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PubMed1999

The pH-dependent structural variation of complementarity-determining region H3 in the crystal structures of the Fv fragment from an anti-dansyl monoclonal antibody.

The Fv fragment from an anti-dansyl antibody was optimally crystallized into two crystal forms having slightly different lattice dimensions at pH 5.25 and 6.75. The two crystal structures were determined and refined at high resolution at 112 K (at 1.45 A for the crystal at pH 5.25 and at 1.55 A for that at pH 6.75). In the two crystal structures, marked differences were identified in the first half of CDRH3 s having an amino acid sequence of Ile95H-Tyr96H-Tyr97H-His98H-Tyr99H-Pro1 00H-Trp100aH-Phe100bH-Ala101H- Tyr102H. NMR pH titration experiments revealed the p Kavalues of four histidine residues (His27dL, His93L, His55H and His98H) exposed to solvent. Only His98H (p Ka=6.3) completely changed its protonation state between the two crystallization conditions. In addition, the environmental structures including hydration water molecules around the four histidine residues were carefully compared. While the hydration structures around His27dL, His93L and His55H were almost invariant between the two crystal structures, those around His98Hs showed great difference in spite of the small conformational difference of His98H between the two crystal structures. These spectroscopic and crystallographic findings suggested that the change in the protonation state in His98H was responsible for the structural differences between pH 5.25 and 6.75. In addition, the most plausible binding site of the dansyl group was mapped into the present structural models with our previous NMR experimental results. The complementarity-determining regions H1, H3 and the N-terminal region in the VH domain formed the site. The side-chain of Tyr96H occupied the site and interacted with Phe27H of H1, giving a clue for the binding mode of the dansyl group in the site.

Antibodies, Monoclonal↗
PubMed1992

Comparison of the NMR solution structure with the X-ray crystal structure of the activation domain from procarboxypeptidase B.

The NMR solution structure of the activation domain isolated from porcine procarboxypeptidase B is compared with the X-ray crystal structure of the corresponding segment in the intact proenzyme. For the region of the polypeptide chain that has a well-defined three-dimensional structure in solution, i.e., the backbone atoms of residues 11-76 and 25 amino acid side chains in this segment that form a hydrophobic core in the activation domain, the root-mean-square distance between the two structures is 1.1.A. There are no significant differences in average atom positions between the two structures, but only the NMR structure shows increased structural disorder in three outlying loops located along the same edge of the activation domain. These regions of increased structural disorder in the free domain coincide only partially with the interface to the enzyme domain in the proenzyme.

Amino Acid Sequence↗
PubMed2006

Habitat structure, trophic structure and ecosystem function: interactive effects in a bromeliad-insect community.

Although previous studies have shown that ecosystem functions are affected by either trophic structure or habitat structure, there has been little consideration of their combined effects. Such interactions may be particularly important in systems where habitat and trophic structure covary. I use the aquatic insects in bromeliads to examine the combined effects of trophic structure and habitat structure on a key ecosystem function: detrital processing. In Costa Rican bromeliads, trophic structure naturally covaries with both habitat complexity and habitat size, precluding any observational analysis of interactions between factors. I therefore designed mesocosms that allowed each factor to be manipulated separately. Increases in mesocosm complexity reduced predator (damselfly larva) efficiency, resulting in high detritivore abundances, indirectly increasing detrital processing rates. However, increased complexity also directly reduced the per capita foraging efficiency of the detritivores. Over short time periods, these trends effectively cancelled each other out in terms of detrital processing. Over longer time periods, more complex patterns emerged. Increases in mesocosm size also reduced both predator efficiency and detritivore efficiency, leading to no net effect on detrital processing. In many systems, ecosystem functions may be impacted by strong interactions between trophic structure and habitat structure, cautioning against examining either effect in isolation.

Animals↗
PubMed2003

Structuring parameters for assessment of bone quality using a morphological filter and star volume analysis: structuring property in the cancellous bone of the human femoral head.

