Structure determination and functional analysis of a chromate reductase from Gluconacetobacter hansenii

Environmental protection through biological mechanisms that aid in the reductive immobilization of toxic metals (e.g., chromate and uranyl) has been identified to involve specific NADH-dependent flavoproteins that promote cell viability. To understand the enzyme mechanisms responsible for metal reduction, the enzyme kinetics of a putative chromate reductase from Gluconacetobacter hansenii (Gh-ChrR) was measured and the crystal structure of the protein determined at 2.25 Å resolution. Gh-ChrR catalyzes the NADH-dependent reduction of chromate, ferricyanide, and uranyl anions under aerobic conditions. Kinetic measurements indicate that NADH acts as a substrate inhibitor; catalysis requires chromate binding prior to NADH association. The crystal structure of Gh-ChrR shows the protein is a homotetramer with one bound flavin mononucleotide (FMN) per subunit. A bound anion is visualized proximal to the FMN at the interface between adjacent subunits within a cationic pocket, which is positioned at an optimal distance for hydride transfer. Site-directed substitutions of residues proposed to involve in both NADH and metal anion binding (N85A or R101A) result in 90–95% reductions in enzyme efficiencies for NADH-dependent chromate reduction. In comparison site-directed substitution of a residue (S118A) participating in the coordination of FMN in the active site results in only modest (50%) reductions in catalytic efficiencies, consistent with the presence of a multitude of side chains that position the FMN in the active site. The proposed proximity relationships between metal anion binding site and enzyme cofactors is discussed in terms of rational design principles for the use of enzymes in chromate and uranyl bioremediation.

Chemical shift assignments for Rv0577, a putative glyoxylase associated with virulence from Mycobacterium tuberculosis

Approximately one-third of mankind has been exposed to Mycobacterium tuberculosis, the etiological agent responsible for tuberculosis (TB). As part of an effort to develop a new generation of anti-TB agents, the chemical shifts for the 261-residue, virulence-associated protein Rv0577 from M. tuberculosis has been extensively assigned.

Crystal structure of cce_0566 from Cyanothece 51142, a protein associated with nitrogen fixation in the DUF269 family

The crystal structure for cce_0566 (171 aa, 19.4 kDa), a DUF269 annotated protein from the diazotrophic cyanobacterium Cyanothece sp. ATCC 51142, was determined to 1.60Å resolution. Cce_0566 is a homodimer with each molecule composed of eight α-helices folded on one side of a three strand anti-parallel β-sheet. Hydrophobic interactions between the side chains of largely conserved residues on the surface of each β-sheet hold the dimer together. The fold observed for cce_0566 may be unique to proteins in the DUF269 family, hence, the protein may also have a function unique to nitrogen fixation. A solvent accessible cleft containing conserved charged residues near the dimer interface could represent the active site or ligand-binding surface for the protein's biological function.

Solution structure of Rv2377c-founding member of the MbtH-like protein family

The Mycobacterium tuberculosis protein Rv2377c (71 residues, MW=8.4kDa) has been characterized using nuclear magnetic resonance (NMR) and circular dichroism (CD) spectroscopy. Rv2377c was the first identified member of the MbtH-like family of proteins. MbtH-like proteins have been implicated in siderophore biosynthesis, however, their precise biochemical function remain unknown. Size exclusion chromatography and NMR spectroscopy show that Rv2377c is a monomer in solution. Circular dichroism spectroscopy indicates that Rv2377c unfolds upon heating and will reversibly fold into its native conformation upon cooling. Using NMR-based methods the solution structure of Rv2377c was determined and some of the dynamic properties of the protein studied. The protein contains a three-strand, anti-parallel beta-sheet (beta3:beta1:beta2) nestled against one C-terminal alpha-helix (S44-N55). Weak or absent amide cross peaks in the (1)H-(15)N HSQC spectrum for many of the beta1 and beta2 residues suggest intermediate motion on the ms to mus time scale at the beta1:beta2 interface. Amide cross peaks in the (1)H-(15)N HSQC spectrum are absent for all but one residue at the C-terminus (W56-D71), a region that includes a highly conserved sequence WXDXR, suggesting this region is intrinsically disordered. The latter observation differs with the crystal structure of another MbtH-like protein, PA2412 from Pseudomonas aeruginosa, where a second ordered alpha-helix was observed at the extreme C-terminus.

