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PubMed2004

Structural exon database, SEDB, mapping exon boundaries on multiple protein structures.

UNLABELLED: Comparative analysis of exon/intron organization of genes and their resulting protein structures is important for understanding evolutionary relationships between species, rules of protein organization and protein functionality. We present Structural Exon Database (SEDB), with a Web interface, an application that allows users to retrieve the exon/intron organization of genes and map the location of the exon boundaries and the intron phase onto a multiple structural alignment. SEDB is linked with Friend, an integrated analytical multiple sequence/structure viewer, which allows simultaneous visualization of exon boundaries on structure and sequence alignments. With SEDB researchers can study the correlations of gene structure with the properties of the encoded three-dimensional protein structures across eukaryotic organisms. AVAILABILITY: SEDB is publicly available at http://glinka.bio.neu.edu/SEDB/SEDB.html SUPPLEMENTARY INFORMATION: On the SEDB Web site.

Databases, Genetic↗
PubMed1998

Crystal structures of open and closed forms of binary and ternary complexes of the large fragment of Thermus aquaticus DNA polymerase I: structural basis for nucleotide incorporation.

The crystal structures of two ternary complexes of the large fragment of Thermus aquaticus DNA polymerase I (Klentaq1) with a primer/template DNA and dideoxycytidine triphosphate, and that of a binary complex of the same enzyme with a primer/template DNA, were determined to a resolution of 2.3, 2.3 and 2.5 A, respectively. One ternary complex structure differs markedly from the two other structures by a large reorientation of the tip of the fingers domain. This structure, designated 'closed', represents the ternary polymerase complex caught in the act of incorporating a nucleotide. In the two other structures, the tip of the fingers domain is rotated outward by 46 degrees ('open') in an orientation similar to that of the apo form of Klentaq1. These structures provide the first direct evidence in DNA polymerase I enzymes of a large conformational change responsible for assembling an active ternary complex.

Amino Acid Sequence↗
PubMed2005

Differences in the intramolecular structure of structured oils do not affect pancreatic lipase activity in vitro or the absorption by rats of (n-3) fatty acids.

The fatty acid composition and intramolecular structure of dietary triacylglycerols (TAGs) influence their absorption. We compared the in vitro pancreatic lipase activity and the lymphatic transport in rats of fish oil and 2 enzymatically interesterified oils containing 10:0 and (n-3) PUFAs of marine origin to investigate whether the positional distribution of fatty acids influenced the overall bioavailability of (n-3) PUFAs in the body. The structured oils had the (n-3) PUFA either mainly at the sn-1,3 position (LML, M = medium-chain fatty acid, L = long-chain fatty acid) or mainly at the sn-2 position (MLM). Oils were administered to lymph-cannulated rats and lymph was collected for 24 h. The fatty acid composition as well as the lipid class distribution of lymph samples was determined. In vitro pancreatic lipase activity was greater when fish oil was the substrate than when the structured oils were the substrates (P < 0.001 at 40 min). This was consistent with a greater 8-h recovery of total fatty acids from fish oil compared with the 2 structured oils (P < 0.05). The absorption profiles of MLM and LML in rats and their in vitro rates of lipase activity did not differ. This indicates that the absorption rate is highly influenced by the lipase activity, which in turn is affected by the fatty acid composition and intramolecular structure. The lipid class distribution in lymph collected from the 3 groups of rats did not differ. In conclusion, the intramolecular structure did not affect the overall absorption of (n-3) PUFAs.

Animals↗
PubMed1998

An Integrated Sequence-Structure Database incorporating matching mRNA sequence, amino acid sequence and protein three-dimensional structure data.

We have constructed a non-homologous database, termed the Integrated Sequence-Structure Database (ISSD) which comprises the coding sequences of genes, amino acid sequences of the corresponding proteins, their secondary structure and straight phi,psi angles assignments, and polypeptide backbone coordinates. Each protein entry in the database holds the alignment of nucleotide sequence, amino acid sequence and the PDB three-dimensional structure data. The nucleotide and amino acid sequences for each entry are selected on the basis of exact matches of the source organism and cell environment. The current version 1.0 of ISSD is available on the WWW at http://www.protein.bio.msu.su/issd/ and includes 107 non-homologous mammalian proteins, of which 80 are human proteins. The database has been used by us for the analysis of synonymous codon usage patterns in mRNA sequences showing their correlation with the three-dimensional structure features in the encoded proteins. Possible ISSD applications include optimisation of protein expression, improvement of the protein structure prediction accuracy, and analysis of evolutionary aspects of the nucleotide sequence-protein structure relationship.

