Crystal structure of the cell cycle-regulatory protein suc1 reveals a beta-hinge conformational switch.

The Schizosaccharomyces pombe cell cycle-regulatory protein suc1, named as the suppressor of cdc2 temperature-sensitive mutations, is essential for cell cycle progression. To understand suc1 structure-function relationships and to help resolve conflicting interpretations of suc1 function based on genetic studies of suc1 and its functional homologs in both lower and higher eukaryotes, we have determined the crystal structure of the beta-interchanged suc1 dimer. Each domain consists of three alpha-helices and a four-stranded beta-sheet, completed by the interchange of terminal beta-strands between the two subunits. This beta-interchanged suc1 dimer, when compared with the beta-hairpin single-domain folds of suc1, reveals a beta-hinge motif formed by the conserved amino acid sequence HVPEPH. This beta-hinge mediates the subunit conformation and assembly of suc1: closing produces the intrasubunit beta-hairpin and single-domain fold, whereas opening leads to the intersubunit beta-strand interchange and interlocked dimer assembly reported here. This conformational switch markedly changes the surface accessibility of sequence-conserved residues available for recognition of cyclin-dependent kinase, suggesting a structural mechanism for beta-hinge-mediated regulation of suc1 biological function. Thus, suc1 belongs to the family of domain-swapping proteins, consisting of intertwined and dimeric protein structures in which the dual assembly modes regulate their function.

Crystal structure of the I-domain from the CD11a/CD18 (LFA-1, alpha L beta 2) integrin.

We report the 1.8-A crystal structure of the CD11a I-domain with bound manganese ion. The CD11a I-domain contains binding sites for intercellular adhesion molecules 1 and 3 and can exist in both low- and high-affinity states. The metal-bound form reported here is likely to represent a high-affinity state. The CD11a I-domain structure reveals a strained hydrophobic ridge adjacent to the bound metal ion that may serve as a ligand-binding surface and is likely to rearrange in the absence of bound metal ion. The CD11a I-domain is homologous to domains found in von Willebrand factor, and mapping of mutations found in types 2a and 2b von Willebrand disease onto this structure allows consideration of the molecular basis of these forms of the disease.

Crystal structure of the large fragment of Thermus aquaticus DNA polymerase I at 2.5-A resolution: structural basis for thermostability.

The crystal structure of the large fragment of the Thermus aquaticus DNA polymerase (Klentaq1), determined at 2.5-A resolution, demonstrates a compact two-domain architecture. The C-terminal domain is identical in fold to the equivalent region of the Klenow fragment of Escherichia coli DNA polymerase I (Klenow pol I). Although the N-terminal domain of Klentaq1 differs greatly in sequence from its counterpart in Klenow pol I, it has clearly evolved from a common ancestor. The structure of Klentaq1 reveals the strategy utilized by this protein to maintain activity at high temperatures and provides the structural basis for future improvements of the enzyme.

The crystal structure of Pseudomonas aeruginosa exotoxin domain III with nicotinamide and AMP: conformational differences with the intact exotoxin.

Domain III of Pseudomonas aeruginosa exotoxin A catalyses the transfer of ADP-ribose from NAD to a modified histidine residue of elongation factor 2 in eukaryotic cells, thus inactivating elongation factor 2. This domain III is inactive in the intact toxin but is active in the isolated form. We report here the 2.5-A crystal structure of this isolated domain crystallized in the presence of NAD and compare it with the corresponding structure in the intact Pseudomonas aeruginosa exotoxin A. We observe a significant conformational difference in the active site region from Arg-458 to Asp-463. Contacts with part of domain II in the intact toxin prevent the adoption of the isolated domain conformation and provide a structural explanation for the observed inactivity. Additional electron density in the active site region corresponds to separate AMP and nicotinamide and indicates that the NAD has been hydrolyzed. The structure has been compared with the catalytic domain of the diphtheria toxin, which was crystallized with ApUp.

Crystal and molecular structure of paclitaxel (taxol).