Structure of a Nudix hydrolase (MutT) in the Mg(2+)-bound state from Bartonella henselae, the bacterium responsible for cat scratch fever

Cat scratch fever (also known as cat scratch disease and bartonellosis) is an infectious disease caused by the proteobacterium Bartonella henselae following a cat scratch. Although the infection usually resolves spontaneously without treatment in healthy adults, bartonellosis may lead to severe complications in young children and immunocompromised patients, and there is new evidence suggesting that B. henselae may be associated with a broader range of clinical symptoms then previously believed. The genome of B. henselae contains genes for two putative Nudix hydrolases, BH02020 and BH01640 (KEGG). Nudix proteins play an important role in regulating the intracellular concentration of nucleotide cofactors and signaling molecules. The amino-acid sequence of BH02020 is similar to that of the prototypical member of the Nudix superfamily, Escherichia coli MutT, a protein that is best known for its ability to neutralize the promutagenic compound 7,8-dihydro-8-oxoguanosine triphosphate. Here, the crystal structure of BH02020 (Bh-MutT) in the Mg(2+)-bound state was determined at 2.1 Å resolution (PDB entry 3hhj). As observed in all Nudix hydrolase structures, the α-helix of the highly conserved `Nudix box' in Bh-MutT is one of two helices that sandwich a four-stranded mixed β-sheet with the central two β-strands parallel to each other. The catalytically essential divalent cation observed in the Bh-MutT structure, Mg(2+), is coordinated to the side chains of Glu57 and Glu61. The structure is not especially robust; a temperature melt obtained using circular dichroism spectroscopy shows that Bh-MutT irreversibly unfolds and precipitates out of solution upon heating, with a T(m) of 333 K.

Solution-state NMR structure and biophysical characterization of zinc-substituted rubredoxin B (Rv3250c) from Mycobacterium tuberculosis

Owing to the evolution of multi-drug-resistant and extremely drug-resistant Mycobacterium tuberculosis strains, there is an urgent need to develop new antituberculosis strategies to prevent TB epidemics in the industrial world. Among the potential new drug targets are two small nonheme iron-binding proteins, rubredoxin A (Rv3251c) and rubredoxin B (Rv3250c), which are believed to play a role in electron-transfer processes. Here, the solution structure and biophysical properties of one of these two proteins, rubredoxin B (Mt-RubB), determined in the zinc-substituted form are reported. The zinc-substituted protein was prepared by expressing Mt-RubB in minimal medium containing excess zinc acetate. Size-exclusion chromatography and NMR spectroscopy indicated that Mt-RubB was a monomer in solution. The structure (PDB entry 2kn9) was generally similar to those of other rubredoxins, containing a three-stranded antiparallel β-sheet (β2-β1-β3) and a metal tetrahedrally coordinated to the S atoms of four cysteine residues (Cys9, Cys12, Cys42 and Cys45). The first pair of cysteine residues is at the C-terminal end of the first β-strand and the second pair of cysteine residues is towards the C-terminal end of the loop between β2 and β3. The structure shows the metal buried deeply within the protein, an observation that is supported by the inability to remove the metal with excess EDTA at room temperature. Circular dichroism spectroscopy shows that this stability extends to high temperature, with essentially no change being observed in the CD spectrum of Mt-RubB upon heating to 353 K.

