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Sample records for acid pdb entries

  1. Re-refinement from deposited X-ray data can deliver improved models for most PDB entries.

    Joosten, R.P.; Womack, T.; Vriend, G.; Bricogne, G.

    2009-01-01

    The deposition of X-ray data along with the customary structural models defining PDB entries makes it possible to apply large-scale re-refinement protocols to these entries, thus giving users the benefit of improvements in X-ray methods that have occurred since the structure was deposited. Automated

  2. Re-refinement from deposited X-ray data can deliver improved models for most PDB entries

    Joosten, Robbie P. [CMBI, NCMLS, Radboud University Nijmegen Medical Centre, PO Box 9101, 6500 HB Nijmegen (Netherlands); Womack, Thomas [Global Phasing, Sheraton House, Castle Park, Cambridge CB3 0AX (United Kingdom); Vriend, Gert, E-mail: vriend@cmbi.ru.nl [CMBI, NCMLS, Radboud University Nijmegen Medical Centre, PO Box 9101, 6500 HB Nijmegen (Netherlands); Bricogne, Gérard [Global Phasing, Sheraton House, Castle Park, Cambridge CB3 0AX (United Kingdom); CMBI, NCMLS, Radboud University Nijmegen Medical Centre, PO Box 9101, 6500 HB Nijmegen (Netherlands)

    2009-02-01

    An evaluation of validation and real-space intervention possibilities for improving existing automated (re-)refinement methods. The deposition of X-ray data along with the customary structural models defining PDB entries makes it possible to apply large-scale re-refinement protocols to these entries, thus giving users the benefit of improvements in X-ray methods that have occurred since the structure was deposited. Automated gradient refinement is an effective method to achieve this goal, but real-space intervention is most often required in order to adequately address problems detected by structure-validation software. In order to improve the existing protocol, automated re-refinement was combined with structure validation and difference-density peak analysis to produce a catalogue of problems in PDB entries that are amenable to automatic correction. It is shown that re-refinement can be effective in producing improvements, which are often associated with the systematic use of the TLS parameterization of B factors, even for relatively new and high-resolution PDB entries, while the accompanying manual or semi-manual map analysis and fitting steps show good prospects for eventual automation. It is proposed that the potential for simultaneous improvements in methods and in re-refinement results be further encouraged by broadening the scope of depositions to include refinement metadata and ultimately primary rather than reduced X-ray data.

  3. Re-refinement from deposited X-ray data can deliver improved models for most PDB entries.

    Joosten, Robbie P; Womack, Thomas; Vriend, Gert; Bricogne, Gérard

    2009-02-01

    The deposition of X-ray data along with the customary structural models defining PDB entries makes it possible to apply large-scale re-refinement protocols to these entries, thus giving users the benefit of improvements in X-ray methods that have occurred since the structure was deposited. Automated gradient refinement is an effective method to achieve this goal, but real-space intervention is most often required in order to adequately address problems detected by structure-validation software. In order to improve the existing protocol, automated re-refinement was combined with structure validation and difference-density peak analysis to produce a catalogue of problems in PDB entries that are amenable to automatic correction. It is shown that re-refinement can be effective in producing improvements, which are often associated with the systematic use of the TLS parameterization of B factors, even for relatively new and high-resolution PDB entries, while the accompanying manual or semi-manual map analysis and fitting steps show good prospects for eventual automation. It is proposed that the potential for simultaneous improvements in methods and in re-refinement results be further encouraged by broadening the scope of depositions to include refinement metadata and ultimately primary rather than reduced X-ray data. PMID:19171973

  4. PDB2Graph: A toolbox for identifying critical amino acids map in proteins based on graph theory.

    Niknam, Niloofar; Khakzad, Hamed; Arab, Seyed Shahriar; Naderi-Manesh, Hossein

    2016-05-01

    The integrative and cooperative nature of protein structure involves the assessment of topological and global features of constituent parts. Network concept takes complete advantage of both of these properties in the analysis concomitantly. High compatibility to structural concepts or physicochemical properties in addition to exploiting a remarkable simplification in the system has made network an ideal tool to explore biological systems. There are numerous examples in which different protein structural and functional characteristics have been clarified by the network approach. Here, we present an interactive and user-friendly Matlab-based toolbox, PDB2Graph, devoted to protein structure network construction, visualization, and analysis. Moreover, PDB2Graph is an appropriate tool for identifying critical nodes involved in protein structural robustness and function based on centrality indices. It maps critical amino acids in protein networks and can greatly aid structural biologists in selecting proper amino acid candidates for manipulating protein structures in a more reasonable and rational manner. To introduce the capability and efficiency of PDB2Graph in detail, the structural modification of Calmodulin through allosteric binding of Ca(2+) is considered. In addition, a mutational analysis for three well-identified model proteins including Phage T4 lysozyme, Barnase and Ribonuclease HI, was performed to inspect the influence of mutating important central residues on protein activity. PMID:27043857

  5. Data mining the PDB for glyco-related data.

    Lütteke, Thomas; von der Lieth, Claus W

    2009-01-01

    The 3D structural data of glycoprotein or protein-carbohydrate complexes that are found in the Protein Data Bank (PDB) are an interesting data source for glycobiologists. Unfortunately, carbohydrate components are difficult to find with the means provided by the PDB. The GLYCOSCIENCES.de internet portal offers a variety of tools and databases to locate and analyze these structures. This chapter describes how to find PDB entries that feature a specific carbohydrate structure and how to locate carbohydrate residues in a 3D structure file and to check their consistency. In addition to this, methods to statistically analyze torsion angles and the abundance of amino acids both in the neighborhood of glycosylation sites and in the spatial vicinity of non-covalently bound carbohydrate chains are summarized. PMID:19277543

  6. PDB_REDO: automated re-refinement of X-ray structure models in the PDB

    Joosten, R.P.; Salzemann, J.; Bloch, V.; Stockinger, H.; Berglund, A; Blanchet, C.; Bongcam-Rudloff, E.; Combet, C.; Da Costa, A.L.; Deleage, G.; Diarena, M.; Fabbretti, R.; Fettahi, G.; Flegel, V.; Gisel, A.

    2009-01-01

    Structural biology, homology modelling and rational drug design require accurate three-dimensional macromolecular coordinates. However, the coordinates in the Protein Data Bank (PDB) have not all been obtained using the latest experimental and computational methods. In this study a method is presented for automated re-refinement of existing structure models in the PDB. A large-scale benchmark with 16 807 PDB entries showed that they can be improved in terms of fit to the deposited experimenta...

  7. PDB_REDO: automated re-refinement of X-ray structure models in the PDB.

    Joosten, Robbie P; Salzemann, Jean; Bloch, Vincent; Stockinger, Heinz; Berglund, Ann-Charlott; Blanchet, Christophe; Bongcam-Rudloff, Erik; Combet, Christophe; Da Costa, Ana L; Deleage, Gilbert; Diarena, Matteo; Fabbretti, Roberto; Fettahi, Géraldine; Flegel, Volker; Gisel, Andreas; Kasam, Vinod; Kervinen, Timo; Korpelainen, Eija; Mattila, Kimmo; Pagni, Marco; Reichstadt, Matthieu; Breton, Vincent; Tickle, Ian J; Vriend, Gert

    2009-06-01

    Structural biology, homology modelling and rational drug design require accurate three-dimensional macromolecular coordinates. However, the coordinates in the Protein Data Bank (PDB) have not all been obtained using the latest experimental and computational methods. In this study a method is presented for automated re-refinement of existing structure models in the PDB. A large-scale benchmark with 16 807 PDB entries showed that they can be improved in terms of fit to the deposited experimental X-ray data as well as in terms of geometric quality. The re-refinement protocol uses TLS models to describe concerted atom movement. The resulting structure models are made available through the PDB_REDO databank (http://www.cmbi.ru.nl/pdb_redo/). Grid computing techniques were used to overcome the computational requirements of this endeavour. PMID:22477769

  8. Protein Data Bank (PDB)

    U.S. Department of Health & Human Services — The Protein Data Bank (PDB) archive is the single worldwide repository of information about the 3D structures of large biological molecules, including proteins and...

  9. PDBCOP: PDB comparison program

    Fejfarová, Karla; Dohnálek, Jan; Hašek, Jindřich

    2015-01-01

    Roč. 22, č. 1 (2015), s. 35. ISSN 1211-5894. [Discussions in Structural Molecular Biology /13./. 19.03.2015-21.03.2015, Nové Hrady] R&D Projects: GA MŠk(CZ) EE2.3.30.0029; GA MŠk(CZ) ED1.1.00/02.0109 Institutional support: RVO:61389013 ; RVO:86652036 Keywords : crystal structure * protein * PDB Subject RIV: CE - Biochemistry

  10. Mirrors in the PDB: left-handed α-turns guide design with D-amino acids

    Nanda Vikas

    2009-09-01

    Full Text Available Abstract Background Incorporating variable amino acid stereochemistry in molecular design has the potential to improve existing protein stability and create new topologies inaccessible to homochiral molecules. The Protein Data Bank has been a reliable, rich source of information on molecular interactions and their role in protein stability and structure. D-amino acids rarely occur naturally, making it difficult to infer general rules for how they would be tolerated in proteins through an analysis of existing protein structures. However, protein elements containing short left-handed turns and helices turn out to contain useful information. Molecular mechanisms used in proteins to stabilize left-handed elements by L-amino acids are structurally enantiomeric to potential synthetic strategies for stabilizing right-handed elements with D-amino acids. Results Propensities for amino acids to occur in contiguous αL helices correlate with published thermodynamic scales for incorporation of D-amino acids into αR helices. Two backbone rules for terminating a left-handed helix are found: an αR conformation is disfavored at the amino terminus, and a βR conformation is disfavored at the carboxy terminus. Helix capping sidechain-backbone interactions are found which are unique to αL helices including an elevated propensity for L-Asn, and L-Thr at the amino terminus and L-Gln, L-Thr and L-Ser at the carboxy terminus. Conclusion By examining left-handed α-turns containing L-amino acids, new interaction motifs for incorporating D-amino acids into right-handed α-helices are identified. These will provide a basis for de novo design of novel heterochiral protein folds.

  11. PDB explorer -- a web based algorithm for protein annotation viewer and 3D visualization.

    Nayarisseri, Anuraj; Shardiwal, Rakesh Kumar; Yadav, Mukesh; Kanungo, Neha; Singh, Pooja; Shah, Pratik; Ahmed, Sheaza

    2014-12-01

    The PDB file format, is a text format characterizing the three dimensional structures of macro molecules available in the Protein Data Bank (PDB). Determined protein structure are found in coalition with other molecules or ions such as nucleic acids, water, ions, Drug molecules and so on, which therefore can be described in the PDB format and have been deposited in PDB database. PDB is a machine generated file, it's not human readable format, to read this file we need any computational tool to understand it. The objective of our present study is to develop a free online software for retrieval, visualization and reading of annotation of a protein 3D structure which is available in PDB database. Main aim is to create PDB file in human readable format, i.e., the information in PDB file is converted in readable sentences. It displays all possible information from a PDB file including 3D structure of that file. Programming languages and scripting languages like Perl, CSS, Javascript, Ajax, and HTML have been used for the development of PDB Explorer. The PDB Explorer directly parses the PDB file, calling methods for parsed element secondary structure element, atoms, coordinates etc. PDB Explorer is freely available at http://www.pdbexplorer.eminentbio.com/home with no requirement of log-in. PMID:25118648

  12. Outcome of the First wwPDB/CCDC/D3R Ligand Validation Workshop.

    Adams, Paul D; Aertgeerts, Kathleen; Bauer, Cary; Bell, Jeffrey A; Berman, Helen M; Bhat, Talapady N; Blaney, Jeff M; Bolton, Evan; Bricogne, Gerard; Brown, David; Burley, Stephen K; Case, David A; Clark, Kirk L; Darden, Tom; Emsley, Paul; Feher, Victoria A; Feng, Zukang; Groom, Colin R; Harris, Seth F; Hendle, Jorg; Holder, Thomas; Joachimiak, Andrzej; Kleywegt, Gerard J; Krojer, Tobias; Marcotrigiano, Joseph; Mark, Alan E; Markley, John L; Miller, Matthew; Minor, Wladek; Montelione, Gaetano T; Murshudov, Garib; Nakagawa, Atsushi; Nakamura, Haruki; Nicholls, Anthony; Nicklaus, Marc; Nolte, Robert T; Padyana, Anil K; Peishoff, Catherine E; Pieniazek, Susan; Read, Randy J; Shao, Chenghua; Sheriff, Steven; Smart, Oliver; Soisson, Stephen; Spurlino, John; Stouch, Terry; Svobodova, Radka; Tempel, Wolfram; Terwilliger, Thomas C; Tronrud, Dale; Velankar, Sameer; Ward, Suzanna C; Warren, Gregory L; Westbrook, John D; Williams, Pamela; Yang, Huanwang; Young, Jasmine

    2016-04-01

    Crystallographic studies of ligands bound to biological macromolecules (proteins and nucleic acids) represent an important source of information concerning drug-target interactions, providing atomic level insights into the physical chemistry of complex formation between macromolecules and ligands. Of the more than 115,000 entries extant in the Protein Data Bank (PDB) archive, ∼75% include at least one non-polymeric ligand. Ligand geometrical and stereochemical quality, the suitability of ligand models for in silico drug discovery and design, and the goodness-of-fit of ligand models to electron-density maps vary widely across the archive. We describe the proceedings and conclusions from the first Worldwide PDB/Cambridge Crystallographic Data Center/Drug Design Data Resource (wwPDB/CCDC/D3R) Ligand Validation Workshop held at the Research Collaboratory for Structural Bioinformatics at Rutgers University on July 30-31, 2015. Experts in protein crystallography from academe and industry came together with non-profit and for-profit software providers for crystallography and with experts in computational chemistry and data archiving to discuss and make recommendations on best practices, as framed by a series of questions central to structural studies of macromolecule-ligand complexes. What data concerning bound ligands should be archived in the PDB? How should the ligands be best represented? How should structural models of macromolecule-ligand complexes be validated? What supplementary information should accompany publications of structural studies of biological macromolecules? Consensus recommendations on best practices developed in response to each of these questions are provided, together with some details regarding implementation. Important issues addressed but not resolved at the workshop are also enumerated. PMID:27050687

  13. PDB_REDO: constructive validation, more than just looking for errors.

    Joosten, Robbie P; Joosten, Krista; Murshudov, Garib N; Perrakis, Anastassis

    2012-04-01

    Developments of the PDB_REDO procedure that combine re-refinement and rebuilding within a unique decision-making framework to improve structures in the PDB are presented. PDB_REDO uses a variety of existing and custom-built software modules to choose an optimal refinement protocol (e.g. anisotropic, isotropic or overall B-factor refinement, TLS model) and to optimize the geometry versus data-refinement weights. Next, it proceeds to rebuild side chains and peptide planes before a final optimization round. PDB_REDO works fully automatically without the need for intervention by a crystallographic expert. The pipeline was tested on 12 000 PDB entries and the great majority of the test cases improved both in terms of crystallographic criteria such as R(free) and in terms of widely accepted geometric validation criteria. It is concluded that PDB_REDO is useful to update the otherwise `static' structures in the PDB to modern crystallographic standards. The publically available PDB_REDO database provides better model statistics and contributes to better refinement and validation targets. PMID:22505269

  14. Widespread occurrence of the tfd-II genes in soil bacteria revealed by nucleotide sequence analysis of 2,4-dichlorophenoxyacetic acid degradative plasmids pDB1 and p712.

    Kim, Dong-Uk; Kim, Min-Sun; Lim, Jong-Sung; Ka, Jong-Ok

    2013-05-01

    Variovorax sp. strain DB1 and Pseudomonas pickettii strain 712 are 2,4-dicholorophenoxy-acetic acid (2,4-D)-degrading bacteria, which were isolated from agricultural soils in Republic of Korea and USA, respectively. Each strain harbors a 2,4-D degradative plasmid and is able to utilize 2,4-D as the sole source of carbon for its growth. The 2,4-D degradative plasmid pDB1 of strain DB1 consisted of a 65,269-bp circular molecule with a G+C content of 66.23% and had 68 ORFs. The 2,4-D degradative plasmid p712 of strain 712 was composed of a 62,798-bp circular molecule with a 62.11% G+C content and had 62 ORFs. The plasmids pDB1 and p712 share significantly homologous 2,4-D degradative genes with high similarity to the tfdR, tfdB-II, tfdC-II, tfdD-II, tfdE-II, tfdF-II, tfdK and tfdA genes of plasmid pJP4 of Alcaligenes eutrophus isolated from Australia. In a phylogenetic analysis with trfA, traL, and trbA genes, pDB1 belonged to IncP-1β with pJP4, while p712 belonged to IncP-1ε with pKJK5 and pEMT3. The results indicated that, in spite of the differences in their backbone regions, the 2,4-D catabolic genes of the two plasmids were closely related and also related to the well-known 2,4-D degradative plasmid pJP4 even though all were isolated from different geographic regions. Other similarities in the genetic organization and the presence of IS1071 suggested that these catabolic genes may be on a transposable element, leading to widespread occurrence in soil bacteria. PMID:23376020

  15. Entry of double-stranded deoxyribonucleic acid during transformation of Neisseria gonorrhoeae.

    Biswas, G D; Sparling, P F

    1981-01-01

    The state of donor deoxyribonucleic acid after entry into competent cells was examined by assaying the transformed cell lysates for donor-marker transforming activity and density of donor deoxyribonucleic acid in CsCl gradients. The experiments showed that deoxyribonucleic acid entered in native, double-stranded form.

  16. NMR structure calculation for all small molecule ligands and non-standard residues from the PDB Chemical Component Dictionary

    An algorithm, CYLIB, is presented for converting molecular topology descriptions from the PDB Chemical Component Dictionary into CYANA residue library entries. The CYANA structure calculation algorithm uses torsion angle molecular dynamics for the efficient computation of three-dimensional structures from NMR-derived restraints. For this, the molecules have to be represented in torsion angle space with rotations around covalent single bonds as the only degrees of freedom. The molecule must be given a tree structure of torsion angles connecting rigid units composed of one or several atoms with fixed relative positions. Setting up CYANA residue library entries therefore involves, besides straightforward format conversion, the non-trivial step of defining a suitable tree structure of torsion angles, and to re-order the atoms in a way that is compatible with this tree structure. This can be done manually for small numbers of ligands but the process is time-consuming and error-prone. An automated method is necessary in order to handle the large number of different potential ligand molecules to be studied in drug design projects. Here, we present an algorithm for this purpose, and show that CYANA structure calculations can be performed with almost all small molecule ligands and non-standard amino acid residues in the PDB Chemical Component Dictionary

  17. NMR structure calculation for all small molecule ligands and non-standard residues from the PDB Chemical Component Dictionary

    Yilmaz, Emel Maden; Güntert, Peter, E-mail: guentert@em.uni-frankfurt.de [Goethe University Frankfurt am Main, Center for Biomolecular Magnetic Resonance, Institute of Biophysical Chemistry (Germany)

    2015-09-15

    An algorithm, CYLIB, is presented for converting molecular topology descriptions from the PDB Chemical Component Dictionary into CYANA residue library entries. The CYANA structure calculation algorithm uses torsion angle molecular dynamics for the efficient computation of three-dimensional structures from NMR-derived restraints. For this, the molecules have to be represented in torsion angle space with rotations around covalent single bonds as the only degrees of freedom. The molecule must be given a tree structure of torsion angles connecting rigid units composed of one or several atoms with fixed relative positions. Setting up CYANA residue library entries therefore involves, besides straightforward format conversion, the non-trivial step of defining a suitable tree structure of torsion angles, and to re-order the atoms in a way that is compatible with this tree structure. This can be done manually for small numbers of ligands but the process is time-consuming and error-prone. An automated method is necessary in order to handle the large number of different potential ligand molecules to be studied in drug design projects. Here, we present an algorithm for this purpose, and show that CYANA structure calculations can be performed with almost all small molecule ligands and non-standard amino acid residues in the PDB Chemical Component Dictionary.

  18. NMR structure calculation for all small molecule ligands and non-standard residues from the PDB Chemical Component Dictionary.