Paclitaxel (formerly called taxol), an important anticancer drug, inhibits cell replication by binding to and stabilizing microtubule polymers. As drug-receptor interactions are governed by the three-dimensional stereochemistries of both participants, we have determined the crystal structure of paclitaxel to identify its conformational preferences that may be related to biological activity. The monoclinic crystals contain two independent paclitaxel molecules in the asymmetric unit plus several water and dioxane solvent molecules. Taxane ring conformation is very similar in both paclitaxel molecules and is similar to the taxane ring conformation found in the crystal structure of the paclitaxel analogue docetaxel (formerly called taxotere). The two paclitaxel molecules have carbon-13 side-chain conformations that differ from each other and from that of the corresponding side chain in the docetaxel crystal structure. The carbon-13 side-chain conformation of one paclitaxel molecule is similar to what was proposed from NMR studies done in polar solvents, while that of the other paclitaxel molecule is different and hitherto unobserved. The paclitaxel molecules interact with each other and with solvent atoms through an extensive network of hydrogen bonds. Analysis of the hydrogen-bonding network together with structure-activity studies may suggest which atoms of paclitaxel are important for binding to microtubule receptors.

The crystal structure of an N-terminal two-domain fragment of vascular cell adhesion molecule 1 (VCAM-1): a cyclic peptide based on the domain 1 C-D loop can inhibit VCAM-1-alpha 4 integrin interaction.

Vascular cell adhesion molecule 1 (VCAM-1) represents a structurally and functionally distinct class of immunoglobulin superfamily molecules that bind leukocyte integrins and are involved in inflammatory and immune functions. X-ray crystallography defines the three-dimensional structure of the N-terminal two-domain fragment that participates in ligand binding. Residues in domain 1 important for ligand binding reside in the C-D loop, which projects markedly from one face of the molecule near the contact between domains 1 and 2. A cyclic peptide that mimics this loop inhibits binding of alpha 4 beta 1 integrin-bearing cells to VCAM-1. These data demonstrate how crystallographic structural information can be used to design a small molecule inhibitor of biological function.

Stable loop in the crystal structure of the intercalated four-stranded cytosine-rich metazoan telomere.

In most metazoans, the telomeric cytosine-rich strand repeating sequence is d(TAACCC). The crystal structure of this sequence was solved to 1.9-A resolution. Four strands associate via the cytosine-containing parts to form a four-stranded intercalated structure held together by C.C+ hydrogen bonds. The base-paired strands are parallel to each other, and the two duplexes are intercalated into each other in opposite orientations. One TAA end forms a highly stabilized loop with the 5' thymine Hoogsteen-base-paired to the third adenine. The 5' end of this loop is in close proximity to the 3' end of one of the other intercalated cytosine strands. Instead of being entirely in a DNA duplex, this structure suggests the possibility of an alternative conformation for the cytosine-rich telomere strands.

Crystal structure of an H-2Kb-ovalbumin peptide complex reveals the interplay of primary and secondary anchor positions in the major histocompatibility complex binding groove.

Sequence analysis of peptides naturally presented by major histocompatibility complex (MHC) class I molecules has revealed allele-specific motifs in which the peptide length and the residues observed at certain positions are restricted. Nevertheless, peptides containing the standard motif often fail to bind with high affinity or form physiologically stable complexes. Here we present the crystal structure of a well-characterized antigenic peptide from ovalbumin [OVA-8, ovalbumin-(257-264), SIINFEKL] in complex with the murine MHC class I H-2Kb molecule at 2.5-A resolution. Hydrophobic peptide residues Ile-P2 and Phe-P5 are packed closely together into binding pockets B and C, suggesting that the interplay of peptide anchor (P5) and secondary anchor (P2) residues can couple the preferred sequences at these positions. Comparison with the crystal structures of H-2Kb in complex with peptides VSV-8 (RGYVYQGL) and SEV-9 (FAPGNYPAL), where a Tyr residue is used as the C pocket anchor, reveals that the conserved water molecule that binds into the B pocket and mediates hydrogen bonding from the buried anchor hydroxyl group could not be likewise positioned if the P2 side chain were of significant size. Based on this structural evidence, H-2Kb has at least two submotifs: one with Tyr at P5 (or P6 for nonamer peptides) and a small residue at P2 (i.e., Ala or Gly) and another with Phe at P5 and a medium-sized hydrophobic residue at P2 (i.e., Ile). Deciphering of these secondary submotifs from both crystallographic and immunological studies of MHC peptide binding should increase the accuracy of T-cell epitope prediction.