Structural genomics of infectious disease drug targets: the SSGCID

The Seattle Structural Genomics Center for Infectious Disease (SSGCID) is a consortium of researchers at Seattle BioMed, Emerald BioStructures, the University of Washington and Pacific Northwest National Laboratory that was established to apply structural genomics approaches to drug targets from infectious disease organisms. The SSGCID is currently funded over a five-year period by the National Institute of Allergy and Infectious Diseases (NIAID) to determine the three-dimensional structures of 400 proteins from a variety of Category A, B and C pathogens. Target selection engages the infectious disease research and drug-therapy communities to identify drug targets, essential enzymes, virulence factors and vaccine candidates of biomedical relevance to combat infectious diseases. The protein-expression systems, purified proteins, ligand screens and three-dimensional structures produced by SSGCID constitute a valuable resource for drug-discovery research, all of which is made freely available to the greater scientific community. This issue of Acta Crystallographica Section F, entirely devoted to the work of the SSGCID, covers the details of the high-throughput pipeline and presents a series of structures from a broad array of pathogenic organisms. Here, a background is provided on the structural genomics of infectious disease, the essential components of the SSGCID pipeline are discussed and a survey of progress to date is presented.

Solution structure of an arsenate reductase-related protein, YffB, from Brucella melitensis, the etiological agent responsible for brucellosis

Brucella melitensis is the etiological agent responsible for brucellosis. Present in the B. melitensis genome is a 116-residue protein related to arsenate reductases (Bm-YffB; BR0369). Arsenate reductases (ArsC) convert arsenate ion (H(2)AsO(4)(-)), a compound that is toxic to bacteria, to arsenite ion (AsO(2)(-)), a product that may be efficiently exported out of the cell. Consequently, Bm-YffB is a potential drug target because if arsenate reduction is the protein's major biological function then disabling the cell's ability to reduce arsenate would make these cells more sensitive to the deleterious effects of arsenate. Size-exclusion chromatography and NMR spectroscopy indicate that Bm-YffB is a monomer in solution. The solution structure of Bm-YffB (PDB entry 2kok) shows that the protein consists of two domains: a four-stranded mixed β-sheet flanked by two α-helices on one side and an α-helical bundle. The α/β domain is characteristic of the fold of thioredoxin-like proteins and the overall structure is generally similar to those of known arsenate reductases despite the marginal sequence similarity. Chemical shift perturbation studies with (15)N-labeled Bm-YffB show that the protein binds reduced glutathione at a site adjacent to a region similar to the HX(3)CX(3)R catalytic sequence motif that is important for arsenic detoxification activity in the classical arsenate-reductase family of proteins. The latter observation supports the hypothesis that the ArsC-YffB family of proteins may function as glutathione-dependent thiol reductases. However, comparison of the structure of Bm-YffB with the structures of proteins from the classical ArsC family suggest that the mechanism and possibly the function of Bm-YffB and other related proteins (ArsC-YffB) may differ from those of the ArsC family of proteins.

Inaugural structure from the DUF3349 superfamily of proteins, Mycobacterium tuberculosis Rv0543c

The first structure for a member of the DUF3349 (PF11829) family of proteins, Rv0543c from Mycobacterium tuberculosis, has been determined using NMR-based methods and some of its biophysical properties characterized. Rv0543c is a 100 residue, 11.3 kDa protein that both size exclusion chromatography and NMR spectroscopy show to be a monomer in solution. The structure of the protein consists of a bundle of five α-helices, α1 (M1-Y16), α2 (P21-C33), α3 (S37-G52), α4 (G58-H65) and α5 (S72-G87), held together by a largely conserved group of hydrophobic amino acid side chains. Heteronuclear steady-state {¹H}-¹⁵N NOE, T₁, and T₂ values are similar through-out the sequence indicating that the backbones of the five helices are in a single motional regime. The thermal stability of Rv0543c, characterized by circular dichroism spectroscopy, indicates that Rv0543c irreversibly unfolds upon heating with an estimated melting temperature of 62.5 °C. While the biological function of Rv0543c is still unknown, the presence of DUF3349 proteins predominantly in Mycobacterium and Rhodococcus bacterial species suggests that Rv0543 may have a biological function unique to these bacteria, and consequently, may prove to be an attractive drug target to combat tuberculosis.