    Yilmaz, Emel Maden; Güntert, Peter

    2015-09-01

    An algorithm, CYLIB, is presented for converting molecular topology descriptions from the PDB Chemical Component Dictionary into CYANA residue library entries. The CYANA structure calculation algorithm uses torsion angle molecular dynamics for the efficient computation of three-dimensional structures from NMR-derived restraints. For this, the molecules have to be represented in torsion angle space with rotations around covalent single bonds as the only degrees of freedom. The molecule must be given a tree structure of torsion angles connecting rigid units composed of one or several atoms with fixed relative positions. Setting up CYANA residue library entries therefore involves, besides straightforward format conversion, the non-trivial step of defining a suitable tree structure of torsion angles, and to re-order the atoms in a way that is compatible with this tree structure. This can be done manually for small numbers of ligands but the process is time-consuming and error-prone. An automated method is necessary in order to handle the large number of different potential ligand molecules to be studied in drug design projects. Here, we present an algorithm for this purpose, and show that CYANA structure calculations can be performed with almost all small molecule ligands and non-standard amino acid residues in the PDB Chemical Component Dictionary. PMID:26123317

  19. Entry of Bluetongue Virus Capsid Requires the Late Endosome-specific Lipid Lysobisphosphatidic Acid.

    Patel, Avnish; Mohl, Bjorn-Patrick; Roy, Polly

    2016-06-01

    The entry of viruses into host cells is one of the key processes of infection. The mechanisms of cellular entry for enveloped virus have been well studied. The fusion proteins as well as the facilitating cellular lipid factors involved in the viral fusion entry process have been well characterized. The process of non-enveloped virus cell entry, in comparison, remains poorly defined, particularly for large complex capsid viruses of the family Reoviridae, which comprises a range of mammalian pathogens. These viruses enter cells without the aid of a limiting membrane and thus cannot fuse with host cell membranes to enter cells. Instead, these viruses are believed to penetrate membranes of the host cell during endocytosis. However, the molecular mechanism of this process is largely undefined. Here we show, utilizing an in vitro liposome penetration assay and cell biology, that bluetongue virus (BTV), an archetypal member of the Reoviridae, utilizes the late endosome-specific lipid lysobisphosphatidic acid for productive membrane penetration and viral entry. Further, we provide preliminary evidence that lipid lysobisphosphatidic acid facilitates pore expansion during membrane penetration, suggesting a mechanism for lipid factor requirement of BTV. This finding indicates that despite the lack of a membrane envelope, the entry process of BTV is similar in specific lipid requirements to enveloped viruses that enter cells through the late endosome. These results are the first, to our knowledge, to demonstrate that a large non-enveloped virus of the Reoviridae has specific lipid requirements for membrane penetration and host cell entry. PMID:27036941

  20. Proteins of Unknown Function in the Protein Data Bank (PDB: An Inventory of True Uncharacterized Proteins and Computational Tools for Their Analysis

    Nurul Nadzirin

    2012-10-01

    Full Text Available Proteins of uncharacterized functions form a large part of many of the currently available biological databases and this situation exists even in the Protein Data Bank (PDB. Our analysis of recent PDB data revealed that only 42.53% of PDB entries (1084 coordinate files that were categorized under “unknown function” are true examples of proteins of unknown function at this point in time. The remainder 1465 entries also annotated as such appear to be able to have their annotations re-assessed, based on the availability of direct functional characterization experiments for the protein itself, or for homologous sequences or structures thus enabling computational function inference.

  1. PDB: CBRC-BTAU-01-1602 [SEVENS

    Full Text Available (Identity=90%) PDB:1FFX Chain:B (X-ray Resolution=3.95),Region:346-794(Identity=90%) PDB:1IA0 Chain:B (EM Resolution...=15.00),Region:346-794(Identity=90%) PDB:1JFF Chain:B (EM Resolution=3.50),Region:346-794(Identity=9...0%) PDB:1SA0 Chain:B (X-ray Resolution=3.58),Region:346-794(Identity=90%) PDB:1SA1 Chain:B (X-ray Resoluti...on=4.20),Region:346-794(Identity=90%) PDB:2WBE Chain:B (EM Resolution=9.40),Region:...346-794(Identity=89%) PDB:1Z2B Chain:B (X-ray Resolution=4.10),Region:346-794(Identity=89%) PDB:3DCO Chain:B (EM Resolution

  2. PDB: CBRC-MDOM-01-0507 [SEVENS

    Full Text Available (Identity=93%) PDB:1FFX Chain:B (X-ray Resolution=3.95),Region:324-795(Identity=93%) PDB:1IA0 Chain:B (EM Resolution...=15.00),Region:324-795(Identity=93%) PDB:1JFF Chain:B (EM Resolution=3.50),Region:324-795(Identity=9...3%) PDB:1SA0 Chain:B (X-ray Resolution=3.58),Region:324-795(Identity=93%) PDB:1SA1 Chain:B (X-ray Resoluti...on=4.20),Region:324-795(Identity=93%) PDB:2WBE Chain:B (EM Resolution=9.40),Region:...324-795(Identity=92%) PDB:1Z2B Chain:B (X-ray Resolution=4.10),Region:324-795(Identity=92%) PDB:3DCO Chain:B (EM Resolution

  3. PDB: CBRC-MDOM-02-0275 [SEVENS

    Full Text Available (Identity=96%) PDB:1FFX Chain:B (X-ray Resolution=3.95),Region:374-798(Identity=96%) PDB:1IA0 Chain:B (EM Resolution...=15.00),Region:374-798(Identity=96%) PDB:1JFF Chain:B (EM Resolution=3.50),Region:374-798(Identity=9...6%) PDB:1SA0 Chain:B (X-ray Resolution=3.58),Region:374-798(Identity=96%) PDB:1SA1 Chain:B (X-ray Resoluti...on=4.20),Region:374-798(Identity=96%) PDB:2WBE Chain:B (EM Resolution=9.40),Region:...374-798(Identity=95%) PDB:1Z2B Chain:B (X-ray Resolution=4.10),Region:374-798(Identity=95%) PDB:3DCO Chain:B (EM Resolution

  4. PDB: CBRC-PVAM-01-1491 [SEVENS

    Full Text Available (Identity=90%) PDB:1FFX Chain:B (X-ray Resolution=3.95),Region:337-792(Identity=90%) PDB:1IA0 Chain:B (EM Resolution...=15.00),Region:337-792(Identity=90%) PDB:1JFF Chain:B (EM Resolution=3.50),Region:337-792(Identity=9...0%) PDB:1SA0 Chain:B (X-ray Resolution=3.58),Region:337-792(Identity=90%) PDB:1SA1 Chain:B (X-ray Resoluti...on=4.20),Region:337-792(Identity=90%) PDB:2WBE Chain:B (EM Resolution=9.40),Region:...337-792(Identity=89%) PDB:1Z2B Chain:B (X-ray Resolution=4.10),Region:337-792(Identity=89%) PDB:3DCO Chain:B (EM Resolution

  5. PDB: CBRC-AGAM-03-0006 [SEVENS

    Full Text Available (Identity=90%) PDB:1FFX Chain:B (X-ray Resolution=3.95),Region:493-923(Identity=90%) PDB:1IA0 Chain:B (EM Resolution...=15.00),Region:493-923(Identity=90%) PDB:1JFF Chain:B (EM Resolution=3.50),Region:493-923(Identity=9...0%) PDB:1SA0 Chain:B (X-ray Resolution=3.58),Region:493-923(Identity=90%) PDB:1SA1 Chain:B (X-ray Resoluti...on=4.20),Region:493-923(Identity=90%) PDB:2WBE Chain:B (EM Resolution=9.40),Region:...493-923(Identity=89%) PDB:1Z2B Chain:B (X-ray Resolution=4.10),Region:493-923(Identity=89%) PDB:3DCO Chain:B (EM Resolution

  6. PDB: CBRC-RNOR-19-0067 [SEVENS

    Full Text Available (Identity=92%) PDB:1FFX Chain:B (X-ray Resolution=3.95),Region:352-778(Identity=92%) PDB:1IA0 Chain:B (EM Resolution...=15.00),Region:352-778(Identity=92%) PDB:1JFF Chain:B (EM Resolution=3.50),Region:352-778(Identity=9...2%) PDB:1SA0 Chain:B (X-ray Resolution=3.58),Region:352-778(Identity=92%) PDB:1SA1 Chain:B (X-ray Resoluti...on=4.20),Region:352-778(Identity=92%) PDB:2WBE Chain:B (EM Resolution=9.40),Region:...352-778(Identity=91%) PDB:1Z2B Chain:B (X-ray Resolution=4.10),Region:352-778(Identity=91%) PDB:3DCO Chain:B (EM Resolution

  7. PDB: CBRC-CJAC-01-0391 [SEVENS

    Full Text Available on:421-804(Identity=82%) PDB:1FFX Chain:B (X-ray Resolution=3.95),Region:421-804(Identity=82%) PDB:1IA0 Chain:B (EM Resolution...=15.00),Region:421-804(Identity=82%) PDB:1JFF Chain:B (EM Resolution=3.50),Region:421-804(...Identity=82%) PDB:1SA0 Chain:B (X-ray Resolution=3.58),Region:421-804(Identity=82...%) PDB:1SA1 Chain:B (X-ray Resolution=4.20),Region:421-788(Identity=82%) PDB:1TUB Chain:B (EM Resolution=3.7...0),Region:421-788(Identity=82%) PDB:1TVK Chain:B (EM Resolution=2.89),Region:421-804(Identity=82%) PDB:2WBE Chain:B (EM Resolution

  8. PDB: CBRC-TGUT-37-0329 [SEVENS

    Full Text Available (Identity=87%) PDB:1FFX Chain:B (X-ray Resolution=3.95),Region:577-967(Identity=87%) PDB:1IA0 Chain:B (EM Resolution...=15.00),Region:577-967(Identity=87%) PDB:1JFF Chain:B (EM Resolution=3.50),Region:577-967(Identity=8...7%) PDB:1SA0 Chain:B (X-ray Resolution=3.58),Region:577-967(Identity=87%) PDB:1SA1 Chain:B (X-ray Resoluti...on=4.20),Region:577-967(Identity=87%) PDB:2WBE Chain:B (EM Resolution=9.40),Region:...577-967(Identity=87%) PDB:1Z2B Chain:B (X-ray Resolution=4.10),Region:577-967(Identity=87%) PDB:3DCO Chain:B (EM Resolution

  9. PDB: CBRC-XTRO-01-3362 [SEVENS

    Full Text Available (Identity=84%) PDB:1FFX Chain:B (X-ray Resolution=3.95),Region:362-748(Identity=84%) PDB:1IA0 Chain:B (EM Resolution...=15.00),Region:362-748(Identity=84%) PDB:1JFF Chain:B (EM Resolution=3.50),Region:362-748(Identity=8...4%) PDB:1SA0 Chain:B (X-ray Resolution=3.58),Region:362-748(Identity=84%) PDB:1SA1 Chain:B (X-ray Resoluti...on=4.20),Region:362-748(Identity=84%) PDB:2WBE Chain:B (EM Resolution=9.40),Region:...362-750(Identity=84%) PDB:1Z2B Chain:B (X-ray Resolution=4.10),Region:362-750(Identity=84%) PDB:3DCO Chain:B (EM Resolution

  10. PDB: CBRC-PABE-07-0039 [SEVENS

    Full Text Available (Identity=96%) PDB:1FFX Chain:B (X-ray Resolution=3.95),Region:377-801(Identity=96%) PDB:1IA0 Chain:B (EM Resolution...=15.00),Region:377-801(Identity=96%) PDB:1JFF Chain:B (EM Resolution=3.50),Region:377-801(Identity=9...6%) PDB:1SA0 Chain:B (X-ray Resolution=3.58),Region:377-801(Identity=96%) PDB:1SA1 Chain:B (X-ray Resoluti...on=4.20),Region:377-801(Identity=96%) PDB:2WBE Chain:B (EM Resolution=9.40),Region:...377-801(Identity=95%) PDB:1Z2B Chain:B (X-ray Resolution=4.10),Region:377-801(Identity=95%) PDB:3DCO Chain:B (EM Resolution

  11. PDB: CBRC-OANA-01-2184 [SEVENS

    Full Text Available (Identity=91%) PDB:1FFX Chain:B (X-ray Resolution=3.95),Region:381-814(Identity=91%) PDB:1IA0 Chain:B (EM Resolution...=15.00),Region:381-814(Identity=91%) PDB:1JFF Chain:B (EM Resolution=3.50),Region:381-814(Identity=9...1%) PDB:1SA0 Chain:B (X-ray Resolution=3.58),Region:381-814(Identity=91%) PDB:1SA1 Chain:B (X-ray Resoluti...on=4.20),Region:381-814(Identity=91%) PDB:2WBE Chain:B (EM Resolution=9.40),Region:...381-814(Identity=90%) PDB:1Z2B Chain:B (X-ray Resolution=4.10),Region:381-814(Identity=90%) PDB:3DCO Chain:B (EM Resolution

  12. PDB: CBRC-FCAT-01-1094 [SEVENS

    Full Text Available (Identity=92%) PDB:1FFX Chain:B (X-ray Resolution=3.95),Region:394-820(Identity=92%) PDB:1IA0 Chain:B (EM Resolution...=15.00),Region:394-820(Identity=92%) PDB:1JFF Chain:B (EM Resolution=3.50),Region:394-820(Identity=9...2%) PDB:1SA0 Chain:B (X-ray Resolution=3.58),Region:394-820(Identity=92%) PDB:1SA1 Chain:B (X-ray Resoluti...on=4.20),Region:394-820(Identity=92%) PDB:2WBE Chain:B (EM Resolution=9.40),Region:...394-820(Identity=92%) PDB:1Z2B Chain:B (X-ray Resolution=4.10),Region:394-820(Identity=92%) PDB:3DCO Chain:B (EM Resolution

  13. PDB: CBRC-RMAC-04-0031 [SEVENS

    Full Text Available (Identity=95%) PDB:1FFX Chain:B (X-ray Resolution=3.95),Region:385-812(Identity=95%) PDB:1IA0 Chain:B (EM Resolution...=15.00),Region:385-812(Identity=95%) PDB:1JFF Chain:B (EM Resolution=3.50),Region:385-812(Identity=9...5%) PDB:1SA0 Chain:B (X-ray Resolution=3.58),Region:385-812(Identity=95%) PDB:1SA1 Chain:B (X-ray Resoluti...on=4.20),Region:385-812(Identity=95%) PDB:2WBE Chain:B (EM Resolution=9.40),Region:...385-812(Identity=95%) PDB:1Z2B Chain:B (X-ray Resolution=4.10),Region:385-812(Identity=95%) PDB:3DCO Chain:B (EM Resolution

  14. PDB: CBRC-CFAM-05-0065 [SEVENS

    Full Text Available (Identity=92%) PDB:1FFX Chain:B (X-ray Resolution=3.95),Region:383-810(Identity=92%) PDB:1IA0 Chain:B (EM Resolution...=15.00),Region:383-810(Identity=92%) PDB:1JFF Chain:B (EM Resolution=3.50),Region:383-810(Identity=9...2%) PDB:1SA0 Chain:B (X-ray Resolution=3.58),Region:383-810(Identity=92%) PDB:1SA1 Chain:B (X-ray Resoluti...on=4.20),Region:383-810(Identity=92%) PDB:2WBE Chain:B (EM Resolution=9.40),Region:...383-810(Identity=91%) PDB:1Z2B Chain:B (X-ray Resolution=4.10),Region:383-810(Identity=91%) PDB:3DCO Chain:B (EM Resolution

  15. PDB: CBRC-PABE-08-0030 [SEVENS

    Full Text Available CBRC-PABE-08-0030 1U34,2JNC,2JND, Region:45-139(Identity=85%) PDB:1U34 Chain:A (NMR...),Region:45-139(Identity=85%) PDB:2JNC Chain:A (NMR),Region:45-139(Identity=85%) PDB:2JND Chain:A (NMR), ...

  16. PDB: CBRC-RNOR-04-0137 [SEVENS

    Full Text Available CBRC-RNOR-04-0137 1U34,2JNC,2JND, Region:39-132(Identity=95%) PDB:1U34 Chain:A (NMR...),Region:39-132(Identity=95%) PDB:2JNC Chain:A (NMR),Region:39-132(Identity=95%) PDB:2JND Chain:A (NMR), ...

  17. PDB: CBRC-BTAU-01-2619 [SEVENS

    Full Text Available CBRC-BTAU-01-2619 1U34,2JNC,2JND, Region:43-137(Identity=85%) PDB:1U34 Chain:A (NMR...),Region:43-137(Identity=85%) PDB:2JNC Chain:A (NMR),Region:43-137(Identity=85%) PDB:2JND Chain:A (NMR), ...

  18. PDB: CBRC-PCAP-01-1657 [SEVENS

    Full Text Available CBRC-PCAP-01-1657 1U34,2JNC,2JND, Region:43-137(Identity=80%) PDB:1U34 Chain:A (NMR...),Region:43-137(Identity=80%) PDB:2JNC Chain:A (NMR),Region:43-137(Identity=80%) PDB:2JND Chain:A (NMR), ...

  19. PDB: CBRC-ACAR-01-1016 [SEVENS

    Full Text Available 2E4H, Region:331-779(Identity=95%) PDB:3E22 Chain:A (X-ray Resolution=3.80),Region:331-779(Identity=97%) PDB:3DCO Chain:A (EM Resolut...ion=1.90),Region:331-779(Identity=97%) PDB:3EDL Chain:A (EM Resolution=28.00),Regio...n:331-779(Identity=96%) PDB:1FFX Chain:A (X-ray Resolution=3.95),Region:331-779(I...dentity=96%) PDB:1IA0 Chain:A (EM Resolution=15.00),Region:331-779(Identity=96%) PDB:1JFF Chain:A (EM Resolution...=3.50),Region:331-779(Identity=96%) PDB:1SA0 Chain:A (X-ray Resolution=3.58),Region:331-779(Identity=96%

  20. PDB: CBRC-FRUB-02-0211 [SEVENS

    Full Text Available 3E22, Region:369-811(Identity=95%) PDB:1Z2B Chain:A (X-ray Resolution=4.10),Region:369-814(Identity=95%) PDB:3DCO Chain:A (EM Resolut...ion=1.90),Region:369-814(Identity=95%) PDB:3EDL Chain:A (EM Resolution=28.00),Regio...n:369-814(Identity=94%) PDB:1FFX Chain:A (X-ray Resolution=3.95),Region:369-814(I...dentity=94%) PDB:1IA0 Chain:A (EM Resolution=15.00),Region:369-814(Identity=94%) PDB:1JFF Chain:A (EM Resolution...=3.50),Region:369-814(Identity=94%) PDB:1SA0 Chain:A (X-ray Resolution=3.58),Region:369-814(Identity=94%

  1. PDB: CBRC-FRUB-02-0776 [SEVENS

    Full Text Available 2E4H, Region:1326-1773(Identity=90%) PDB:2WBE Chain:A (EM Resolution=9.40),Region:1326-1773(Identity=91%) PDB:3DCO Chain:A (EM Resolu...tion=1.90),Region:1326-1773(Identity=91%) PDB:3EDL Chain:A (EM Resolution=28.00),Re...gion:1326-1773(Identity=91%) PDB:3DU7 Chain:A (X-ray Resolution=4.10),Region:1326...-1773(Identity=91%) PDB:3E22 Chain:A (X-ray Resolution=3.80),Region:1326-1773(Identity=90%) PDB:1FFX Chain:A (X-ray Resolution...=3.95),Region:1326-1773(Identity=90%) PDB:1IA0 Chain:A (EM Resolution=15.00),Region:1326-1

  2. PDB: CBRC-DRER-10-0153 [SEVENS

    Full Text Available 3DU7,3E22, Region:383-831(Identity=93%) PDB:3DCO Chain:A (EM Resolution=1.90),Region:383-831(Identity=93%) PDB:3EDL Chain:A (EM Resol...ution=28.00),Region:383-831(Identity=93%) PDB:1FFX Chain:A (X-ray Resolution=3.95),...Region:383-831(Identity=93%) PDB:1IA0 Chain:A (EM Resolution=15.00),Region:383-83...1(Identity=93%) PDB:1JFF Chain:A (EM Resolution=3.50),Region:383-831(Identity=93%) PDB:1SA0 Chain:A (X-ray Resolution...=3.58),Region:383-831(Identity=93%) PDB:1SA1 Chain:A (X-ray Resolution=4.20),Region:383-821(Identit

  3. PDB: CBRC-TNIG-22-0159 [SEVENS

    Full Text Available 2WBE,3DU7,2E4H, Region:346-770(Identity=93%) PDB:3E22 Chain:A (X-ray Resolution=3.80),Region:346-770(Identit...y=95%) PDB:3DCO Chain:A (EM Resolution=1.90),Region:346-770(Identity=95%) PDB:3EDL Chain:A (EM Resolution=28....00),Region:346-770(Identity=94%) PDB:1FFX Chain:A (X-ray Resolution=3.95),Region...:346-770(Identity=94%) PDB:1IA0 Chain:A (EM Resolution=15.00),Region:346-770(Identity=94%) PDB:1JFF Chain:A (EM Resolution...=3.50),Region:346-770(Identity=94%) PDB:1SA0 Chain:A (X-ray Resolution=3.58),Region:346-770(Id

  4. PDB: CBRC-TGUT-37-0154 [SEVENS

    Full Text Available 2E4H, Region:400-819(Identity=93%) PDB:3DU7 Chain:A (X-ray Resolution=4.10),Region:400-819(Identity=93%) PDB...:3E22 Chain:A (X-ray Resolution=3.80),Region:400-819(Identity=93%) PDB:2WBE Chain:A (EM Resolution=9.40),Reg...ion:400-819(Identity=93%) PDB:3DCO Chain:A (EM Resolution=1.90),Region:400-819(Id...entity=93%) PDB:3EDL Chain:A (EM Resolution=28.00),Region:400-819(Identity=93%) PDB:1FFX Chain:A (X-ray Resolution...=3.95),Region:400-819(Identity=93%) PDB:1IA0 Chain:A (EM Resolution=15.00),Region:400-819(Identity=93%

  5. Identification of a D-amino acid decapeptide HIV-1 entry inhibitor

    Entry of human immunodeficiency virus type 1 (HIV-1) virion into host cells involves three major steps, each being a potential target for the development of entry inhibitors: gp120 binding to CD4, gp120-CD4 complex interacting with a coreceptor, and gp41 refolding to form a six-helix bundle. Using a D-amino acid decapeptide combinatorial library, we identified peptide DC13 as having potent HIV-1 fusion inhibitory activity, and effectively inhibiting infection by several laboratory-adapted and primary HIV-1 strains. While DC13 did not block binding of gp120 to CD4, nor disrupt the gp41 six-helix bundle formation, it effectively blocked the binding of an anti-CXCR4 monoclonal antibody and chemokine SDF-1α to CXCR4-expressing cells. However, because R5-using primary viruses were also neutralized, the antiviral activity of DC13 implies additional mode(s) of action. These results suggest that DC13 is a useful HIV-1 coreceptor antagonist for CXCR4 and, due to its biostability and simplicity, may be of value for developing a new class of HIV-1 entry inhibitors

