Local atomic order in the Al-Cu-Fe melts corresponding to crystalline and quasicrystalline phases

The local atomic order in the Al₇₀Cu₂₀Fe₁₀ and Al_61.9Cu_25.4Fe_12.7 melts that correspond to the tetragonal τ₂ and quasicrystalline phases was studied. The structures of these ternary melts were investigated by high-temperature X-ray diffraction and Reverse Monte Carlo simulation at various temperatures. The structural models of the melts are analyzed using the Voronoi polyhedra and the Delaunay simplexes. The specific features in the structure factor curves were comprehensively discussed: a shoulder in the second maximum and a prepeak on the left side of the principal maximum. The prepeak in the structure factor curves in the diffraction vector range 11–22 nm^?1 is shown to be caused by chemical local atomic ordering, and the shoulder on the right side of the second maximum is shown to result from the presence of icosahedral polytetrahedral clusters in the melts.     

Three-dimensional structure of annexins

Annexins constitute a family of structurally related calcium- and phospholipid-binding proteins whose molecular structure has been investigated in detail in the crystalline and membrane-bound form. Their polypeptide chain is folded into four or eight alpha-helical domains of similar structure with a central hydrophilic pore. Bound to phospholipid membranes, the four-domain arrangement of the annexin molecule is conserved. A peripheral binding mode has been well documented by electron microscopy and a variety of other techniques.     

Three-dimensional structure of cell adhesion molecules

Recent structural data have provided insights into various forms of specific cell adhesion interactions, including both protein-protein and protein-glycoconjugate recognition events. The major advances have been made in the structural characterization of cadherin-cadherin and integrin-ligand mediated adhesion.     

Three-dimensional structure of the yeast ribosome

The 80S ribosome from Saccharomyces cerevisiae has been reconstructed from cryo electron micrographs to a resolution of 35 A. It is strikingly similar to the 70S ribosome from Escherichia coli, while displaying the characteristic eukaryotic features familiar from reconstructions of ribosomes from higher eukaryotes. Aside from the elaboration of a number of peripherally located features on the two subunits and greater overall size, the largest difference between the yeast and E.coli ribosomes is in a mass increase on one side of the large (60S) subunit. It thus appears more elliptical than the characteristically globular 50S subunit from E.coli. The interior of the 60S subunit reveals a variable diameter tunnel spanning the subunit between the interface canyon and a site on the lower back of the subunit, presumably the exit site through which the nascent polypeptide chain emerges from the ribosome.     

A lock-in model for the atomic structure of interphase boundaries between metals and ionic crystals

The low energy interphase boundaries between noble metals (Au, Cu) and various ionic crystals (LiF, KCl, NaCl, MgO, A1₂O₃, mica) were determined at 550°C by means of the boundary energy induced rotation of small (~ 1 μm) spheres. The systems were chosen so that the effect of lattice mismatch (varied between 1.3 and 35.1%), the effect of lattice structure (cubic/cubic and hexagonal/cubic) and chemical effects could be studied. The results obtained suggest that boundary models based on the coincidence concept are not applicable to interphase boundaries between noble metals and ionic crystals because the low energy boundaries observed were not of the coincidence type and existing coincidence orientation relationships did not result in low energy boundaries. However, the atomic structure of the low energy interphase boundaries observed may be understood in terms of the following “lock-in model”. A low energy interphase boundary results if the close packed rows of atoms at the “surface” of the metal crystal fit into the “valleys” between close packed rows of atoms at the “surface” of the ionic crystal. This model seems to predict correctly the experimentally observed correlations between the interfacial energy and the boundary inclination, the lattice mismatch and the lattice structure of the two phases involved.     

Three-dimensional model of a hairpin ribozyme

On the basis of the mutational and chemical-modification analysis, we propose the new secondary structure of a hairpin ribozyme, which contains three stems, a triple helix and the reverse Watson-Crick g+1C44 base pair at the 3' side of the cleavage site. The computational approach to the tertiary structure of a hairpin ribozyme have been carried out.     

Three-dimensional structure of the tyrosine kinase c-Src

The structure of a large fragment of the c-Src tyrosine kinase, comprising the regulatory and kinase domains and the carboxy-terminal tall, has been determined at 1.7 A resolution in a closed, inactive state. Interactions among domains, stabilized by binding of the phosphorylated tail to the SH2 domain, lock the molecule in a conformation that simultaneously disrupts the kinase active site and sequesters the binding surfaces of the SH2 and SH3 domains. The structure shows how appropriate cellular signals, or transforming mutations in v-Src, could break these interactions to produce an open, active kinase.     