Crystal structure of the receptor binding domain of the botulinum C-D mosaic neurotoxin reveals potential roles of lysines 1118 and 1136 in membrane interactions

The botulinum neurotoxins (BoNTs) produced by different strains of the bacterium Clostridium botulinum are responsible for the disease botulism and include a group of immunologically distinct serotypes (A, B, E, and F) that are considered to be the most lethal natural proteins known for humans. Two BoNT serotypes, C and D, while rarely associated with human infection, are responsible for deadly botulism outbreaks afflicting animals. Also associated with animal infections is the BoNT C-D mosaic protein (BoNT/CD), a BoNT subtype that is essentially a hybrid of the BoNT/C (∼two-third) and BoNT/D (∼one-third) serotypes. While the amino acid sequence of the heavy chain receptor binding (HCR) domain of BoNT/CD (BoNT/CD-HCR) is very similar to the corresponding amino acid sequence of BoNT/D, BoNT/CD-HCR binds synaptosome membranes better than BoNT/D-HCR. To obtain structural insights for the different membrane binding properties, the crystal structure of BoNT/CD-HCR (S867-E1280) was determined at 1.56 Å resolution and compared to previously reported structures for BoNT/D-HCR. Overall, the BoNT/CD-HCR structure is similar to the two sub-domain organization observed for other BoNT HCRs: an N-terminal jellyroll barrel motif and a C-terminal β-trefoil fold. Comparison of the structure of BoNT/CD-HCR with BoNT/D-HCR indicates that K1118 has a similar structural role as the equivalent residue, E1114, in BoNT/D-HCR, while K1136 has a structurally different role than the equivalent residue, G1132, in BoNT/D-HCR. Lysine-1118 forms a salt bridge with E1247 and may enhance membrane interactions by stabilizing the putative membrane binding loop (K1240-N1248). Lysine-1136 is observed on the surface of the protein. A sulfate ion bound to K1136 may mimic a natural interaction with the negatively changed phospholipid membrane surface. Liposome-binding experiments demonstrate that BoNT/CD-HCR binds phosphatidylethanolamine liposomes more tightly than BoNT/D-HCR.

A multi-pronged search for a common structural motif in the secretion signal of Salmonella enterica serovar Typhimurium type III effector proteins

Many pathogenic Gram-negative bacteria use a type III secretion system (T3SS) to deliver effector proteins into the host cell where they reprogram host defenses and facilitate pathogenesis. The first 20-30 N-terminal residues usually contain the 'secretion signal' that targets effector proteins for translocation, however, a consensus sequence motif has never been discerned. Recent machine-learning approaches, such as support vector machine (SVM)-based Identification and Evaluation of Virulence Effectors (SIEVE), have improved the ability to identify effector proteins from genomics sequence information. While these methods all suggest that the T3SS secretion signal has a characteristic amino acid composition bias, it is still unclear if the amino acid pattern is important and if there are any unifying structural properties that direct recognition. To address these issues a peptide corresponding to the secretion signal for Salmonella enterica serovar Typhimurium effector SseJ was synthesized (residues 1-30, SseJ) along with scrambled peptides of the same amino acid composition that produced high (SseJ-H) and low (SseJ-L) SIEVE scores. The secretion properties of these three peptides were tested using a secretion signal-CyaA fusion assay and their structural properties probed using circular dichroism, nuclear magnetic resonance, and ion mobility spectrometry-mass spectrometry. The secretion predictions from SIEVE matched signal-CyaA fusion experimental results with J774 macrophages suggesting that the SseJ secretion signal has some sequence order dependence. The structural studies showed that the SseJ, SseJ-H, and SseJ-L peptides were intrinsically disordered in aqueous solution with a small predisposition to adopt nascent helical structure only in the presence of structure stabilizing agents such as 1,1,1,3,3,3-hexafluoroisopropanol. Intrinsic disorder may be a universal feature of effector secretion signals as similar conclusions were reached following structural characterization of peptides corresponding to the N-terminal regions of the S. Typhimurium effectors SptP, SopD-2, GtgE, and the Yersinia pestis effector YopH.

