An algorithm to find distant repeats in a pair of protein sequences

Distant repeats between a pair of protein sequences can be exploited to study the various aspects of proteins such as structure-function relationship, disorders due to protein malfunction, evolutionary analysis, etc. An in-depth analysis of the distant repeats would facilitate to establish a stable evolutionary relation of the repeats with respect to their three-dimensional structure. To this effect, an algorithm has been devised to identify the distant repeats in a pair of protein sequences by essentially using the scores of PAM (Percent Accepted Mutation) matrices. The proposed algorithm will be of much use to researchers involved in the comparative study of various organisms based on the amino-acid repeats in protein sequences. (C) 2010 Elsevier B.V. All rights reserved.

Measurement of complex optical flow with use of an augmented generalized gradient scheme

We present a method for measuring the local velocities and first-order variations in velocities in a timevarying image. The scheme is an extension of the generalized gradient model that encompasses the local variation of velocity within a local patch of the image. Motion within a patch is analyzed in parallel by 42 different spatiotemporal filters derived from 6 linearly independent spatiotemporal kernels. No constraints are imposed on the image structure, and there is no need for smoothness constraints on the velocity field. The aperture problem does not arise so long as there is some two-dimensional structure in the patch being analyzed. Among the advantages of the scheme is that there is no requirement to calculate second or higher derivatives of the image function. This makes the scheme robust in the presence of noise. The spatiotemporal kernels are of simple form, involving Gaussian functions, and are biologically plausible receptive fields. The validity of the scheme is demonstrated by application to both synthetic and real video images sequences and by direct comparison with another recently published scheme Biol. Cybern. 63, 185 (1990)] for the measurement of complex optical flow.

Measurement of complex optical flow with use of an augmented generalized gradient scheme

We present a method for measuring the local velocities and first-order variations in velocities in a time-varying image. The scheme is an extension of the generalized gradient model that encompasses the local variation of velocity within a local patch of the image. Motion within a patch is analyzed in parallel by 42 different spatiotemporal filters derived from 6 linearly independent spatiotemporal kernels. No constraints are imposed on the image structure, and there is no need for smoothness constraints on the velocity field. The aperture problem does not arise so long as there is some two-dimensional structure in the patch being analyzed. Among the advantages of the scheme is that there is no requirement to calculate second or higher derivatives of the image function. This makes the scheme robust in the presence of noise. The spatiotemporal kernels are of simple form, involving Gaussian functions, and are biologically plausible receptive fields. The validity of the scheme is demonstrated by application to both synthetic and real video images sequences and by direct comparison with another recently published scheme [Biol. Cybern. 63, 185 (1990)] for the measurement of complex optical flow.

RPS: Repeats in Protein Sequences

Repeats are two or more contiguous segments of amino acid residues that are believed to have arisen as a result of intragenic duplication, recombination and mutation events. These repeats can be utilized for protein structure prediction and can provide insights into the protein evolution and phylogenetic relationship. Therefore, to aid structural biologists and phylogeneticists in their research, a computing resource (a web server and a database), Repeats in Protein Sequences (RPS), has been created. Using RPS, users can obtain useful information regarding identical, similar and distant repeats (of varying lengths) in protein sequences. In addition, users can check the frequency of occurrence of the repeats in sequence databases such as the Genome Database, PIR and SWISS-PROT and among the protein sequences available in the Protein Data Bank archive. Furthermore, users can view the three-dimensional structure of the repeats using the Java visualization plug-in Jmol. The proposed computing resource can be accessed over the World Wide Web at http://bioserver1.physics.iisc.ernet.in/rps/.

BSSB: BLAST Server for Structural Biologists

The Basic Local Alignment Search Tool (BLAST) is one of the most widely used sequence alignment programs with which similarity searches, for both protein and nucleic acid sequences, can be performed against large databases at high speed. A large number of tools exist for processing BLAST output, but none of them provide three-dimensional structure visualization. This shortcoming has been addressed in the proposed tool BLAST Server for Structural Biologists (BSSB), which maps a BLAST output onto the three-dimensional structure of the subject protein. The three-dimensional structure of the subject protein is represented using a three-color coding scheme (identical: red; similar: yellow; and mismatch: white) based on the pairwise alignment obtained. Thus, the user will be able to visualize a possible three-dimensional structure for the query protein sequence. This information can be used to gain a deeper insight into the sequence-structure correlation. Furthermore, the additional structure-level information enables the user to make coherent and logical decisions regarding the type of input model structure or fragment that can be used for molecular replacement calculations. This tool is freely available to all users at http://bioserver1.physics.iisc.ernet.in/bssb/.

