecular-replacement model has been determined and refinement is in progress.

Ab initio crystallographic structure determination of insulin from protein to electron density without crystal handling.

Insulin crystals suitable for cryogenic data collection and structure determination by single-wavelength anomalous scattering (SAS) were obtained by a self-optimization screening process in a single capillary tube without manipulation of the crystals at any time. Using the counter-diffusion crystallization technique, screening for optimal conditions for crystal growth, incorporation of a strong anomalous scattering halide and cryogenic solution took place simultaneously in a single capillary tube. The crystals in the capillaries can be placed directly in the cryostream for data collection using a conventional home-laboratory X-ray source. High-redundancy data were used to obtain a Patterson solution from the anomalous signal of iodine. As a result, the anomalous scattering-atom position was determined and the phase calculated, giving rise to an initial electron-density map at 2.4 A resolution. This entire procedure from crystal growth to the determination of an initial structure was performed within four weeks.