High-level expression, purification, crystallization and preliminary X-ray crystallographic studies of the receptor-binding domain of botulinum neurotoxin serotype D

Botulinum neurotoxins (BoNTs) are highly toxic proteins for humans and animals that are responsible for the deadly neuroparalytic disease botulism. Here, details of the expression and purification of the receptor-binding domain (HCR) of BoNT/D in Escherichia coli are presented. Using a codon-optimized cDNA, BoNT/D_HCR was expressed at a high level (150-200 mg per litre of culture) in the soluble fraction. Following a three-step purification protocol, very pure (>98%) BoNT/D_HCR was obtained. The recombinant BoNT/D_HCR was crystallized and the crystals diffracted to 1.65 Å resolution. The crystals belonged to space group P2(1)2(1)2(1), with unit-cell parameters a=60.8, b=89.7, c=93.9 Å. Preliminary crystallographic data analysis revealed the presence of one molecule in the asymmetric unit.

Circular dichroism studies on the Deinococcus radiodurans Nudix hydrolase DR_0079: an atypical thermal melt

The crystal structure for the Deinococcus radiodurans Nudix protein DR_0079 was recently determined in the metal-free form at 1.9 A resolution (2O5F). The protein adopts the fundamental fold common to the Nudix family of proteins, a large mixed b-sheet sandwiched between the a-helix of the "Nudix box" and a second a-helix. The protein's physical properties were further characterized by circular dichroism (CD) spectroscopy. A CD thermal melt at 220 nm identifies an inflection point at approximately 52 degrees C. However, unlike typical CD thermal melts, the negative ellipticity at 220 nm becomes more negative upon passing through the inflection point. Both NMR spectroscopy and size exclusion chromatography indicate that heating effects the irreversible formation of a large molecular weight complex. After cooling, the negative ellipiticity at 220 nm increases further, and overall, the CD spectrum at 25 degrees C suggests that heat-treated DR_0079 has more a-helical and b-sheet structure than non-heat treated DR_0079.

The Seattle Structural Genomics Center for Infectious Disease (SSGCID)

The NIAID-funded Seattle Structural Genomics Center for Infectious Disease (SSGCID) is a consortium established to apply structural genomics approaches to potential drug targets from NIAID priority organisms for biodefense and emerging and re-emerging diseases. The mission of the SSGCID is to determine approximately 400 protein structures over the next five years. In order to maximize biomedical impact, ligand-based drug-lead discovery campaigns will be pursued for a small number of high-impact targets. Here we review the center's target selection processes, which include pro-active engagement of the infectious disease research and drug therapy communities to identify drug targets, essential enzymes, virulence factors and vaccine candidates of biomedical relevance to combat infectious diseases. This is followed by a brief overview of the SSGCID structure determination pipeline and ligand screening methodology. Finally, specifics of our resources available to the scientific community are presented. Physical materials and data produced by SSGCID will be made available to the scientific community, with the aim that they will provide essential groundwork benefiting future research and drug discovery.

Structural characterization of Burkholderia pseudomallei adenylate kinase (Adk): profound asymmetry in the crystal structure of the 'open' state

In all organisms adenylate kinases (Adks) play a vital role in cellular energy metabolism and nucleic acid synthesis. Due to differences in catalytic properties between the Adks found in prokaryotes and in the cytoplasm of eukaryotes, there is interest in targeting this enzyme for new drug therapies against infectious bacterial agents. Here we report the 2.1A resolution crystal structure for the 220-residue Adk from Burkholderia pseudomallei (BpAdk), the etiological agent responsible for the infectious disease melioidosis. The general structure of apo BpAdk is similar to other Adk structures, composed of a CORE subdomain with peripheral ATP-binding (ATP(bd)) and LID subdomains. The two molecules in the asymmetric unit have significantly different conformations, with a backbone RMSD of 1.46 A. These two BpAdk conformations may represent 'open' Adk sub-states along the preferential pathway to the 'closed' substrate-bound state.