  6. PDB: CBRC-PABE-06-0012 [SEVENS

    Full Text Available ion=3.10),Region:38-64(Identity=100%) PDB:1NRO Chain:R (X-ray Resolution=3.10),Regi...on:38-60(Identity=100%) PDB:1NRP Chain:R (X-ray Resolution=3.00),Region:40-60(Identity=100%) PDB:1NRQ Chain:R (X-ray Resolution...=3.50),Region:43-60(Identity=100%) PDB:1NRR Chain:R (X-ray Resolution...=2.40),Region:49-57(Identity=100%) PDB:3BEF Chain:C (X-ray Resolution=2.20), ... ...CBRC-PABE-06-0012 1NRN,1NRO,1NRP,1NRQ,1NRR,3BEF, Region:38-60(Identity=100%) PDB:1NRN Chain:R (X-ray Resolut

  7. PDB: CBRC-PHAM-01-0359 [SEVENS

    Full Text Available ion=3.10),Region:38-64(Identity=100%) PDB:1NRO Chain:R (X-ray Resolution=3.10),Regi...on:38-60(Identity=100%) PDB:1NRP Chain:R (X-ray Resolution=3.00),Region:40-60(Identity=100%) PDB:1NRQ Chain:R (X-ray Resolution...=3.50),Region:43-60(Identity=100%) PDB:1NRR Chain:R (X-ray Resolution...=2.40),Region:49-57(Identity=100%) PDB:3BEF Chain:C (X-ray Resolution=2.20), ... ...CBRC-PHAM-01-0359 1NRN,1NRO,1NRP,1NRQ,1NRR,3BEF, Region:38-60(Identity=100%) PDB:1NRN Chain:R (X-ray Resolut

  8. PDB: CBRC-PTRO-06-0019 [SEVENS

    Full Text Available ion=3.10),Region:38-64(Identity=100%) PDB:1NRO Chain:R (X-ray Resolution=3.10),Regi...on:38-60(Identity=100%) PDB:1NRP Chain:R (X-ray Resolution=3.00),Region:40-60(Identity=100%) PDB:1NRQ Chain:R (X-ray Resolution...=3.50),Region:43-60(Identity=100%) PDB:1NRR Chain:R (X-ray Resolution...=2.40),Region:49-57(Identity=100%) PDB:3BEF Chain:C (X-ray Resolution=2.20), ... ...CBRC-PTRO-06-0019 1NRN,1NRO,1NRP,1NRQ,1NRR,3BEF, Region:38-60(Identity=100%) PDB:1NRN Chain:R (X-ray Resolut

  9. PDB: CBRC-RMAC-06-0015 [SEVENS

    Full Text Available ion=3.10),Region:38-64(Identity=100%) PDB:1NRO Chain:R (X-ray Resolution=3.10),Regi...on:38-60(Identity=100%) PDB:1NRP Chain:R (X-ray Resolution=3.00),Region:40-60(Identity=100%) PDB:1NRQ Chain:R (X-ray Resolution...=3.50),Region:43-60(Identity=100%) PDB:1NRR Chain:R (X-ray Resolution...=2.40),Region:49-57(Identity=100%) PDB:3BEF Chain:C (X-ray Resolution=2.20), ... ...CBRC-RMAC-06-0015 1NRN,1NRO,1NRP,1NRQ,1NRR,3BEF, Region:38-60(Identity=100%) PDB:1NRN Chain:R (X-ray Resolut

  10. PDB: CBRC-PABE-06-0013 [SEVENS

    Full Text Available ion=3.10),Region:21-47(Identity=100%) PDB:1NRO Chain:R (X-ray Resolution=3.10),Regi...on:21-43(Identity=100%) PDB:1NRP Chain:R (X-ray Resolution=3.00),Region:23-43(Identity=100%) PDB:1NRQ Chain:R (X-ray Resolution...=3.50),Region:26-43(Identity=100%) PDB:1NRR Chain:R (X-ray Resolution...=2.40),Region:32-40(Identity=100%) PDB:3BEF Chain:C (X-ray Resolution=2.20), ... ...CBRC-PABE-06-0013 1NRN,1NRO,1NRP,1NRQ,1NRR,3BEF, Region:21-43(Identity=100%) PDB:1NRN Chain:R (X-ray Resolut

  11. PDB: CBRC-HSAP-05-0018 [SEVENS

    Full Text Available ion=3.10),Region:38-64(Identity=100%) PDB:1NRO Chain:R (X-ray Resolution=3.10),Regi...on:38-60(Identity=100%) PDB:1NRP Chain:R (X-ray Resolution=3.00),Region:40-60(Identity=100%) PDB:1NRQ Chain:R (X-ray Resolution...=3.50),Region:43-60(Identity=100%) PDB:1NRR Chain:R (X-ray Resolution...=2.40),Region:49-57(Identity=100%) PDB:3BEF Chain:C (X-ray Resolution=2.20), ... ...CBRC-HSAP-05-0018 1NRN,1NRO,1NRP,1NRQ,1NRR,3BEF, Region:38-60(Identity=100%) PDB:1NRN Chain:R (X-ray Resolut

  12. PDB: CBRC-CFAM-23-0006 [SEVENS

    Full Text Available CBRC-CFAM-23-0006 1OF2,1OGT,3B3I, Region:402-410(Identity=100%) PDB:1OF2 Chain:C (X-ray Resolution...=2.20),Region:402-410(Identity=100%) PDB:1OGT Chain:C (X-ray Resolution=1.47),Region:402-410(Identity=100%) PDB:3B3I Chain:C (X-ray Resolution=1.86), ...

  13. PDB: CBRC-PABE-18-0028 [SEVENS

    Full Text Available CBRC-PABE-18-0028 3EHS,3EHT,3EHU, Region:36-131(Identity=100%) PDB:3EHS Chain:A (X-ray Resolution...=2.76),Region:36-131(Identity=100%) PDB:3EHT Chain:A (X-ray Resolution=3.40),Region:36-131(Identity=100%) PDB:3EHU Chain:A (X-ray Resolution=1.96), ...

  14. PDB: CBRC-OPRI-01-1523 [SEVENS

    Full Text Available CBRC-OPRI-01-1523 1OF2,1OGT,3B3I, Region:401-409(Identity=100%) PDB:1OF2 Chain:C (X-ray Resolution...=2.20),Region:401-409(Identity=100%) PDB:1OGT Chain:C (X-ray Resolution=1.47),Region:401-409(Identity=100%) PDB:3B3I Chain:C (X-ray Resolution=1.86), ...

  15. PDB: CBRC-MLUC-01-0880 [SEVENS

    Full Text Available CBRC-MLUC-01-0880 3EHS,3EHT,3EHU, Region:22-117(Identity=91%) PDB:3EHS Chain:A (X-ray Resolution...=2.76),Region:22-117(Identity=91%) PDB:3EHT Chain:A (X-ray Resolution=3.40),Region:22-117(Identity=91%) PDB:3EHU Chain:A (X-ray Resolution=1.96), ...

  16. Acid hydrolysis of cellulose as the entry point into biorefinery schemes.

    Rinaldi, Roberto; Schüth, Ferdi

    2009-01-01

    Cellulose is a major source of glucose because it is readily available, renewable, and does not compete with the food supply. Hydrolysis of cellulose is experiencing a new research and development cycle in which this reaction is carried out over solid catalysts and coupled to other reactions for increased efficiency. Cellulose is typically not soluble in conventional solvents and very resistant to chemical and biological transformations. This Review focuses on aspects related to the hydrolysis of cellulose as this process is a significant entry point into the biorefinery scheme based on carbohydrates for the production of biofuels and biochemicals. Structural features of cellulose, conventional acid-catalyzed reactions, and the use of solid acid catalysts for hydrolysis are discussed. The longterm success of the biorefinery concept depends on the development of energetically efficient processes to convert cellulose directly or indirectly into biofuels and chemicals. PMID:19950346

  17. PDB: CBRC-PTRO-06-0041 [SEVENS

    Full Text Available CBRC-PTRO-06-0041 2R4R,2RH1,3D4S,2R4S, Region:85-449(Identity=99%) PDB:2R4R Chain:A (X-ray Resolution...=3.40),Region:85-449(Identity=99%) PDB:2RH1 Chain:A (X-ray Resolution=2.40),Region:85-449(...Identity=99%) PDB:3D4S Chain:A (X-ray Resolution=2.80),Region:108-449(Identity=99%) PDB:2R4S Chain:A (X-ray Resolution=3.40), ...

  18. PDB: CBRC-HSAP-05-0044 [SEVENS

    Full Text Available CBRC-HSAP-05-0044 2R4R,2RH1,3D4S,2R4S, Region:1-365(Identity=99%) PDB:2R4R Chain:A (X-ray Resolution...=3.40),Region:1-365(Identity=99%) PDB:2RH1 Chain:A (X-ray Resolution=2.40),Region:1-365(Ide...ntity=99%) PDB:3D4S Chain:A (X-ray Resolution=2.80),Region:24-365(Identity=99%) PDB:2R4S Chain:A (X-ray Resolution=3.40), ...

  19. PDB: CBRC-RMAC-06-0031 [SEVENS

    Full Text Available CBRC-RMAC-06-0031 2R4R,2RH1,3D4S,2R4S, Region:1-367(Identity=98%) PDB:2R4R Chain:A (X-ray Resolution...=3.40),Region:1-367(Identity=98%) PDB:2RH1 Chain:A (X-ray Resolution=2.40),Region:1-367(Ide...ntity=98%) PDB:3D4S Chain:A (X-ray Resolution=2.80),Region:24-367(Identity=97%) PDB:2R4S Chain:A (X-ray Resolution=3.40), ...

  20. PDB: CBRC-PABE-06-0027 [SEVENS

    Full Text Available CBRC-PABE-06-0027 2R4R,2RH1,3D4S,2R4S, Region:126-492(Identity=98%) PDB:2R4R Chain:A (X-ray Resolution...=3.40),Region:126-492(Identity=98%) PDB:2RH1 Chain:A (X-ray Resolution=2.40),Region:126-4...92(Identity=98%) PDB:3D4S Chain:A (X-ray Resolution=2.80),Region:149-492(Identity=98%) PDB:2R4S Chain:A (X-ray Resolution=3.40), ...

  1. PDB: CBRC-CJAC-01-1334 [SEVENS

    Full Text Available CBRC-CJAC-01-1334 2R4R,2RH1,3D4S,2R4S, Region:32-398(Identity=96%) PDB:2R4R Chain:A (X-ray Resolution...=3.40),Region:32-398(Identity=96%) PDB:2RH1 Chain:A (X-ray Resolution=2.40),Region:32-398(...Identity=96%) PDB:3D4S Chain:A (X-ray Resolution=2.80),Region:55-398(Identity=96%) PDB:2R4S Chain:A (X-ray Resolution=3.40), ...

  2. Local Unfolding of Fatty Acid Binding Protein to Allow Ligand Entry for Binding.

    Xiao, Tianshu; Fan, Jing-Song; Zhou, Hu; Lin, Qingsong; Yang, Daiwen

    2016-06-01

    Fatty acid binding proteins are responsible for the transportation of fatty acids in biology. Despite intensive studies, the molecular mechanism of fatty acid entry to and exit from the protein cavity is still unclear. Here a cap-closed variant of human intestinal fatty acid binding protein was generated by mutagenesis, in which the helical cap is locked to the β-barrel by a disulfide linkage. Structure determination shows that this variant adopts a closed conformation, but still uptakes fatty acids. Stopped-flow experiments indicate that a rate-limiting step exists before the ligand association and this step corresponds to the conversion of the closed form to the open one. NMR relaxation dispersion and H-D exchange data demonstrate the presence of two excited states: one is native-like, but the other adopts a locally unfolded structure. Local unfolding of helix 2 generates an opening for ligands to enter the protein cavity, and thus controls the ligand association rate. PMID:27105780

  3. PDB: CBRC-TGUT-02-0002 [SEVENS

    Full Text Available CBRC-TGUT-02-0002 2E4U,2E4V,2E4W,2E4X,2E4Y, Region:25-575(Identity=89%) PDB:2E4U Chain:A (X-ray Resolut...ion=2.35),Region:25-575(Identity=89%) PDB:2E4V Chain:A (X-ray Resolution=2.40),Region:25...-575(Identity=89%) PDB:2E4W Chain:A (X-ray Resolution=2.40),Region:25-575(Identity=89%) PDB:2E4X Chain:A (X-ray Resolut...ion=2.75),Region:25-575(Identity=89%) PDB:2E4Y Chain:A (X-ray Resolution=3.40), ...

  4. PDB: CBRC-BTAU-01-2536 [SEVENS

    Full Text Available CBRC-BTAU-01-2536 3ODU,3OE0,3OE6,3OE8,3OE9, Region:10-324(Identity=92%) PDB:3ODU Chain:A (X-ray Resolution...=2.5),Region:10-324(Identity=92%) PDB:3OE0 Chain:A (X-ray Resolution=2.9),Region:10-3...30(Identity=92%) PDB:3OE6 Chain:A (X-ray Resolution=3.2),Region:10-324(Identity=92%) PDB:3OE8 Chain:A (X-ray Resolution...=3.1),Region:10-324(Identity=92%) PDB:3OE9 Chain:A (X-ray Resolution=3.1), ...

  5. PDB: CBRC-MMUR-01-1429 [SEVENS

    Full Text Available CBRC-MMUR-01-1429 2E4U,2E4V,2E4W,2E4X,2E4Y, Region:25-575(Identity=96%) PDB:2E4U Chain:A (X-ray Resolution...=2.35),Region:25-575(Identity=96%) PDB:2E4V Chain:A (X-ray Resolution=2.40),Region:25...-575(Identity=96%) PDB:2E4W Chain:A (X-ray Resolution=2.40),Region:25-575(Identity=96%) PDB:2E4X Chain:A (X-ray Resolution...=2.75),Region:25-575(Identity=96%) PDB:2E4Y Chain:A (X-ray Resolution=3.40), ...

  6. PDB: CBRC-PHAM-01-1532 [SEVENS

    Full Text Available CBRC-PHAM-01-1532 3ODU,3OE0,3OE6,3OE8,3OE9, Region:8-323(Identity=97%) PDB:3ODU Chain:A (X-ray Resolution...=2.5),Region:8-323(Identity=97%) PDB:3OE0 Chain:A (X-ray Resolution=2.9),Region:8-329(...Identity=97%) PDB:3OE6 Chain:A (X-ray Resolution=3.2),Region:8-323(Identity=97%) PDB:3OE8 Chain:A (X-ray Resolution...=3.1),Region:8-323(Identity=97%) PDB:3OE9 Chain:A (X-ray Resolution=3.1), ...

  7. PDB: CBRC-PABE-03-0008 [SEVENS

    Full Text Available CBRC-PABE-03-0008 3ODU,3OE0,3OE6,3OE8,3OE9, Region:8-324(Identity=99%) PDB:3ODU Chain:A (X-ray Resolution...=2.5),Region:8-324(Identity=99%) PDB:3OE0 Chain:A (X-ray Resolution=2.9),Region:8-330(...Identity=99%) PDB:3OE6 Chain:A (X-ray Resolution=3.2),Region:8-324(Identity=99%) PDB:3OE8 Chain:A (X-ray Resolution...=3.1),Region:8-324(Identity=99%) PDB:3OE9 Chain:A (X-ray Resolution=3.1), ...

  8. PDB: CBRC-TTRU-01-0390 [SEVENS

    Full Text Available CBRC-TTRU-01-0390 3ODU,3OE0,3OE6,3OE8,3OE9, Region:2-320(Identity=93%) PDB:3ODU Chain:A (X-ray Resolution...=2.5),Region:2-320(Identity=93%) PDB:3OE0 Chain:A (X-ray Resolution=2.9),Region:2-326(...Identity=93%) PDB:3OE6 Chain:A (X-ray Resolution=3.2),Region:2-320(Identity=93%) PDB:3OE8 Chain:A (X-ray Resolution...=3.1),Region:2-320(Identity=93%) PDB:3OE9 Chain:A (X-ray Resolution=3.1), ...

  9. PDB: CBRC-OGAR-01-0515 [SEVENS

    Full Text Available CBRC-OGAR-01-0515 3ODU,3OE0,3OE6,3OE8,3OE9, Region:2-318(Identity=94%) PDB:3ODU Chain:A (X-ray Resolution...=2.5),Region:2-318(Identity=94%) PDB:3OE0 Chain:A (X-ray Resolution=2.9),Region:2-324(...Identity=94%) PDB:3OE6 Chain:A (X-ray Resolution=3.2),Region:2-318(Identity=94%) PDB:3OE8 Chain:A (X-ray Resolution...=3.1),Region:2-318(Identity=94%) PDB:3OE9 Chain:A (X-ray Resolution=3.1), ...

  10. PDB: CBRC-CFAM-14-0054 [SEVENS

    Full Text Available CBRC-CFAM-14-0054 2E4U,2E4V,2E4W,2E4X,2E4Y, Region:25-571(Identity=89%) PDB:2E4U Chain:A (X-ray Resolution...=2.35),Region:25-571(Identity=89%) PDB:2E4V Chain:A (X-ray Resolution=2.40),Region:25...-571(Identity=89%) PDB:2E4W Chain:A (X-ray Resolution=2.40),Region:25-571(Identity=89%) PDB:2E4X Chain:A (X-ray Resolution...=2.75),Region:25-571(Identity=89%) PDB:2E4Y Chain:A (X-ray Resolution=3.40), ...

  11. PDB: CBRC-CJAC-01-1379 [SEVENS

    Full Text Available CBRC-CJAC-01-1379 3ODU,3OE0,3OE6,3OE8,3OE9, Region:8-323(Identity=97%) PDB:3ODU Chain:A (X-ray Resolution...=2.5),Region:8-323(Identity=97%) PDB:3OE0 Chain:A (X-ray Resolution=2.9),Region:8-329(...Identity=97%) PDB:3OE6 Chain:A (X-ray Resolution=3.2),Region:8-323(Identity=97%) PDB:3OE8 Chain:A (X-ray Resolution...=3.1),Region:8-323(Identity=97%) PDB:3OE9 Chain:A (X-ray Resolution=3.1), ...

  12. PDB: CBRC-MDOM-04-0074 [SEVENS

    Full Text Available CBRC-MDOM-04-0074 3ODU,3OE0,3OE6,3OE8,3OE9, Region:18-334(Identity=82%) PDB:3ODU Chain:A (X-ray Resolution...=2.5),Region:18-334(Identity=82%) PDB:3OE0 Chain:A (X-ray Resolution=2.9),Region:18-3...40(Identity=82%) PDB:3OE6 Chain:A (X-ray Resolution=3.2),Region:18-334(Identity=82%) PDB:3OE8 Chain:A (X-ray Resolution...=3.1),Region:18-334(Identity=82%) PDB:3OE9 Chain:A (X-ray Resolution=3.1), ...

  13. PDB: CBRC-HSAP-02-0054 [SEVENS

    Full Text Available CBRC-HSAP-02-0054 3ODU,3OE0,3OE6,3OE8,3OE9, Region:8-323(Identity=99%) PDB:3ODU Chain:A (X-ray Resolution...=2.5),Region:8-323(Identity=99%) PDB:3OE0 Chain:A (X-ray Resolution=2.9),Region:8-329(...Identity=99%) PDB:3OE6 Chain:A (X-ray Resolution=3.2),Region:8-323(Identity=99%) PDB:3OE8 Chain:A (X-ray Resolution...=3.1),Region:8-323(Identity=99%) PDB:3OE9 Chain:A (X-ray Resolution=3.1), ...

  14. PDB: CBRC-MDOM-02-0383 [SEVENS

    Full Text Available CBRC-MDOM-02-0383 1EWK,1EWT,1EWV,1ISR,1ISS, Region:33-522(Identity=96%) PDB:1EWK Chain:A (X-ray Resolution...=2.20),Region:33-522(Identity=96%) PDB:1EWT Chain:A (X-ray Resolution=3.70),Region:33...-522(Identity=96%) PDB:1EWV Chain:A (X-ray Resolution=4.00),Region:33-522(Identity=96%) PDB:1ISR Chain:A (X-ray Resolution...=4.00),Region:33-522(Identity=96%) PDB:1ISS Chain:A (X-ray Resolution=3.30), ...

  15. PDB: CBRC-LAFR-01-1328 [SEVENS

    Full Text Available CBRC-LAFR-01-1328 3ODU,3OE0,3OE6,3OE8,3OE9, Region:2-311(Identity=93%) PDB:3ODU Chain:A (X-ray Resolution...=2.5),Region:2-311(Identity=93%) PDB:3OE0 Chain:A (X-ray Resolution=2.9),Region:2-317(...Identity=93%) PDB:3OE6 Chain:A (X-ray Resolution=3.2),Region:2-311(Identity=93%) PDB:3OE8 Chain:A (X-ray Resolution...=3.1),Region:2-311(Identity=93%) PDB:3OE9 Chain:A (X-ray Resolution=3.1), ...

  16. PDB: CBRC-ETEL-01-1471 [SEVENS

    Full Text Available CBRC-ETEL-01-1471 3ODU,3OE0,3OE6,3OE8,3OE9, Region:52-369(Identity=87%) PDB:3ODU Chain:A (X-ray Resolution...=2.5),Region:52-369(Identity=87%) PDB:3OE0 Chain:A (X-ray Resolution=2.9),Region:52-3...75(Identity=87%) PDB:3OE6 Chain:A (X-ray Resolution=3.2),Region:52-369(Identity=87%) PDB:3OE8 Chain:A (X-ray Resolution...=3.1),Region:52-369(Identity=87%) PDB:3OE9 Chain:A (X-ray Resolution=3.1), ...