This study examines structuring parameters for the assessment of bone quality based on the relationship of bone strength to the trabecular structure or bone mineral density (BMD). Thirty-nine human cancellous bone blocks sampled from resected Ward's triangle area were investigated. The trabecular bone pattern of each bone block was binarized into its corresponding trabecular skeletal pattern using computed radiography with a morphological filter. Every binarized trabecular skeletal pattern was quantified to find the trabecular skeletal pixel percentage (SkP = volume parameter of trabecular skeletal signal component) and skeletal star volume (Vt = connection parameter of trabecular skeletal structure). After BMD and elasticity for each bone block was measured by dual X-ray absorptiometry and the breaking test, the correlations to SkP and Vt were determined. In addition, an attempt was made to detect changes of the trabecular structure in the Ward's triangle area of the femoral head after patients had received treatment for osteoporosis. This evaluation used the structuring parameters SkP and Vt. The results showed that the larger the BMD value, the greater the elasticity, although some samples with similar BMD values had considerably different elasticities. With increased Vt values the trabecular skeletal pattern that had horizontal skeletal elements orientated perpendicular to the loading direction showed higher elasticity. No correlation between SkP and either elasticity or BMD was observed in either the subset (sequential images of morphological filter) or sumset images (combined with subset images). On the other hand, the correlation coefficient between Vt and elasticity was similar to that between BMD and elasticity for subset image ( n = 6). For sumset images (3-6 and 4-7), the correlation coefficient of Vt was equal or higher than that of BMD and the connectivity of the trabecular skeletal structure was more closely linked to bone strength as compared to BMD. Therefore, it was concluded that because no high correlation could be detected between Vt and BMD, BMD and the connectivity of trabeculae are independently related to bone strength. In addition, this method was used to evaluate patients after treatment for osteoporosis, and noticeable changes were seen in the bone trabecular skeletal structure in the Ward's triangle area of the femoral head. In reference to these clinical images, variations in SkP and Vt were quantitatively assessed. These results suggest that the SkP and Vt obtained using computed radiography, morphological filter, and star volume analysis are useful structuring parameters for the assessment of bone quality.

Aged↗
PubMed2002

Solution structure of cyanoferricytochrome c: ligand-controlled conformational flexibility and electronic structure of the heme moiety.

The solution structure of cyanoferricytochrome c has been determined using NMR spectroscopy. As a result of including additional constraints derived from pseudocontact shifts, a high-resolution NMR structure was obtained with high accuracy. In order to study the conformational transition between the native protein and its ligand adducts, the present structure was compared with the solution structures of the wild-type cytochrome c and the imidazole-cytochrome c complex. Like the solution structure of imidazole-cytochrome c, the heme crevice is widened by the swinging out of residues 77-85 and a noticeable shift of the 50s helix. However, unlike imidazole, cyanide exerts less significant perturbation on the conformation of the heme cavity, which is revealed by a more compact residue package in the distal pocket. Furthermore, comparison of the solution structure of CN-iso-1Met80Ala cytochrome c with the structure of cyanoferricytochrome c indicated that the binding of cyanide has a different impact on the distal cavity conformation in the two proteins. In addition, the magnetic properties of the present system are discussed and a comprehensive study of the electronic structure of ligand-cytochrome c complexes and the native protein is also described. Electronic supplementary material to this paper can be obtained by using the Springer Link server located at http://dx.doi.org/10.1007/s00775-001-0334-y.

Amino Acid Sequence↗
PubMed1981

A computer method for construction of secondary structure from polynucleotide sequence. Possible structure of the bacterial replication origin.

A computer method to search the possible secondary structure of a long polynucleotide was developed. As a criterion for the stabilization of a secondary structure, free energy originating from base-pairing was employed, since the structure in solution would be at the free energy minimum. The method is summarized as follows: all possible helices are collected from a given nucleotide sequence under restrictions that the length of a helix is greater than N0 bases (e.g., four bases) and the free energy of the helix calculated according to free energies of two successive sequence-dependent basepairs is lower than E0 (e.g., -5 kcal/mol). The search of secondary structures of low free energy is performed by connecting one helix to another without allowing any base-pairing between loops. For connecting single-stranded regions, destabilizing free energy of 2--3 kcal/mol is added. The method was first applied to several tRNAs and the clover-leaf structure of tRNA was obtained as a free energy minimum. Then, possible secondary structures of the replication origin regions of the Escherichia coli and Salmonella typhimurium chromosomes were examined by the method, assuming that one of the strands in the origin region takes a specific secondary structure. The lowest-energy structure for the E. coli origin was found to be approximately identical to that for the S. typhimurium origin region.