A solution NMR investigation into the murine amelogenin splice-variant LRAP (Leucine-Rich Amelogenin Protein)

Amelogenins are the dominant proteins present in ameloblasts during the early stages of enamel biomineralization, making up >90% of the matrix protein. Along with the full-length protein there are several splice-variant isoforms of amelogenin present including LRAP (Leucine-Rich Amelogenin Protein), a protein that consists of the first 33 and the last 26 residues of full-length amelogenin. Using solution-state NMR spectroscopy we have assigned the (1)H-(15)N HSQC spectrum of murine LRAP (rp(H)LRAP) in 2% acetic acid at pH 3.0 by making extensive use of previous chemical shift assignments for full-length murine amelogenin (rp(H)M180). This correlation was possible because LRAP, like the full-length protein, is intrinsically disordered under these solution conditions. The major difference between the (1)H-(15)N HSQC spectra of rp(H)M180 and rp(H)LRAP was an additional set of amide resonances for each of the seven non-proline residues between S12 and Y12 near the N-terminus of rp(H)LRAP indicating that the N-terminal region of LRAP exists in two different conformations. Analysis of the proline carbon chemical shifts suggests that the molecular basis for the two states is not a cis-trans isomerization of one or more of the proline residues in the N-terminal region. Starting from 2% acetic acid, where rp(H)LRAP was monomeric in solution, NaCl addition effected residue specific changes in molecular dynamics manifested by the reduction in intensity and disappearance of (1)H-(15)N HSQC cross peaks. As observed for the full-length protein, these perturbations may signal early events governing supramolecular self-assembly of rp(H)LRAP into nanospheres. However, the different patterns of (1)H-(15)N HSQC cross peak perturbation between rp(H)LRAP and rp(H)M180 in high salt suggest that the termini may behave differently in their respective nanospheres, and perhaps, these differences contribute to the cell signaling properties attributable to LRAP but not to the full-length protein.

Backbone and side chain (1)H, (13)C, and (15)N NMR assignments for the organic hydroperoxide resistance protein (Ohr) from Burkholderia pseudomallei

Burkholderia pseudomallei is a NIAID Category B microorganism responsible for melioidosis. Here we report backbone and side chain NMR assignments for the 139-residue, homodimeric, organic hydroperoxide resistance protein (Ohr) from this organism.

Structural characterization of the protein cce_0567 from Cyanothece 51142, a metalloprotein associated with nitrogen fixation in the DUF683 family

The genomes of many cyanobacteria contain the sequence for a small protein with a common "Domain of Unknown Function" grouped into the DUF683 protein family. While the biological function of DUF683 is still not known, their genomic location within nitrogen fixation clusters suggests that DUF683 proteins may play a role in the process. The diurnal cyanobacterium Cyanothece sp. PCC 51142 contains a gene for a protein that falls into the DUF683 family, cce_0567 (78 aa, 9.0 kDa). In an effort to elucidate the biochemical role DUF683 proteins may play in nitrogen fixation, we have determined the first crystal structure for a protein in this family, cce_0567, to 1.84 A resolution. Cce_0567 crystallized in space group P2(1) with two protein molecules and one Ni(2+) cation per asymmetric unit. The protein is composed of two alpha-helices, residues P11 to G41 (alpha1) and L49-E74 (alpha2), with the second alpha-helix containing a short 3(10)-helix (Y46-N48). A four-residue linker (L42-D45) between the helices allows them to form an anti-parallel bundle and cross over each other towards their termini. In solution it is likely that two molecules of cce_0567 form a rod-like dimer by the stacking interactions of approximately 1/2 of the protein. Histidine-36 is highly conserved in all known DUF683 proteins and the N2 nitrogen of the H36 side chain of each molecule in the dimer is coordinated with Ni(2+) in the crystal structure. The divalent cation Ni(2+) was titrated into (15)N-labeled cce_0567 and chemical shift perturbations were observed only in the (1)H-(15)N HSQC spectra for residues at, or near, the site of Ni(2+) binding observed in the crystal structure. There was no evidence for an increase in the size of cce_0567 upon binding Ni(2+), even in large molar excess of Ni(2+), indicating that a metal was not required for dimer formation. Circular dichroism spectroscopy indicated that cce_0567 was extremely robust, with a melting temperature of approximately 62 degrees C that was reversible.