An open-framework zincoborate formed by Zn6B12O24 clusters

A novel zincoborate, Zn(H2O)B2O4.xH(2)O (xapproximate to0.12), I, with open architecture has been synthesized hydrothermally. The 3-dimensional structure is built up of Zn6B12O24 clusters formed by the capping of the polycyclic borate anion, B12O2412-, by Zn3O3 clusters. The open-framework structure of I has one-dimensional 8-membered channels wherein the water molecules reside. Formation of trimeric Zn3O3 clusters as well as the presence of boron in dual coordination, both triangular and tetrahedral, are important structural features of this new zincoborate.

Revisiting the Mechanism of the Triosephosphate Isomerase Reaction: The Role of the Fully Conserved Glutamic Acid 97 Residue

An analysis of 503 available triosephosphate isomerase sequences revealed nine fully conserved residues. Of these, four residues-K12, H95, E97 and E165-are capable of proton transfer and are all arrayed around the dihydroxyacetone phosphate substrate in the three-dimensional structure. Specific roles have been assigned to the residues K12, H95 and E165, but the nature of the involvement of E97 has not been established. Kinetic and structural characterization is reported for the E97Q and E97D mutants of Plasmodium falciparum triosephosphate isomerase (Pf TIM). A 4000-fold reduction in k(cat) is observed for E97Q, whereas the E97D mutant shows a 100-fold reduction. The control mutant, E165A, which lacks the key catalytic base, shows an approximately 9000-fold drop in activity. The integrity of the overall fold and stability of the dimeric structure have been demonstrated by biophysical studies. Crystal structures of E97Q and E97D mutants have been determined at 2.0 angstrom resolution. In the case of the isosteric replacement of glutamic acid by glutamine in the E97Q mutant a large conformational change for the critical K12 side chain is observed, corresponding to a trans-to-gauche transition about the C gamma-C delta (chi(3)) bond. In the E97D mutant, the K12 side chain maintains the wild-type orientation, but the hydrogen bond between K12 and D97 is lost. The results are interpreted as a direct role for E97 in the catalytic proton transfer cycle. The proposed mechanism eliminates the need to invoke the formation of the energetically unfavourable imidazolate anion at H95, a key feature of the classical mechanism.

Usefulness of in Situ Single Crystal to Single Crystal Transformation (SCSC) Studies in Understanding the Temperature-Dependent Dimensionality Cross-over and Structural Reorganization in Copper-Containing Metal-Organic Frameworks (MOFs)

Two copper-containing compounds [Cu(3)(mu(3)-OH)(2)-(H(2)O)(2){(SO(3))-C(6)H(3)-(COO)(2)}(CH(3)COO)] , I, and [Cu(5)(mu(3)-OH)(2)(H(2)O)(6){(NO(2))-C(6)H(3)-(COO)(2)}(4)]center dot 5H(2)O, II, were prepared using sulphoisophthalic and nitroisophthalic acids. The removal of the coordinated water molecules in the compounds was investigated using in situ single crystal to single crystal (SCSC) transformation studies, temperature-dependent powder X-ray diffraction (PXRD), and thermogravimetric analysis (TGA). The efficacy of SCSC transformation studies were established by the observation of dimensionality cross-over from a two-dimensional (I) to a three-dimensional structure, Cu(6)(mu(3)-OH)(4){(SO(3))-C(6)H(3)-(COO)(2)}(2)(CH(3)COO)(2), Ia, during the removal of the coordinated water molecules. Compound H exhibited a structural reorganization forming Cu(5)(mu(2)-OH)(2){(NO(2))C(6)H(3)-(COO)(2))(4)], Ha, possessing trimeric (Cu(3)O(12)) and dimeric (Cu(2)O(8)) copper clusters. The PXRD studies indicate that the three-dimensional structure (Ia) is transient and unstable, reverting back to the more stable two-dimensional structure (I) on cooling to room temperature. Compound Ha appears to be more stable at room temperature. The rehydration/dehydration studies using a modified TGA setup suggest complete rehydration of the water molecules, indicating that the water molecules in both compounds are labile. A possible model for the observed changes in the structures has been proposed. Magnetic studies indicate changes in the exchanges between the copper centers in Ha, whereas no such behavior was observed in Ia.

