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At least 1,369 records · Page 76Linked to original sources
PubMed1997

Structural characterization of an alpha-amylase inhibitor from a wild common bean (Phaseolus vulgaris): insight into the common structural features of leguminous alpha-amylase inhibitors.

The primary structures of two subunits of an alpha-amylase inhibitor (alpha AI-2) from a wild common bean (Phaseolus vulgaris) were revealed by a comparison of the amino acid sequence previously deduced from the nucleotide sequence with the amino- and carboxyl-terminal amino acid sequences determined by conventional methods. The polypeptide molecular weight of alpha AI-2 obtained by the light-scattering technique, considered together with the sequence molecular weights revealed for the subunits, indicated that alpha AI-2 has the subunit stoichiometry of an alpha 2 beta 2 complex. These structural features were closely similar to those recently elucidated for a white kidney bean (P. vulgaris) alpha-amylase inhibitor, which is quite different in the inhibitory specificity from alpha AI-2. The post-translational processing of the precursor glycoproteins to form the tetrameric structure appeared to require an Arg residue close to the processing site. Further, the proper associations of the subunits into the tetrameric structures seemed to be strictly controlled by a few amino acids on the subunit interfaces.

Amino Acid Sequence↗
PubMed2001

Does the trabecular bone structure depicted by high-resolution MRI of the calcaneus reflect the true bone structure?

RATIONALE AND OBJECTIVES: The purpose of this study was to compare trabecular bone structure parameters assessed with high-resolution magnetic resonance imaging (HR-MRI) with those determined in specimen sections. METHODS: High-resolution MR images were obtained for 30 calcaneus specimens with a three-dimensional, T1-weighted spin-echo sequence (spatial in-plane resolution 0.195 mm, slice thicknesses of 0.3 and 0.9 mm). Thirty-eight sections were obtained from the specimens, and contact radiography was performed. In the corresponding sections, structural parameters analogous to bone histomorphometry were determined. RESULTS: Significant correlations between MRI-derived structural parameters and those derived from macro pathological sections were found: r values of up to 0.75 were obtained (P < 0.01). The highest correlations were found for apparent bone volume/total volume and trabecular thickness. Image thresholding techniques showed a significant impact on these correlations (P < 0.01). The thinner MR sections were less susceptible to the different thresholding algorithms. CONCLUSIONS: Trabecular bone structure depicted by HR-MR images is significantly correlated with that shown in macro sections (P < 0.01); however, a number of limitations have to be considered, including the substantial impact of thresholding techniques and slice thickness.

Aged↗
PubMed2002

Interaction between seasonal density-dependence structures and length of the seasons explain the geographical structure of the dynamics of voles in Hokkaido: an example of seasonal forcing.

The grey-sided vole (Clethrionomys rufocanus) is distributed over the entire island of Hokkaido, Japan, across which it exhibits multi-annual density cycles in only parts of the island (the north-eastern part); in the remaining part of the island, only seasonal density changes occur. Using annual sampling of 189 grey-sided vole populations, we deduced the geographical structure in their second-order density dependence. Building upon our earlier suggestion, we deduce the seasonal density-dependent structure for these populations. Strong direct and delayed density dependence is found to occur during winter, whereas no density dependence is seen during the summer period. The direct density dependence during winter may be seen as a result of food being limited during that season: the delayed density dependence during the winter is consistent with vole-specialized predators (e.g. the least weasel) responding to vole densities so as to have a negative effect on the net growth rate of voles in the following year. We conclude that the observed geographical structure of the population dynamics may be properly seen as a result of the length of the summer in interaction with the differential seasonal density-dependent structure. Altogether, this indicates that the geographical pattern in multi-annual density dynamics in the grey-sided vole may be a result of seasonal forcing.

Animals↗
PubMed2003

(3 + 1)-dimensional structure refinement of the fresnoite framework-structure type compound Ba(2)TiGe(2)O(8).