A solution NMR investigation into the early events of amelogenin nanosphere self-assembly initiated with sodium chloride or calcium chloride

Using solution-state NMR spectroscopy, new insights into the early events governing amelogenin supramolecular self-assembly have been identified using sodium chloride and calcium chloride to trigger the association. Two-dimensional 1H-15N HSQC spectra were recorded for 15N- and 13C-labeled murine amelogenin as a function of increasing NaCl and CaCl2 concentration beginning with solution conditions of 2% acetic acid at pH 3.0, where amelogenin was monomeric. Residue specific changes in molecular dynamics, manifested by the reduction in intensity and disappearance of 1H-15N HSQC cross-peaks, were observed with the addition of either salt to the protein. With increasing NaCl concentrations, residues between T21 and R31 near the N-terminus were affected first, suggesting that these residues may initiate amelogenin dimerization, the first step in nanosphere assembly. At higher NaCl concentrations, more residues near the N-terminus (Y12-I51) were affected, and with further additions of NaCl, residues near the C-terminus (L141-T171) began to show a similar change in molecular dynamics. With increasing CaCl2 concentrations, a similar stepwise change in molecular dynamics involving essentially the same set of amelogenin residues was observed. As the concentration of either salt was increased, a concomitant increase in the estimated overall rotational correlation time (tau(c)) was observed, consistent with assembly. Self-assembly into a dimer or trimer was established with dynamic light scattering studies under similar conditions that showed an increase in diameter of the smallest species from 4.1 nm in the absence of salt to 10 nm in the presence of salt. These results suggest a possible stepwise interaction mechanism, starting with the N-terminus and followed by the C-terminus, leading to amelogenin nanosphere assembly.

A Bayesian integration model of high-throughput proteomics and metabolomics data for improved early detection of microbial infections

High-throughput (HTP) technologies offer the capability to evaluate the genome, proteome, and metabolome of an organism at a global scale. This opens up new opportunities to define complex signatures of disease that involve signals from multiple types of biomolecules. However, integrating these data types is difficult due to the heterogeneity of the data. We present a Bayesian approach to integration that uses posterior probabilities to assign class memberships to samples using individual and multiple data sources; these probabilities are based on lower-level likelihood functions derived from standard statistical learning algorithms. We demonstrate this approach on microbial infections of mice, where the bronchial alveolar lavage fluid was analyzed by three HTP technologies, two proteomic and one metabolomic. We demonstrate that integration of the three datasets improves classification accuracy to approximately 89% from the best individual dataset at approximately 83%. In addition, we present a new visualization tool called Visual Integration for Bayesian Evaluation (VIBE) that allows the user to observe classification accuracies at the class level and evaluate classification accuracies on any subset of available data types based on the posterior probability models defined for the individual and integrated data.

Functional and structural characterization of DR_0079 from Deinococcus radiodurans, a novel Nudix hydrolase with a preference for cytosine (deoxy)ribonucleoside 5'-Di- and triphosphates