Algorithms↗
PubMed1986

The structure of sugar chains of Japanese quail ovomucoid. The occurrence of oligosaccharides not expected from the classical biosynthetic pathway for N-glycans; a method for the assessment of the structure of glycans present in picomolar amounts.

While the structure of the major oligosaccharide of Japanese quail ovomucoid was reported earlier (Hase, S. et al. (1982) J. Biochem. 91, 735-737), the structures of the minor oligosaccharide units were investigated for the first time in the present studies. For this purpose, the glycans of the protein were liberated from the polypeptide chain by hydrazinolysis. After N-acetylation, the reducing ends of the oligosaccharides obtained were coupled with 2-aminopyridine, and then the resulting fluorescent derivatives were purified by Bio-Gel P-2 column chromatography and reversed-phase HPLC. The chemical structures of two minor oligosaccharide units were determined with the aid of exoglycosidases, and by methylation analysis and Smith degradation. The results demonstrated that the ovomucoid contains the following two monoantennary glycans: Man alpha 1-6(Gal beta 1-4GlcNAc beta 1-2Man alpha 1-3)Man beta 1-4GlcNAc beta 1-4GlcNAc and Gal beta 1-4GlcNAc beta 1-2Man alpha 1-6(Man alpha 1-3)Man beta 1-4GlcNAc beta 1-4GlcNAc. The latter structure was not predicted by the classical metabolic pathway for the N-glycans to be formed. The structures of three additional minor heterosaccharides were deduced from their elution positions on HPLC together with the results of determination of their molecular sizes and the HPLC elution positions of their enzymatic degradation products. It is noteworthy that for the latter procedure for the estimation of the structures of oligosaccharides only minute quantities of glycans (several hundreds pmol) are required.

Amino Acids↗
PubMed1987

Origin of structural domains of the serum-albumin gene family and a predicted structure of the gene for vitamin D-binding protein.

We have recently determined complete DNA sequences for the human albumin and alpha-fetoprotein [AFP] genes and thus have identified their detailed structures. Each is composed of three domains of four exons, three of which are internal and one of which is a domain-linking exon. Equivalent exons in each domain show sufficient sequence and structural similarity to be considered homologous; additional unique exons at each end of the gene show no similarity to the internal triplicated structures. Since earlier, conflicting evolutionary models were based on analysis of single gene structures, we derived from five genes a series of consensus sequences representing the three internal exons as well as the domain-linking exon. The five genes were human and rat albumin and human, mouse, and rat AFP genes. Structurally equivalent exons of the different domains are shown to have arisen from a single exon in a one-domain precursor. Exons that bridge the domains arose from an unequal crossover that fused two exons of the precursor. Our model suggests that part of the coding sequence of the one-domain precursor may have been derived from an intron, by way of loss of a splice site. The consensus sequences were used to propose an intron-exon structure for the related gene encoding the serum vitamin D-binding protein (DBP). DBP is truncated relative to albumin and AFP, and we submit that this results from deletion of two internal exons in the third domain of the gene rather than from premature termination of the coding sequence.

Amino Acid Sequence↗
PubMed1990

Structural effects induced by removal of a disulfide-bridge: the X-ray structure of the C30A/C51A mutant of basic pancreatic trypsin inhibitor at 1.6 A.

The X-ray structure of a variant of basic pancreatic trypsin inhibitor (BPTI) has been analyzed to determine the structural accommodation resulting from removal of a disulfide cross-link in a protein. The disulfide removed, Cys30-Cys51, has been implicated in both the folding pathway of the protein and its overall thermal stability. In the variant studied, C30A/C51A, the disulfide cysteines were replaced by less bulky alanines. The atomic displacements observed for C30A/C51A indicate a set of concerted shifts of two segments of chains, which together significantly diminish a packing defect at the site of the removed cysteine sulfur atoms. The observed structural changes are distributed asymmetrically around the sites of mutation, indicating that the adjacent beta-sheet is more resistant to the perturbation than the alpha-helix on the opposite side of the disulfide bond. The thermal parameters of groups involved in the structural accommodation are not significantly altered. A comparison of the X-ray structures reported for native BPTI determined in three different crystal forms indicates that the magnitude of its conformational variability exceeds that of the structural changes caused by the disulfide removal. This emphasizes the necessity of using isomorphous crystal systems to determine the relatively small effects due to mutation.