Study of dopamine reactivity on platinum single crystal electrode surfaces

Dopamine is the biological molecule responsible, among other functions, of the heart beat and blood pressure regulation. Its loss, in the human body, can result in serious diseases such as Parkinson's, schizophrenia or depression. Structurally, this molecule belongs to the group of catecholamines, together with epinephrine (adrenaline) and norepinephrine (noradrenaline). The hydroquinone moiety of the molecule can be easily oxidized to quinone, rendering the electrochemical methods a convenient approach for the development of dopamine biosensors. The reactivity of similar aromatic molecules, such as catechol and hydroquinone, at well-ordered platinum surfaces, has recently been investigated in our group. In this paper, we extend these studies to the structurally related molecule dopamine. The study has been performed in neutral pH, since this is closer to the natural conditions for these molecules in biological media. Cyclic voltammetry and in situ infra-red spectroscopy have been combined to extract information about the behavior of this molecule on well-defined platinum surfaces. Dopamine appears to be electrochemically active and reveals interesting adsorption phenomena at low potentials (0.15–0.25 V vs RHE), sensitive to the single crystal orientation. The adsorption of dopamine on these surfaces is very strong, taking place at much lower potentials than the electron transfer from solution species. Specifically, the voltammetry of Pt(1 1 1) and Pt(1 0 0) in dopamine solutions shows an oxidation peak at potentials close to the onset of hydrogen evolution, which is related to the desorption of hydrogen and the adsorption of dopamine. On the other hand, adsorption on Pt(1 1 0) is irreversible and the surface appears totally blocked. Spectroscopic results indicate that dopamine is adsorbed flat on the surface. At potentials higher than 0.6 V vs RHE the three basal planes show a common redox process. The initial formation of the quinone moiety is followed by a chemical step resulting in the formation of 5,6-dihydroxyindoline quinone as final product. This oxidation process has also been investigated by vibrational spectroscopy.

Interaction of water with methanesulfonic acid on Pt single crystal electrodes

The electrochemical behavior of methanesulfonic acid on platinum single crystal electrode surfaces is investigated by cyclic voltammetry and infrared spectroscopy measurements. The results are compared with the voltammetric profiles of perchloric and trifluoromethanesulfonic acids. The differences are interpreted in terms of the effect of the anion on the structure of water. No adsorbed species are detected by infrared spectroscopy.

Adsorption and first stages of polymerization of aniline on platinum single crystal electrodes

The present communication studies the adsorption of aniline on platinum single crystal electrodes and the electrochemical properties of the first layers of polyaniline(PANI) grown on those platinum surfaces. The adsorption process was studied in aqueous acidic solution (0.1 M HClO4) and the electrochemical properties of thin films of PANI in both aqueous (1 M HClO4) and non-aqueous media (tetrabutyl ammonium hexafluorophosphate (TBAPF6) with additions of methanesulphonic acid in acetonitrile). First of all, it was found that the adsorption of aniline on platinum single crystal surfaces is a surface sensitive process, and even more important that the adsorption features found at low concentrations (5 × 10−5 M) can be directly correlated to the electrochemical properties of thin films of PANI in the very early stages of polymerization. The Pt(1 1 0) surface was found to be more suitable to obtain polymers with more reversible redox transitions when studied in aqueous media (1 M HClO4). This is in good agreement with the higher polymerization rates found on this surface compared to Pt(1 0 0) and Pt(1 1 1). Finally the differences in ionic exchange rate were greatly enhanced when they were studied in organic media. The AC 250 Hz response in the case of the thin films synthesized on Pt(1 1 0) is about twice greater than that obtained in the other basal planes using polymer layers with the same thickness.

Characterization of the interfaces between Au(hkl) single crystal basal plane electrodes and [Emmim][Tf2N] ionic liquid

The interface between Au(hkl) basal planes and the ionic liquid 1-Ethyl-2,3-dimethyl imidazolium bis(trifluoromethyl)sulfonil imide was investigated by using both cyclic voltammetry and laser-induced temperature jump. Cyclic voltammetry showed characteristic features, revealing surface sensitive processes at the interfaces Au(hkl)/[Emmim][Tf2N]. From laser-induced heating the potential of maximum entropy (pme) is determined. Pme is close to the potential of zero charge (pzc) and, therefore, the technique provides relevant interfacial information. The following order for the pme values has been found: Au(111) > Au(100) > Au(110). This order correlates well with work function data and values of pzc in aqueous solutions.