The incommensurately modulated structure of the fresnoite framework-structure type compound Ba(2)TiGe(2)O(8) has been solved using a (3 + 1)-dimensional superspace approach. The structure is orthorhombic and adopts the superspace group Cmm2(0,beta,1/2)s00 with beta approximately 0.635 at room temperature. The refinement was based on neutron powder diffraction data obtained from a powdered single crystal grown by Czochralski pulling. The modulation parameters that were obtained support the idea that frozen-in rigid-unit modes cause the modulation. The modulation is mainly manifested by positional displacements of O atoms. Barium ions are either eightfold, ninefold or tenfold coordinated in the one-dimensional modulated structure. A significant improvement of the bond-valence sum for both barium positions is achieved by the introduction of the positional modulation. This finding strongly suggests that underbonded barium positions are critically involved in provoking the incommensurate modulation in Ba(2)TiGe(2)O(8).

Journal Article↗
PubMed2004

Quininium (R)-mandelate, a structure with large Z' described as an incommensurately modulated structure in (3+1)-dimensional superspace.

Quininium (R)-mandelate, C(20)H(25)N(2)O(2)(+).C(8)H(7)O(3)(-), is an organic salt with an incommensurately modulated structure. The superspace approach is required for a precise description of the structure at room temperature. In addition to the main reflections, the diffraction pattern also exhibits higher-order satellite reflections. The large number of first- and second-order satellite reflections with relatively strong intensities indicates a significant modulation. No average structure solution could be obtained on the basis of the main reflections only and hence the structure solution was performed in two suitable superstructure approximations, including satellite intensities. Positional modulation functions and modulation functions for the anisotropic atomic displacement parameters were introduced. The modulation originates from a competition between intramolecular and intermolecular forces, which is reflected, in the superspace formalism, in the modification of hydrogen bonds along the internal space variable t.

Journal Article↗
PubMed2005

Structure of KNbOB2O5--a commensurately modulated structure.

Members of the AMOB2O5 (A = K, Rb, Cs, Tl; M = Nb, Ta) family of compounds can be described as modulated structures with a single superspace group and very similar modulation functions. Single-crystal X-ray diffraction data (Mo Kalpha radiation) are used to solve and refine the structure of KNbOB2O5 in these terms for the first time. The average structure is solved and refined in the space group Pmn2(1). Subsequently, the atomic modulation functions are determined using JANA2000 and superspace-group symmetry Pmn2(1)(0,0.375,0)s. The commensurately modulated structure is finally refined as a superstructure in the space group Pbn2(1) using SHELXS97 converging to R(1) = 0.024.

Journal Article↗
PubMed2000

Structure of the inclusion complex of beta-cyclodextrin with 1,12-dodecanedioic acid using synchrotron radiation data; a detailed dimeric beta-cyclodextrin structure

A detailed crystal structure study of the dimeric inclusion complex of beta-cyclodextrin (betaCD) with 1,12-dodecanedioic acid is presented [IUPAC name: beta-cyclodextrin-1,12-dodecanedioic acid (2/1)]. The structure was solved with synchrotron high-resolution data (0.65 A) at 100 K [crystal data: P1, Z= 1, a = 18.153 (7), b = 15.456 (8), c = 15.251 (4) A, alpha = 102.81 (2), beta = 113.13 (2), gamma = 99.90 (3)degrees, V = 3,673 (3) A3, R = 0.0474 for 25,134 unique reflections with I > 2sigma(I)]. Moreover, the room-temperature structure is used for comparison [crystal data: P1, Z = 1, a = 18.220 (3), b = 15.488 (3), c = 15.409 (3) A, alpha = 102.903 (6), beta = 113.122 (5), gamma = 99.708 (5)degrees, V = 3735.2 (12) A3, R = 0.0828 for 8,235 unique reflections with I > 2sigma(I)]. Combining the high-resolution data and the low-temperature made possible the location of the disordered guest molecule, 1,12-dodecanedioic acid, inside the wide cavity of the macrocycle formed by two betaCD monomers. Moreover, almost all the H atoms of the betaCD macrocycle and many of the water molecules have been located in the low-temperature structure. Thus, for the first time, it has been possible to show in detail, up to now only given by neutron diffraction data, that two betaCD monomers self-assemble through O3...O3 intermolecular hydrogen bonds to form the betaCD dimer, as well as describe the hydrogen-bonding scheme between the dimer's hydroxyl groups among themselves and with water molecules in the lattice. The long guest threads through two host molecules forming a [3]pseudorotaxane. Its polar carboxyl groups, fully hydrated at the primary faces of the betaCD dimers, influence their packing so that those faces are exposed to the solvent. This is in contrast to the packing of the beta-cyclodextrin complexes of the corresponding aliphatic monoacids, where the dimeric complexes form channels in order to isolate the terminal methyl group from the water environment of the lattice.

