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Atomic Interactions (atomic + interaction)
Selected AbstractsAtomic Interactions and Profile of Small Molecules Disrupting Protein,Protein Interfaces: the TIMBAL DatabaseCHEMICAL BIOLOGY & DRUG DESIGN, Issue 5 2009Alícia P. Higueruelo Growing evidence of the possibility of modulating protein,protein interactions with small molecules is opening the door to new approaches and concepts in drug discovery. In this paper, we describe the creation of TIMBAL, a hand-curated database holding an up to date collection of small molecules inhibiting multi-protein complexes. This database has been analysed and profiled in terms of molecular properties. Protein,protein modulators tend to be large lipophilic molecules with few hydrogen bond features. An analysis of TIMBAL's intersection with other structural databases, including CREDO (protein,small molecule from the PDB) and PICCOLO (protein,protein from the PDB) reveals that TIMBAL molecules tend to form mainly hydrophobic interactions with only a few hydrogen bonding contacts. With respect to potency, TIMBAL molecules are slightly less efficient than an average medicinal chemistry hit or lead. The database provides a resource that will allow further insights into the types of molecules favoured by protein interfaces and provide a background to continuing work in this area. Access at http://www-cryst.bioc.cam.ac.uk/timbal [source] Mass and lifetime measurements of exotic nuclei in storage ringsMASS SPECTROMETRY REVIEWS, Issue 5 2008Bernhard Franzke Abstract Mass and lifetime measurements lead to the discovery and understanding of basic properties of matter. The isotopic nature of the chemical elements, nuclear binding, and the location and strength of nuclear shells are the most outstanding examples leading to the development of the first nuclear models. More recent are the discoveries of new structures of nuclides far from the valley of stability. A new generation of direct mass measurements which allows the exploration of extended areas of the nuclear mass surface with high accuracy has been opened up with the combination of the Experimental Storage Ring ESR and the FRragment Separator FRS at GSI Darmstadt. In-flight separated nuclei are stored in the ring. Their masses are directly determined from the revolution frequency. Dependent on the half-life two complementary methods are applied. Schottky Mass Spectrometry SMS relies on the measurement of the revolution frequency of electron cooled stored ions. The cooling time determines the lower half-life limit to the order of seconds. For Isochronous Mass Spectrometry IMS the ring is operated in an isochronous ion-optical mode. The revolution frequency of the individual ions coasting in the ring is measured using a time-of-flight method. Nuclides with lifetimes down to microseconds become accessible. With SMS masses of several hundreds nuclides have been measured simultaneously with an accuracy in the 2,×,10,7 -range. This high accuracy and the ability to study large areas of the mass surface are ideal tools to discover new nuclear structure properties and to guide improvements for theoretical mass models. In addition, nuclear half-lives of stored bare and highly charged ions have been measured. This new experimental development is a significant progress since nuclear decay characteristics are mostly known for neutral atoms. For bare and highly charged ions new nuclear decay modes become possible, such as bound-state beta decay. Dramatic changes in the nuclear lifetime have been observed in highly charged ions compared to neutral atoms due to blocking of nuclear decay channels caused by the modified atomic interaction. High ionization degrees prevail in hot stellar matter and thus these experiments have great relevance for the understanding of the synthesis of elements in the universe and astrophysical scenarios in general. © 2008 Wiley Periodicals, Inc., Mass Spec Rev 27: 428,469, 2008 [source] Crystal structure of the parasite inhibitor chagasin in complex with papain allows identification of structural requirements for broad reactivity and specificity determinants for target proteasesFEBS JOURNAL, Issue 3 2009Izabela Redzynia A complex of chagasin, a protein inhibitor from Trypanosoma cruzi, and papain, a classic family C1 cysteine protease, has been crystallized. Kinetic studies revealed that inactivation of papain by chagasin is very fast (kon = 1.5 × 106 m,1·s,1), and results in the formation of a very tight, reversible complex (Ki = 36 pm), with similar or better rate and equilibrium constants than those for cathepsins L and B. The high-resolution crystal structure shows an inhibitory wedge comprising three loops, which forms a number of contacts responsible for the high-affinity binding. Comparison with the structure of papain in complex with human cystatin B reveals that, despite entirely different folding, the two inhibitors utilize very similar atomic interactions, leading to essentially identical affinities for the enzyme. Comparisons of the chagasin,papain complex with high-resolution structures of chagasin in complexes with cathepsin L, cathepsin B and falcipain allowed the creation of a consensus map of the structural features that are important for efficient inhibition of papain-like enzymes. The comparisons also revealed a number of unique interactions that can be used to design enzyme-specific inhibitors. As papain exhibits high structural similarity to the catalytic domain of the T. cruzi enzyme cruzipain, the present chagasin,papain complex provides a reliable model of chagasin,cruzipain interactions. Such information, coupled with our identification of specificity-conferring interactions, should