Aprotinin↗
PubMed2001

Commensurate structure of Ca(2)CoSi(2)O(7), a new twinned orthorhombic structure.

The crystal structure of the commensurate phase of Ca(2)CoSi(2)O(7), dicalcium cobalt disilicate, has been derived from the modulated structure described in (3 + 2)-dimensional space. The structure is orthorhombic P2(1)2(1)2; a = 23.510 (4), b = 23.510 (4), c = 5.025 (1) A (at 170 K), Z = 18. Since the crystal is twinned and the apparent diffraction symmetry is 4/mmm, the parameters were refined by a newly developed least-squares program for the refinement of twinned crystals. The structure is essentially similar to the known structure of the melilite group, but with regular arrangement of the bundles along [001] formed with four arrays of the sixfold coordinated Ca polyhedra and an array of CoO(4) tetrahedra. The distribution of the bundles found in the present structure is different from that reported by Riester et al. [(2000), Z. Kristallogr. 215, 102-109].

Journal Article↗
PubMed2002

Structure prediction as a tool for solution of the crystal structures of metallo-organic complexes using powder X-ray diffraction data.

A simulated-annealing direct-space approach has been applied to predict the crystal structures of a series of metallo-organic complexes containing Zn, Cu and Ni. The prediction methodology generates a set of energetically reasonable crystal structures among which the actual structure is present, but it is not always possible to specify unambiguously the known crystal structure solely on the basis of energy. In each case, however, the ambiguity may be resolved by recourse to laboratory powder X-ray diffraction (PXRD) data. In this manner, structure prediction is shown to be a powerful tool for structure solution using PXRD data, with the additional advantage that indexing of the PXRD profile is not required at the outset.

Journal Article↗
PubMed2004

Structure of incommensurate ammonium tetrafluoroberyllate studied by structure refinements and the maximum entropy method.

Incommensurately modulated ammonium tetrafluoroberyllate (AFB) occurs in a narrow temperature interval between the paraelectric room-temperature phase with space group Pnma (Ti = 178 K) and the ferroelectric low-temperature phase with space group Pna2(1) (Tc = 173 K). The structure is determined from accurate single-crystal X-ray diffraction data collected with synchrotron radiation at 175 K. The superspace group of the structure is Pnma(alpha00)0ss with alpha = 0.4796 (4). Both structure refinements and the maximum entropy method lead to the same structure model, which involves only single harmonic modulations. The building units of the structure are BeF4(2-) and NH4+ complex ions with approximately tetrahedral point symmetry. They are relatively rigid and the modulations consist mainly of translations of the tetrahedra and their rotations around a fixed axis. The modulation is related to changes in the network of the hydrogen bonds. The low-temperature superstructure can be described as a commensurately modulated structure with the same superspace symmetry. The first harmonic modulations of the low-temperature and incommensurate phases are related by a scale factor with a value of approximately two. In addition, the low-temperature phase exhibits a second harmonic modulation that is responsible for shifts along c and the ferroelectricity in this phase. The experimental data of the incommensurate phase do not contain any evidence for the presence of a second harmonic in the modulation functions. This suggests that the development of the second harmonic, i.e. the development of the spontaneous polarization, is responsible for the lock-in transition.

Journal Article↗
PubMed1999

Crystal structure of moganite-type phosphorus oxynitride: relationship to other twinned-quartz-based structures.

The structure of moganite-type phosphorus oxynitride quenched from high-pressure high-temperature conditions has been refined using neutron powder diffraction data. This moganite-type structure, space group I2/a, Z = 12, is slightly less distorted with respect to the Imab aristotype than is moganite (a monoclinic form of silica). A close topological relationship has been identified between the moganite-type and orthorhombic BeH(2) structures indicating that SiO(2), PON and BeH(2) all adopt structures belonging to the twinned-quartz-based group. This group represents another possible structure type for systems composed of corner-sharing AX(4) tetrahedra. Structures of this group are obvious candidates for intermediate phases between the cristobalite and quartz types.