Journal Article↗
PubMed2000

Structure, phase transitions and ionic conductivity of K3NdSi6O15 x xH2O. II. Structure of beta-K3NdSi6O15

Hydrothermally grown crystals of beta-K3NdSi6O15, potassium neodymium silicate, have been studied by single-crystal X-ray methods. Under appropriate conditions, the compound crystallizes in space group Bb2(1)m and has lattice constants a = 14.370 (2), b = 15.518 (2) and c = 14.265 (2) A. There are 30 atom sites in the asymmetric unit of the basic structure. With eight formula units per unit cell, the calculated density is 2.798 Mg m(-3). Refinement was carried out to a residual, wR(F2), of 0.1177 [R(F) = 0.0416] using anisotropic temperature factors for all atoms. The structure is based on (Si2O5(2-))infinity layers, connected by Nd polyhedra to form a three-dimensional framework. Potassium ion sites, some of which are only partially occupied, are located within channels that run between the silicate layers. The silica-neodymia framework of beta-K3NdSi6O15, in particular the linkages formed between the silicate layers and Nd polyhedra, bears some similarities to that of the essentially isocompositional phase alpha-K3NdSi6O15 x 2H2O. In both, the silicate layers are corrugated so as to accommodate a simple cubic array of NdO6 octahedra with lattice constant approximately 7.5 A. Furthermore, the Si2O5 layers in beta-K3NdSi6O15 are topologically identical to those of the mineral sazhinite, Na2HCeSi6O15. Although beta-K3NdSi6O15 and sazhinite are not isostructural, the structures of each can be described as slight distortions of a high-symmetry parent structure with space group Pbmm.

Journal Article↗
PubMed2002

Structure of ribosomal protein L1 from Methanococcus thermolithotrophicus. Functionally important structural invariants on the L1 surface.

The crystal structure of ribosomal protein L1 from the archaeon Methanococcus thermolithotrophicus has been determined at 2.7 A resolution. The crystals belong to space group P2(1)2(1)2(1), with unit-cell parameters a = 67.0, b = 70.1, c = 106.3 A and two molecules per asymmetric unit. The structure was solved by the molecular-replacement method with AMoRe and refined with CNS to an R value of 18.9% and an R(free) of 25.4% in the resolution range 30-2.7 A. Comparison of this structure with those obtained previously for two L1 proteins from other sources (the bacterium Thermus thermophilus and the archaeon M. jannaschii) as well as detailed analysis of intermolecular contacts in the corresponding L1 crystals reveal structural invariants on the molecular surface which are probably important for binding the 23S ribosomal RNA and protein function within the ribosome.

Amino Acid Sequence↗
PubMed2003

Structure of DNA helicase RepA in complex with sulfate at 1.95 A resolution implicates structural changes to an "open" form.

The structure of a new crystal form (space group C2), grown at pH 8.0 and diffracting to 1.95 A resolution, of the replicative homo-hexameric DNA helicase RepA encoded by plasmid RSF1010 is reported. In contrast to previous crystals grown at pH 6.0 in space group P2(1) (Niedenzu et al., 2001), only one half (a trimer) of the RepA hexamer occupies the asymmetric unit of the space-group C2 crystals. The new crystal packing explains the pH-dependent hexamer-hexamer association mechanism of RepA. The C-terminus (264)VLERQRKSKGVPRGEA(279), which could not be modelled in the previous structure, is clearly defined in the present electron density except for the last four amino acids. Sulfate anions occupy the six ATPase active sites of RepA at positions where the product phosphates are supposed to bind. Binding of sulfate anions induces conformational changes both at the ATPase active sites and throughout the whole molecular structure. In agreement with electron microscopy, the above studies implicate structural changes to an "open" form that may occur upon binding and hydrolysis of nucleotide 5'-triphosphates and could be essential for DNA duplex-unwinding activity.