Base Sequence↗
PubMed1986

Water structure in vitamin B12 coenzyme crystals. II. Structural characteristics of the solvent networks.

The geometrical details of the solvent structure in vitamin B12 coenzyme crystals with respect to hydrogen bonding and nonbonded contacts, are described. The individual H-bond geometries varied over wide ranges, similar to those observed in small molecule structures. Large deviations from tetrahedral coordination were found around a majority of the waters. The mutual positions and orientations of the water molecules could not be adequately explained in terms of the H-bonding relationships present in the structure. However, additional investigations, which focused on the short range nonbonded contacts around water positions in a variety of crystal hydrates, revealed several structural regularities (Savage, 1986b). These features relate to the nonbonded O...O, H...O, and H...H interactions, and give rise to a set of repulsive restrictions that are seen to be very much stronger stereochemical restraints than those associated with H-bonding. The short-range restrictions appear largely to govern the local orientational correlations and packing arrangements of the water structure within the coenzyme (and other hydrate) crystals. In more general terms, the inclusion of the nonbonding relationships as well as the attractive H-bonding interactions, leads to a significant increase in our understanding of water structure(s). The repulsive restrictions can be used as stereochemical restraints in the interpretation and refinement of solvent structures within larger hydrate systems, such as protein crystals. They may also be included in potential functions used to simulate solvent structures in aqueous solutions and hydrate systems.

Hydrogen Bonding↗
PubMed2000

Separating the elements of habitat structure: independent effects of habitat complexity and structural components on rocky intertidal gastropods.

It has been difficult to understand the effects of habitat structure on assemblages because the different elements of habitat structure are often confounded. For example, few studies consider that the effects of structural components of a habitat (rocks, trees, pits, pneumatophores) may be separate from the complexity (e.g. surface area {SA}) they create. From prior observations and experiments, I developed three hypotheses about the effects of habitat structure on gastropods on rocky intertidal shores in Botany Bay, Australia. (1) The complexity of habitats positively affects the density and richness of gastropods. (2) The fractal dimension (D) represents elements of complexity that affect the density and richness of gastropods better than other indices of complexity. (3) The effects of specific structural components on the density and richness of gastropods are independent of their complexity. To test these hypotheses, treatments composed of pits and pneumatophores were used to independently manipulate complexity and structural components in experiments repeated at five different times on two shores. There was support for hypotheses (1) and (3) at most times and places but not for hypothesis (2). Richness, total density, and the densities of two of the three most common gastropods were greater in treatments with greater complexity. D was not definitively better than other indices of complexity, but D and SA were recommended for further consideration. When complexity was held constant, species richness and the density of most gastropods, except Austrocochlea porcata, was greater in treatments with pits than with pneumatophores. A common mechanistic explanation for the effects of habitat complexity on rocky intertidal gastropods relies on a specific characteristic of pits; they pool water and reduce desiccation stress. This assumption may be appropriate for many gastropods, but it was inappropriate for A. porcata. Habitat complexity affected its density, but this was not because of a characteristic specific to pits. The complexity and structural components of habitats have separate effects on assemblages, and it confuses the study of habitat structure to combine them.

Journal Article↗
PubMed1997

A new structural class of serine protease inhibitors revealed by the structure of the hirustasin-kallikrein complex.

