Structural plasticity in Mycobacterium tuberculosis uracil-DNA glycosylase (MtUng) and its functional implications

17 independent crystal structures of family I uracil-DNA glycosylase from Mycobacterium tuberculosis (MtUng) and its complexes with uracil and its derivatives, distributed among five distinct crystal forms, have been determined. Thermodynamic parameters of binding in the complexes have been measured using isothermal titration calorimetry. The two-domain protein exhibits open and closed conformations, suggesting that the closure of the domain on DNA binding involves conformational selection. Segmental mobility in the enzyme molecule is confined to a 32-residue stretch which plays a major role in DNA binding. Uracil and its derivatives can bind to the protein in two possible orientations. Only one of them is possible when there is a bulky substituent at the 50 position. The crystal structures of the complexes provide a reasonable rationale for the observed thermodynamic parameters. In addition to providing fresh insights into the structure, plasticity and interactions of the protein molecule, the results of the present investigation provide a platform for structure-based inhibitor design.

Donut-Shaped Fingerprint In Homologous Polypeptide Relationships-A Topological Feature Related To Pathogenic Structural Changes In Conformational Disease

Features of homologous relationship of proteins can provide us a general picture of protein universe, assist protein design and analysis, and further our comprehension of the evolution of organisms. Here we carried Out a Study of the evolution Of protein molecules by investigating homologous relationships among residue segments. The motive was to identify detailed topological features of homologous relationships for short residue segments in the whole protein universe. Based on the data of a large number of non-redundant Proteins, the universe of non-membrane polypeptide was analyzed by considering both residue mutations and structural conservation. By connecting homologous segments with edges, we obtained a homologous relationship network of the whole universe of short residue segments, which we named the graph of polypeptide relationships (GPR). Since the network is extremely complicated for topological transitions, to obtain an in-depth understanding, only subgraphs composed of vital nodes of the GPR were analyzed. Such analysis of vital subgraphs of the GPR revealed a donut-shaped fingerprint. Utilization of this topological feature revealed the switch sites (where the beginning of exposure Of previously hidden "hot spots" of fibril-forming happens, in consequence a further opportunity for protein aggregation is Provided; 188-202) of the conformational conversion of the normal alpha-helix-rich prion protein PrPC to the beta-sheet-rich PrPSc that is thought to be responsible for a group of fatal neurodegenerative diseases, transmissible spongiform encephalopathies. Efforts in analyzing other proteins related to various conformational diseases are also introduced. (C) 2009 Elsevier Ltd. All rights reserved.

Structural studies of the hipersaline adaptation of proteins belonging to halophilic archaea

183 p.

Degeneration of postovulatory follicles in the Iberian sardine Sardina pilchardus: structural changes and factors affecting resorption

Inaccuracy in the aging of postovulatory follicles (POFs) and in estimating the effect of temperature on the resorption rate of POFs may introduce bias in the determination of the daily spawning age classes with the daily egg production method (DEPM). To explore the above two bias problems with f ield-collected European pilchard (Sardina pilchardus, known regionally as the Iberian sardine), a method was developed in which the time elapsed from spawning (POF age) was estimated from the size of POFs (i.e., from the cross-sectional area in histological sections). The potential effect of the preservative type and embedding material on POF size and the effect of ambient water temperature on POF resorption rate are taken into account with this method. A highly significant loglinear relationship was found between POF area and age; POF area shrank by approximately 50% per day. POFs were also shown to shrink faster at higher temperatures (approximately 3% per degree), but this temperature effect is unlikely to be an important source of bias in the assignment of females to daily spawning classes. The embedding material was also shown to influence the size of POFs, the latter being significantly larger in resin than in paraffin sections. In conclusion, the size of POFs provides an indirect, reliable estimation of the time elapsed from spawning and may thus be used to test both the validity of POF staging criteria for identifying daily classes of spawners and the effect of other factors (such as temperature and laboratory processing) in applications of the DEPM to S. pilchardus and other fish species.

