Data mining crystallization databases: knowledge-based approaches to optimize protein crystal screens

Protein crystallization is a major bottleneck in protein X-ray crystallography, the workhorse of most structural proteomics projects. Because the principles that govern protein crystallization are too poorly understood to allow them to be used in a strongly predictive sense, the most common crystallization strategy entails screening a wide variety of solution conditions to identify the small subset that will support crystal nucleation and growth. We tested the hypothesis that more efficient crystallization strategies could be formulated by extracting useful patterns and correlations from the large data sets of crystallization trials created in structural proteomics projects. A database of crystallization conditions was constructed for 755 different proteins purified and crystallized under uniform conditions. Forty-five percent of the proteins formed crystals. Data mining identified the conditions that crystallize the most proteins, revealed that many conditions are highly correlated in their behavior, and showed that the crystallization success rate is markedly dependent on the organism from which proteins derive. Of the proteins that crystallized in a 48-condition experiment, 60% could be crystallized in as few as 6 conditions and 94% in 24 conditions. Consideration of the full range of information coming from crystal screening trials allows one to design screens that are maximally productive while consuming minimal resources, and also suggests further useful conditions for extending existing screens.     

Ecdysteroids: isolation,chemical transformations,and biological activity

Phytochemistry Reviews - Ecdysteroids are polyhydroxylated sterols, and are widespread in the plant and animal world. To date, over 520 ecdysteroids have been isolated from natural sources. The...     

Computed tomography in the x-ray diagnosis of pneumonia

Experience in the use of CT in combined radiodiagnosis of pneumonia was analysed. It has been concluded that CT objectively reflects morphological inflammatory pulmonary changes and permits their all-round assessment over time. The diagnosis of pneumonia in CT is based on classical x-ray symptoms. As compared to survey radiography CT reveals symptoms of pneumonia to the full at earlier stages. CT is an important additional method of investigation of inflammatory pulmonary diseases, but it should not be used separately without survey radiography. In a majority of cases when CT is performed there is no need in x-ray tomography.     

Sequence‐ and activity‐based screening of microbial genomes for novel dehalogenases

Dehalogenases are environmentally important enzymes that detoxify organohalogens by cleaving their carbon-halogen bonds. Many microbial genomes harbour enzyme families containing dehalogenases, but a sequence-based identification of genuine dehalogenases with high confidence is challenging because of the low sequence conservation among these enzymes. Furthermore, these protein families harbour a rich diversity of other enzymes including esterases and phosphatases. Reliable sequence determinants are necessary to harness genome sequencing-efforts for accelerating the discovery of novel dehalogenases with improved or modified activities. In an attempt to extract dehalogenase sequence fingerprints, 103 uncharacterized potential dehalogenase candidates belonging to the α/β hydrolase (ABH) and haloacid dehalogenase-like hydrolase (HAD) superfamilies were screened for dehalogenase, esterase and phosphatase activity. In this first biochemical screen, 1 haloalkane dehalogenase, 1 fluoroacetate dehalogenase and 5 l -2-haloacid dehalogenases were found (success rate 7%), as well as 19 esterases and 31 phosphatases. Using this functional data, we refined the sequence-based dehalogenase selection criteria and applied them to a second functional screen, which identified novel dehalogenase activity in 13 out of only 24 proteins (54%), increasing the success rate eightfold. Four new l -2-haloacid dehalogenases from the HAD superfamily were found to hydrolyse fluoroacetate, an activity never previously ascribed to enzymes in this superfamily.     

Sequencing three crocodilian genomes to illuminate the evolution of archosaurs and amniotes

The International Crocodilian Genomes Working Group (ICGWG) will sequence and assemble the American alligator (Alligator mississippiensis), saltwater crocodile (Crocodylus porosus) and Indian gharial (Gavialis gangeticus) genomes. The status of these projects and our planned analyses are described.     

Crystal structures of putative phosphoglycerate kinases from B. anthracis and C. jejuni

Phosphoglycerate kinase (PGK) is indispensable during glycolysis for anaerobic glucose degradation and energy generation. Here we present comprehensive structure analysis of two putative PGKs from Bacillus anthracis str. Sterne and Campylobacter jejuni in the context of their structural homologs. They are the first PGKs from pathogenic bacteria reported in the Protein Data Bank. The crystal structure of PGK from Bacillus anthracis str. Sterne (BaPGK) has been determined at 1.68 ? while the structure of PGK from Campylobacter jejuni (CjPGK) has been determined at 2.14 ? resolution. The proteins' monomers are composed of two domains, each containing a Rossmann fold, hinged together by a helix which can be used to adjust the relative position between two domains. It is also shown that apo-forms of both BaPGK and CjPGK adopt open conformations as compared to the substrate and ATP bound forms of PGK from other species.     

Crystal structure of a putative isochorismatase hydrolase from Oleispira antarctica

Isochorismatase-like hydrolases (IHL) constitute a large family of enzymes divided into five structural families (by SCOP). IHLs are crucial for siderophore-mediated ferric iron acquisition by cells. Knowledge of the structural characteristics of these molecules will enhance the understanding of the molecular basis of iron transport, and perhaps resolve which of the mechanisms previously proposed in the literature is the correct one. We determined the crystal structure of the apo-form of a putative isochorismatase hydrolase OaIHL (PDB code: 3LQY) from the antarctic γ-proteobacterium Oleispira antarctica, and did comparative sequential and structural analysis of its closest homologs. The characteristic features of all analyzed structures were identified and discussed. We also docked isochorismate to the determined crystal structure by in silico methods, to highlight the interactions of the active center with the substrate. The putative isochorismate hydrolase OaIHL from O. antarctica possesses the typical catalytic triad for IHL proteins. Its active center resembles those IHLs with a D–K–C catalytic triad, rather than those variants with a D–K–X triad. OaIHL shares some structural and sequential features with other members of the IHL superfamily. In silico docking results showed that despite small differences in active site composition, isochorismate binds to in the structure of OaIHL in a similar mode to its binding in phenazine biosynthesis protein PhzD (PDB code 1NF8).     

Vascular endothelium: target or victim of cytostatic therapy?

Chemotherapy continues to be the main therapeutic approach in the treatment of hematological malignancies including acute leukemia. Generally, chemotherapy is used to eliminate cancer cells and to restore normal bone marrow function. Simultaneous action of cytostatic drugs on bone marrow angiogenesis decreases the formation of new capillaries and improves therapeutic effect. However, chemotherapeutic agents may also be cytodestructive for cellular elements of other tissues, particularly the vascular endothelium, which can lead to various cardiovascular complications. In this work, we studied the effects of 2 cytostatic drugs, cytosine arabinoside (ara-C) and daunorubicin (DNR), on cultured human vascular (i.e., umbilical) endothelial cells (ECs). Ara-C and DNR were added to cultured cells at concentrations ranging from 1 ng/mL to 100 microg/mL. Drug effects were studied using phase-contrast microscopy, cell viability tests, BRDU incorporation, immunohistochemistry, flow cytometry, and cell cloning. At various concentrations, ara-C and DNR are able to induce morphological and functional changes in cultured cells related to either cytostatic or cytotoxic action. Moreover, ara-C-treated cultured cells displayed significant disturbances in cell adhesion molecule expression and interaction with blood leukocytes. Preliminary data obtained on acute leukemia patients undergoing standard cytostatic therapy ("7+3" regimen) have shown that concentration of the circulating ECs was significantly increased compared with the control group and could be as high as 500-1500 cells/mL of blood. Results obtained suggest that anticancer chemotherapy may induce systemic damage of vascular endothelium related to massive cell loss and (or) alterations of endothelial function.