BACKGROUND: Hirustasin belongs to a class of serine protease inhibitors characterized by a well conserved pattern of cysteine residues. Unlike the closely related inhibitors, antistasin/ghilanten and guamerin, which are selective for coagulation factor Xa or neutrophil elastase, hirustasin binds specifically to tissue kallikrein. The conservation of the pattern of cysteine residues and the significant sequence homology suggest that these related inhibitors possess a similar three-dimensional structure to hirustasin. RESULTS: The crystal structure of the complex between tissue kallikrein and hirustasin was analyzed at 2.4 resolution. Hirustasin folds into a brick-like structure that is dominated by five disulfide bridges and is sparse in secondary structural elements. The cysteine residues are connected in an abab cdecde pattern that causes the polypeptide chain to fold into two similar motifs. As a hydrophobic core is absent from hirustasin the disulfide bridges maintain the tertiary structure and present the primary binding loop to the active site of the protease. The general structural topography and disulfide connectivity of hirustasin has not previously been described. CONCLUSIONS: The crystal structure of the kallikrein-hirustasin complex reveals that hirustasin differs from other serine protease inhibitors in its conformation and its disulfide bond connectivity, making it the prototype for a new class of inhibitor. The disulfide pattern shows that the structure consists of two domains, but only the C-terminal domain interacts with the protease. The disulfide pattern of the N-terminal domain is related to the pattern found in other proteins. Kallikrein recognizes hirustasin by the formation of an antiparallel beta sheet between the protease and the inhibitor. The P1 arginine binds in a deep negatively charged pocket of the enzyme. An additional pocket at the periphery of the active site accommodates the sidechain of the P4 valine.

Amino Acid Sequence↗
PubMed1998

Function from structure? The crystal structure of human phosphatidylethanolamine-binding protein suggests a role in membrane signal transduction.

BACKGROUND: Proteins belonging to the phosphatidylethanolamine-binding protein (PEBP) family are highly conserved throughout nature and have no significant sequence homology with other proteins of known structure or function. A variety of biological roles have previously been described for members of this family, including lipid binding, roles as odorant effector molecules or opioids, interaction with the cell-signalling machinery, regulation of flowering plant stem architecture, and a function as a precursor protein of a bioactive brain neuropeptide. To date, no experimentally derived structural information has been available for this protein family. In this study we have used X-ray crystallography to determine the three-dimensional structure of human PEBP (hPEBP), in an attempt to clarify the biological role of this unique protein family. RESULTS: The crystal structures of two forms of hPEBP have been determined: one in the native state (at 2.05 A resolution) and one in complex with cacodylate (at 1.75 A resolution). The crystal structures reveal that hPEBP adopts a novel protein topology, dominated by the presence of a large central beta sheet, and is expected to represent the archaetypal fold for this family of proteins. Two potential functional sites have been identified from the structure: a putative ligand-binding site and a coupled cleavage site. hPEBP forms a dimer in the crystal with a distinctive dipole moment that may orient the oligomer for membrane binding. CONCLUSIONS: The crystal structure of hPEBP suggests that the ligand-binding site could accommodate the phosphate head groups of membrane lipids, therefore allowing the protein to adhere to the inner leaf of bilipid membranes where it would be ideally positioned to relay signals from the membrane to the cytoplasm. The structure also suggests that ligand binding may lead to coordinated release of the N-terminal region of the protein to form the hippocampal neurostimulatory peptide, which is known to be active in the development of the hippocampus. These studies are consistent with a primary biological role for hPEBP as a transducer of signals from the interior membrane surface.

Amino Acid Sequence↗
PubMed2003

Small-angle scattering: a view on the properties, structures and structural changes of biological macromolecules in solution.

A self-contained presentation of the main concepts and methods for interpretation of X-ray and neutron-scattering patterns of biological macromolecules in solution, including a reminder of the basics of X-ray and neutron scattering and a brief overview of relevant aspects of modern instrumentation, is given. For monodisperse solutions the experimental data yield the scattering intensity of the macromolecules, which depends on the contrast between the solvent and the particles as well as on their shape and internal scattering density fluctuations, and the structure factor, which is related to the interactions between macromolecules. After a brief analysis of the information content of the scattering intensity, the two main approaches for modelling the shape and/or structure of macromolecules and the global minimization schemes used in the calculations are presented. The first approach is based, in its more advanced version, on the spherical harmonics approximation and relies on few parameters, whereas the second one uses bead models with thousands of parameters. Extensions of bead modelling can be used to model domain structure and missing parts in high-resolution structures. Methods for computing the scattering patterns from atomic models including the contribution of the hydration shell are discussed and examples are given, which also illustrate that significant differences sometimes exist between crystal and solution structures. These differences are in some cases explainable in terms of rigid-body motions of parts of the structures. Results of two extensive studies--on ribosomes and on the allosteric protein aspartate transcarbamoylase--illustrate the application of the various methods. The unique bridge between equilibrium structures and thermodynamic or kinetic aspects provided by scattering techniques is illustrated by modelling of intermolecular interactions, including crystallization, based on an analysis of the structure factor and recent time-resolved work on assembly and protein folding.