  17. PDB: CBRC-MMUS-10-0003 [SEVENS

    Full Text Available CBRC-MMUS-10-0003 1EWK,1EWT,1EWV,1ISR,1ISS, Region:33-522(Identity=99%) PDB:1EWK Chain:A (X-ray Resolution...=2.20),Region:33-522(Identity=99%) PDB:1EWT Chain:A (X-ray Resolution=3.70),Region:33...-522(Identity=99%) PDB:1EWV Chain:A (X-ray Resolution=4.00),Region:33-522(Identity=99%) PDB:1ISR Chain:A (X-ray Resolution...=4.00),Region:33-522(Identity=99%) PDB:1ISS Chain:A (X-ray Resolution=3.30), ...

  18. PDB: CBRC-RMAC-04-0056 [SEVENS

    Full Text Available CBRC-RMAC-04-0056 1EWK,1EWT,1EWV,1ISR,1ISS, Region:33-522(Identity=98%) PDB:1EWK Chain:A (X-ray Resolution...=2.20),Region:33-522(Identity=98%) PDB:1EWT Chain:A (X-ray Resolution=3.70),Region:33...-522(Identity=98%) PDB:1EWV Chain:A (X-ray Resolution=4.00),Region:33-522(Identity=98%) PDB:1ISR Chain:A (X-ray Resolution...=4.00),Region:33-522(Identity=98%) PDB:1ISS Chain:A (X-ray Resolution=3.30), ...

  19. PDB: CBRC-RNOR-04-0019 [SEVENS

    Full Text Available CBRC-RNOR-04-0019 2E4U,2E4V,2E4W,2E4X,2E4Y, Region:25-575(Identity=100%) PDB:2E4U Chain:A (X-ray Resolution...=2.35),Region:25-575(Identity=100%) PDB:2E4V Chain:A (X-ray Resolution=2.40),Region:...25-575(Identity=100%) PDB:2E4W Chain:A (X-ray Resolution=2.40),Region:25-575(Identity=100%) PDB:2E4X Chain:A (X-ray Resolution...=2.75),Region:25-575(Identity=100%) PDB:2E4Y Chain:A (X-ray Resolution=3.40), ...

  20. PDB: CBRC-CFAM-01-0008 [SEVENS

    Full Text Available CBRC-CFAM-01-0008 1EWK,1EWT,1EWV,1ISR,1ISS, Region:33-522(Identity=98%) PDB:1EWK Chain:A (X-ray Resolution...=2.20),Region:33-522(Identity=98%) PDB:1EWT Chain:A (X-ray Resolution=3.70),Region:33...-522(Identity=98%) PDB:1EWV Chain:A (X-ray Resolution=4.00),Region:33-522(Identity=98%) PDB:1ISR Chain:A (X-ray Resolution...=4.00),Region:33-522(Identity=98%) PDB:1ISS Chain:A (X-ray Resolution=3.30), ...

  1. PDB: CBRC-TGUT-10-0011 [SEVENS

    Full Text Available CBRC-TGUT-10-0011 3ODU,3OE0,3OE6,3OE8,3OE9, Region:13-329(Identity=81%) PDB:3ODU Chain:A (X-ray Resolution...=2.5),Region:13-329(Identity=81%) PDB:3OE0 Chain:A (X-ray Resolution=2.9),Region:13-3...35(Identity=82%) PDB:3OE6 Chain:A (X-ray Resolution=3.2),Region:13-329(Identity=81%) PDB:3OE8 Chain:A (X-ray Resolution...=3.1),Region:13-329(Identity=81%) PDB:3OE9 Chain:A (X-ray Resolution=3.1), ...

  2. PDB: CBRC-SARA-01-0838 [SEVENS

    Full Text Available CBRC-SARA-01-0838 3ODU,3OE0,3OE6,3OE8,3OE9, Region:8-324(Identity=89%) PDB:3ODU Chain:A (X-ray Resolution...=2.5),Region:8-324(Identity=89%) PDB:3OE0 Chain:A (X-ray Resolution=2.9),Region:8-330(...Identity=90%) PDB:3OE6 Chain:A (X-ray Resolution=3.2),Region:8-324(Identity=89%) PDB:3OE8 Chain:A (X-ray Resolution...=3.1),Region:8-324(Identity=89%) PDB:3OE9 Chain:A (X-ray Resolution=3.1), ...

  3. PDB: CBRC-GGOR-01-0300 [SEVENS

    Full Text Available CBRC-GGOR-01-0300 3ODU,3OE0,3OE6,3OE8,3OE9, Region:8-271(Identity=98%) PDB:3ODU Chain:A (X-ray Resolution...=2.5),Region:8-271(Identity=98%) PDB:3OE0 Chain:A (X-ray Resolution=2.9),Region:8-271(...Identity=98%) PDB:3OE6 Chain:A (X-ray Resolution=3.2),Region:8-271(Identity=98%) PDB:3OE8 Chain:A (X-ray Resolution...=3.1),Region:8-271(Identity=98%) PDB:3OE9 Chain:A (X-ray Resolution=3.1), ...

  4. PDB: CBRC-TGUT-05-0017 [SEVENS

    Full Text Available CBRC-TGUT-05-0017 1EWK,1EWT,1EWV,1ISR,1ISS, Region:33-520(Identity=81%) PDB:1EWK Chain:A (X-ray Resolution...=2.20),Region:33-520(Identity=81%) PDB:1EWT Chain:A (X-ray Resolution=3.70),Region:33...-520(Identity=81%) PDB:1EWV Chain:A (X-ray Resolution=4.00),Region:33-520(Identity=81%) PDB:1ISR Chain:A (X-ray Resolution...=4.00),Region:33-520(Identity=81%) PDB:1ISS Chain:A (X-ray Resolution=3.30), ...

  5. PDB: CBRC-PCAP-01-1190 [SEVENS

    Full Text Available CBRC-PCAP-01-1190 2E4U,2E4V,2E4W,2E4X,2E4Y, Region:1-485(Identity=92%) PDB:2E4U Chain:A (X-ray Resolution...=2.35),Region:1-485(Identity=92%) PDB:2E4V Chain:A (X-ray Resolution=2.40),Region:1-48...5(Identity=92%) PDB:2E4W Chain:A (X-ray Resolution=2.40),Region:1-485(Identity=92%) PDB:2E4X Chain:A (X-ray Resolution...=2.75),Region:1-485(Identity=92%) PDB:2E4Y Chain:A (X-ray Resolution=3.40), ...

  6. PDB: CBRC-MMUS-05-0006 [SEVENS

    Full Text Available CBRC-MMUS-05-0006 2E4U,2E4V,2E4W,2E4X,2E4Y, Region:25-575(Identity=98%) PDB:2E4U Chain:A (X-ray Resolution...=2.35),Region:25-575(Identity=98%) PDB:2E4V Chain:A (X-ray Resolution=2.40),Region:25...-575(Identity=98%) PDB:2E4W Chain:A (X-ray Resolution=2.40),Region:25-575(Identity=98%) PDB:2E4X Chain:A (X-ray Resolution...=2.75),Region:25-575(Identity=98%) PDB:2E4Y Chain:A (X-ray Resolution=3.40), ...

  7. PDB: CBRC-GGAL-07-0011 [SEVENS

    Full Text Available CBRC-GGAL-07-0011 3ODU,3OE0,3OE6,3OE8,3OE9, Region:9-325(Identity=81%) PDB:3ODU Chain:A (X-ray Resolution...=2.5),Region:9-325(Identity=81%) PDB:3OE0 Chain:A (X-ray Resolution=2.9),Region:9-331(...Identity=81%) PDB:3OE6 Chain:A (X-ray Resolution=3.2),Region:9-325(Identity=81%) PDB:3OE8 Chain:A (X-ray Resolution...=3.1),Region:9-325(Identity=81%) PDB:3OE9 Chain:A (X-ray Resolution=3.1), ...

  8. PDB: CBRC-RMAC-03-0043 [SEVENS

    Full Text Available CBRC-RMAC-03-0043 2E4U,2E4V,2E4W,2E4X,2E4Y, Region:25-575(Identity=96%) PDB:2E4U Chain:A (X-ray Resolution...=2.35),Region:25-575(Identity=96%) PDB:2E4V Chain:A (X-ray Resolution=2.40),Region:25...-575(Identity=96%) PDB:2E4W Chain:A (X-ray Resolution=2.40),Region:25-575(Identity=96%) PDB:2E4X Chain:A (X-ray Resolution...=2.75),Region:25-575(Identity=96%) PDB:2E4Y Chain:A (X-ray Resolution=3.40), ...

  9. PDB: CBRC-PVAM-01-1450 [SEVENS

    Full Text Available CBRC-PVAM-01-1450 3ODU,3OE0,3OE6,3OE8,3OE9, Region:113-429(Identity=92%) PDB:3ODU Chain:A (X-ray Resolution...=2.5),Region:113-429(Identity=92%) PDB:3OE0 Chain:A (X-ray Resolution=2.9),Region:11...3-435(Identity=92%) PDB:3OE6 Chain:A (X-ray Resolution=3.2),Region:113-429(Identity=92%) PDB:3OE8 Chain:A (X-ray Resolution...=3.1),Region:113-429(Identity=92%) PDB:3OE9 Chain:A (X-ray Resolution=3.1), ...

  10. PDB: CBRC-TSYR-01-0036 [SEVENS

    Full Text Available CBRC-TSYR-01-0036 2E4U,2E4V,2E4W,2E4X,2E4Y, Region:1-551(Identity=97%) PDB:2E4U Chain:A (X-ray Resolution...=2.35),Region:1-551(Identity=97%) PDB:2E4V Chain:A (X-ray Resolution=2.40),Region:1-55...1(Identity=97%) PDB:2E4W Chain:A (X-ray Resolution=2.40),Region:1-551(Identity=97%) PDB:2E4X Chain:A (X-ray Resolution...=2.75),Region:1-551(Identity=97%) PDB:2E4Y Chain:A (X-ray Resolution=3.40), ...

  11. PDB: CBRC-MEUG-01-2373 [SEVENS

    Full Text Available CBRC-MEUG-01-2373 1EWK,1EWT,1EWV,1ISR,1ISS, Region:33-522(Identity=90%) PDB:1EWK Chain:A (X-ray Resolution...=2.20),Region:33-522(Identity=90%) PDB:1EWT Chain:A (X-ray Resolution=3.70),Region:33...-522(Identity=90%) PDB:1EWV Chain:A (X-ray Resolution=4.00),Region:33-522(Identity=90%) PDB:1ISR Chain:A (X-ray Resolution...=4.00),Region:33-522(Identity=90%) PDB:1ISS Chain:A (X-ray Resolution=3.30), ...

  12. PDB: CBRC-OANA-01-1931 [SEVENS

    Full Text Available CBRC-OANA-01-1931 3ODU,3OE0,3OE6,3OE8,3OE9, Region:37-348(Identity=84%) PDB:3ODU Chain:A (X-ray Resolution...=2.5),Region:37-348(Identity=84%) PDB:3OE0 Chain:A (X-ray Resolution=2.9),Region:37-3...54(Identity=84%) PDB:3OE6 Chain:A (X-ray Resolution=3.2),Region:37-348(Identity=84%) PDB:3OE8 Chain:A (X-ray Resolution...=3.1),Region:37-348(Identity=84%) PDB:3OE9 Chain:A (X-ray Resolution=3.1), ...

  13. PDB: CBRC-PABE-08-0035 [SEVENS

    Full Text Available CBRC-PABE-08-0035 2E4U,2E4V,2E4W,2E4X,2E4Y, Region:25-575(Identity=96%) PDB:2E4U Chain:A (X-ray Resolution...=2.35),Region:25-575(Identity=96%) PDB:2E4V Chain:A (X-ray Resolution=2.40),Region:25...-575(Identity=96%) PDB:2E4W Chain:A (X-ray Resolution=2.40),Region:25-575(Identity=96%) PDB:2E4X Chain:A (X-ray Resolution...=2.75),Region:25-575(Identity=96%) PDB:2E4Y Chain:A (X-ray Resolution=3.40), ...

  14. PDB: CBRC-EEUR-01-1356 [SEVENS

    Full Text Available CBRC-EEUR-01-1356 3ODU,3OE0,3OE6,3OE8,3OE9, Region:35-347(Identity=90%) PDB:3ODU Chain:A (X-ray Resolution...=2.5),Region:35-347(Identity=90%) PDB:3OE0 Chain:A (X-ray Resolution=2.9),Region:35-3...53(Identity=90%) PDB:3OE6 Chain:A (X-ray Resolution=3.2),Region:35-347(Identity=90%) PDB:3OE8 Chain:A (X-ray Resolution...=3.1),Region:35-347(Identity=90%) PDB:3OE9 Chain:A (X-ray Resolution=3.1), ...

  15. PDB: CBRC-MLUC-01-0762 [SEVENS

    Full Text Available CBRC-MLUC-01-0762 3ODU,3OE0,3OE6,3OE8,3OE9, Region:3-319(Identity=93%) PDB:3ODU Chain:A (X-ray Resolution...=2.5),Region:3-319(Identity=93%) PDB:3OE0 Chain:A (X-ray Resolution=2.9),Region:3-325(...Identity=93%) PDB:3OE6 Chain:A (X-ray Resolution=3.2),Region:3-319(Identity=93%) PDB:3OE8 Chain:A (X-ray Resolution...=3.1),Region:3-319(Identity=93%) PDB:3OE9 Chain:A (X-ray Resolution=3.1), ...

  16. PDB: CBRC-PTRO-07-0089 [SEVENS

    Full Text Available CBRC-PTRO-07-0089 1EWK,1EWT,1EWV,1ISR,1ISS, Region:33-522(Identity=98%) PDB:1EWK Chain:A (X-ray Resolution...=2.20),Region:33-522(Identity=98%) PDB:1EWT Chain:A (X-ray Resolution=3.70),Region:33...-522(Identity=98%) PDB:1EWV Chain:A (X-ray Resolution=4.00),Region:33-522(Identity=98%) PDB:1ISR Chain:A (X-ray Resolution...=4.00),Region:33-522(Identity=98%) PDB:1ISS Chain:A (X-ray Resolution=3.30), ...

  17. PDB: CBRC-RNOR-01-0027 [SEVENS

    Full Text Available CBRC-RNOR-01-0027 1EWK,1EWT,1EWV,1ISR,1ISS, Region:33-522(Identity=100%) PDB:1EWK Chain:A (X-ray Resolution...=2.20),Region:33-522(Identity=100%) PDB:1EWT Chain:A (X-ray Resolution=3.70),Region:...33-522(Identity=100%) PDB:1EWV Chain:A (X-ray Resolution=4.00),Region:33-522(Identity=100%) PDB:1ISR Chain:A (X-ray Resolution...=4.00),Region:33-522(Identity=100%) PDB:1ISS Chain:A (X-ray Resolution=3.30), ...

  18. Solution structure of human intestinal fatty acid binding protein: Implications for ligand entry and exit

    Zhang Fengli [Boston University School of Medicine, Department of Biophysics (United States); Luecke, Christian [Johann Wolfgang Goethe-Universitaet (Germany); Baier, Leslie J. [NIDDK, NIH, Phoenix Epidemiology and Clinical Research Branch (United States); Sacchettini, James C. [Texas A and M University, Department of Biochemistry and Biophysics (United States); Hamilton, James A. [Boston University School of Medicine, Department of Biophysics (United States)

    1997-04-15

    The human intestinal fatty acid binding protein (I-FABP) is a small (131 amino acids) protein which binds dietary long-chain fatty acids in the cytosol of enterocytes. Recently, an alanine to threonine substitution at position 54 in I-FABP has been identified which affects fatty acid binding and transport, and is associated with the development of insulin resistance in several populations including Mexican-Americans and Pima Indians. To investigate the molecular basis of the binding properties of I-FABP, the 3D solution structure of the more common form of human I-FABP (Ala54) was studied by multidimensional NMR spectroscopy.Recombinant I-FABP was expressed from E. coli in the presence and absence of 15N-enriched media. The sequential assignments for non-delipidated I-FABP were completed by using 2D homonuclear spectra (COSY, TOCSY and NOESY) and 3D heteronuclear spectra(NOESY-HMQC and TOCSY-HMQC). The tertiary structure of human I-FABP was calculated by using the distance geometry program DIANA based on 2519 distance constraints obtained from the NMR data. Subsequent energy minimization was carried out by using the program SYBYL in the presence of distance constraints. The conformation of human I-FABP consists of 10 antiparallel {beta}-strands which form two nearly orthogonal {beta}-sheets of five strands each, and two short {alpha}-helices that connect the {beta}-strands A and B. The interior of the protein consists of a water-filled cavity between the two {beta}-sheets. The NMR solution structure of human I-FABP is similar to the crystal structure of rat I-FABP.The NMR results show significant conformational variability of certain backbone segments around the postulated portal region for the entry and exit of fatty acid ligand.

  19. An Integrated Sequence-Structure Database incorporating matching mRNA sequence, amino acid sequence and protein three-dimensional structure data.

    Adzhubei, I A; Adzhubei, A. A.; Neidle, S.

    1998-01-01

    We have constructed a non-homologous database, termed the Integrated Sequence-Structure Database (ISSD) which comprises the coding sequences of genes, amino acid sequences of the corresponding proteins, their secondary structure and straight phi,psi angles assignments, and polypeptide backbone coordinates. Each protein entry in the database holds the alignment of nucleotide sequence, amino acid sequence and the PDB three-dimensional structure data. The nucleotide and amino acid sequences for ...

  20. PDB: CBRC-RMAC-02-0036 [SEVENS

    Full Text Available C BRC -RMAC -02-0036 1OF2,1OGT,3B3I, Region:400-408(Identity=100%) PDB:1OF2 C hain:C ... (X-ray Resoluti ... on=2.20),Region:400-408(Identity=100%) PDB:1OGT C hain:C ... (X-ray Resolution=1.47),Region:400-408(Ident ... ity=100%) PDB:3B3I C hain:C ... (X-ray Resolution=1.86), ...

  1. PDB: CBRC-PTRO-04-0013 [SEVENS

    Full Text Available C BRC -PTRO-04-0013 1OF2,1OGT,3B3I, Region:401-409(Identity=100%) PDB:1OF2 C hain:C ... (X-ray Resoluti ... on=2.20),Region:401-409(Identity=100%) PDB:1OGT C hain:C ... (X-ray Resolution=1.47),Region:401-409(Ident ... ity=100%) PDB:3B3I C hain:C ... (X-ray Resolution=1.86), ...

  2. PDB: CBRC-TTRU-01-0897 [SEVENS

    Full Text Available C BRC -TTRU-01-0897 1OF2,1OGT,3B3I, Region:408-416(Identity=100%) PDB:1OF2 C hain:C ... (X-ray Resoluti ... on=2.20),Region:408-416(Identity=100%) PDB:1OGT C hain:C ... (X-ray Resolution=1.47),Region:408-416(Ident ... ity=100%) PDB:3B3I C hain:C ... (X-ray Resolution=1.86), ...

  3. PDB: CBRC-GGOR-01-1356 [SEVENS

    Full Text Available C BRC -GGOR-01-1356 1OF2,1OGT,3B3I, Region:417-425(Identity=100%) PDB:1OF2 C hain:C ... (X-ray Resoluti ... on=2.20),Region:417-425(Identity=100%) PDB:1OGT C hain:C ... (X-ray Resolution=1.47),Region:417-425(Ident ... ity=100%) PDB:3B3I C hain:C ... (X-ray Resolution=1.86), ...

  4. PDB: CBRC-BTAU-01-1625 [SEVENS

    Full Text Available C BRC -BTAU-01-1625 1OF2,1OGT,3B3I, Region:401-409(Identity=100%) PDB:1OF2 C hain:C ... (X-ray Resoluti ... on=2.20),Region:401-409(Identity=100%) PDB:1OGT C hain:C ... (X-ray Resolution=1.47),Region:401-409(Ident ... ity=100%) PDB:3B3I C hain:C ... (X-ray Resolution=1.86), ...

  5. PDB: CBRC-MMUS-09-0212 [SEVENS

    Full Text Available C BRC -MMUS-09-0212 1OF2,1OGT,3B3I, Region:402-410(Identity=100%) PDB:1OF2 C hain:C ... (X-ray Resoluti ... on=2.20),Region:402-410(Identity=100%) PDB:1OGT C hain:C ... (X-ray Resolution=1.47),Region:402-410(Ident ... ity=100%) PDB:3B3I C hain:C ... (X-ray Resolution=1.86), ...

  6. PDB: CBRC-MMUR-01-1589 [SEVENS

    Full Text Available C BRC -MMUR-01-1589 1OF2,1OGT,3B3I, Region:367-375(Identity=100%) PDB:1OF2 C hain:C ... (X-ray Resoluti ... on=2.20),Region:367-375(Identity=100%) PDB:1OGT C hain:C ... (X-ray Resolution=1.47),Region:367-375(Ident ... ity=100%) PDB:3B3I C hain:C ... (X-ray Resolution=1.86), ...

  7. PDB: CBRC-HSAP-03-0017 [SEVENS

    Full Text Available C BRC -HSAP-03-0017 1OF2,1OGT,3B3I, Region:400-408(Identity=100%) PDB:1OF2 C hain:C ... (X-ray Resoluti ... on=2.20),Region:400-408(Identity=100%) PDB:1OGT C hain:C ... (X-ray Resolution=1.47),Region:400-408(Ident ... ity=100%) PDB:3B3I C hain:C ... (X-ray Resolution=1.86), ...

  8. PDB: CBRC-CJAC-01-0834 [SEVENS

    Full Text Available C BRC -C JAC -01-0834 1OF2,1OGT,3B3I, Region:400-408(Identity=100%) PDB:1OF2 C hain:C ... (X-ray Resoluti ... on=2.20),Region:400-408(Identity=100%) PDB:1OGT C hain:C ... (X-ray Resolution=1.47),Region:400-408(Ident ... ity=100%) PDB:3B3I C hain:C ... (X-ray Resolution=1.86), ...