be important for the development of drugs for treatment of the devastating Chagas disease caused by this parasite. [source] Molecular mechanics in the context of the finite element methodINTERNATIONAL JOURNAL FOR NUMERICAL METHODS IN ENGINEERING, Issue 7 2009Jens Wackerfuß Abstract In molecular mechanics, the formalism of the finite element method can be exploited in order to analyze the behavior of atomic structures in a computationally efficient way. Based on the atom-related consideration of the atomic interactions, a direct correlation between the type of the underlying interatomic potential and the design of the related finite element is established. Each type of potential is represented by a specific finite element. A general formulation that unifies the various finite elements is proposed. Arbitrary diagonal- and cross-terms dependent on bond length, valence angle, dihedral angle, improper dihedral angle and inversion angle can also be considered. The finite elements are formulated in a geometrically exact setting; the related formulas are stated in detail. The mesh generation can be performed using well-known procedures typically used in molecular dynamics. Although adjacent elements overlap, a double counting of the element contributions (as a result of the assembly process) cannot occur a priori. As a consequence, the assembly process can be performed efficiently line by line. The presented formulation can easily be implemented in standard finite element codes; thus, already existing features (e.g. equation solver, visualization of the numerical results) can be employed. The formulation is applied to various interatomic potentials that are frequently used to describe the mechanical behavior of carbon nanotubes. The effectiveness and robustness of this method are demonstrated by means of several numerical examples. Copyright © 2008 John Wiley & Sons, Ltd. [source] DFT calculations on the electronic structures of BiOX (X = F, Cl, Br, I) photocatalysts with and without semicore Bi 5d statesJOURNAL OF COMPUTATIONAL CHEMISTRY, Issue 2 2009Wen Lai Huang Abstract The electronic structures of BiOX (X = F, Cl, Br, I) photocatalysts have been calculated with and without Bi 5d states using the experimental lattice parameters, via the plane-wave pseudopotential method based on density functional theory (DFT). BiOF exhibits a direct band gap of 3.22 or 3.12 eV corresponding to the adoption of Bi 5d states or not. The indirect band gaps of BiOCl, BiOBr, and BiOI are 2.80, 2.36, and 1.75 eV, respectively, if calculated with Bi 5d states, whereas the absence of Bi 5d states reduces them to 2.59, 2.13, and 1.53 eV successively. The calculated gap characteristics and the falling trend of gap width with the increasing X atomic number agree with the experimental results, despite the common DFT underestimation of gap values. The shapes of valence-band tops and conduction-band bottoms are almost independent of the involvement of Bi 5d states. The indirect characteristic becomes more remarkable, and the conduction-band bottom flattens in the sequence of BiOCl, BiOBr, and BiOI. Both O 2p and X np (n = 2, 3, 4, and 5 for X = F, Cl, Br, and I, respectively) states dominate the valence bands, whereas Bi 6p states contribute the most to the conduction bands. With the growing X atomic number, the localized X np states shift closer toward the valence-band tops, and the valence and conduction bandwidths evolve in opposite trends. Atomic and bond populations have also been explored to elucidate the atomic interactions, along with the spatial distribution of orbital density. © 2008 Wiley Periodicals, Inc. J Comput Chem, 2009 [source] Molecular dynamics simulation of annihilation of 60° dislocations in Si crystalsPHYSICA STATUS SOLIDI (B) BASIC SOLID STATE PHYSICS, Issue 2 2009Qingyuan Meng Abstract The annihilation of two 60° shuffle dislocations is studied via the molecular dynamics method. The Stillinger,Weber (SW) potential and environment-dependent interatomic potential (EDIP) are used to describe the atomic interactions. The simulation results show that the complete annihilation of the 60° dislocations takes place only when the two dislocations lie on the same slip plane. The annihilation process may occur without external shear stress when the temperature is higher than a critical value. It is found that the critical temperature increases exponentially as a function of distance between the two dislocations. Also revealed in this simulation is an incomplete annihilation occurring when the distance between the slip planes of the two dislocations is less than about 1 nm. If the distance between the two slip planes is larger than about 1 nm, the dislocations will glide on their own slip planes as if no interaction exists between them. (© 2009 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim) [source] Tight binding modelling of electronic band structure in conventional InGaN/GaN and dilute GaAsN/GaAs nitride heterostructuresPHYSICA STATUS SOLIDI (C) - CURRENT TOPICS IN SOLID STATE PHYSICS, Issue 2 2007H. Hakan Gürel Abstract We utilize a semi-empirical sp3s * tight binding model to investigate the strain and composition effects on electronic structure of conventional InGaN/GaN and dilute GaAsN/GaAs cubic nitride heterostructures. The model includes the second nearest neighbor (2NN) atomic interactions, spin-orbit splitting and nonlinear composition variation of atomic energies and bond lengths of ternaries. Results show that band gaps of conventional InGaN increase with composition for 0 < x < 1. However, the , band gap of dilute GaAsN decreases with composition for x < 0.25 and then starts to increase for 0.26 < x < 1. (© 2007 