Journal Article↗
PubMed1999

Correlation between structural parameters of garnet and garnet-like structures.

Statistical analysis of structural parameters of garnet and garnet-like structures retrieved from the Inorganic Crystal Structure Database has revealed strong correlations between them. The degree of correlation depends on doping site and garnet type. Structural parameters are not equally sensitive to changes imposed by doping. The strongest correlation exists between the unit-cell parameter and the doping-ion radius. In the case of doping at the dodecahedral sites, the most sensitive parameter is the shortest dodecahedral distance. Principal component analysis (PCA) clearly shows that the first component explains most of the variation of structural data. It has a geometric basis and correlates with the effective radii of the doping ion. Partial correlation helps to identify the strongest relations between pairs of variables when the influence of other structural variables on them is controlled. It appears that in some cases partial correlation has a different sign when compared with the results of the standard correlation technique.

Journal Article↗
PubMed2001

Practical experience with the use of halides for phasing macromolecular structures: a powerful tool for structural genomics.

The crystal structure of pepstatin-insensitive carboxyl proteinase (PCP) from Pseudomonas sp. 101, an enzyme with no overall sequence similarity to any other proteinases of known structure, was solved using crystals soaked in sodium bromide solution and then cryocooled. A data set collected at the bromine peak absorption wavelength was sufficient for calculation of an excellent map and the entire process of phasing and tracing the maps required almost no direct human intervention. The process of structure solution using single-wavelength data was compared with three-wavelength multiwavelength anomalous diffraction (MAD); although the latter resulted in slightly better maps, the use of this much more labor-intensive approach did not significantly improve the ability to solve the structure. The successful phasing approaches are compared with several less successful attempts utilizing other crystal forms of the enzyme and the practical aspects of the use of bromine as a heavy-atom derivative are discussed. In conclusion, the use of halides with single-wavelength diffraction data fulfills the requirements of being a first-choice method of high-throughput structure solution for the emerging field of structural genomics.

Aspartic Acid Endopeptidases↗
PubMed1994

Comparison of two crystal structures of TGF-beta2: the accuracy of refined protein structures.

Transforming growth factor-beta is a multifunctional cell-growth regulator and is a member of the TGF-beta superfamily of cytokines. Each monomer is 112 amino acids long and the mature active form is a 25 kDa homodimer. Recently, the crystal structure of TGF-beta2 has been determined independently in two laboratories [Daopin, Piez, Ogawa & Davies (1992). Science, 257, 369-373; Schlunegger & Grütter (1992). Nature (London), 358, 430-434] and subsequently refined to higher resolutions [Daopin, Li & Davies (1993). Proteins Struct. Funct. Genet. In the press; Schlunegger & Grütter (1993). J. Mol. Biol. In the press]. A detailed structural comparison shows that the two structures are nearly identical with the differences mostly located on the mobile regions of the molecule. The r.m.s. differences between the two structures are 0.10 A for 104 pairs of C(alpha) atoms, 0.15 A for 434 pairs of main-chain atoms, 0.33 A for 860 out of 890 pairs of protein atoms and a correlation of 90% between the temperature B factors of all protein atoms. Based on a comparison of the water molecules, a B value of 60.0 A(2) is recommended as the cut off for modeling new waters. The structural identity is striking because in one case the material was expressed in vivo in CHO cells whereas in the other case it was expressed in E. coli and had to be refolded in vitro. The overall coordinate errors are estimated to be 0.21 A from the Luzzati plot, 0.18 A from the sigma(A) plot, 0.24 A with Cruickshank's equations and 0.25 A using the empirical method of Perry & Stroud. These estimates are comparable to the r.m.s. structure superposition. The r.m.s. differences correlate very well with the crystallographic B values and the relation is best described with the Cruickshank formula. In addition to the estimation of an overall error, a new application of the Cruickshank formula is presented here to estimate the local errors.