Macromolecular Substances↗
PubMed1991

Three-dimensional structure of murine anti-p-azophenylarsonate Fab 36-71. 2. Structural basis of hapten binding and idiotypy.

Comparison between the structures and solvent-accessible surfaces of the antigen-binding fragments of two murine anti-p-azophenylarsonate monoclonal antibodies, one bearing a major cross-reactive idiotype of A/J strain mice (36-71) and one lacking the idiotype (R19.9; Lascombe et al., 1989), highlight the structural basis for the determination of hapten affinity and idiotypy. Since the sequence of R 19.9 is identical with the germline-encoded sequence at 16 positions in both heavy-chain and light-chain variable regions where somatic mutations and junctional differences have occurred to produce the 36-71 sequence, the structure of R 19.9 can be used to model the structure of the germline-encoded antibody (36-65) in the regions around these sites. These 16 sequence differences exclude the third heavy-chain complementarity-determining region because R 19.9 utilizes a D gene segment not associated with the predominant idiotype, which is 4 residues longer than the canonical D gene segment utilized in the sequences of 36-71 and 36-65. This difference between the structures of R 19.9 and 36-71 does not affect the validity of using the structure of R 19.9 to model the structure of 36-65 since the third heavy-chain complementarity-determining region is highly solvent-exposed in both 36-71 and R 19.9, and does not interact with any of these 16 sites. Comparing the structures of 36-71 and R 19.9 suggests that only three of the differences in the heavy-chain sequences, and three of the differences in the light-chain sequences of 36-71 and 36-65, increase the affinity for hapten.(ABSTRACT TRUNCATED AT 250 WORDS)

Amino Acid Sequence↗
PubMed1986

Three-dimensional structure of the kringle sequence: structure of prothrombin fragment 1.

The three-dimensional structure of bovine prothrombin fragment 1 has been solved at 2.8-A resolution. The electron density clearly reveals four disulfide bridges along with more than 80% of the side chains completely in density, which correspond faithfully to the kringle sequence, its preceding 30 residues, and the dodecapeptide carboxy terminal; the polysaccharide and the first 35 residues of the amino terminal of fragment 1 are disordered or about 40% of the structure. The folding of the kringle sequence is based upon close disulfide van der Waals contacts between Cys-87-Cys-127 and Cys-115-Cys-139 (4.1 A between midpoints of the bridges), two antiparallel strands of highly conserved (113-118, 124-129) beta-structure, and the stacking of some conserved aromatic residues, all near the center of the folded structure. Moreover, the overall folding appears to be duplicated as a pair of stacked duplex loops with an antiparallel open loop. The overall shape of the kringle structure approximates an eccentric oblate ellipsoid of dimensions 11 X 28 X 30 A. The residues immediately preceding the kringle are dominated by alpha-helical structure (Phe-41-Cys-48; Leu-56-Glu-63). Residues Phe-41-Trp-42 and Tyr-45, which are conserved in factor IX, factor X, protein C, and protein Z, form another aromatic stacked cluster while the Cys-48-Cys-61 disulfide loop corresponds to the well-known alpha/beta structural unit. The dodecapeptide carboxy-terminal interkringle chain extends along the periphery of the kringle in its plane and forms a beta-structure with the kringle-closing Ser-140-Val-143 tetrapeptide.

Amino Acid Sequence↗
PubMed1988

A study of the structure of human complement component factor H by Fourier transform infrared spectroscopy and secondary structure averaging methods.