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim) [source] A new approach to calculating powder diffraction patterns based on the Debye scattering equationACTA CRYSTALLOGRAPHICA SECTION A, Issue 1 2010Noel William Thomas A new method is defined for the calculation of X-ray and neutron powder diffraction patterns from the Debye scattering equation (DSE). Pairwise atomic interactions are split into two contributions, the first from lattice-pair vectors and the second from cell-pair vectors. Since the frequencies of lattice-pair vectors can be directly related to crystallite size, application of the DSE is thereby extended to crystallites of lengths up to ~200,nm. The input data correspond to unit-cell parameters, atomic coordinates and displacement factors. The calculated diffraction patterns are characterized by full backgrounds as well as complete reflection profiles. Four illustrative systems are considered: sodium chloride (NaCl), ,-quartz, monoclinic lead zirconate titanate (PZT) and kaolinite. The effects of varying crystallite size on diffraction patterns are calculated for NaCl, quartz and kaolinite, and a method of modelling static structural disorder is defined for kaolinite. The idea of partial diffraction patterns is introduced and a treatment of atomic displacement parameters is included. Although the method uses pair distribution functions as an intermediate stage, it is anticipated that further progress in reducing computational times will be made by proceeding directly from crystal structure to diffraction pattern. [source] Features of the electron density in magnesium diboride: reconstruction from X-ray diffraction data and comparison with TB-LMTO and FPLO calculationsACTA CRYSTALLOGRAPHICA SECTION B, Issue 5 2003S. Lee Features of the electron density in MgB2 reconstructed from room-temperature single-crystal X-ray diffraction intensities using a multipole model are considered. Topological analysis of the total electron density has been applied to characterize the atomic interactions in magnesium diboride. The shared-type B,B interaction in the B-atom layer reveals that both , and , components of the bonding are strong. A closed-shell-type weak B,B , interaction along the c axis of the unit cell has also been found. The Mg,B closed-shell interaction exhibits a bond path that is significantly curved towards the vertical Mg-atom chain ([110] direction). The latter two facts reflect two sorts of bonding interactions along the [001] direction. Integration of the electron density over the zero-flux atomic basins reveals a charge transfer of ,1.4,(1) electrons from the Mg atoms to the B-atom network. The calculated electric-field gradients at nuclear positions are in good agreement with experimental NMR values. The anharmonic displacement of the B atoms is also discussed. Calculations of the electron density by tight-binding linear muffin-tin orbital (TB-LMTO) and full-potential non-orthogonal local orbital (FPLO) methods confirm the results of the reconstruction from X-ray diffraction; for example, a charge transfer of 1.5 and 1.6 electrons, respectively, was found. [source] Electron density and energy density view on the atomic interactions in SrTiO3ACTA CRYSTALLOGRAPHICA SECTION B, Issue 4 2002Elizabeth A. Zhurova The results of topological analysis of the electron density in an SrTiO3 crystal based on the experimental (at 145,K) and theoretical data are presented and discussed. The features of the electron density lead to the conclusion that the Ti,O interaction is of the partly polar covalent (or intermediate) type. Complicated atomic shapes defined by the zero-flux surfaces in the electron density are revealed. It is found that, in general, they are far from spherical and have very slight asphericity in the close-packed layers. The topological coordination numbers of Sr and Ti are the same as the geometrical numbers, whereas the topological coordination for the O atom (6) differs from the geometrical value (12). The latter results from the specific shape of the Ti-atom basin, which prevents bond-path formation between the O atoms. The analysis of the kinetic and potential energy densities derived from the electron density using the density functional theory formulae revealed the stabilizing crystal-forming role of the O atoms in SrTiO3. Structural homeomorphism between the experimental electron density and the potential and kinetic energy densities is observed. [source] Multiple crystal structures of actin dimers and their implications for interactions in the actin filamentACTA CRYSTALLOGRAPHICA SECTION D, Issue 4 2008Michael R. Sawaya The structure of actin in its monomeric form is known at high resolution, while the structure of filamentous F-actin is only understood at considerably lower resolution. Knowing precisely how the monomers of actin fit together would lead to a deeper understanding of the dynamic behavior of the actin filament. Here, a series of crystal structures of actin dimers are reported which were prepared by cross-linking in either the longitudinal or the lateral direction in the filament state. Laterally cross-linked dimers, comprised of monomers belonging to different protofilaments, are found to adopt configurations in crystals that are not related to the native structure of filamentous actin. In contrast, multiple structures of longitudinal dimers consistently reveal the same interface between monomers within a single protofilament. The reappearance of the same longitudinal interface in multiple crystal structures adds weight to arguments that the interface visualized is similar to that in actin filaments. Highly conserved atomic interactions involving residues 199,205 and 287,291 are highlighted. [source] | |||||||||||||