Adenosine Triphosphatases↗
PubMed1994

Accuracy and precision in protein crystal structure analysis: two independent refinements of the structure of poplar plastocyanin at 173 K.

The structure of the copper protein plastocyanin from poplar leaves (Populus nigra var. italica) at 173 K has been subjected to two independent refinements, using a single set of synchrotron X-ray data at 1.6 A resolution. Energy-restrained refinement using the program EREF resulted in lower root-mean-square deviations from ideal geometry (e.g. 0.011 A for bond lengths) but a higher residual R (0.153) than restrained least-squares refinement using the program PROLSQ (0.014 A, 0.132). Electron-density difference maps in both refinements provided evidence for disorder at some side chains and solvent atoms, and the PROLSQ refinement made allowance for this disorder. The number of solvent sites identified at the 4sigma(rho) level was 171 in the EREF refinement and 189 in the PROLSQ refinement; 159 of the solvent sites are common to both refinements within 1 A. The root-mean-square differences between the atomic positions produced by the two refinements are 0.08 A for C(alpha) atoms, 0.08 A for backbone atoms and 0.12 A for all non-H atoms (excluding six obvious outliers) of the protein molecule. The two sets of Cu-ligand bond lengths differ by up to 0.07 A, and the ligand-Cu-ligand angles by up to 7 degrees. At 173 K the volume of the unit cell is 4.2% smaller than at 295 K. Greater order in the solvent region is indicated by the location of 79 more solvent sites, the identification of extensive networks of hydrogen-bonded rings of solvent molecules, and a general decrease in the thermal parameters. Within the unit cell, the protein molecules are significantly translated and rotated from their positions at ambient temperature. An important structural change at low temperature is a 180 degrees flip of the peptide group at Ser48-Gly49. Nearly all other significant differences between the structures of the protein at 173 and 295 K occur at exposed side chains. If the backbone atoms in the 173 and 295 K structures are superposed, excluding atoms involved in the peptide flip, the root-mean- square difference between the positions of 393 atoms is 0.25 A. Two internal water molecules, not included in previous descriptions of poplar plastocyanin, have been located. The plastocyanin Cu-site geometry at 173 K is not significantly different from that at 295 K. If plastocyanin undergoes a change in Cu-site geometry at low temperature, as has been suggested on the basis of resonance Raman spectroscopic evidence, then the change is not detected within the limits of precision of the present results.

Journal Article↗
PubMed1995

Small-molecule crystal structures as a structural basis for drug design.

For a long time, the crystal structures of small molecules were regarded as useful only for establishing the stereochemical formulae of the crystallized compounds. Recently, chemists have realized that in the study of the environment in the solid state there exists valuable structural information on the binding characteristics of chemical groups. Numerous comparisons have been made which show the nearly perfect correlation between small-molecule structural results, and the observed binding in receptor-substrate complexes. Moreover, the observed conformations of flexible substrates interacting with the neighbouring molecules in their crystal structures, can lead to valuable hypotheses on their conformation when bound in the active site of a biological macromolecule.

Journal Article↗
PubMed1996

Three-dimensional structure of cytochrome c' from two Alcaligenes species and the implications for four-helix bundle structures.