Fish muscle structural proteins

Based on the differences in their physico-chemical properties proteins are broadly categorised as sarcoplasmic or fibrillar. The properties are important in fish technology. The authors review some of these physico-chemical properties of the proteins which have distinguished themselves as 'structural' or 'textural' proteins. As denaturation in these proteins caused by a variety of factors manifests itself in terms in the quality attributes of the product, relevant mechanisms have been particularly highlighted.

Structural analysis of human CCR2b and primate CCR2b by molecular modeling and molecular dynamics simulation

CCR2b, a chemokine receptor for MCP-1, -2, -3, -4, plays an important role in a variety of diseases involving infection, inflammation, and/or injury, as well as being a coreceptor for HIV-1 infection. Two models of human CCR2b (hCCR2b) were generated by h

Protein three-dimensional structural databases: Domains, structurally aligned homologues and superfamilies

This paper reports the availability of a database of protein structural domains (DDBASE), an alignment database of homologous proteins (HOMSTRAD) and a database of structurally aligned superfamilies (CAMPASS) on the World Wide Web (WWW). DDBASE contains information on the organization of structural domains and their boundaries; it includes only one representative domain from each of the homologous families. This database has been derived by identifying the presence of structural domains in proteins on the basis of inter-secondary structural distances using the program DIAL [Sowdhamini & Blundell (1995), Protein Sci. 4, 506-520]. The alignment of proteins in superfamilies has been performed on the basis of the structural features and relationships of individual residues using the program COMPARER [Sali & Blundell (1990), J. Mol. Biol. 212, 403-428]. The alignment databases contain information on the conserved structural features in homologous proteins and those belonging to superfamilies. Available data include the sequence alignments in structure-annotated formats and the provision for viewing superposed structures of proteins using a graphical interface. Such information, which is freely accessible on the WWW, should be of value to crystallographers in the comparison of newly determined protein structures with previously identified protein domains or existing families.

Structural and functional properties of the hemoglobin components from the Caspian Sea Acipenser persicus and Acipenser stellatus

Hemoglobin (Hb) variability is a commonly used index of phylogenetic differentiation and molecular adaptation in fish. In the current study, the structural and functional characteristics of Hbs from two Sturgeon species of the Southern Caspian Sea Basin were investigated. After extraction and separation of hemoglobin from whole blood , the polyacrylamide gel electrophoresis (SDSPAGE), native-PAGE and isoelectric focusing (IEF) were used to confirm Hb variability in these fishes. Ion-exchange on CM-cellulose chromatography was used for purification of the dominant Hbs from these fishes. The accuracy of the methods was confirmed by IEF and SDS-PAGE. Spectral studies using fluorescence spectrophotometery, circular dichroism spectropolarimetry (CD) analysis and UV–vis spectrophotometery. Oxygen affinities of these Hbs were compared using Hb-oxygen dissociation curves. Also, the dominant Hbs from these blood fishes were utilized for further experiments. The behavior of Hbs during the denaturation process by n-dodecyl trimethylammonium bromide (DTAB) is investigated by UV–vis spectrophotometer and circular dichroism spectropolarimetry. The thermal denaturation properties of the Hbs wereinvestigated by differential scanning calorimetry (DSC) and Hbs aggregation performed chemically in the presence of dithiotreitol (DTT) by UV–vis spectrophotometer and chemometric study. The results demonstrate a significant relationship between stability of fish hemoglobins and the ability of fish for entering to deeper depths. The UV–Vis absorption spectra identified species of hemoglobin and showed the concentration of oxyHb and metHb decreases and deoxyHb increases upon interaction with DTAB. Besides the UV–vis spectrophotometry, the interaction of DTAB with hemoglobins has been studied using circular dichroism spectropolarimetry analysis. This experiment was utilized to measure the unfolding mechanism and compared alpha-helix secondary structure under different conditions for Hbs. The results reveal that the Acipenser stellatus Hb in comparison with Acipenser persicus Hb has more stability and more structural compactness. Besides, the results confirm the hypothesis that there is a meaningful relation between average habitat depth, partial oxygen pressure, oxygen affinity, structural compactness of Hb, and its stability.