Oxidation of Ethanol and Its Derivatives on Well Defined Pt Single Crystal Electrodes Vicinal to Pt(111): A Comparative Study

The oxidation of ethanol (EtOH) at Pt(111) electrodes is dominated by the 4e path leading to acetic acid. The inclusion of surface defects such as those present on stepped surfaces leads to an increase of the reactivity towards the most desirable 12e path leading to CO2 as final product. This path is also favored when the methyl group is more oxidized, as in the case of ethylene glycol (EG) that spontaneously decomposes to CO on Pt(111) electrodes, thus showing a more effective breaking of the C-C bond. Some trends in reactivity can be envisaged when other derivative molecules are compared at well-ordered electrodes. This strategy was used in the past, but the improvement in the electrode pretreatment and the overall information available on the subject suggest that relevant information is still missing.

Topological spin waves in the atomic-scale magnetic skyrmion crystal

We study the spin waves of the triangular skyrmion crystal that emerges in a two-dimensional spin lattice model as a result of the competition between Heisenberg exchange, Dzyalonshinkii–Moriya interactions, Zeeman coupling and uniaxial anisotropy. The calculated spin wave bands have a finite Berry curvature that, in some cases, leads to non-zero Chern numbers, making this system topologically distinct from conventional magnonic systems. We compute the edge spin-waves, expected from the bulk-boundary correspondence principle, and show that they are chiral, which makes them immune to elastic backscattering. Our results illustrate how topological phases can occur in self-generated emergent superlattices at the mesoscale.

Tight-Binding Approximations in 1D and 2D Coupled-Cavity Photonic Crystal Structures

Light confinement and controlling an optical field has numerous applications in the field of telecommunications for optical signals processing. When the wavelength of the electromagnetic field is on the order of the period of a photonic microstructure, the field undergoes reflection, refraction, and coherent scattering. This produces photonic bandgaps, forbidden frequency regions or spectral stop bands where light cannot exist. Dielectric perturbations that break the perfect periodicity of these structures produce what is analogous to an impurity state in the bandgap of a semiconductor. The defect modes that exist at discrete frequencies within the photonic bandgap are spatially localized about the cavity-defects in the photonic crystal. In this thesis the properties of two tight-binding approximations (TBAs) are investigated in one-dimensional and two-dimensional coupled-cavity photonic crystal structures We require an efficient and simple approach that ensures the continuity of the electromagnetic field across dielectric interfaces in complex structures. In this thesis we develop \textrm{E} -- and \textrm{D} --TBAs to calculate the modes in finite 1D and 2D two-defect coupled-cavity photonic crystal structures. In the \textrm{E} -- and \textrm{D} --TBAs we expand the coupled-cavity \overrightarrow{E} --modes in terms of the individual \overrightarrow{E} -- and \overrightarrow{D} --modes, respectively. We investigate the dependence of the defect modes, their frequencies and quality factors on the relative placement of the defects in the photonic crystal structures. We then elucidate the differences between the two TBA formulations, and describe the conditions under which these formulations may be more robust when encountering a dielectric perturbation. Our 1D analysis showed that the 1D modes were sensitive to the structure geometry. The antisymmetric \textrm{D} mode amplitudes show that the \textrm{D} --TBA did not capture the correct (tangential \overrightarrow{E} --field) boundary conditions. However, the \textrm{D} --TBA did not yield significantly poorer results compared to the \textrm{E} --TBA. Our 2D analysis reveals that the \textrm{E} -- and \textrm{D} --TBAs produced nearly identical mode profiles for every structure. Plots of the relative difference between the \textrm{E} and \textrm{D} mode amplitudes show that the \textrm{D} --TBA did capture the correct (normal \overrightarrow{E} --field) boundary conditions. We found that the 2D TBA CC mode calculations were 125-150 times faster than an FDTD calculation for the same two-defect PCS. Notwithstanding this efficiency, the appropriateness of either TBA was found to depend on the geometry of the structure and the mode(s), i.e. whether or not the mode has a large normal or tangential component.