Network approach for capturing ligand-induced subtle global changes in protein structures

Ligand-induced conformational changes in proteins are of immense functional relevance. It is a major challenge to elucidate the network of amino acids that are responsible for the percolation of ligand-induced conformational changes to distal regions in the protein from a global perspective. Functionally important subtle conformational changes (at the level of side-chain noncovalent interactions) upon ligand binding or as a result of environmental variations are also elusive in conventional studies such as those using root-mean-square deviations (r.m.s.d.s). In this article, the network representation of protein structures and their analyses provides an efficient tool to capture these variations (both drastic and subtle) in atomistic detail in a global milieu. A generalized graph theoretical metric, using network parameters such as cliques and/or communities, is used to determine similarities or differences between structures in a rigorous manner. The ligand-induced global rewiring in the protein structures is also quantified in terms of network parameters. Thus, a judicious use of graph theory in the context of protein structures can provide meaningful insights into global structural reorganizations upon perturbation and can also be helpful for rigorous structural comparison. Data sets for the present study include high-resolution crystal structures of serine proteases from the S1A family and are probed to quantify the ligand-induced subtle structural variations.

Bis{2-4-(methylsulfanyl)phenyl]-1H-benzimidazol-3-ium} tetrabromidocuprate(II) dihydrate

The asymmetric unit of the title compound, (C14H13N2S)(2)CuBr4]center dot 2H(2)O, contains two cations, one anion and two solvent water molecules that are connected via O-H center dot center dot center dot Br, N-H center dot center dot center dot Br and N-H center dot center dot center dot O hydrogen bonds into a two-dimensional polymeric structure. The cations are arranged in a head-to-tail fashion and form stacks along 100]. The central Cu-II atom of the anion is in a distorted tetrahedral environment.

Bis(acetylacetonato-kappa 2 O,O')(pyridine-kappa N)zinc(II)

In the title compound, Zn(C5H7O2)(2)(C5H5N)], the metal atom has square-pyramidal coordination geometry with the basal plane defined by the four O atoms of the chelating acetylacetonate ligands and with the axial position occupied by the pyridine N atom. The crystal packing is characterized by a C-H...O hydrogen-bonded ribbon structure approximately parallel to 10 ].

N-3-benzoyl-2 ',3 '-di-O-benzoyluridine

The structure of N-3-benzoyl-2',3'-di-O-benzoyluridine, C30H24N2O9, has two molecules in the asymmetric unit. The uracil bases of both the molecules are in the anti conformation with respect to the ribose moiety and the furanosyl rings adopt a C3'-endo conformation. The orientation about the C4'-C5' bond is gauche-gauche. The two crystallographically independent molecules are linked through several C-H ... O hydrogen bonds. The nucleoside molecules pack as columns along the a axis and these columns repeat along the c axis.

N-4-anisoylcytidine dihydrate

The title compound, C17H19N3O7. 2H(2)O, has C2'-endo, C3'-exo puckering, The orientation of the base with respect to the sugar is anti and the geometry about C4'-C5' is gauche,trans. The angle between the cytidine base and the phenyl ring of the anisoyl group is 15.5(2)degrees.

N-6-anisoyladenosine monohydrate

The title compound, C18H19N5O6. H2O, has a syn conformation about the glycosidic bond. Its furanose ring shows a C2'-endo-C3'-exo twist conformation and trans-gauche geometry about the C4'-C5' bond. The angle between the adenine base and the phenyl ring of the anisoyl group is 22.9 degrees. Adenine and anisoyl groups stack along the b axis at a separation of 3.4 Angstrom.

3-nitroacetanilide

The title compound, also known as N-(3-nitrophenyl)acetamide, C8H8N2O3, is an organic non-linear optical material. It crystallizes in the monoclinic system in the chiral space group P2(1), and there are four independent molecules in the asymmetric unit.

4-Chlorobenzohydrazide

The crystal structure of the title compound, C7H7N2OCl, has been determined in the monoclinic space group P2(1)/c at room temperature. The structure is stabilized by intermolecular N-H...O and N-H...N hydrogen bonds.

Least path criterion (LPC) for unique indexing in a two-dimensional decagonal quasilattice

The least path criterion or least path length in the context of redundant basis vector systems is discussed and a mathematical proof is presented of the uniqueness of indices obtained by applying the least path criterion. Though the method has greater generality, this paper concentrates on the two-dimensional decagonal lattice. The order of redundancy is also discussed; this will help eventually to correlate with other redundant but desirable indexing sets.

PDB Goodies - a web-based GUI to manipulate the Protein Data Bank file

PDB Goodies is a web-based graphical user interface (GUI) to manipulate the Protein Data Bank file containing the three-dimensional atomic coordinates of protein structures. The program also allows users to save the manipulated three-dimensional atomic coordinate file on their local client system. These fragments are used in various stages of structure elucidation and analysis. This software is incorporated with all the three-dimensional protein structures available in the Protein Data Bank, which presently holds approximately 18 000 structures. In addition, this program works on a three-dimensional atomic coordinate file (Protein Data Bank format) uploaded from the client machine. The program is written using CGI/PERL scripts and is platform independent. The program PDB Goodies can be accessed over the World Wide Web at http:// 144.16.71.11/pdbgoodies/.