The three-dimensional structures of two cytochromes c' have been determined in order to analyse the common features of proteins of this family and their relationship with other four-helix bundle structures. The structure of cytochrome c' from Alcaligenes sp was determined by molecular replacement supplemented with the iron anomalous scattering and the use of a single isomorphous heavy-atom derivative, and was refined using synchrotron data to 1.8 A resolution. The final model, comprising 956 protein atoms (one monomer) and 89 water molecules, has a final R value of 0.188 for all data in the range 20.0-1.8 A resolution (14 673 reflections). The structure of the cytochrome c' from Alcaligenes denitrificans is isomorphous and essentially identical (r.m.s. deviation for all atoms 0.36 A). Although its amino-acid sequence has not been determined chemically, only four differences from that of Alcaligenes sp cytochrome c' were identified by the X-ray analysis. The final model for Alcaligenes denitrificans cytochrome c', comprising 953 protein atoms and 75 water molecules, gave a final R factor of 0.167 for all data in the range 20.0-2.15 A (8220 reflections). The cytochrome c' monomer forms a classic four-helix bundle, determined by the packing of hydrophobic side chains around the enclosed haem group. There are very few cross-linking hydrogen bonds between the helices, the principal side-chain hydrogen bonding involving one of the haem propionates and a conserved Arg residue. The cytochrome c' dimer is created by a crystallographic twofold axis. Monomer-monomer contacts primarily involve the two A helices, with size complementarity of side chains in a central solvent-excluded portion of the interface and hydrogen bonding at the periphery. Both species have a pyroglutamic acid N-terminal residue. The haem iron is five-coordinate, 0.32 A out of the haem plane towards the fifth ligand, His120. The unusual magnetic properties of the Fe atom may be linked to a conserved basic residue, Arg124, adjacent to His120.

Journal Article↗
PubMed1996

High-resolution structure (1.33 A) of a HEW lysozyme tetragonal crystal grown in the APCF apparatus. Data and structural comparison with a crystal grown under microgravity from SpaceHab-01 mission.

Crystals of tetragonal hen egg-white lysozyme were grown using Advanced Protein Crystallization Facility (APCF) apparatus under a microgravity environment (SpaceHab-01 mission) and ground control conditions. Crystals were grown from NaCl as a crystallizing agent at pH 4.3. The X-ray diffraction patterns of the best diffracting ground- and space-grown crystals were recorded using synchrotron radiation and an image plate on the W32 beamline at LURE. Both ground- and space-grown crystals showed nearly equivalent maximum resolution of 1.3-1.4 A. Refinements were carried out with the program X-PLOR with final R values of 18.45 and 18.27% for structures from ground- and space- grown crystals, respectively. The two structures are nearly identical with the root-mean-square difference on all protein atoms being 0.13 A. Some residues of the two refined structures show multiple alternative conformations. Two ions were localized into the electron-density maps of the two structures: one chloride ion at the interface between two symmetry-related molecules and one sodium ion stabilizing the loop Ser60-Leu75. The sodium ion is surrounded by six ligands which form a bipyramid around it at distances of 2.2-2.6 A.

Journal Article↗
PubMed1997

Structure of human plasminogen kringle 4 at 1.68 a and 277 K. A possible structural role of disordered residues.

Despite considerable effort to elucidate the functional role of the kringle domains, relatively little is known about interactions with other protein domains. Most of the crystal structures describe the interactions at the kringle active site. This study suggests a novel way to interpret structural results such as disorder located away from an active site. The crystal structure of human plasminogen kringle 4 (PGK4) has been refined against 10-1.68 A resolution X-ray data (R(merge) = 3.7%) to the standard crystallographic R = 14.7% using the program X-PLOR. The crystals of PGK4 showed significant instability in cell dimensions (changes more than 1.5 A) even at 277 K. The refinement revealed structural details not observed before [Mulichak, Tulinsky & Ravichandran (1991). Biochemistry, 30, 10576-10588], such as clear density for additional side chains and more extensive disorder. Discrete disorder was detected for residues S73, S78, T80, S89, S91, S92, Ml12, S132, C138 and K142. Most of the disordered residues form two patches on the surface of the protein. This localized disorder suggests that these residues may play a role in quaternary interactions and possibly form an interface with the other domains of proteins that contain kringles, such as plasminogen. Although, an additional residue D65 was refined at the beginning of the sequence, still more residues near the peptide cleavage site must be disordered in the crystal.

Journal Article↗
PubMed2003

High-resolution crystal structures of ribonuclease A complexed with adenylic and uridylic nucleotide inhibitors. Implications for structure-based design of ribonucleolytic inhibitors.