The atomic structure of protein-protein recognition sites

The non-covalent assembly of proteins that fold separately is central to many biological processes, and differs from the permanent macromolecular assembly of protein subunits in oligomeric proteins. We performed an analysis of the atomic structure of the recognition sites seen in 75 protein-protein complexes of known three-dimensional structure: 24 protease-inhibitor, 19 antibody-antigen and 32 other complexes, including nine enzyme-inhibitor and 11 that are involved in signal transduction.The size of the recognition site is related to the conformational changes that occur upon association. Of the 75 complexes, 52 have "standard-size" interfaces in which the total area buried by the components in the recognition site is 1600 (+/-400) A2. In these complexes, association involves only small changes of conformation. Twenty complexes have "large" interfaces burying 2000 to 4660 A2, and large conformational changes are seen to occur in those cases where we can compare the structure of complexed and free components. The average interface has approximately the same non-polar character as the protein surface as a whole, and carries somewhat fewer charged groups. However, some interfaces are significantly more polar and others more non-polar than the average. Of the atoms that lose accessibility upon association, half make contacts across the interface and one-third become fully inaccessible to the solvent. In the latter case, the Voronoi volume was calculated and compared with that of atoms buried inside proteins. The ratio of the two volumes was 1.01 (+/-0.03) in all but 11 complexes, which shows that atoms buried at protein-protein interfaces are close-packed like the protein interior. This conclusion could be extended to the majority of interface atoms by including solvent positions determined in high-resolution X-ray structures in the calculation of Voronoi volumes. Thus, water molecules contribute to the close-packing of atoms that insure complementarity between the two protein surfaces, as well as providing polar interactions between the two proteins.     

Three-dimensional model of Tetrahymena group I intron

The modelling of the folding structure of Tetrahymena group I intron have been carried out, using the molecular mechanics programs; Insight II and Discover. This model has long-range interactions between the P2.1 loop region and the 3' exon, and between the P9.1a and P5c loop regions.     

Three-dimensional structure of O-acetylserine sulfhydrylase from Salmonella typhimurium

The dependence of hormonal responses to exercise on sexual maturation was tested in three-year longitudinal experiment on 34 girls (11-12 years old at the beginning of the study). Sexual maturation of the girls was evaluated using Tanner scale. Girls were divided into three groups: maturation stages 1-2, 2-4 and 4-5. Children performed a 20-min cycle exercise at 60% of maximal oxygen uptake (VO max) once a year. Cortisol, insulin, somatotropin, beta-estradiol, progesterone and testosterone were determined in venous blood by RIA procedures. High basal levels of beta-estradiol and somatotropin appeared in stages 2-4 (387 +/- 92 pmol.l-1) and 12.9 +/- 2.85 ng.ml-1, respectively) and 4-5 (358 +/- 54 pmol.l-1) and 14.3 +/- 1.53 ng.ml-1, respectively). The basal progesterone level increased with maturation, testosterone appeared in the blood in stages 2-4 and 4-5. The exercise resulted in increased levels of cortisol and somatotropin, and a drop in insulin in all girls. The cortisol response was most pronounced in stage 1-2. Postexercise insulin concentration was the highest in stage 4-5. beta-estradiol level increased by 23% in stages 1-2 and 4-5, while the response was insignificant in stages 2-4. Exercise-induced progesterone increase was significant in stage 4-5. In conclusion, sexual maturation associates with several quantitative changes in exercise-induced hormonal responses.     

Three-dimensional structure of functional motor proteins on microtubules

BACKGROUND: Kinesins are a superfamily of motor proteins that use ATP hydrolysis to fuel movement along microtubules and participate in many crucial phases of the eukaryotic cell cycle. Usually these motors are heterotetramers of two heavy and two light chains, and have globular motor domains on the two heavy chains. Most kinesins move towards the microtubule 'plus end', but some, such as ncd (nonclaret disjunctional protein), move in the opposite direction. Heavy chain dimers produced by overexpression are viable motors. RESULTS: In order to establish whether the opposite directionality of kinesin and ncd dimers is related to notable conformational differences, we have used electron cryo-microscopy and three-dimensional reconstruction methods to investigate the structure of kinesin and ncd dimers attached to microtubules in the presence of AMP-PNP (5'-adenylylimidodiphosphate), a nonhydrolyzable ATP analogue. Three-dimensional maps of the motor-microtubule complexes show the motors to have one unattached, and one attached head per tubulin dimer. The polarity of the reconstructions was determined for each individual microtubule. Attachment occurs on the crest of a protofilament at the end of the tubulin dimer that points towards the plus end of the microtubule. The attached head extends over the next tubulin molecule along the protofilament. The unattached heads of kinesin and ncd have distinctly different conformations. CONCLUSIONS: The attached heads of kinesin and ncd appear to be similar and to interact with the same region of the plus end-oriented tubulin subunits. The free heads, however, are quite different, which suggests that directionality could be determined by differences in the dimer conformations. Work is in progress to obtain three-dimensional maps in the presence of different nucleotides with the aim of understanding how these motors move along microtubules.