  9. PDB: CBRC-PABE-04-0051 [SEVENS

    Full Text Available C BRC -PABE-04-0051 1OF2,1OGT,3B3I, Region:400-408(Identity=100%) PDB:1OF2 C hain:C ... (X-ray Resoluti ... on=2.20),Region:400-408(Identity=100%) PDB:1OGT C hain:C ... (X-ray Resolution=1.47),Region:400-408(Ident ... ity=100%) PDB:3B3I C hain:C ... (X-ray Resolution=1.86), ...

  10. PDB: CBRC-PHAM-01-0319 [SEVENS

    Full Text Available C BRC -PHAM-01-0319 1OF2,1OGT,3B3I, Region:389-397(Identity=100%) PDB:1OF2 C hain:C ... (X-ray Resoluti ... on=2.20),Region:389-397(Identity=100%) PDB:1OGT C hain:C ... (X-ray Resolution=1.47),Region:389-397(Ident ... ity=100%) PDB:3B3I C hain:C ... (X-ray Resolution=1.86), ...

  11. Boronic acid-modified lipid nanocapsules: a novel platform for the highly efficient inhibition of hepatitis C viral entry

    Khanal, Manakamana; Barras, Alexandre; Vausselin, Thibaut; Fénéant, Lucie; Boukherroub, Rabah; Siriwardena, Aloysius; Dubuisson, Jean; Szunerits, Sabine

    2015-01-01

    The search for viral entry inhibitors that selectively target viral envelope glycoproteins has attracted increasing interest in recent years. Amongst the handful of molecules reported to show activity as hepatitis C virus (HCV) entry inhibitors are a variety of glycan-binding proteins including the lectins, cyanovirin-N (CV-N) and griffithsin. We recently demonstrated that boronic acid-modified nanoparticles are able to reduce HCV entry through a similar mechanism to that of lectins. A major obstacle to any further development of these nanostructures as viral entry inhibitors is their only moderate maximal inhibition potential. In the present study, we report that lipid nanocapsules (LNCs), surface-functionalized with amphiphilic boronic acid (BA) through their post-insertion into the semi-rigid shell of the LNCs, are indeed far superior as HCV entry inhibitors when compared with previously reported nanostructures. These 2nd generation particles (BA-LNCs) are shown to prevent HCV infection in the micromolar range (IC50 = 5.4 μM of BA moieties), whereas the corresponding BA monomers show no significant effects even at the highest analyzed concentration (20 μM). The new BA-LNCs are the most promising boronolectin-based HCV entry inhibitors reported to date and are thus observed to show great promise in the development of a pseudolectin-based therapeutic agent.The search for viral entry inhibitors that selectively target viral envelope glycoproteins has attracted increasing interest in recent years. Amongst the handful of molecules reported to show activity as hepatitis C virus (HCV) entry inhibitors are a variety of glycan-binding proteins including the lectins, cyanovirin-N (CV-N) and griffithsin. We recently demonstrated that boronic acid-modified nanoparticles are able to reduce HCV entry through a similar mechanism to that of lectins. A major obstacle to any further development of these nanostructures as viral entry inhibitors is their only moderate maximal

  12. Millisecond Timescale Dynamics of Human Liver Fatty Acid Binding Protein: Testing of Its Relevance to the Ligand Entry Process

    Long, Dong; Yang, Daiwen

    2010-01-01

    For over a decade, scientists have been attempting to know more about the conformational dynamics of fatty acid binding proteins (FABPs), to answer the puzzling question of how ligands could access the internalized binding site(s). Conformational exchange of FABPs on the microsecond to millisecond timescales has been found in many FABPs and offers an important hypothesis for the ligand entry mechanism. Despite the potential significance, the validity of this hypothesis has not been verified y...

  13. Sialic acid-dependent cell entry of human enterovirus D68

    Liu, Yue; Sheng, Ju; Baggen, Jim; Meng, Geng; Xiao, Chuan; Thibaut, Hendrik J; van Kuppeveld, Frank J M; Rossmann, Michael G

    2015-01-01

    Human enterovirus D68 (EV-D68) is a causative agent of childhood respiratory diseases and has now emerged as a global public health threat. Nevertheless, knowledge of the tissue tropism and pathogenesis of EV-D68 has been hindered by a lack of studies on the receptor-mediated EV-D68 entry into host

  14. Improving links between literature and biological data with text mining: a case study with GEO, PDB and MEDLINE.

    Névéol, Aurélie; Wilbur, W John; Lu, Zhiyong

    2012-01-01

    High-throughput experiments and bioinformatics techniques are creating an exploding volume of data that are becoming overwhelming to keep track of for biologists and researchers who need to access, analyze and process existing data. Much of the available data are being deposited in specialized databases, such as the Gene Expression Omnibus (GEO) for microarrays or the Protein Data Bank (PDB) for protein structures and coordinates. Data sets are also being described by their authors in publications archived in literature databases such as MEDLINE and PubMed Central. Currently, the curation of links between biological databases and the literature mainly relies on manual labour, which makes it a time-consuming and daunting task. Herein, we analysed the current state of link curation between GEO, PDB and MEDLINE. We found that the link curation is heterogeneous depending on the sources and databases involved, and that overlap between sources is low, mining tools can automatically provide valuable evidence to help curators broaden the scope of articles and database entries that they review. As a result, we made recommendations to improve the coverage of curated links, as well as the consistency of information available from different databases while maintaining high-quality curation. Database URLs: http://www.ncbi.nlm.nih.gov/PubMed, http://www.ncbi.nlm.nih.gov/geo/, http://www.rcsb.org/pdb/ PMID:22685160

  15. PDB: CBRC-GGOR-01-1431 [SEVENS

    Full Text Available CBRC-GGOR-01-1431 2PED,3C9L,3CAP,1EDX,1F88,3DQB,1GZM,1HZX,1JFP,1L9H,1LN6,1U19,2G87,2HPY,2I35,2I3 ... M,1RY1,1EDS,1EDV,1EDW,1FDF,1NZS,1VQX, Region:1-348(Identity =93%) PDB:2PED Chain:A (X-ray Resolution=2.95),Regi ... on:1-348(Identity =93%) PDB:3C9L Chain:A (X-ray Resolution=2.65),Regi ...

  16. PDB: CBRC-OANA-01-1800 [SEVENS

    Full Text Available CBRC-OANA-01-1800 2I37,2PED,3C9L,3CAP,1EDX,1F88,3DQB,1GZM,1HZX,1JFP,1L9H,1LN6,1U19,2G87,2HPY,2I3 ... Y,1RY1,1EDS,1EDV,1EDW,1FDF,1NZS,1VQX, Region:1-353(Identity =89%) PDB:2I37 Chain:A (X-ray Resolution=4.15),Regi ... on:1-353(Identity =89%) PDB:2PED Chain:A (X-ray Resolution=2.95),Regi ...

  17. PDB: CBRC-PVAM-01-0804 [SEVENS

    Full Text Available CBRC-PVAM-01-0804 2PED,3C9L,3CAP,1EDX,1F88,3DQB,1GZM,1HZX,1JFP,1L9H,1LN6,1U19,2G87,2HPY,2I35,2I3 ... M,1RY1,1EDS,1EDV,1EDW,1FDF,1NZS,1VQX, Region:1-348(Identity =94%) PDB:2PED Chain:A (X-ray Resolution=2.95),Regi ... on:1-348(Identity =94%) PDB:3C9L Chain:A (X-ray Resolution=2.65),Regi ...

  18. PDB: CBRC-TTRU-01-1321 [SEVENS

    Full Text Available CBRC-TTRU-01-1321 2I37,2PED,3C9L,3CAP,1EDX,1F88,3DQB,1GZM,1HZX,1JFP,1L9H,1LN6,1U19,2G87,2HPY,2I3 ... Y,1RY1,1EDS,1EDV,1EDW,1FDF,1NZS,1VQX, Region:1-348(Identity =92%) PDB:2I37 Chain:A (X-ray Resolution=4.15),Regi ... on:1-348(Identity =92%) PDB:2PED Chain:A (X-ray Resolution=2.95),Regi ...

  19. PDB: CBRC-RMAC-11-0073 [SEVENS

    Full Text Available CBRC-RMAC-11-0073 2PED,3C9L,3CAP,1EDX,1F88,3DQB,1GZM,1HZX,1JFP,1L9H,1LN6,1U19,2G87,2HPY,2I35,2I3 ... M,1RY1,1EDS,1EDV,1EDW,1FDF,1NZS,1VQX, Region:1-348(Identity =93%) PDB:2PED Chain:A (X-ray Resolution=2.95),Regi ... on:1-348(Identity =93%) PDB:3C9L Chain:A (X-ray Resolution=2.65),Regi ...

  20. PDB: CBRC-RNOR-04-0298 [SEVENS

    Full Text Available CBRC-RNOR-04-0298 2PED,3C9L,3CAP,1EDX,1F88,3DQB,1GZM,1HZX,1JFP,1L9H,1LN6,1U19,2G87,2HPY,2I35,2I3 ... M,1RY1,1EDS,1EDV,1EDW,1FDF,1NZS,1VQX, Region:1-348(Identity =93%) PDB:2PED Chain:A (X-ray Resolution=2.95),Regi ... on:1-348(Identity =93%) PDB:3C9L Chain:A (X-ray Resolution=2.65),Regi ...

  1. PDB: CBRC-CPOR-01-1479 [SEVENS

    Full Text Available CBRC-CPOR-01-1479 2I37,2PED,3C9L,3CAP,1EDX,1F88,3DQB,1GZM,1HZX,1JFP,1L9H,1LN6,1U19,2G87,2HPY,2I3 ... Y,1RY1,1EDS,1EDV,1EDW,1FDF,1NZS,1VQX, Region:1-354(Identity =88%) PDB:2I37 Chain:A (X-ray Resolution=4.15),Regi ... on:1-354(Identity =88%) PDB:2PED Chain:A (X-ray Resolution=2.95),Regi ...

  2. PDB: CBRC-PTRO-04-0067 [SEVENS

    Full Text Available CBRC-PTRO-04-0067 2PED,3C9L,3CAP,1EDX,1F88,3DQB,1GZM,1HZX,1JFP,1L9H,1LN6,1U19,2G87,2HPY,2I35,2I3 ... M,1RY1,1EDS,1EDV,1EDW,1FDF,1NZS,1VQX, Region:1-348(Identity =93%) PDB:2PED Chain:A (X-ray Resolution=2.95),Regi ... on:1-348(Identity =93%) PDB:3C9L Chain:A (X-ray Resolution=2.65),Regi ...

  3. PDB: CBRC-HSAP-03-0075 [SEVENS

    Full Text Available CBRC-HSAP-03-0075 2PED,3C9L,3CAP,1EDX,1F88,3DQB,1GZM,1HZX,1JFP,1L9H,1LN6,1U19,2G87,2HPY,2I35,2I3 ... M,1RY1,1EDS,1EDV,1EDW,1FDF,1NZS,1VQX, Region:1-348(Identity =93%) PDB:2PED Chain:A (X-ray Resolution=2.95),Regi ... on:1-348(Identity =93%) PDB:3C9L Chain:A (X-ray Resolution=2.65),Regi ...

  4. PDB: CBRC-MMUS-06-0155 [SEVENS

    Full Text Available CBRC-MMUS-06-0155 2PED,3C9L,3CAP,1EDX,1F88,3DQB,1GZM,1HZX,1JFP,1L9H,1LN6,1U19,2G87,2HPY,2I35,2I3 ... M,1RY1,1EDS,1EDV,1EDW,1FDF,1NZS,1VQX, Region:1-348(Identity =93%) PDB:2PED Chain:A (X-ray Resolution=2.95),Regi ... on:1-348(Identity =93%) PDB:3C9L Chain:A (X-ray Resolution=2.65),Regi ...

  5. PDB: CBRC-MDOM-06-0154 [SEVENS

    Full Text Available CBRC-MDOM-06-0154 2PED,3C9L,3CAP,1EDX,1F88,3DQB,1GZM,1HZX,1JFP,1L9H,1LN6,1U19,2G87,2HPY,2I35,2I3 ... M,1RY1,1EDS,1EDV,1EDW,1FDF,1NZS,1VQX, Region:1-348(Identity =93%) PDB:2PED Chain:A (X-ray Resolution=2.95),Regi ... on:1-348(Identity =93%) PDB:3C9L Chain:A (X-ray Resolution=2.65),Regi ...

  6. PDB: CBRC-PABE-04-0004 [SEVENS

    Full Text Available CBRC-PABE-04-0004 2PED,3C9L,3CAP,1EDX,1F88,3DQB,1GZM,1HZX,1JFP,1L9H,1LN6,1U19,2G87,2HPY,2I35,2I3 ... M,1RY1,1EDS,1EDV,1EDW,1FDF,1NZS,1VQX, Region:1-348(Identity =93%) PDB:2PED Chain:A (X-ray Resolution=2.95),Regi ... on:1-348(Identity =93%) PDB:3C9L Chain:A (X-ray Resolution=2.65),Regi ...

  7. PDB: CBRC-CFAM-20-0004 [SEVENS

    Full Text Available CBRC-CFAM-20-0004 2PED,3C9L,3CAP,1EDX,1F88,3DQB,1GZM,1HZX,1JFP,1L9H,1LN6,1U19,2G87,2HPY,2I35,2I3 ... M,1RY1,1EDS,1EDV,1EDW,1FDF,1NZS,1VQX, Region:1-348(Identity =94%) PDB:2PED Chain:A (X-ray Resolution=2.95),Regi ... on:1-348(Identity =94%) PDB:3C9L Chain:A (X-ray Resolution=2.65),Regi ...

  8. PDB: CBRC-BTAU-01-2416 [SEVENS

    Full Text Available CBRC-BTAU-01-2416 2PED,3C9L,3CAP,1EDX,1F88,3DQB,1GZM,1HZX,1JFP,1L9H,1LN6,1U19,2G87,2HPY,2I35,2I3 ... M,1RY1,1EDS,1EDV,1EDW,1FDF,1NZS,1VQX, Region:1-348(Identity =100%) PDB:2PED Chain:A (X-ray Resolution=2.95),Reg ... ion:1-348(Identity =100%) PDB:3C9L Chain:A (X-ray Resolution=2.65),Reg ...

  9. PDB: CBRC-FCAT-01-1134 [SEVENS

    Full Text Available CBRC-FCAT-01-1134 2PED,3C9L,3CAP,1EDX,1F88,3DQB,1GZM,1HZX,1JFP,1L9H,1LN6,1U19,2G87,2HPY,2I35,2I3 ... M,1RY1,1EDS,1EDV,1EDW,1FDF,1NZS,1VQX, Region:1-348(Identity =95%) PDB:2PED Chain:A (X-ray Resolution=2.95),Regi ... on:1-348(Identity =95%) PDB:3C9L Chain:A (X-ray Resolution=2.65),Regi ...

  10. PDB: CBRC-PHAM-01-1599 [SEVENS

    Full Text Available CBRC-PHAM-01-1599 2PED,3C9L,3CAP,1EDX,1F88,3DQB,1GZM,1HZX,1JFP,1L9H,1LN6,1U19,2G87,2HPY,2I35,2I3 ... M,1RY1,1EDS,1EDV,1EDW,1FDF,1NZS,1VQX, Region:1-348(Identity =93%) PDB:2PED Chain:A (X-ray Resolution=2.95),Regi ... on:1-348(Identity =93%) PDB:3C9L Chain:A (X-ray Resolution=2.65),Regi ...

  11. PDB: CBRC-OPRI-01-1186 [SEVENS

    Full Text Available CBRC-OPRI-01-1186 2PED,3C9L,3CAP,1EDX,1F88,3DQB,1GZM,1HZX,1JFP,1L9H,1LN6,1U19,2G87,2HPY,2I35,2I3 ... M,1RY1,1EDS,1EDV,1EDW,1FDF,1NZS,1VQX, Region:1-348(Identity =91%) PDB:2PED Chain:A (X-ray Resolution=2.95),Regi ... on:1-348(Identity =91%) PDB:3C9L Chain:A (X-ray Resolution=2.65),Regi ...

  12. Continuous mutual improvement of macromolecular structure models in the PDB and of X-ray crystallographic software: the dual role of deposited experimental data

    Terwilliger, Thomas C., E-mail: terwilliger@lanl.gov [Los Alamos National Laboratory, Mail Stop M888, Los Alamos, NM 87507 (United States); Bricogne, Gerard, E-mail: terwilliger@lanl.gov [Global Phasing Ltd, Sheraton House, Castle Park, Cambridge CB3 0AX (United Kingdom); Los Alamos National Laboratory, Mail Stop M888, Los Alamos, NM 87507 (United States)

    2014-10-01

    Macromolecular structures deposited in the PDB can and should be continually reinterpreted and improved on the basis of their accompanying experimental X-ray data, exploiting the steady progress in methods and software that the deposition of such data into the PDB on a massive scale has made possible. Accurate crystal structures of macromolecules are of high importance in the biological and biomedical fields. Models of crystal structures in the Protein Data Bank (PDB) are in general of very high quality as deposited. However, methods for obtaining the best model of a macromolecular structure from a given set of experimental X-ray data continue to progress at a rapid pace, making it possible to improve most PDB entries after their deposition by re-analyzing the original deposited data with more recent software. This possibility represents a very significant departure from the situation that prevailed when the PDB was created, when it was envisioned as a cumulative repository of static contents. A radical paradigm shift for the PDB is therefore proposed, away from the static archive model towards a much more dynamic body of continuously improving results in symbiosis with continuously improving methods and software. These simultaneous improvements in methods and final results are made possible by the current deposition of processed crystallographic data (structure-factor amplitudes) and will be supported further by the deposition of raw data (diffraction images). It is argued that it is both desirable and feasible to carry out small-scale and large-scale efforts to make this paradigm shift a reality. Small-scale efforts would focus on optimizing structures that are of interest to specific investigators. Large-scale efforts would undertake a systematic re-optimization of all of the structures in the PDB, or alternatively the redetermination of groups of structures that are either related to or focused on specific questions. All of the resulting structures should be

  13. Continuous mutual improvement of macromolecular structure models in the PDB and of X-ray crystallographic software: the dual role of deposited experimental data

    Macromolecular structures deposited in the PDB can and should be continually reinterpreted and improved on the basis of their accompanying experimental X-ray data, exploiting the steady progress in methods and software that the deposition of such data into the PDB on a massive scale has made possible. Accurate crystal structures of macromolecules are of high importance in the biological and biomedical fields. Models of crystal structures in the Protein Data Bank (PDB) are in general of very high quality as deposited. However, methods for obtaining the best model of a macromolecular structure from a given set of experimental X-ray data continue to progress at a rapid pace, making it possible to improve most PDB entries after their deposition by re-analyzing the original deposited data with more recent software. This possibility represents a very significant departure from the situation that prevailed when the PDB was created, when it was envisioned as a cumulative repository of static contents. A radical paradigm shift for the PDB is therefore proposed, away from the static archive model towards a much more dynamic body of continuously improving results in symbiosis with continuously improving methods and software. These simultaneous improvements in methods and final results are made possible by the current deposition of processed crystallographic data (structure-factor amplitudes) and will be supported further by the deposition of raw data (diffraction images). It is argued that it is both desirable and feasible to carry out small-scale and large-scale efforts to make this paradigm shift a reality. Small-scale efforts would focus on optimizing structures that are of interest to specific investigators. Large-scale efforts would undertake a systematic re-optimization of all of the structures in the PDB, or alternatively the redetermination of groups of structures that are either related to or focused on specific questions. All of the resulting structures should be

  14. soaPDB: a web application for searching the Protein Data Bank, organizing results, and receiving automatic email alerts

    Lesburg, Charles A.; Duca, José S.

    2008-01-01

    soaPDB is a web application that allows generation and organization of saved PDB searches, and offers automatic email alerts. This tool is used from a web interface to store PDB searches and results in a backend relational database. Written using the Ruby on Rails open-source web framework, soaPDB is easy to deploy, maintain and customize. soaPDB is freely available upon request for local installation and is also available at http://soapdb.dyndns.org:3000.

  15. All-trans retinoic acid promotes neural lineage entry by pluripotent embryonic stem cells via multiple pathways

    Fang Bo

    2009-07-01

    Full Text Available Abstract Background All-trans retinoic acid (RA is one of the most important morphogens with pleiotropic actions. Its embryonic distribution correlates with neural differentiation in the developing central nervous system. To explore the precise effects of RA on neural differentiation of mouse embryonic stem cells (ESCs, we detected expression of RA nuclear receptors and RA-metabolizing enzymes in mouse ESCs and investigated the roles of RA in adherent monolayer culture. Results Upon addition of RA, cell differentiation was directed rapidly and exclusively into the neural lineage. Conversely, pharmacological interference with RA signaling suppressed this neural differentiation. Inhibition of fibroblast growth factor (FGF signaling did not suppress significantly neural differentiation in RA-treated cultures. Pharmacological interference with extracellular signal-regulated kinase (ERK pathway or activation of Wnt pathway effectively blocked the RA-promoted neural specification. ERK phosphorylation was enhanced in RA-treated cultures at the early stage of differentiation. Conclusion RA can promote neural lineage entry by ESCs in adherent monolayer culture systems. This effect depends on RA signaling and its crosstalk with the ERK and Wnt pathways.