NMRof peptides

Developments and applications of NMR spectroscopy especially with biomolecules has taken big strides over the decades. This review gives a brief overview of peptide analysis by NMR as carried out in the author’s laboratory. A brief introduction to peptide biomolecules and NMR useful parameters are discussed in the beginning. This is followed by diagnostics features observed in NMR for identification of secondary structures. It further goes on to show how a three dimensional structure could be obtained by all-important NOE and hydrogen bond information. Use of heteronuclear experiments, which could be done at natural abundance is also highlighted in getting more details of peptide structures.Applications using Solid state NMR at natural abundance in connecting peptide solution and x-ray structures is demonstrated with couple of examples.

Crystallization and preliminary X-ray studies of MutT1 (MSMEG_2390) from Mycobacterium smegmatis

MutT1 (MSMEG_2390) from Mycobacterium smegmatis has been crystallized and the crystals have been characterized using X-ray diffraction. The crystals belonged to space group P2(1)2(1)2(1). The Matthews coefficient suggested the possibility of one protein molecule in the asymmetric unit of the orthorhombic unit cell. Solution of the structure using the known three-dimensional structure of a bacterial MutT1 is anticipated.

Solid State and Solution Mediated Multistep Sequential Transformations in Metal-Organic Coordination Networks

Sequential transformation in a family of metal-organic framework compounds has been investigated employing both a solid-state as well as a solution mediated route. The compounds, cobalt oxy-bis(benzoate) and manganese oxybis(benzoate) having a two-dimensional structure, were reacted with bipyridine forming cobalt oxy-bis(benzoate)-4,4'-bipyridine and manganese oxy-bis(benzoate)-4,4'-bipyridine, respectively. The bipyridine containing compounds appear to form sequentially through stable intermediates. For the cobalt system, the transformation from a two-dimensional compound, Co(H2O)(2)(OBA)] (OBA = 4,4'-oxy-bis(benzoate)), I, to two different three-dimensional compounds, Co(bpy)(OBA)]center dot bpy, II, (bpy = 4,4'-bipyridine) and Co(bpy)(0.5)(OBA)], III, and reversibility between II and III have been investigated. In the manganese system, transformation from a two-dimensional compound, Mn(H2O)(2)(OBA)], Ia, to two different three-dimensional compounds, Mn (bpy)(OBA)]center dot bpy, Ha and Ha to Mn(bpy)(0.5)(OBA)], Ilia, has been investigated. It has also been possible to identify intermediate products during these transformation reactions. The possible pathways for the formation of the compounds were postulated.

Identification of mycobacterial lectins from genomic data

Sixty-four sequences containing lectin domains with homologs of known three-dimensional structure were identified through a search of mycobacterial genomes. They appear to belong to the -prism II, the C-type, the Microcystis virdis (MV), and the -trefoil lectin folds. The first three always occur in conjunction with the LysM, the PI-PLC, and the -grasp domains, respectively while mycobacterial -trefoil lectins are unaccompanied by any other domain. Thirty heparin binding hemagglutinins (HBHA), already annotated, have also been included in the study although they have no homologs of known three-dimensional structure. The biological role of HBHA has been well characterized. A comparison between the sequences of the lectin from pathogenic and nonpathogenic mycobacteria provides insights into the carbohydrate binding region of the molecule, but the structure of the molecule is yet to be determined. A reasonable picture of the structural features of other mycobacterial proteins containing one or the other of the four lectin domains can be gleaned through the examination of homologs proteins, although the structure of none of them is available. Their biological role is also yet to be elucidated. The work presented here is among the first steps towards exploring the almost unexplored area of the structural biology of mycobacterial lectins. Proteins 2013. (c) 2012 Wiley Periodicals, Inc.