Fourier transform infrared spectroscopy was used to investigate the secondary structure of human complement component factor H in H2O and 2H2O buffers. The spectra show a broad amide I band which after second-derivative calculations is shown to be composed of three components at 1645, 1663, and 1685 cm-1 in H2O and at 1638, 1661, and 1680 cm-1 in 2H2O. The frequencies of these components are consistent with the existence of an extensive antiparallel beta-strand secondary structure. The exchange properties of the amide protons of factor H as measured in 2H2O buffers are rapid and lead to an estimate of NH proton nonexchange that is comparable with those for small globular proteins. Human factor H is constructed from a linear sequence of 20 short consensus repeats with a mean of 61 residues in each one. To investigate the secondary structure further, secondary structure predictions were carried out on the basis of an alignment scheme for 101 sequences for these repeats as found in human factor H and 12 other proteins. These predictions were averaged in order to improve the reliability of the calculations. Both the Robson and the Chou-Fasman methods indicate significant beta-structural contents. Residues 21-51 in the 61-residue repeat show a clear prediction of four strands of beta-structure and four beta-turns. A structural model based on antiparallel beta-strands in the secondary structure is proposed and discussed.(ABSTRACT TRUNCATED AT 250 WORDS)

Amino Acid Sequence↗
PubMed1990

Secondary structure of the mammalian 70-kilodalton heat shock cognate protein analyzed by circular dichroism spectroscopy and secondary structure prediction.

Heat shock proteins are rapidly synthesized when cells are exposed to stressful agents that cause protein damage. The 70-kDa heat shock induced proteins and their closely related constitutively expressed cognate proteins bind to unfolded and aberrant polypeptides and to hydrophilic peptides. The structural features of the 70-kDa heat shock proteins that confer the ability to associate with diverse polypeptides are unknown. In this study, we have used circular dichroism (CD) spectroscopy and secondary structure prediction to analyze the secondary structure of the mammalian 70-kDa heat shock cognate protein (hsc 70). The far-ultraviolet CD spectrum of hsc 70 indicates a large fraction of alpha-helix in the protein and resembles the spectra one obtains from proteins of the alpha/beta structural class. Analysis of the CD spectra with deconvolution methods yielded estimates of secondary structure content. The results indicate about 40% alpha-helix and 20% aperiodic structure within hsc 70 and between 16-41% beta-sheet and 21-0% beta-turn. The Garnier-Osguthorpe-Robson method of secondary structure prediction was applied to the rat hsc 70 amino acid sequence. The predicted estimates of alpha-helix and aperiodic structure closely matched the values derived from the CD analysis, whereas the predicted estimates of beta-sheet and beta-turn were midway between the CD-derived values. Present evidence suggests that the polypeptide ligand binding domain of the 70-kDa heat shock protein resides within the C-terminal 160 amino acids [Milarski, K. L., & Morimoto, R. I. (1989) J. Cell Biol. 109, 1947-1962].(ABSTRACT TRUNCATED AT 250 WORDS)

Amino Acid Sequence↗
PubMed2003

Structural consequences of metallothionein dimerization: solution structure of the isolated Cd4-alpha-domain and comparison with the holoprotein dimer.

The NMR determination of the structure of Cd(7)-metallothionein was done previously using a relatively large protein concentration that favors dimer formation. The reactivity of the protein is also affected under this condition. To examine the influence of protein concentration on metallothionein conformation, the isolated Cd(4)-alpha-domain was prepared from rabbit metallothionein-2 (MT 2), and its three-dimensional structure was determined by heteronuclear, (1)H-(111)Cd, and homonuclear, (1)H-(1)H NMR, correlation experiments. The three-dimensional structure was refined using distance and angle constraints derived from these two-dimensional NMR data sets and a distance geometry/simulated annealing protocol. The backbone superposition of the alpha-domain from rabbit holoprotein Cd(7)-MT 2 and the isolated rabbit Cd(4)-alpha was measured at a RMSD of 2.0 A. Nevertheless, the conformations of the two Cd-thiolate clusters were distinctly different at two of the cadmium centers. In addition, solvent access to the sulfhydryl ligands of the isolated Cd(4)-alpha cluster was 130% larger due to this small change in cluster geometry. To probe whether these differences were an artifact of the structure calculation, the Cd(4)-alpha-domain structure in rabbit Cd(7)-MT 2 was redetermined, using the previously defined set of NOEs and the present calculation protocol. All calculations employed the same ionic radius for Cd(2+) and same cadmium-thiolate bond distance. The newly calculated structure matched the original with an RMSD of 1.24 A. It is hypothesized that differences in the two alpha-domain structures result from a perturbation of the holoprotein structure because of head-to-tail dimerization under the conditions of the NMR experiments.