  16. Drug Promiscuity in PDB: Protein Binding Site Similarity Is Key.

    V Joachim Haupt

    Full Text Available Drug repositioning applies established drugs to new disease indications with increasing success. A pre-requisite for drug repurposing is drug promiscuity (polypharmacology - a drug's ability to bind to several targets. There is a long standing debate on the reasons for drug promiscuity. Based on large compound screens, hydrophobicity and molecular weight have been suggested as key reasons. However, the results are sometimes contradictory and leave space for further analysis. Protein structures offer a structural dimension to explain promiscuity: Can a drug bind multiple targets because the drug is flexible or because the targets are structurally similar or even share similar binding sites? We present a systematic study of drug promiscuity based on structural data of PDB target proteins with a set of 164 promiscuous drugs. We show that there is no correlation between the degree of promiscuity and ligand properties such as hydrophobicity or molecular weight but a weak correlation to conformational flexibility. However, we do find a correlation between promiscuity and structural similarity as well as binding site similarity of protein targets. In particular, 71% of the drugs have at least two targets with similar binding sites. In order to overcome issues in detection of remotely similar binding sites, we employed a score for binding site similarity: LigandRMSD measures the similarity of the aligned ligands and uncovers remote local similarities in proteins. It can be applied to arbitrary structural binding site alignments. Three representative examples, namely the anti-cancer drug methotrexate, the natural product quercetin and the anti-diabetic drug acarbose are discussed in detail. Our findings suggest that global structural and binding site similarity play a more important role to explain the observed drug promiscuity in the PDB than physicochemical drug properties like hydrophobicity or molecular weight. Additionally, we find ligand

  17. Hydrolyzable Tannins (Chebulagic Acid and Punicalagin) Target Viral Glycoprotein-Glycosaminoglycan Interactions To Inhibit Herpes Simplex Virus 1 Entry and Cell-to-Cell Spread▿

    Lin, Liang-Tzung; Chen, Ting-Ying; Chung, Chueh-Yao; Noyce, Ryan S.; Grindley, T. Bruce; McCormick, Craig; Lin, Ta-Chen; Wang, Guey-Horng; Lin, Chun-Ching; Richardson, Christopher D.

    2011-01-01

    Herpes simplex virus 1 (HSV-1) is a common human pathogen that causes lifelong latent infection of sensory neurons. Non-nucleoside inhibitors that can limit HSV-1 recurrence are particularly useful in treating immunocompromised individuals or cases of emerging acyclovir-resistant strains of herpesvirus. We report that chebulagic acid (CHLA) and punicalagin (PUG), two hydrolyzable tannins isolated from the dried fruits of Terminalia chebula Retz. (Combretaceae), inhibit HSV-1 entry at noncytot...

  18. Design, synthesis and biological evaluation of novel L-ascorbic acid-conjugated pentacyclic triterpene derivatives as potential influenza virus entry inhibitors.

    Wang, Han; Xu, Renyang; Shi, Yongying; Si, Longlong; Jiao, Pingxuan; Fan, Zibo; Han, Xu; Wu, Xingyu; Zhou, Xiaoshu; Yu, Fei; Zhang, Yongmin; Zhang, Liangren; Zhang, Lihe; Zhou, Demin; Xiao, Sulong

    2016-03-01

    Since the influenza viruses can rapidly evolve, it is urgently required to develop novel anti-influenza agents possessing a novel mechanism of action. In our previous study, two pentacyclic triterpene derivatives (Q8 and Y3) have been found to have anti-influenza virus entry activities. Keeping the potential synergy of biological activity of pentacyclic triterpenes and l-ascorbic acid in mind, we synthesized a series of novel l-ascorbic acid-conjugated pentacyclic triterpene derivatives (18-26, 29-31, 35-40 and 42-43). Moreover, we evaluated these novel compounds for their anti-influenza activities against A/WSN/33 virus in MDCK cells. Among all evaluated compounds, the 2,3-O,O-dibenzyl-6-deoxy-l-ascorbic acid-betulinic acid conjugate (30) showed the most significant anti-influenza activity with an EC50 of 8.7 μM, and no cytotoxic effects on MDCK cells were observed. Time-of-addition assay indicated that compound 30 acted at an early stage of the influenza life cycle. Further analyses revealed that influenza virus-induced hemagglutination of chicken red blood cells was inhibited by treatment of compound 30, and the interaction between the influenza hemagglutinin (HA) and compound 30 was determined by surface plasmon resonance (SPR) with a dissociation constant of KD = 3.76 μM. Finally, silico docking studies indicated that compound 30 and its derivative 31 were able to occupy the binding pocket of HA for sialic acid receptor. Collectively, these results suggested that l-ascorbic acid-conjugated pentacyclic triterpenes were promising anti-influenza entry inhibitors, and HA protein associated with viral entry was a promising drug target. PMID:26866456

  19. Structural and functional studies of a phosphatidic acid-binding antifungal plant defensin MtDef4: Identification of an RGFRRR motif governing fungal cell entry

    Sagaram, Uma S.; El-Mounadi, Kaoutar; Buchko, Garry W.; Berg, Howard R.; Kaur, Jagdeep; Pandurangi, Raghoottama; Smith, Thomas J.; Shah, Dilip

    2013-12-04

    A highly conserved plant defensin MtDef4 potently inhibits the growth of a filamentous fungus Fusarium graminearum. MtDef4 is internalized by cells of F. graminearum. To determine its mechanism of fungal cell entry and antifungal action, NMR solution structure of MtDef4 has been determined. The analysis of its structure has revealed a positively charged patch on the surface of the protein consisting of arginine residues in its γ-core signature, a major determinant of the antifungal activity of MtDef4. Here, we report functional analysis of the RGFRRR motif of the γ-core signature of MtDef4. The replacement of RGFRRR to AAAARR or to RGFRAA not only abolishes fungal cell entry but also results in loss of the antifungal activity of MtDef4. MtDef4 binds strongly to phosphatidic acid (PA), a precursor for the biosynthesis of membrane phospholipids and a signaling lipid known to recruit cytosolic proteins to membranes. Mutations of RGFRRR which abolish fungal cell entry of MtDef4 also impair its binding to PA. Our results suggest that RGFRRR motif is a translocation signal for entry of MtDef4 into fungal cells and that this positively charged motif likely mediates interaction of this defensin with PA as part of its antifungal action.

  20. PDB_REDO: constructive validation, more than just looking for errors

    Joosten, Robbie P.; Joosten, Krista; Murshudov, Garib N.; Perrakis, Anastassis

    2012-01-01

    Developments of the PDB_REDO procedure that combine re-refinement and rebuilding within a unique decision-making framework to improve structures in the PDB are presented. PDB_REDO uses a variety of existing and custom-built software modules to choose an optimal refinement protocol (e.g. anisotropic, isotropic or overall B-factor refinement, TLS model) and to optimize the geometry versus data-refinement weights. Next, it proceeds to rebuild side chains and peptide planes before a final optimiz...

  1. soaPDB: a web application for searching the Protein Data Bank, organizing results, and receiving automatic email alerts.

    Lesburg, Charles A; Duca, José S

    2008-07-01

    soaPDB is a web application that allows generation and organization of saved PDB searches, and offers automatic email alerts. This tool is used from a web interface to store PDB searches and results in a backend relational database. Written using the Ruby on Rails open-source web framework, soaPDB is easy to deploy, maintain and customize. soaPDB is freely available upon request for local installation and is also available at http://soapdb.dyndns.org:3000. PMID:18487276

  2. Structure-activity relationships of 3-O-β-chacotriosyl ursolic acid derivatives as novel H5N1 entry inhibitors.

    Song, Gaopeng; Shen, Xintian; Li, Sumei; Li, Yibin; Liu, Yunpeng; Zheng, Yushan; Lin, Ruheng; Fan, Jihong; Ye, Hanming; Liu, Shuwen

    2015-03-26

    A series of methyl ursolate 3-O-β-chacotrioside analogs have been designed, synthesized and evaluated as H5N1 entry inhibitors based on a small molecule inhibitor saponin 3 previously discovered by us. Detailed structure-activity relationships (SARs) studies on the aglycone of compound 3 indicated that both the type of pentacyclic triterpene and the subtle modification of ursolic acid as an aglycon had key influences on the antiviral activity. These results suggested that either the introduction of a disubstituted amide structure at the 17-COOH of ursolic acid or alteration of the C-3 configuration of ursolic acid from 3β-to 3α-forms was helpful to significantly improve the selective index while keeping their antiviral activities. PMID:25728024

  3. Web servers and services for electrostatics calculations with APBS and PDB2PQR

    Unni, Samir; Huang, Yong; Hanson, Robert; Tobias, Malcolm; Krishnan, Sriram; Li, Wilfred W.; Nielsen, Jens E.; Baker, Nathan A.

    2011-01-01

    APBS and PDB2PQR are widely utilized free software packages for biomolecular electrostatics calculations. Using the Opal toolkit, we have developed a Web services framework for these software packages that enables the use of APBS and PDB2PQR by users who do not have local access to the necessary amount of computational capabilities. This not only increases accessibility of the software to a wider range of scientists, educators, and students but it also increases the availability of electrosta...

  4. Primary Biliary Acids Inhibit Hepatitis D Virus (HDV) Entry into Human Hepatoma Cells Expressing the Sodium-Taurocholate Cotransporting Polypeptide (NTCP)

    Veloso Alves Pereira, Isabel; Buchmann, Bettina; Sandmann, Lisa; Sprinzl, Kathrin; Schlaphoff, Verena; Döhner, Katinka; Vondran, Florian; Sarrazin, Christoph; Manns, Michael P.; Pinto Marques Souza de Oliveira, Cláudia; Sodeik, Beate; Ciesek, Sandra; von Hahn, Thomas

    2015-01-01

    Background The sodium-taurocholate cotransporting polypeptide (NTCP) is both a key bile acid (BA) transporter mediating uptake of BA into hepatocytes and an essential receptor for hepatitis B virus (HBV) and hepatitis D virus (HDV). In this study we aimed to characterize to what extent and through what mechanism BA affect HDV cell entry. Methods HuH-7 cells stably expressing NTCP (HuH-7/NTCP) and primary human hepatocytes (PHH) were infected with in vitro generated HDV particles. Infectivity in the absence or presence of compounds was assessed using immunofluorescence staining for HDV antigen, standard 50% tissue culture infectious dose (TCID50) assays and quantitative PCR. Results Addition of primary conjugated and unconjugated BA resulted in a dose dependent reduction in the number of infected cells while secondary, tertiary and synthetic BA had a lesser effect. This effect was observed both in HuH-7/NTCP and in PHH. Other replication cycle steps such as replication and particle assembly and release were unaffected. Moreover, inhibitory BA competed with a fragment from the large HBV envelope protein for binding to NTCP-expressing cells. Conversely, the sodium/BA-cotransporter function of NTCP seemed not to be required for HDV infection since infection was similar in the presence or absence of a sodium gradient across the plasma membrane. When chenodeoxycolic acid (15 mg per kg body weight) was administered to three chronically HDV infected individuals over a period of up to 16 days there was no change in serum HDV RNA. Conclusions Primary BA inhibit NTCP-mediated HDV entry into hepatocytes suggesting that modulation of the BA pool may affect HDV infection of hepatocytes. PMID:25646622

  5. Web servers and services for electrostatics calculations with APBS and PDB2PQR.

    Unni, Samir; Huang, Yong; Hanson, Robert M; Tobias, Malcolm; Krishnan, Sriram; Li, Wilfred W; Nielsen, Jens E; Baker, Nathan A

    2011-05-01

    APBS and PDB2PQR are widely utilized free software packages for biomolecular electrostatics calculations. Using the Opal toolkit, we have developed a Web services framework for these software packages that enables the use of APBS and PDB2PQR by users who do not have local access to the necessary amount of computational capabilities. This not only increases accessibility of the software to a wider range of scientists, educators, and students but also increases the availability of electrostatics calculations on portable computing platforms. Users can access this new functionality in two ways. First, an Opal-enabled version of APBS is provided in current distributions, available freely on the web. Second, we have extended the PDB2PQR web server to provide an interface for the setup, execution, and visualization of electrostatic potentials as calculated by APBS. This web interface also uses the Opal framework which ensures the scalability needed to support the large APBS user community. Both of these resources are available from the APBS/PDB2PQR website: http://www.poissonboltzmann.org/. PMID:21425296

  6. Expression of Vibrio harveyi Acyl-ACP Synthetase Allows Efficient Entry of Exogenous Fatty Acids into the Escherichia coli Fatty Acid and Lipid A Synthetic Pathways

    Jiang, Yanfang; Morgan-Kiss, Rachael M.; Campbell, John W.; Chan, Chi Ho; Cronan, John E.

    2010-01-01

    Although the Escherichia coli fatty acid synthesis (FAS) pathway is the best studied type II fatty acid synthesis system, a major experimental limitation has been the inability to feed intermediates into the pathway in vivo because exogenously-supplied free fatty acids are not efficiently converted to the acyl-acyl carrier protein (ACP) thioesters required by the pathway. We report that expression of Vibrio harveyi acyl-ACP synthetase (AasS), a soluble cytosolic enzyme that ligates free fatty acids to ACP to form acyl-ACPs, allows exogenous fatty acids to enter the E. coli fatty acid synthesis pathway. The free fatty acids are incorporated intact and can be elongated or directly incorporated into complex lipids by acyltransferases specific for acyl-ACPs. Moreover, expression of AasS strains and supplementation with the appropriate fatty acid restored growth to E. coli mutant strains that lack essential fatty acid synthesis enzymes. Thus, this strategy provides a new tool for circumventing the loss of enzymes essential for FAS function. PMID:20028080

  7. Comparison of temporal trends in VOCs as measured with PDB samplers and low-flow sampling methods

    Harte, P.T.

    2002-01-01

    Analysis of temporal trends in tetrachloroethylene (PCE) concentration determined by two sample techniques showed that passive diffusion bag (pdb) samplers adequately sample the large variation in PCE concentrations at the site. The slopes of the temporal trends in concentrations were comparable between the two techniques, and the pdb sample concentration generally reflected the instantaneous concentration sampled by the low-flow technique. Thus, the pdb samplers provided an appropriate sampling technique for PCE at these wells. One or two wells did not make the case for widespread application of pdb samples at all sites. However, application of pdb samples in some circumstances was appropriate for evaluating temporal and spatial variations in VOC concentrations, thus, should be considered as a useful tool in hydrogeology.

  8. LIBP-Pred: web server for lipid binding proteins using structural network parameters; PDB mining of human cancer biomarkers and drug targets in parasites and bacteria.

    González-Díaz, Humberto; Munteanu, Cristian R; Postelnicu, Lucian; Prado-Prado, Francisco; Gestal, Marcos; Pazos, Alejandro

    2012-03-01

    Lipid-Binding Proteins (LIBPs) or Fatty Acid-Binding Proteins (FABPs) play an important role in many diseases such as different types of cancer, kidney injury, atherosclerosis, diabetes, intestinal ischemia and parasitic infections. Thus, the computational methods that can predict LIBPs based on 3D structure parameters became a goal of major importance for drug-target discovery, vaccine design and biomarker selection. In addition, the Protein Data Bank (PDB) contains 3000+ protein 3D structures with unknown function. This list, as well as new experimental outcomes in proteomics research, is a very interesting source to discover relevant proteins, including LIBPs. However, to the best of our knowledge, there are no general models to predict new LIBPs based on 3D structures. We developed new Quantitative Structure-Activity Relationship (QSAR) models based on 3D electrostatic parameters of 1801 different proteins, including 801 LIBPs. We calculated these electrostatic parameters with the MARCH-INSIDE software and they correspond to the entire protein or to specific protein regions named core, inner, middle, and surface. We used these parameters as inputs to develop a simple Linear Discriminant Analysis (LDA) classifier to discriminate 3D structure of LIBPs from other proteins. We implemented this predictor in the web server named LIBP-Pred, freely available at , along with other important web servers of the Bio-AIMS portal. The users can carry out an automatic retrieval of protein structures from PDB or upload their custom protein structural models from their disk created with LOMETS server. We demonstrated the PDB mining option performing a predictive study of 2000+ proteins with unknown function. Interesting results regarding the discovery of new Cancer Biomarkers in humans or drug targets in parasites have been discussed here in this sense. PMID:22234525

  9. The PDB database is a rich source of alpha-helical anti-microbial peptides to combat disease causing pathogens.

    Chakraborty, Sandeep; Phu, My; de Morais, Tâmara Prado; Nascimento, Rafael; Goulart, Luiz Ricardo; Rao, Basuthkar J; Asgeirsson, Bjarni; Dandekar, Abhaya M

    2014-01-01

    The therapeutic potential of α-helical anti-microbial peptides (AH-AMP) to combat pathogens is fast gaining prominence. Based on recently published open access software for characterizing α-helical peptides (PAGAL), we elucidate a search methodology (SCALPEL) that leverages the massive structural data pre-existing in the PDB database to obtain AH-AMPs belonging to the host proteome. We provide in vitro validation of SCALPEL on plant pathogens ( Xylella fastidiosa, Xanthomonas arboricola and Liberibacter crescens) by identifying AH-AMPs that mirror the function and properties of cecropin B, a well-studied AH-AMP. The identified peptides include a linear AH-AMP present within the existing structure of phosphoenolpyruvate carboxylase (PPC20), and an AH-AMP mimicing the properties of the two α-helices of cecropin B from chitinase (CHITI25). The minimum inhibitory concentration of these peptides are comparable to that of cecropin B, while anionic peptides used as control failed to show any inhibitory effect on these pathogens. Substitute therapies in place of conventional chemotherapies using membrane permeabilizing peptides like these might also prove effective to target cancer cells. The use of native structures from the same organism could possibly ensure that administration of such peptides will be better tolerated and not elicit an adverse immune response. We suggest a similar approach to target Ebola epitopes, enumerated using PAGAL recently, by selecting suitable peptides from the human proteome, especially in wake of recent reports of cationic amphiphiles inhibiting virus entry and infection. PMID:26629331

  10. Defining and searching for structural motifs using DeepView/Swiss-PdbViewer

    Johansson Maria U; Zoete Vincent; Michielin Olivier; Guex Nicolas

    2012-01-01

    Abstract Background Today, recognition and classification of sequence motifs and protein folds is a mature field, thanks to the availability of numerous comprehensive and easy to use software packages and web-based services. Recognition of structural motifs, by comparison, is less well developed and much less frequently used, possibly due to a lack of easily accessible and easy to use software. Results In this paper, we describe an extension of DeepView/Swiss-PdbViewer through which structura...

  11. Chemical modification of B4C cap layers on Pd/B4C multilayers

    Supruangnet, Ratchadaporn; Morawe, Christian; Peffen, Jean-Christophe; Nakajima, Hideki; Rattanasuporn, Surachet; Photongkam, Pat; Jearanaikoon, Nichada; Busayaporn, Wutthikri

    2016-03-01

    Chemical modifications of B4C cap layers on sputtered Pd/B4C multilayer coatings for X-ray optical applications were investigated using X-ray reflectivity, photoemission electron spectroscopy, photoemission electron microscopy, transmission electron microscopy, energy dispersive X-ray spectroscopy, and infrared spectroscopy. The results indicate oxidation down to probing depths of about 10 nm and strong evidence for the formation of B2O3 crystals at the sample surface, while B4C like compounds are absent.

  12. High-resolution structure of the M14-type cytosolic carboxypeptidase from Burkholderia cenocepacia refined exploiting PDB-REDO strategies

    Rimsa, Vadim; Eadsforth, Thomas C. [University of Dundee, Dundee DD1 5EH, Scotland (United Kingdom); Joosten, Robbie P. [Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam (Netherlands); Hunter, William N., E-mail: w.n.hunter@dundee.ac.uk [University of Dundee, Dundee DD1 5EH, Scotland (United Kingdom)

    2014-02-01

    The structure of a bacterial M14-family carboxypeptidase determined exploiting microfocus synchrotron radiation and highly automated refinement protocols reveals its potential to act as a polyglutamylase. A potential cytosolic metallocarboxypeptidase from Burkholderia cenocepacia has been crystallized and a synchrotron-radiation microfocus beamline allowed the acquisition of diffraction data to 1.9 Å resolution. The asymmetric unit comprises a tetramer containing over 1500 amino acids, and the high-throughput automated protocols embedded in PDB-REDO were coupled with model–map inspections in refinement. This approach has highlighted the value of such protocols for efficient analyses. The subunit is constructed from two domains. The N-terminal domain has previously only been observed in cytosolic carboxypeptidase (CCP) proteins. The C-terminal domain, which carries the Zn{sup 2+}-containing active site, serves to classify this protein as a member of the M14D subfamily of carboxypeptidases. Although eukaryotic CCPs possess deglutamylase activity and are implicated in processing modified tubulin, the function and substrates of the bacterial family members remain unknown. The B. cenocepacia protein did not display deglutamylase activity towards a furylacryloyl glutamate derivative, a potential substrate. Residues previously shown to coordinate the divalent cation and that contribute to peptide-bond cleavage in related enzymes such as bovine carboxypeptidase are conserved. The location of a conserved basic patch in the active site adjacent to the catalytic Zn{sup 2+}, where an acetate ion is identified, suggests recognition of the carboxy-terminus in a similar fashion to other carboxypeptidases. However, there are significant differences that indicate the recognition of substrates with different properties. Of note is the presence of a lysine in the S1′ recognition subsite that suggests specificity towards an acidic substrate.