Improved facilities for marine biology in East Africa

In 1967 the then University College of Dar es Salaam built a small laboratory on the shore at Kunduchi, 16 km from the main campus and 24 km north of Dar es Salaam. This was used for undergraduate field courses, and as a base for staff from the University to carry out research. It soon became apparent that the urgent need for studies of the marine environment in the East African area, and the lack of existing facilities, necessitated the development of the Kunduchi Marine Biology station into a research establishment with its own staff of full time scientists. This operation began in 1970: necessary structural modifications have been made to the building, staff have been recruited, and the station has been equipped with an adequate range of field and laboratory apparatus. A varied programme of research is now actively under way.

Network structure preserving model reduction with weak a priori structural information

This paper extends a state projection method for structure preserving model reduction to situations where only a weaker notion of system structure is available. This weaker notion of structure, identifying the causal relationship between manifest variables of the system, is especially relevant is settings such as systems biology, where a clear partition of state variables into distinct subsystems may be unknown, or not even exist. The resulting technique, like similar approaches, does not provide theoretical performance guarantees, so an extensive computational study is conducted, and it is observed to work fairly well in practice. Moreover, conditions characterizing structurally minimal realizations and sufficient conditions characterizing edge loss resulting from the reduction process, are presented. ©2009 IEEE.

Structural and functional characterization of the human CCR5 receptor in complex with HIV gp120 envelope glycoprotein and CD4 receptor by molecular modeling studies

The entry of human immunodeficiency virus (HIV) into cells depends on a sequential interaction of the gp120 envelope glycoprotein with the cellular receptors CD4 and members of the chemokine receptor family. The CC chemokine receptor CCR5 is such a receptor for several chemokines and a major coreceptor for the entry of R5 HIV type-1 (HIV-1) into cells. Although many studies focus on the interaction of CCR5 with HIV-1, the corresponding interaction sites in CCR5 and gp120 have not been matched. Here we used an approach combining protein structure modeling, docking and molecular dynamics simulation to build a series of structural models of the CCR5 in complexes with gp120 and CD4. Interactions such as hydrogen bonds, salt bridges and van der Waals contacts between CCR5 and gp120 were investigated. Three snapshots of CCR5-gp120-CD4 models revealed that the initial interactions of CCR5 with gp120 are involved in the negatively charged N-terminus (Nt) region of CCR5 and positively charged bridging sheet region of gp120. Further interactions occurred between extracellular loop2 (ECL2) of CCR5 and the base of V3 loop regions of gp120. These interactions may induce the conformational changes in gp120 and lead to the final entry of HIV into the cell. These results not only strongly support the two-step gp120-CCR5 binding mechanism, but also rationalize extensive biological data about the role of CCR5 in HIV-1 gp120 binding and entry, and may guide efforts to design novel inhibitors.

Studies of polysaccharides from three edible species of Nostoc (cyanobacteria) with different colony morphologies: Structural characterization and effect on the complement system of polysaccharides from Nostoc commune

The cyanobacterium Nostoc commune Vaucher produces quite complex extracellular polysaccharides. The cyanobacterium is nitrogen fixing, and on growing the cyanobacterium in media with and without nitrogen, different types of extracellular polysaccharides were obtained. These were also different from the polysaccharides present in N. commune collected in the field. High pH anion exchange chromatography (HPAEC) of weak acid hydrolysates of the culture-grown material demonstrated that, in this case, HPAEC was useful for comparison of the different polymers. The main differences between the polymers from the field group and the culture-grown samples were the presence of substantial amounts of arabinose, 2-O-methylglucose, and glucuronic acid in the latter. Methylation studies also revealed a difference in the branching points on the glucose units between the field and cultured samples, being 1,4,6 for the first and 1,3,6 for the latter. The field acidic fraction gave, on weak acid hydrolysis and separation on BioGel P2 and HPAEC, 12 oligosaccharide fractions that were isolated and studied by different mass spectroscopy techniques. The structures of the oligosaccharides were determined, and two different series that can originate from two repeating pentamers were identified: GlcAl-4/6GlcM1-4Ga11-4Glc1-4Xyl and GlcAl-4/6Glc1-4Ga11-4Glc1-4Xyl. The difference between these oligosaccharides lies in the methyl substituent on carbon 2 of the glucose unit next to the nonreducing glucuronic acid unit. The polysaccharides from field material were shown to have a strong effect on the complement system.