Journal Article↗
PubMed1996

An eye lens protein-water structure: 1.2 A resolution structure of gammaB-crystallin at 150 K.

gammabeta-crystallin is a structural protein of the eye lens with a role in the maintenance of an even distribution of protein and water over distances around the wavelength of light, preserving lens transparency. The structure of the 174-residue bovine protein has already been determined at room temperature to 1.47 A resolution. By flash freezing the protein crystals, data have now been collected to a nominal resolution limit of 1.2 A as radiation damage was essentially eliminated. The protein-water model has been refined against this data using the program RESTRAIN converging to an R factor of 18.5% with all data. Atomic positions are clearly indicated in the electron-density maps. Discrete bimodal disorder has been visualized for a few side chains. Out of a total of 498 water molecules present in the crystal asymmetric unit, 394 have been modelled and refined at unit occupancy. The solvent structure is extremely well ordered with an average B value of 23.4 A(2). Partially occupied sites have been identified where disorder in the protein induces concomitant disorder in the local solvent structure. The solvent structure covers 97% of the solvent-exposed surface of the protein in the crystal. 126 water molecules are distributed in second and higher hydration shells. There are networks of hydrogen-bonded solvent extending up to 64 molecules in a network, comprising trimers and tetramers as well as five- and six-membered water-ring structures. The hydration of the protein surface is dominated by arginine and aspartate side chains. Extensive cages of highly ordered solvent molecules are also observed around exposed non-polar groups.

Journal Article↗
PubMed1997

Structure of apo duck ovotransferrin: the structures of the N and C lobes are in the open form.

The structure of apo duck ovotransferrin (APODOT) has been determined at a resolution of 4.0 A by the molecular replacement method using the structure of duck ovotransferrin (DOT) as the search model. The DOT structure contains two iron binding sites; one in the N-terminal lobe lying between domains N1 and N2 and one in the C-terminal lobe between domains C1 and C2. Both lobes have a closed structure. Models of various forms of both the N and C lobes were used in the search. The final model was refined to give an R factor of 0.22. The comparison of the structure of APODOT with that of DOT shows that both the N and the C lobes are in an open form, where the N2 and C2 domains undergo large rigid-body rotations of 51.6 and 49.9 degrees relative to the N1 and C1 domains, respectively. The interface between the N and C lobes, which is formed by the N1-C1 contact in the core of the molecule does not change significantly. The DOT molecule may be described in terms of three rigid bodies; the N1 and C1 domains as one rigid body forming the static core of the molecule and the N2 and C2 domains as two other rigid bodies which, on the release of iron, move away from the static core of the molecule to form the open structure of APODOT.

Journal Article↗
PubMed2002

Solution structure of a yeast ubiquitin-like protein Smt3: the role of structurally less defined sequences in protein-protein recognitions.

Smt3 belongs to a growing family of ubiquitin-related proteins involved in posttranslational protein modification. Independent studies demonstrate an essential function of Smt3 in the regulation of nucleocytoplasmic transport, and suggest a role in cell-cycle regulation. Here we report the high-resolution NMR structure of yeast Smt3 in the complex free form. Our comparison of the Smt3 NMR structure with the Smt3 crystal structure in complex with the C-Terminal Ulp1 protease domain revealed large structural differences in the binding surface, which is also involved in the Smt3-Ubc-9 interaction detected by NMR. The structural differences in the region indicate the important functions of conserved residues in less structurally defined sequences.

Amino Acid Sequence↗
PubMed2002

The structure of spider toxin huwentoxin-II with unique disulfide linkage: evidence for structural evolution.

The three-dimensional structure of huwentoxin-II (HWTX-II), an insecticidal peptide purified from the venom of spider Selenocosmia huwena with a unique disulfide bond linkage as I-III, II-V, and IV-VI, has been determined using 2D (1)H-NMR. The resulting structure of HWTX-II contains two beta-turns (C4-S7 and K24-W27) and a double-stranded antiparallel beta-sheet (W27-C29 and C34-K36). Although the C-terminal double-stranded beta-sheet cross-linked by two disulfide bonds (II-V and IV-VI in HWTX-II, II-V and III-VI in the ICK molecules) is conserved both in HWTX-II and the ICK molecules, the structure of HWTX-II is unexpected absence of the cystine knot because of its unique disulfide linkage. It suggests that HWTX-II adopts a novel scaffold different from the ICK motif that is adopted by all other spider toxin structures elucidated thus far. Furthermore, the structure of HWTX-II, which conforms to the disulfide-directed beta-hairpin (DDH) motif, not only supports the hypothesis that the ICK is a minor elaboration of the more ancestral DDH motif but also suggests that HWTX-II may have evolved from the same structural ancestor.

Amino Acid Sequence↗