Solvothermal routes to capped oxide and chalcogenide nanoparticles

We review our recent contributions to the use of solvothermal methods for the preparation of different oxide and chalcogenide nanoparticles. We have prepared sub 10-nm,gamma-Fe2O3 ZnFe2O4, and CoFe2O4 particles by the decomposition of the corresponding cupferron complexes in the presence of n-octylamine or n-dodecylamine in solvothermal toluene. Similarly, dodecanethiol-capped chalcogenide nanoparticles of CdSe have been prepared by reacting cadmium stearates with H2Se under solvothermal conditions. The H2Se is generated in situ by the reduction of Se by tetralin. Using this latter technique, we have also been able to prepare PbSe and PbI2 in toluene under solvothermal conditions, albeit in bulk (rather than nanocrystalline) form. In the preparation of PbI2, HI is prepared by the in situ reduction of I-2 by tetralin.

Materials Research Priorities

R. Chidambaram is the principal scientific advisor to the government of India and is past president of the Materials Research Society-India. He joined the Bhabha Atomic Research Center (BARC) in 1962, became its director in 1990, and is currently the Department of Atomic Energy Homi Bhabha Chair Professor. He served as chair of the Atomic Energy Commission and secretary to the government of India in the Department of Atomic Energy from February 1993 to November 2000. Chidambaram is a fellow of all of the major science academies in India and also of the Third World Academy of Sciences in Trieste, Italy. He chaired the Board of Governors of the International Atomic Energy Agency (IAEA) during 1994–1995. Until recently, he was vice president of the International Union of Crystallography. Chidambaram is currently chair of the council and the governing body of the Technology Information, Forecasting, and Assessment Council (TIFAC). He received his PhD and DSc degrees from the Indian Institute of Science, Bangalore, and holds honorary DSc degrees from several Indian universities.

(4aR, 8aS, 9aR, 10aS)-8a, 9a-Difluoro-1,4,4a, 5,8,8a, 9,9a, 10,10a-decahydroanthracene-4a, 10a-diol hemihydrate

The title compound, C(14)H(18)F(2)O(2)center dot 0.5H(2)O, a hemihydrate of a C(s)-symmetric unsaturated difluorodiol, crystallizes in the centrosymmetric space group P2/m (Z = 4). The asymmetric unit contains two crystallographically independent difluorodiol half-molecules, occupying the mirror planes at (x, 0, z) and (x, 1/2, z), and half a molecule of water, lying on the twofold axis at (0, y, 0). Four difluorodiol molecules self-assemble around each solvent water molecule via O-H center dot center dot center dot O hydrogen bonds in a near tetrahedral symmetry to generate a cylindrical column-like architecture.

Multi-hop Cooperative Wireless Networks: Diversity Multiplexing Tradeoff and Optimal Code Design

We consider single-source single-sink (ss-ss) multi-hop relay networks, with slow-fading links and single-antenna half-duplex relay nodes. While two-hop cooperative relay networks have been studied in great detail in terms of the diversity-multiplexing tradeoff (DMT), few results are available for more general networks. In this paper, we identify two families of networks that are multi-hop generalizations of the two-hop network: K-Parallel-Path (KPP)networks and layered networks.KPP networks, can be viewed as the union of K node-disjoint parallel relaying paths, each of length greater than one. KPP networks are then generalized to KPP(I) networks, which permit interference between paths and to KPP(D) networks, which possess a direct link from source to sink. We characterize the DMT of these families of networks completely for K > 3. Layered networks are networks comprising of layers of relays with edges existing only between adjacent layers, with more than one relay in each layer. We prove that a linear DMT between the maximum diversity dmax and the maximum multiplexing gain of 1 is achievable for single-antenna fully-connected layered networks. This is shown to be equal to the optimal DMT if the number of relaying layers is less than 4.For multiple-antenna KPP and layered networks, we provide an achievable DMT, which is significantly better than known lower bounds for half duplex networks.For arbitrary multi-terminal wireless networks with multiple source-sink pairs, the maximum achievable diversity is shown to be equal to the min-cut between the corresponding source and the sink, irrespective of whether the network has half-duplex or full-duplex relays. For arbitrary ss-ss single-antenna directed acyclic networks with full-duplex relays, we prove that a linear tradeoff between maximum diversity and maximum multiplexing gain is achievable.Along the way, we derive the optimal DMT of a generalized parallel channel and derive lower bounds for the DMT of triangular channel matrices, which are useful in DMT computation of various protocols. We also give alternative and often simpler proofs of several existing results and show that codes achieving full diversity on a MIMO Rayleigh fading channel achieve full diversity on arbitrary fading channels. All protocols in this paper are explicit and use only amplify-and-forward (AF) relaying. We also construct codes with short block-lengths based on cyclic division algebras that achieve the optimal DMT for all the proposed schemes.Two key implications of the results in the paper are that the half-duplex constraint does not entail any rate loss for a large class of cooperative networks and that simple AF protocols are often sufficient to attain the optimal DMT

3-(2-Bromoacetyl)-6-fluoro-2H-chromen-2-one

The non-H atoms of the title compound, C(11)H(6)BrFO(3), are essentially coplanar (r.m.s. deviation for all non-H atoms = 0.074 angstrom). In the crystal, the molecules are linked by C-H center dot center dot center dot O and C-H center dot center dot center dot Br interactions.