Heat and SDS insensitive NDK dimers are largely stabilised by hydrophobic interaction to form functional hexamer in Mycobacterium smegmatis

The primary structure and function of nucleoside diphosphate kinase (NDK), a substrate non-specific enzyme involved in the maintenance of nucleotide pools is also implicated to play pivotal roles in many other cellular processes. NDK is conserved from bacteria to human and forms a homotetramer or hexamer to exhibit its biological activity. However, the nature of the functional oligomeric form of the enzyme differs among different organisms. The functional form of NDKs from many bacterial systems, including that of the human pathogen, Mycobacterium tuberculosis (MtuNDK), is a hexamer, although some bacterial NDKs are tetrameric in nature. The present study addresses the oligomeric property of MsmNDK and how a dimer, the basic subunit of a functional hexamer, is stabilized by hydrogen bonds and hydrophobic interactions. Homology modeling was generated using the three-dimensional structure of MtuNDK as a template; the residues interacting at the monomer-monomer interface of MsmNDK were mapped. Using recombinant enzymes of wild type, catalytically inactive mutant, and monomer-monomer interactive mutants of MsmNDK, the stability of the dimer was verified under heat, SDS, low pH, and methanol. The predicted residues (Gln17, Ser24 and Glu27) were engaged in dimer formation, however the mutated proteins retained the ATPase and GTPase activity even after introducing single (MsmNDK- Q17A, MsmNDK-E27A, and MsmNDK-E27Q) and double (MsmNDK-E27A/Q17A) mutation. However, the monomer monomer interaction could be abolished using methanol, indicating the stabilization of the monomer-monomer interaction by hydrophobic interaction.

Generation of Ligand Specificity and Modes of Oligomerization in beta-Prism I Fold Lectins

beta-Prism I fold lectins constitute one of the five widely occurring structural classes of plant lectins. Each single domain subunit is made up of three Greek key motifs arranged in a threefold symmetric fashion. The threefold symmetry is not reflected in the sequence except in the case of the lectin from banana, a monocot, which carries two sugar-binding sites instead of the one in other lectins of known three-dimensional structure, all from dicots. This is believed to be a consequence of the different evolutionary paths followed by the lectin in monocots and dicots. The galactose-specific lectins among them have two chains produced by posttranslational proteolysis and contain three aromatic residues at the binding site. The extended binding sites of galactose- and mannose-specific lectins have been thoroughly characterized. Ligand binding at the sites involves both conformational selection and induced fit. Molecular plasticity of some of the lectins in the family has been characterized. The plasticity appears to be such as to promote variability in quaternary association which could be dimeric, tetrameric, or octameric. Structural and evolutionary reasons for the variability have been explored, and the relation of oligomerization to ligand binding and conformational selection investigated.

New Structural Topologies in a Series of 3d Metal Complexes with Isomeric Phenylenediacetates and 1,3,5-Tris(1-imidazolyl)benzene Ligand: Syntheses, Structures, and Magnetic and Luminescence Properties

In this article we present the syntheses, characterizations, magnetic and luminescence properties of five 3d-metal complexes, Co(tib)(1,2-phda)](n)center dot(H2O)(n) (1), Co-3(tib)(2)(1,3-phda)(3)(H2O)](n)center dot(H2O)(2n) (2), Co-5(tib)(3)(1,4-phda)(5)(H2O)(3)](n)center dot(H2O)(7n) (3), Zn-3(tib)(2)(1,3-phda)(3)](n)center dot(H2O)(4n) (4), and Mn(tib)(2)(H2O)(2)](n)center dot(1,4-phdaH)(2n)center dot(H2O)(4n) (5), obtained from the use of isomeric phenylenediacetates (phda) and the neutral 1,3,5-tris(1-imidazolyl)benzene (tib) ligand. Single crystal X-ray structures showed that 1 constitutes 3,5-connected 2-nodal nets with a double-layered two-dimensional (2D) structure, while 2 forms an interpenetrated 2D network (3,4-connected 3-nodal net). Complex 3 has a complicated three-dimensional structure with 10-nodal 3,4,5-connected nets. Complex 4, although it resembles 2 in stoichiometry and basic building structures, forms a very different overall 2D assembly. In complex 5 the dicarboxylic acid, upon losing only one of the acidic protons, does not take part in coordination; instead it forms a complicated hydrogen bonding network with water molecules. Magnetic susceptibility measurements over a wide range of temperatures revealed that the metal ions exchange very poorly through the tib ligand, but for the Co(II) complexes the effects of nonquenched orbital contributions are prominent. The 3d(10) metal complex 4 showed strong luminescence with lambda(max) = 415 nm (lambda(ex) = 360 nm).