  13. High-resolution structure of the M14-type cytosolic carboxypeptidase from Burkholderia cenocepacia refined exploiting PDB-REDO strategies

    The structure of a bacterial M14-family carboxypeptidase determined exploiting microfocus synchrotron radiation and highly automated refinement protocols reveals its potential to act as a polyglutamylase. A potential cytosolic metallocarboxypeptidase from Burkholderia cenocepacia has been crystallized and a synchrotron-radiation microfocus beamline allowed the acquisition of diffraction data to 1.9 Å resolution. The asymmetric unit comprises a tetramer containing over 1500 amino acids, and the high-throughput automated protocols embedded in PDB-REDO were coupled with model–map inspections in refinement. This approach has highlighted the value of such protocols for efficient analyses. The subunit is constructed from two domains. The N-terminal domain has previously only been observed in cytosolic carboxypeptidase (CCP) proteins. The C-terminal domain, which carries the Zn2+-containing active site, serves to classify this protein as a member of the M14D subfamily of carboxypeptidases. Although eukaryotic CCPs possess deglutamylase activity and are implicated in processing modified tubulin, the function and substrates of the bacterial family members remain unknown. The B. cenocepacia protein did not display deglutamylase activity towards a furylacryloyl glutamate derivative, a potential substrate. Residues previously shown to coordinate the divalent cation and that contribute to peptide-bond cleavage in related enzymes such as bovine carboxypeptidase are conserved. The location of a conserved basic patch in the active site adjacent to the catalytic Zn2+, where an acetate ion is identified, suggests recognition of the carboxy-terminus in a similar fashion to other carboxypeptidases. However, there are significant differences that indicate the recognition of substrates with different properties. Of note is the presence of a lysine in the S1′ recognition subsite that suggests specificity towards an acidic substrate

  14. Entry and incumbent innovation

    Weinschenk, Philipp

    2010-01-01

    We explore how the threat of entry influences the innovation activity of an incumbent. We show that the incumbent’s investment is hump-shaped in the entry threat. When the entry threat is small and increases, the incumbent invests more to deter entry, or to make it unlikely. This is due to the entry deterrence effect. However, when the threat becomes huge, entry can no longer profitably be deterred or made unlikely and the investment becomes small. Then the Schumpeterian effect dominates. The...

  15. Entry Modes of Starbucks

    Santamaría Sotillo, Beatriz; Ni, Shuang

    2008-01-01

    Topic:When an MNC seeks to enter a foreign country, it must choose the most appropriate entry mode for that specific market, such as exporting, licensing, a turnkey project, franchising, joint ventures or wholly-owned subsidiaries. There are many factors which affect the choice of entry modes. Influential factors contributing to the entry mode decision can have different degrees of impact for each particular country. As a consequence, an MNC has to use different entry modes in order to adapt ...

  16. FeatureMap3D - a tool to map protein features and sequence conservation onto homologous structures in the PDB

    Wernersson, Rasmus; Rapacki, Krzysztof; Stærfeldt, Hans Henrik;

    2006-01-01

    FeatureMap3D is a web-based tool that maps protein features onto 3D structures. The user provides sequences annotated with any feature of interest, such as post-translational modifications, protease cleavage sites or exonic structure and FeatureMap3D will then search the Protein Data Bank (PDB) for...

  17. Characterization of hepatitis C virus recombinants with chimeric E1/E2 envelope proteins and identification of single amino acids in the E2 stem region important for entry

    Carlsen, Thomas H R; Scheel, Troels K H; Ramirez, Santseharay;

    2013-01-01

    . For recovered 1b-E2 recombinants, single E2 stem region amino acid changes were identified at residues 706, 707, and 710. In reverse genetic studies, these mutations increased infectivity titers by ~100-fold, apparently without influencing particle stability or cell binding although introducing slight...... decrease in particle density. In addition, the 1b-E2 exchange led to a decrease in secreted core protein of 25 to 50%, which was further reduced by the E2 stem region mutations. These findings indicated that compensatory mutations permitted robust infectious virus production, without increasing assembly....../release. Studies of E1/E2 heterodimerization showed no differences in intracellular E1/E2 interaction for chimeric constructs with or without E2 stem region mutations. Interestingly, the E2 stem region mutations allowed efficient entry, which was verified in 1a-E1/1b-E2 HCV pseudoparticle assays. A CD81 inhibition...

  18. Web-based visualisation and analysis of 3D electron-microscopy data from EMDB and PDB.

    Lagerstedt, Ingvar; Moore, William J; Patwardhan, Ardan; Sanz-García, Eduardo; Best, Christoph; Swedlow, Jason R; Kleywegt, Gerard J

    2013-11-01

    The Protein Data Bank in Europe (PDBe) has developed web-based tools for the visualisation and analysis of 3D electron microscopy (3DEM) structures in the Electron Microscopy Data Bank (EMDB) and Protein Data Bank (PDB). The tools include: (1) a volume viewer for 3D visualisation of maps, tomograms and models, (2) a slice viewer for inspecting 2D slices of tomographic reconstructions, and (3) visual analysis pages to facilitate analysis and validation of maps, tomograms and models. These tools were designed to help non-experts and experts alike to get some insight into the content and assess the quality of 3DEM structures in EMDB and PDB without the need to install specialised software or to download large amounts of data from these archives. The technical challenges encountered in developing these tools, as well as the more general considerations when making archived data available to the user community through a web interface, are discussed. PMID:24113529

  19. Web-based visualisation and analysis of 3D electron-microscopy data from EMDB and PDB

    Lagerstedt, Ingvar; Moore, William J.; Patwardhan, Ardan; Sanz-García, Eduardo; Best, Christoph; Swedlow, Jason R.; Kleywegt, Gerard J

    2013-01-01

    The Protein Data Bank in Europe (PDBe) has developed web-based tools for the visualisation and analysis of 3D electron microscopy (3DEM) structures in the Electron Microscopy Data Bank (EMDB) and Protein Data Bank (PDB). The tools include: (1) a volume viewer for 3D visualisation of maps, tomograms and models, (2) a slice viewer for inspecting 2D slices of tomographic reconstructions, and (3) visual analysis pages to facilitate analysis and validation of maps, tomograms and models. These tool...

  20. PDB_Hydro: incorporating dipolar solvents with variable density in the Poisson-Boltzmann treatment of macromolecule electrostatics.

    Azuara, Cyril; Lindahl, Erik; Koehl, Patrice; Orland, Henri; Delarue, Marc

    2006-01-01

    We describe a new way to calculate the electrostatic properties of macromolecules which eliminates the assumption of a constant dielectric value in the solvent region, resulting in a Generalized Poisson-Boltzmann-Langevin equation (GPBLE). We have implemented a web server (http://lorentz.immstr.pasteur.fr/pdb_hydro.php) that both numerically solves this equation and uses the resulting water density profiles to place water molecules at preferred sites of hydration. Surface atoms with high or l...

  1. Flavivirus cell entry and membrane fusion

    Smit, Jolanda M.; Moesker, Bastiaan; Rodenhuis-Zybert, Izabela; Wilschut, Jan

    2011-01-01

    Flaviviruses, such as dengue virus and West Nile virus, are enveloped viruses that infect cells through receptor-mediated endocytosis and fusion from within acidic endosomes. The cell entry process of flaviviruses is mediated by the viral E glycoprotein. This short review will address recent advance

  2. Lobbying on Entry

    Perotti, E.C.; Volpin, P.

    2004-01-01

    We develop a model of endogenous lobby formation in which wealth inequality and political accountability undermine entry and financial development. Incumbents seek a low level of effective investor protection to prevent potential entrants from raising capital. They succeed because they can promise larger political contributions than the entrants due to the higher rents earned with less competition. Entry and investor protection improve when wealth distribution becomes less unequal, and the po...

  3. Entry Threat in Duopoly

    Peitz, Martin

    1996-01-01

    Abstract: An oligopolistic market with vertical product differentiation is parametrized in cost parameters. This allows me to study the impact of the technology of the firms (cost parameters) on market structure, conduct, and performance. Firms which differ only by the order of the sequential move to choose a quality use sophisticated entry deterring or entry accomodating strategies. I show that infinitesimal changes in the cost parameters can generate discontinuities in market profits. In pa...

  4. Mitochondrial myopathy in rats fed with a diet containing beta-guanidine propionic acid, an inhibitor of creatine entry in muscle cells.

    Gori, Z.; De Tata, V.; Pollera, M.; Bergamini, E

    1988-01-01

    In rats with phosphoryl-creatine depletion (fed a standard Randoin-Causeret diet containing 1% beta-guanidine propionic acid) abnormal mitochondria were observed in slow skeletal muscles, often containing paracrystalline inclusions very like those induced by ischaemia or mitochondrial poisons and in human mitochondrial myopathy.

  5. Low temperature activation of methane over a zinc-exchanged heteropolyacid as an entry to its selective oxidation to methanol and acetic acid

    Patil, Umesh

    2014-01-01

    A Zn-exchanged heteropolyacid supported onto silica (Zn-HPW/SiO2) activates methane at 25 °C into Zn-methyl. At higher temperatures and with CH4/O2 or CH4/CO2, it gives methanol and acetic acid respectively. This journal is

  6. Structural and Functional Studies of a Phosphatidic Acid-Binding Antifungal Plant Defensin MtDef4: Identification of an RGFRRR Motif Governing Fungal Cell Entry

    Sagaram, Uma Shankar; El-Mounadi, Kaoutar; Buchko, Garry W.; Berg, Howard R.; Kaur, Jagdeep; Raghu S Pandurangi; Thomas J Smith; Dilip M Shah

    2013-01-01

    MtDef4 is a 47-amino acid cysteine-rich evolutionary conserved defensin from a model legume Medicago truncatula. It is an apoplast-localized plant defense protein that inhibits the growth of the ascomycetous fungal pathogen Fusarium graminearum in vitro at micromolar concentrations. Little is known about the mechanisms by which MtDef4 mediates its antifungal activity. In this study, we show that MtDef4 rapidly permeabilizes fungal plasma membrane and is internalized by the fungal cells where ...

  7. Time card entry system

    Montierth, B.S.

    1996-05-01

    The Time Card Entry System was developed to interface with the DOE Headquarters Electronic Time and Attendance (ETA) system. It features pop-up window pick lists for Work Breakdown Structure Numbers and Hour Codes and has extensive processing that ensures that time and attendance reported by the employee fulfills US Government/OMB requirements before Timekeepers process the data at the end of the two week payroll cycle using ETA. Tours of Duty (e.g. ten hour day, four day week with Friday through Sunday off), established in the ETA system, are imported into the Time Card Entry System by the Timekeepers. An individual`s Tour of Duty establishes the basis for validation of time of day and number of hours worked per day. At the end of the two week cycle, data is exported by the Timekeepers from the Time Card Entry System into ETA data files.

  8. Exclusive Dealing and Entry

    João Leão

    2008-01-01

    This paper examines the use of exclusive dealing agreements to prevent the entry of rival firms. An exclusive dealing agreement is a contract between a buyer and a seller where the buyer commits to buy a good exclusively from the seller. One main concern of the literature is to explain how an incumbent seller is able to persuade the buyers to sign an exclusive dealing agreement that deters the entry of a more efficient rival seller. We propose a new explanation when the buyers are downstream ...

  9. Pairwise amino acid secondary structural propensities

    Chemmama, Ilan E.; Chapagain, Prem P.; Gerstman, Bernard S.

    2015-04-01

    We investigate the propensities for amino acids to form a specific secondary structure when they are paired with other amino acids. Our investigations use molecular dynamics (MD) computer simulations, and we compare the results to those from the Protein Data Bank (PDB). Proper comparison requires weighting of the MD results in a manner consistent with the relative frequency of appearance in the PDB of each possible pair of amino acids. We find that the propensity for an amino acid to assume a secondary structure varies dramatically depending on the amino acid that is before or after it in the primary sequence. This cooperative effect means that when selecting amino acids to facilitate the formation of a secondary structure in peptide engineering experiments, the adjacent amino acids must be considered. We also examine the preference for a secondary structure in bacterial proteins and compare the results to those of human proteins.

  10. Deployable Entry-system Project

    National Aeronautics and Space Administration — The Deployable Entry-system ProjecT (ADEPT) will develop requirements for the ADEPT flight test.  Prior entry systems used high mass thermal protection...

  11. Analyzing Modes of Foreign Entry

    Müller, Thomas

    2001-01-01

    This paper studies the entry decision of a multinational enterprise into a foreign market. Two alternative entry modes for a foreign direct investment are considered: Greenfield investment versus acquisition. In contrast to existing approaches, the acquisition price and the profits under both entry modes are endogenously determined. Interestingly, we find that the optimal entry mode decision is a ected by the competition intensity in the market in a non-monotonic way. When markets are very mu...

  12. Corruption, Entry and Pollution

    Eleni Stathopoulou; Dimitrios Varvarigos

    2013-01-01

    We model an economy where imperfectly competitive firms choose whether to employ a dirty technology and pay an emission tax or employ a clean technology and incur the cost of its adoption. Bureaucrats who are entrusted with the task of monitoring the emissions of each firm, are corruptible in the sense that they may accept bribes in order to mislead authorities on the firms’ actual emissions. Market entry is an important element in the relation between corruption and pollution. Particularly, ...

  13. Carbohydrate-Related Inhibitors of Dengue Virus Entry

    Takashi Suzuki

    2013-02-01

    Full Text Available Dengue virus (DENV, which is transmitted by Aedes mosquitoes, causes fever and hemorrhagic disorders in humans. The virus entry process mediated through host receptor molecule(s is crucial for virus propagation and the pathological progression of dengue disease. Therefore, elucidation of the molecular mechanisms underlying virus entry is essential for an understanding of dengue pathology and for the development of effective new anti-dengue agents. DENV binds to its receptor molecules mediated through a viral envelope (E protein, followed by incorporation of the virus-receptor complex inside cells. The fusion between incorporated virus particles and host endosome membrane under acidic conditions is mediated through the function of DENV E protein. Carbohydrate molecules, such as sulfated glycosaminoglycans (GAG and glycosphingolipids, and carbohydrate-recognition proteins, termed lectins, inhibit virus entry. This review focuses on carbohydrate-derived entry inhibitors, and also introduces functionally related compounds with similar inhibitory mechanisms against DENV entry.

  14. An automated system designed for large scale NMR data deposition and annotation: application to over 600 assigned chemical shift data entries to the BioMagResBank from the Riken Structural Genomics/Proteomics Initiative internal database

    Biomolecular NMR chemical shift data are key information for the functional analysis of biomolecules and the development of new techniques for NMR studies utilizing chemical shift statistical information. Structural genomics projects are major contributors to the accumulation of protein chemical shift information. The management of the large quantities of NMR data generated by each project in a local database and the transfer of the data to the public databases are still formidable tasks because of the complicated nature of NMR data. Here we report an automated and efficient system developed for the deposition and annotation of a large number of data sets including 1H, 13C and 15N resonance assignments used for the structure determination of proteins. We have demonstrated the feasibility of our system by applying it to over 600 entries from the internal database generated by the RIKEN Structural Genomics/Proteomics Initiative (RSGI) to the public database, BioMagResBank (BMRB). We have assessed the quality of the deposited chemical shifts by comparing them with those predicted from the PDB coordinate entry for the corresponding protein. The same comparison for other matched BMRB/PDB entries deposited from 2001–2011 has been carried out and the results suggest that the RSGI entries greatly improved the quality of the BMRB database. Since the entries include chemical shifts acquired under strikingly similar experimental conditions, these NMR data can be expected to be a promising resource to improve current technologies as well as to develop new NMR methods for protein studies.

  15. Sport entries and qualification manual

    2014-01-01

    This manual is designed to provide National Olympic Committees (NOCs) with the Olympic Sport Entries process, relevant policies, and instructions for completing the online registration for athletes participating in the Sochi 2014 Olympic Winter Games and to assist NOCs in using the online Sport Entries and Qualification (eSEQ) system to complete the entries of their athletes to the Sochi 2014 Olympic Winter Games.

  16. Entry deterrence and experimentation under demand uncertainty

    Jain, N

    2011-01-01

    We examine the effect of a threat of entry on experimentation about demand by an incumbent monopolist when there is a fixed cost of entry. We show that experimentation may itself be used as a tool for entry deterrence and derive conditions under which experimentation reduces the probability of entry. These conditions depend on the entry rule which in turn depends on entry costs. We show that if experimentation does not deter entry, the monopolist incumbent experiments less. We also characteri...

  17. Bovine Viral Diarrhea Virus Entry Is Dependent on Clathrin-Mediated Endocytosis

    Lecot, Steve; Belouzard, Sandrine; Dubuisson, Jean; Rouillé, Yves

    2005-01-01

    Cellular mechanisms of bovine viral diarrhea virus (BVDV) entry in MDBK cells were investigated. Chloroquine, bafilomycin A1, or ammonium chloride inhibited BVDV infection, indicating that an acidic endosomal pH is required for BVDV entry. The tyrosine kinase inhibitor genistein partially inhibited BVDV infection at a postentry step, whereas BVDV entry was strongly inhibited by chlorpromazine or by the overexpression of a dominant-negative form of EPS15, a protein essential for the formation ...

  18. GOCE Re-Entry Campaign

    Bastida, B.; Flohrer, T.; Lemmens, S.; Krag, H.

    2015-03-01

    Every year ESA, through the Space Debris Office, participates to an Inter-Agency Space Debris Coordination Committee (IADC) Re-entry Test Campaign.. For the campaign of 2013, ESA’s proposal to select GOCE's re-entry was accepted. The campaign opened on the 21st October 2013 after fuel depletion of the drag-compensating ion propulsion. GOCE was expected to enter into a phase of attitude-controlled fine-pointing mode (FPM) until the attitude controllers would be unable to cope with the atmospheric torques and then the satellite would enter in a phase of fully uncontrolled flight. In this paper, we present the evolution of ESA’s daily predictions on the re-entry epoch using different sources of orbital information. The uncertainties on the spacecraft operability (i.e. the physical limits of the attitude controller) led to a non-standard re-entry scenario were different attitudes had to be considered (instead of the commonly assumed random tumbling mode case that is used whenever no information on the physical properties of a re-entering object is available). A daily assessment of the status, in coordination with the flight control team, was required and implied a continuous update on the predicted failure point of the attitude controller. This in turn imposed the need for considering an asymmetric re-entry window. These operation-bound uncertainties were simulated to predict the attitude evolution after failure at different altitudes and their effects evaluated to be taken into account for the re-entry predictions. We present ESA’s re-entry prediction activities for GOCE, internally, and within the IADC, and address specific technical aspects and challenges for re-entry predictions, which are related to the expected and occurred attitude of GOCE during the final re-entry phase.

  19. Brownfield Entry in Emerging Markets

    Meyer, Klaus E.; Saul Estrin

    2001-01-01

    This paper focuses on the brown-field entry mode, as a special case of acquisition, in which the resources transferred by the investor dominate over those provided by the acquired firm. We see this mode as having particular relevance for entry strategies in emerging markets. The choice of entry mode is analyzed on the basis of a framework utilizing both resource-based and transaction-cost theories. The resource requirements have to be matched with resources available to the investor through a...

  20. Financial Intermediation and Entry Deterrence

    Jain, Neelam; Thomas D. Jeitschko; Mirman, Leonard J.

    2001-01-01

    In this paper, we analyze the interaction between an incumbent firm's financial contract with abank and its product market decisions in the face of the threat of entry, in a dynamic model.The main results of the paper are: there exists a separating equilibrium with no limit pricing; thelow-cost incumbent repays more to the bank in the first period, due to the threat of entry; andthere are parameter values for which the bank makes more profits with the threat of entry thanwithout.

  1. Entry Threat and Entry Deterrence: The Timing of Broadband Rollout

    Mo Xiao; Orazem, Peter F.

    2007-01-01

    Past empirical literature provides strong evidence that competition increases when new firms enter a market. However, rarely have economists been able to examine how competition changes with the threat of entry. This paper uses the evolution of the zip code level market structure of facilities-based broadband providers from 1999 to 2004 to investigate how a firm adjusts its entry strategy when facing the threat of additional entrants. We identify the potential entrant into a local market as t...

  2. The PDB database is a rich source of alpha-helical anti-microbial peptides to combat disease causing pathogens [version 2; referees: 2 approved, 1 approved with reservations

    Sandeep Chakraborty

    2015-06-01

    Full Text Available The therapeutic potential of α-helical anti-microbial peptides (AH-AMP to combat pathogens is fast gaining prominence. Based on recently published open access software for characterizing α-helical peptides (PAGAL, we elucidate a search methodology (SCALPEL that leverages the massive structural data pre-existing in the PDB database to obtain AH-AMPs belonging to the host proteome. We provide in vitro validation of SCALPEL on plant pathogens (Xylella fastidiosa, Xanthomonas arboricola and Liberibacter crescens by identifying AH-AMPs that mirror the function and properties of cecropin B, a well-studied AH-AMP. The identified peptides include a linear AH-AMP present within the existing structure of phosphoenolpyruvate carboxylase (PPC20, and an AH-AMP mimicing the properties of the two α-helices of cecropin B from chitinase (CHITI25. The minimum inhibitory concentration of these peptides are comparable to that of cecropin B, while anionic peptides used as control failed to show any inhibitory effect on these pathogens. Substitute therapies in place of conventional chemotherapies using membrane permeabilizing peptides like these might also prove effective to target cancer cells. The use of native structures from the same organism could possibly ensure that administration of such peptides will be better tolerated and not elicit an adverse immune response. We suggest a similar approach to target Ebola epitopes, enumerated using PAGAL recently, by selecting suitable peptides from the human proteome, especially in wake of recent reports of cationic amphiphiles inhibiting virus entry and infection.

  3. Analisis Pengaruh Penanaman Modal Asing Langsung (PMAL) Dan Pengeluaran Pemerintah (PP) Terhadap Produk Domestik Bruto (PDB) Di Indonesia Pasca Krisis Ekonomi 1998

    Simandjorang, Bonataon MTV

    2011-01-01

    Penelitian ini berjudul Analisis Pengaruh Penanaman Modal Asing Langsung (PMAL) dan Pengeluaran Pemerintah (PP) terhadap Produk Domestik Bruto (PDB) Di Indonesia Pasca Krisis Ekonomi 1998. Penelitian ini menggunakan metode ekonometrika melalui model regresi linear berganda (metode OLS) dengan menggunakan data runtut waktu (time series) 12 tahun, yaitu mulai 1999 hingga 2010 yang diperoleh dari Asian Development Bank (ADB) dan Badan Koordinasi Penanaman Modal (BKPM) Republik Indonesia. Hasi...