The genome of the extremely radiation resistant bacterium Deinococcus radiodurans encodes 21 Nudix hydrolases, of which only two have been characterized in detail. Here we report the activity and crystal structure for DR_0079, the first Nudix hydrolase observed to have a marked preference for cytosine ribonucleoside 5'-diphosphate (CDP) and cytosine ribonucleoside 5'-triphosphate (CTP). After CDP and CTP, the next most preferred substrates for DR_0079, with a relative activity of <50%, were the corresponding deoxyribose nucleotides, dCDP and dCTP. Hydrolase activity at the site of the phosphodiester bond was corroborated using (31)P NMR spectroscopy to follow the phosphorus resonances for three substrates, CDP, IDP, and CTP, and their hydrolysis products, CMP + P(i), IMP + P(i), and CMP + PP(i), respectively. Nucleophilic substitution at the beta-phosphorus of CDP and CTP was established, using (31)P NMR spectroscopy, by the appearance of an upfield-shifted P(i) resonance and line-broadened PP(i) resonance, respectively, when the hydrolysis was performed in 40% H(2)(18)O-enriched water. The optimal activity for CDP was at pH 9.0-9.5 with the reaction requiring divalent metal cation (Mg(2+) > Mn(2+) > Co(2+)). The biochemical data are discussed with reference to the crystal structure for DR_0079 that was determined in the metal-free form at 1.9 A resolution. The protein contains nine beta-strands, three alpha-helices, and two 3(10)-helices organized into three subdomains: an N-terminal beta-sheet, a central Nudix core, and a C-terminal helix-turn-helix motif. As observed for all known structures of Nudix hydrolases, the alpha-helix of the "Nudix box" is one of two helices that sandwich a "four-strand" mixed beta-sheet. To identify residues potentially involved in metal and substrate binding, NMR chemical shift mapping experiments were performed on (15)N-labeled DR_0079 with the paramagnetic divalent cation Co(2+) and the nonhydrolyzable substrate thymidine 5'-O-(alpha,beta-methylenediphosphate) and the results mapped onto the crystal structure.

Backbone 1H, 13C, and 15N NMR assignments for the Cyanothece 51142 protein cce_0567: a protein associated with nitrogen fixation in the DUF683 family

Cyanothece 51142 contains a 78-residue protein, cce_0567, that falls into the DUF683 family of proteins associated with nitrogen fixation. Here we report the assignment of most of the main chain and 13C(beta) side chain resonances of the approximately 40 kDa homo-tetramer.

1H, 13C, and 15N resonance assignments of murine amelogenin, an enamel biomineralization protein

Amelogenin is the predominant matrix protein in developing dental enamel. Making extensive use of residue specific 15N-labeled amino acids samples, the majority of the main and side chain resonances for murine amelogenin were assigned in 2% aqueous acetic acid at pH 3.0.

Insights into the structural variation between pentapeptide repeat proteins--crystal structure of Rfr23 from Cyanothece 51142

Cyanothece sp. PCC 51142 contains 35 pentapeptide repeat proteins (PRPs), proteins that contain a minimum of eight tandem repeated five-residues (Rfr) of the general consensus sequence A[N/D]LXX. Published crystal structures of PRPs show that the tandem pentapeptide repeats adopt a type of right-handed quadrilateral beta-helix called an Rfr-fold. To characterize how structural features of Rfr-folds might vary with different amino acid sequences, the crystal structure of Cyanothece Rfr23 (174 residues) was determined at 2.4A resolution. The structure is dominated by an Rfr-fold capped at the N-terminus with a nine-residue alpha-helix (M26(*)-E34). The Rfr-fold of Rfr23 contains four structural features previously unobserved in Rfr-folds. First, Rfr23 is composed entirely of type II beta-turns. Second, the pentapeptide repeats are not consecutive in the primary amino acid sequence. Instead, Rfr23 contains 24-residues protruding outside one corner of the first complete N-terminal coil of the Rfr-fold (L56-P79) (24-residue insertion). Third, a disulfide bond between C39 and C42 bridges the beta-turn between the first and second pentapeptide repeats in the first coil (disulfide bracket). NMR spectroscopy indicates that the reduction of the disulfide bracket with the addition of DTT destroys the entire Rfr-fold. Fourth, a single-residue perturbs the Rfr-fold slightly in the last coil between the C-terminal two pentapeptide repeats (single-residue bulge).