The crystal structures of bovine pancreatic ribonuclease A (RNase A) in complex with 3',5'-ADP, 2',5'-ADP, 5'-ADP, U-2'-p and U-3'-p have been determined at high resolution. The structures reveal that each inhibitor binds differently in the RNase A active site by anchoring a phosphate group in subsite P1. The most potent inhibitor of all five, 5'-ADP (Ki = 1.2 microM), adopts a syn conformation (in contrast to 3',5'-ADP and 2',5'-ADP, which adopt an anti), and it is the beta- rather than the alpha-phosphate group that binds to P1. 3',5'-ADP binds with the 5'-phosphate group in P1 and the adenosine in the B2 pocket. Two different binding modes are observed in the two RNase A molecules of the asymmetric unit for 2',5'-ADP. This inhibitor binds with either the 3' or the 5' phosphate groups in subsite P1, and in each case, the adenosine binds in two different positions within the B2 subsite. The two uridilyl inhibitors bind similarly with the uridine moiety in the B1 subsite but the placement of a different phosphate group in P1 (2' versus 3') has significant implications on their potency against RNase A. Comparative structural analysis of the RNase A, eosinophil-derived neurotoxin (EDN), eosinophil cationic protein (ECP), and human angiogenin (Ang) complexes with these and other phosphonucleotide inhibitors provides a wealth of information for structure-based design of inhibitors specific for each RNase. These inhibitors could be developed to therapeutic agents that could control the biological activities of EDN, ECP, and ANG, which play key roles in human pathologies.

Adenosine Diphosphate↗
PubMed2002

Composites of local structure propensities: evidence for local encoding of long-range structure.

To estimate how extensively the ensemble of denatured-state conformations is constrained by local side-chain-backbone interactions, propensities of each of the 20 amino acids to occur in mono- and dipeptides mapped to discrete regions of the Ramachandran map are computed from proteins of known structure. In addition, propensities are computed for the trans, gauche-, and gauche+ rotamers, with or without consideration of the values of phi and psi. These propensities are used in scoring functions for fragment threading, which estimates the energetic favorability of fragments of protein sequence to adopt the native conformation as opposed to hundreds of thousands of incorrect conformations. As finer subdivisions of the Ramachandran plot, neighboring residue phi/psi angles, and rotamers are incorporated, scoring functions become better at ranking the native conformation as the most favorable. With the best composite propensity function, the native structure can be distinguished from 300,000 incorrect structures for 71% of the 2130 arbitrary protein segments of length 40, 48% of 2247 segments of length 30, and 20% of 2368 segments of length 20. A majority of fragments of length 30-40 are estimated to be folded into the native conformation a substantial fraction of the time. These data suggest that the variations observed in amino acid frequencies in different phi/psi/chi1 environments in folded proteins reflect energetically important local side-chain-backbone interactions, interactions that may severely restrict the ensemble of conformations populated in the denatured state to a relatively small subset with nativelike structure.

Amino Acids↗
PubMed2001

Perceived structure from optic flow: consistent versus variable mapping of 3-D Euclidean structure.

In an earlier study (Börjesson & Lind, 1996), the perception of Euclidean structure from polar projected two-frame apparent motion sequences was studied. The results showed that Euclidean structure is not perceived. However, at larger visual angles a certain consistency in the mapping between distal and perceived structure exists. The aim of the present study was to more precisely examine how this degree of consistency varies as a function of visual angle. In Experiments 1 and 2, slant judgments of simulated and real planes indicated that the degree of consistency is a positive function of visual angle. No definite sign of a Euclidean mapping could, however, be found even in the full view condition. Experiment 3 examined texture gradients and the response method used. The results showed that texture gradients did not influence the degree of consistency of the mapping between distal and judged depth and that the response method was both reliable and valid. However, texture gradients did influence the absolute values of the slant judgments. The role of Euclidean and affine mappings of distal structure is discussed and it is proposed that the perceptually important distinction is not between affine and Euclidean mapping, but rather between two types of affine mappings--consistent and variable.

Analysis of Variance↗