Amino Acid Sequence↗
PubMed2000

A unique distortion in K1/3Ba2/3AgTe2: X-ray diffraction determination and electronic band structure analysis of its incommensurately modulated structure.

The incommensurately modulated structure of a square Te-net, namely that of K1/3Ba2/3AgTe2, is determined from single-crystal X-ray diffraction data within a (3+1)D higher dimension formalism. The phase is shown to crystallize in the monoclinic symmetry, P2(1)(alpha 0 gamma) superspace group with the following lattice parameters: a = 4.6441(10) A, b = 4.6292(12) A, c = 23.765(9) A, and beta = 101.28(2) degrees with q = 0.3248(6)a* -0.071(8)c*, that is, in a symmetry different from that reported for the average structure (tetragonal) or that assumed from electron diffraction measurements (orthorhombic). After the introduction of a crenel function for the Te displacive description, the refinement converged to a residual factor R = 0.033 for 2583 observed reflections and 115 parameters (R = 0.024 and 0.101 for 1925 main reflections and 658 first-order satellites, respectively). The [Ag2-Te2] and the Ba/K layers are found to be only weakly modulated. The modulation of the square Te-net is, however, both substantial and unique. Namely, it results in two different units: a "V"-shaped Te3 trimer and a "W"-shaped Te5 pentamer. To examine both unit types, which are segregated in domains that aperiodically alternate within the Te layers, first principles electronic band structure calculations were carried out for three model commensurate structures using the tight-binding linear-muffin-tin-orbital method (LMTO). The calculations show that the distorted structures of V-pattern (model 2) and W-pattern (model 3) are more stable than the average structure (model 1) and that the V-pattern distortion provides a slightly larger stabilization than does the W-pattern distortion. The Fermi surface calculated for the average structure shows nesting vectors that are consistent with the occurrence of the V- and W-pattern distortions in the Te layers. However, these vectors do not predict the observed modulation vector of the incommensurately distorted structure, because the stabilization energy associated with the distortion is not mainly dominated by the energy lowering of the occupied band levels near the Fermi level.

Journal Article↗
PubMed2001

Supermolecular structure of the enteropathogenic Escherichia coli type III secretion system and its direct interaction with the EspA-sheath-like structure.

Enteropathogenic Escherichia coli (EPEC) secretes several Esp proteins via the type III secretion system (secreton). EspA, EspB, and EspD are required for translocation of the effector proteins into host cells, in which EspB and EspD are thought to form a pore in the host membrane. Recent study has shown that EspA forms a filamentous structure that assembles as a physical bridge between bacteria and host cell surfaces, which then functions as a conduit for the translocation of bacterial effectors into host cells. To investigate the supermolecular structure of the type III secreton in EPEC, we partially purified it from the bacteria membrane and observed it via transmission electron microscopy. The EPEC type III secreton was composed of a basal body and a needle part and was similar to those of Salmonella and Shigella, except for a sheath-like structure at the tip of the needle. The length of sheath-like structures varied; it extended more than 600 nm and was 10 times longer than the Shigella needle part. The putative major needle component, EscF, was required for both secretion of Esp proteins and needle complex formation. Interestingly, elongation of the sheath-like structure was observed under constitutive expression of EspA but not of EscF. Furthermore, the transmission electron microscopy view with immunogold labeled anti-EspA antibodies clearly showed that EspA is a component of the sheath-like structure. This study revealed, to our knowledge for the first time, the supermolecular structure of the EPEC type III secreton and its direct association with the EspA-sheath-like structure.

Amino Acid Sequence↗