  4. Corporate Author Entries. Revision 5

    This reference authority has been created and is maintained to provide standard forms for recording the names of organizations consistently in bibliographic citations. This revision includes approximately 42,000 entries established since 1973

  5. Tactile Data Entry System Project

    National Aeronautics and Space Administration — Building on our successful Phase I Tactile Data Entry program, Barron Associates proposes development of a Glove-Enabled Computer Operations (GECO) system to permit...

  6. Entry, Descent, Landing Animation (Animation)

    2005-01-01

    [figure removed for brevity, see original site] Click on the image for Entry, Descent, Landing animation This animation illustrates the path the Stardust return capsule will follow once it enters Earth's atmosphere.

  7. Orion Entry Handling Qualities Assessments

    Bihari, B.; Tiggers, M.; Strahan, A.; Gonzalez, R.; Sullivan, K.; Stephens, J. P.; Hart, J.; Law, H., III; Bilimoria, K.; Bailey, R.

    2011-01-01

    The Orion Command Module (CM) is a capsule designed to bring crew back from the International Space Station (ISS), the moon and beyond. The atmospheric entry portion of the flight is deigned to be flown in autopilot mode for nominal situations. However, there exists the possibility for the crew to take over manual control in off-nominal situations. In these instances, the spacecraft must meet specific handling qualities criteria. To address these criteria two separate assessments of the Orion CM s entry Handling Qualities (HQ) were conducted at NASA s Johnson Space Center (JSC) using the Cooper-Harper scale (Cooper & Harper, 1969). These assessments were conducted in the summers of 2008 and 2010 using the Advanced NASA Technology Architecture for Exploration Studies (ANTARES) six degree of freedom, high fidelity Guidance, Navigation, and Control (GN&C) simulation. This paper will address the specifics of the handling qualities criteria, the vehicle configuration, the scenarios flown, the simulation background and setup, crew interfaces and displays, piloting techniques, ratings and crew comments, pre- and post-fight briefings, lessons learned and changes made to improve the overall system performance. The data collection tools, methods, data reduction and output reports will also be discussed. The objective of the 2008 entry HQ assessment was to evaluate the handling qualities of the CM during a lunar skip return. A lunar skip entry case was selected because it was considered the most demanding of all bank control scenarios. Even though skip entry is not planned to be flown manually, it was hypothesized that if a pilot could fly the harder skip entry case, then they could also fly a simpler loads managed or ballistic (constant bank rate command) entry scenario. In addition, with the evaluation set-up of multiple tasks within the entry case, handling qualities ratings collected in the evaluation could be used to assess other scenarios such as the constant bank angle

  8. Autonomous gliding entry guidance with

    Guo Jie; Wu Xuzhong; Tang Shengjing

    2015-01-01

    This paper presents a novel three-dimensional autonomous entry guidance for relatively high lift-to-drag ratio vehicles satisfying geographic constraints and other path constraints. The guidance is composed of onboard trajectory planning and robust trajectory tracking. For trajectory planning, a longitudinal sub-planner is introduced to generate a feasible drag-versus-energy profile by using the interpolation between upper boundary and lower boundary of entry corridor to get the desired traje...

  9. Network Competition and Entry Deterrence

    Calzada, Joan; Valletti, Tommaso

    2005-01-01

    We develop a model of logit demand that extends to a multi-firm industry the traditional duopoly framework of network competition with access charges. Firstly, we show that, when incumbents do not face the threat of entry and compete in prices, they inefficiently establish the reciprocal access charge below cost. This inefficiency disappears if incumbents compete in utilities instead of prices. Secondly, we study how incumbents change their choices under the threat of entry when they determin...

  10. Re-entry flight clearance

    Juliana, S.

    2006-01-01

    The objective of the research was to identify and evaluate promising mathematical techniques for re-entry flight clearance. To fulfil this objective, two mathematical methods were investigated and developed: μ analysis for linear models and interval analysis for both linear and non-linear models. The stability of re-entry vehicles in the presence of model uncertainties was chosen as the clearance criterion, which is represented by two mathematical criteria: worst-case eigenvalues (linear...

  11. Stackelberg competition with endogenous entry

    Etro, F.

    2007-01-01

    This paper analyzes market structures where leaders have a first mover advantage and entry by the followers is endogenous. The strategy of the leaders is always more aggressive than the strategy of the followers independently from strategic substitutability or complementarity. Under quantity competition, the leader produces more than any other firm and I determine the conditions for entry deterrence to be optimal (high substitutability and constant or decreasing marginal costs). Under price c...

  12. 19 CFR 142.16 - Entry summary documentation.

    2010-04-01

    ... 19 Customs Duties 2 2010-04-01 2010-04-01 false Entry summary documentation. 142.16 Section 142.16... TREASURY (CONTINUED) ENTRY PROCESS Entry Summary Documentation § 142.16 Entry summary documentation. (a) Entry summary not filed at time of entry. When the entry documentation is filed before the entry...

  13. Entry Mode Choice of Multinational Banks

    Lehner, Maria

    2008-01-01

    When expanding abroad, a multinational bank faces a trade-off between accessing a foreign country via cross border lending or a financial foreign direct investment, i.e. greenfield or acquisition entry. We analyze the entry mode choice of multinational banks and explicitly derive the entry mode pattern in the banking industry. Moreover, we show that in less developed banking markets, a trend towards cross border lending and acquisition entry exists. Greenfield entry prevails in more developed...

  14. Autonomous gliding entry guidance with

    Guo Jie

    2015-10-01

    Full Text Available This paper presents a novel three-dimensional autonomous entry guidance for relatively high lift-to-drag ratio vehicles satisfying geographic constraints and other path constraints. The guidance is composed of onboard trajectory planning and robust trajectory tracking. For trajectory planning, a longitudinal sub-planner is introduced to generate a feasible drag-versus-energy profile by using the interpolation between upper boundary and lower boundary of entry corridor to get the desired trajectory length. The associated magnitude of the bank angle can be specified by drag profile, while the sign of bank angle is determined by lateral sub-planner. Two-reverse mode is utilized to satisfy waypoint constraints and dynamic heading error corridor is utilized to satisfy no-fly zone constraints. The longitudinal and lateral sub-planners are iteratively employed until all of the path constraints are satisfied. For trajectory tracking, a novel tracking law based on the active disturbance rejection control is introduced. Finally, adaptability tests and Monte Carlo simulations of the entry guidance approach are performed. Results show that the proposed entry guidance approach can adapt to different entry missions and is able to make the vehicle reach the prescribed target point precisely in spite of geographic constraints.

  15. Characterization of Hepatitis C Virus Recombinants with Chimeric E1/E2 Envelope Proteins and Identification of Single Amino Acids in the E2 Stem Region Important for Entry

    Carlsen, Thomas H. R.; Scheel, Troels K. H.; Ramirez, Santseharay; Foung, Steven K. H.; Bukh, Jens

    2013-01-01

    The hepatitis C virus (HCV) envelope proteins E1 and E2 play a key role in host cell entry and represent important targets for vaccine and drug development. Here, we characterized HCV recombinants with chimeric E1/E2 complexes in vitro. Using genotype 1a/2a JFH1-based recombinants expressing 1a core-NS2, we exchanged E2 with functional isolate sequences of genotypes 1a (alternative isolate), 1b, and 2a. While the 1a-E2 exchange did not impact virus viability, the 2a-E2 recombinant was nonviab...

  16. Chemical characterization of fatty acids, alkanes, n-diols and alkyl esters produced by a mixed culture of Trichoderma koningii and Penicillium janthinellum grown aerobically on undecanoic acid, potatoe dextrose and their mixture.

    Monreal, Carlos M; Chahal, Amarpreet; Schnitzer, Morris; Rowland, Owen

    2016-05-01

    Little is known about the mixed fungal synthesis of high-value aliphatics derived from the metabolism of simple and complex carbon substrates. Trichoderma koningii and Penicillium janthinellum were fed with undecanoic acid (UDA), potatoe dextrose broth (PDB), and their mixture. Pyrolysis Field Ionization Mass Spectrometry (Py-FIMS) together with (1)H and (13)C Nuclear Magnetic Resonance (NMR) characterized CHCl3 soluble aliphatics in the fungal cell culture. Data from NMR and Py-FIMS analysis were complementary to each other. On average, the mixed fungal species produced mostly fatty acids (28% of total ion intensity, TII) > alkanes (2% of TII) > n-diols (2% of TII) > and alkyl esters (0.8% of TII) when fed with UDA, PDB or UDA+PDB. The cell culture accumulated aliphatics extracellularly, although most of the identified compounds accumulated intracellularly. The mixed fungal culture produced high-value chemicals from the metabolic conversion of simple and complex carbon substrates. PMID:26852878

  17. The pace of MNEs’ sequential entries: Cumulative entry experience and the dynamic process

    Gerald Yong Gao; Yigang Pan

    2010-01-01

    This study examines the pace with which multinational enterprises undertake sequential entries in a foreign market. We focus on learning effects from cumulative entry experience of different modes within a host market. Moreover, we investigate the dynamic process of entry mode switch, and how cumulative entry experience reduces the expansion constraint. Using a dataset of sequential entries by US firms in China during 1979–2002, we find that the impact of cumulative entry experience on the pa...

  18. Poxvirus entry and membrane fusion

    The study of poxvirus entry and membrane fusion has been invigorated by new biochemical and microscopic findings that lead to the following conclusions: (1) the surface of the mature virion (MV), whether isolated from an infected cell or by disruption of the membrane wrapper of an extracellular virion, is comprised of a single lipid membrane embedded with non-glycosylated viral proteins; (2) the MV membrane fuses with the cell membrane, allowing the core to enter the cytoplasm and initiate gene expression; (3) fusion is mediated by a newly recognized group of viral protein components of the MV membrane, which are conserved in all members of the poxvirus family; (4) the latter MV entry/fusion proteins are required for cell to cell spread necessitating the disruption of the membrane wrapper of extracellular virions prior to fusion; and furthermore (5) the same group of MV entry/fusion proteins are required for virus-induced cell-cell fusion. Future research priorities include delineation of the roles of individual entry/fusion proteins and identification of cell receptors

  19. Delayed School Entry in Uganda

    Moyi, Peter

    2011-01-01

    Since 1997 Uganda has seen a large increase in school enrolment. Despite this increased enrolment, universal education has remained elusive. Many children enrol in school, but not at the recommended age, and they drop out before completing school. This article focuses on one of these problems--delayed school entry. What household factors are…

  20. Crystal structure and ligand affinity of avidin in the complex with 4‧-hydroxyazobenzene-2-carboxylic acid

    Strzelczyk, Paweł; Bujacz, Grzegorz

    2016-04-01

    Avidin is a protein found in egg white that binds numerous organic compounds with high affinity, especially biotin and its derivatives. Due to its extraordinary affinity for its ligands, avidin is extensively used in biotechnology. X-ray crystallography and fluorescence-based biophysical techniques were used to show that avidin binds the dye 4‧-hydroxyazobenzene-2-carboxylic acid (HABA) with a lower affinity than biotin. The apparent dissociation constant determined for the avidin complex with HABA by microscale thermophoresis (MST) is 4.12 μM. The crystal structure of avidin-HABA complex was determined at a resolution of 2.2 Å (PDB entry 5chk). The crystals belong to a hexagonal system, in the space group P6422. In that structure, the hydrazone tautomer of HABA is bound at the bottom part of the central calyx near the polar residues. We show interactions of the dye with avidin and compare them with the previously reported avidin-biotin complex.

  1. Crystal structure and ligand affinity of avidin in the complex with 4‧-hydroxyazobenzene-2-carboxylic acid

    Strzelczyk, Paweł; Bujacz, Grzegorz

    2016-04-01

    Avidin is a protein found in egg white that binds numerous organic compounds with high affinity, especially biotin and its derivatives. Due to its extraordinary affinity for its ligands, avidin is extensively used in biotechnology. X-ray crystallography and fluorescence-based biophysical techniques were used to show that avidin binds the dye 4‧-hydroxyazobenzene-2-carboxylic acid (HABA) with a lower affinity than biotin. The apparent dissociation constant determined for the avidin complex with HABA by microscale thermophoresis (MST) is 4.12 μM. The crystal structure of avidin-HABA complex was determined at a resolution of 2.2 Å (PDB entry 5chk). The crystals belong to a hexagonal system, in the space group P6422. In that structure, the hydrazone tautomer of HABA is bound at the bottom part of the central calyx near the polar residues. We show interactions of the dye with avidin and compare them with the previously reported avidin-biotin complex.

  2. Bi-weekly waterfowl survey data entry

    US Fish and Wildlife Service, Department of the Interior — Data sheet for the entry of bi-weekly waterfowl survey data from the state of Kansas. This Excel file contains the data entry sheet and a chart displaying waterfowl...

  3. Sunk Costs and Antitrust Barriers to Entry

    SCHMALENSEE, Richard

    2004-01-01

    US antitrust policy takes as its objective consumer welfare, not total economic welfare. With that objective, Joe Bain's definition of entry barriers is more useful than George Stigler's or definitions based on economic welfare. It follows that economies of scale that involve sunk costs may create antitrust barriers to entry. A simple model shows that sunk costs without scale economies may discourage entry without creating an antitrust entry barrier.

  4. Endogenous Market Structure and Foreign Market Entry

    Markusen, James R.; Frank Stähler

    2009-01-01

    Models dealing with cross-border acquisitions versus greenfield investment usually assume that the entry of a foreign firm into a market has effects on the outputs of all domestic firms in that market, but exit or entry of local firms is not considered. The purpose of this paper is to re-examine the acquisition versus greenfield versus exporting question under fixed versus free entry assumptions for local firms. Our finding is that greenfield entry and exporting options are more attractive re...

  5. Predicting the Diversity of Foreign Entry Modes

    Hashai, Niron; Asmussen, Christian G.; Benito, Gabriel R. G.; Petersen, Bent

    2007-01-01

    This paper expands entry mode literature by referring to multiple modes exerted in different value chain activities within and across host markets, rather than to a single entry mode at the host market level. Scale of operations and knowledge intensity are argued to affect firms’ entry mode diversity across value chain activities and host markets. Analyzing a sample of Israeli based firms we show that larger firms exhibit a higher degree of entry mode diversity both across value chain activit...

  6. BioMagResBank (BMRB) as a partner in the Worldwide Protein Data Bank (wwPDB): new policies affecting biomolecular NMR depositions

    We describe the role of the BioMagResBank (BMRB) within the Worldwide Protein Data Bank (wwPDB) and recent policies affecting the deposition of biomolecular NMR data. All PDB depositions of structures based on NMR data must now be accompanied by experimental restraints. A scheme has been devised that allows depositors to specify a representative structure and to define residues within that structure found experimentally to be largely unstructured. The BMRB now accepts coordinate sets representing three-dimensional structural models based on experimental NMR data of molecules of biological interest that fall outside the guidelines of the Protein Data Bank (i.e., the molecule is a peptide with 23 or fewer residues, a polynucleotide with 3 or fewer residues, a polysaccharide with 3 or fewer sugar residues, or a natural product), provided that the coordinates are accompanied by representation of the covalent structure of the molecule (atom connectivity), assigned NMR chemical shifts, and the structural restraints used in generating model. The BMRB now contains an archive of NMR data for metabolites and other small molecules found in biological systems

  7. Sport entries and qualification manual: Nanjing 2014

    2014-01-01

    Sport entries constitute an important part of the delegation registration process of the Nanjing 2014 Summer Youth Olympic Games. This manual aims to introduce to NOCs the process, relevant policies and requirements regarding sport entries so as to ensure that NOCs can successfully complete the entries for their athletes to the Nanjing 2014 Youth Olympic Games.

  8. 19 CFR 122.42 - Aircraft entry.

    2010-04-01

    ... 19 Customs Duties 1 2010-04-01 2010-04-01 false Aircraft entry. 122.42 Section 122.42 Customs... AIR COMMERCE REGULATIONS Aircraft Entry and Entry Documents; Electronic Manifest Requirements for Passengers, Crew Members, and Non-Crew Members Onboard Commercial Aircraft Arriving In, Continuing...

  9. 76 FR 66875 - Informal Entry Limit and Removal of a Formal Entry Requirement

    2011-10-28

    ... increasing the informal entry limit to $2,500 will save the trade community approximately $11 million in... informal entry from $2,000 to $2,500. Unless exempt under a free trade agreement and in addition to any..., 143, 145, and 148 RIN 1515-AD69 Informal Entry Limit and Removal of a Formal Entry Requirement...

  10. Bargaining agenda, timing, and entry

    Fanti, Luciano; Buccella, Domenico

    2015-01-01

    In a unionised Cournot duopoly, the present paper extensively re-examines the subject of the bargaining scope between firms and unions. It investigates the endogenous equilibrium agenda (Right-to-Manage vs Efficient Bargaining) that can arise under three timing specification of the bargaining game both for a given duopoly and monopoly with threat of entry. A novel result is that, in sequential negotiations, Efficient Bargaining emerges in equilibrium for a range of the unions’ power larger th...

  11. Developing the Brand Entry Strategy

    Gupta, Pramesh

    2004-01-01

    With more than two decades of experience in the flashlight industry, Vinpol is all set to launch the flashlights, under their brand name, into the market. This dissertation describes a process of generating a brand entry strategy for Vinpol. A model is proposed that adapts the approach of 4Ps and Relationship Marketing. The rationale for this report has come about due to initial secondary research which shows that there will be constant growth in the flashlight industry. Some factors that nee...

  12. Marketing Mix Reactions to Entry

    Robinson, William T.

    1988-01-01

    Initial product, distribution, marketing expenditure, and price reactions by incumbents are examined for 115 entrants into oligopolistic markets. The most common reaction pattern is either no reaction or only a single reaction. It is very unusual for entrants to face reactions across the entire marketing mix. Reactions in the first two years after entry are explained as a function of the entrant's strategy, incumbent characteristics, and industry characteristics. The explanation provides insi...

  13. SPANISH COMPANY FOREIGN MARKET ENTRY

    Francisco J. Más; Felipe Ruiz Moreno

    2003-01-01

    The aim of this paper is to analyse the determinants of diversification mode (acquisition versus greenfield) through foreign direct investment considering various theories, such as those of mergers and acquisitions, transaction costs, the learning organisation, the institutional context of the company and the cultural environment of the host country, and to analyse the determinants of entry mode combining diversification mode with ownership structure decision (greenfield wholly-owned subsidia...

  14. Predicting the Diversity of Foreign Entry Modes

    Hashai, Niron; Geisler Asmussen, Christian; Benito, Gabriel;

    2007-01-01

    This paper expands entry mode literature by referring to multiple modes exerted in different value chain activities within and across host markets, rather than to a single entry mode at the host market level. Scale of operations and knowledge intensity are argued to affect firms' entry mode...... diversity across value chain activities and host markets. Analyzing a sample of Israeli based firms we show that larger firms exhibit a higher degree of entry mode diversity both across value chain activities and across host markets. Higher levels of knowledge intensity are also associated with more...... diversity in firms' entry modes across both dimensions....

  15. Atmospheric Entry Experiments at IRS

    Auweter-Kurtz, M.; Endlich, P.; Herdrich, G.; Kurtz, H.; Laux, T.; Löhle, S.; Nazina, N.; Pidan, S.

    2002-01-01

    Entering the atmosphere of celestial bodies, spacecrafts encounter gases at velocities of several km/s, thereby being subjected to great heat loads. The thermal protection systems and the environment (plasma) have to be investigated by means of computational and ground facility based simulations. For more than a decade, plasma wind tunnels at IRS have been used for the investigation of TPS materials. Nevertheless, ground tests and computer simulations cannot re- place space flights completely. Particularly, entry mission phases encounter challenging problems, such as hypersonic aerothermodynamics. Concerning the TPS, radiation-cooled materials used for reuseable spacecrafts and ablator tech- nologies are of importance. Besides the mentioned technologies, there is the goal to manage guidance navigation, con- trol, landing technology and inflatable technologies such as ballutes that aim to keep vehicles in the atmosphere without landing. The requirement to save mass and energy for planned interplanetary missions such as Mars Society Balloon Mission, Mars Sample Return Mission, Mars Express or Venus Sample Return mission led to the need for manoeuvres like aerocapture, aero-breaking and hyperbolic entries. All three are characterized by very high kinetic vehicle energies to be dissipated by the manoeuvre. In this field flight data are rare. The importance of these manoeuvres and the need to increase the knowledge of required TPS designs and behavior during such mission phases point out the need of flight experiments. As result of the experience within the plasma diagnostic tool development and the plasma wind tunnel data base, flight experiments like the PYrometric RE-entry EXperiment PYREX were developed, fully qualified and successfully flown. Flight experiments such as the entry spectrometer RESPECT and PYREX on HOPE-X are in the conceptual phase. To increase knowledge in the scope of atmospheric manoeuvres and entries, data bases have to be created combining both

  16. Endocytic Pathways Involved in Filovirus Entry: Advances, Implications and Future Directions

    Suchita Bhattacharyya

    2012-12-01

    Full Text Available Detailed knowledge of the host-virus interactions that accompany filovirus entry into cells is expected to identify determinants of viral virulence and host range, and to yield targets for the development of antiviral therapeutics. While it is generally agreed that filovirus entry into the host cytoplasm requires viral internalization into acidic endosomal compartments and proteolytic cleavage of the envelope glycoprotein by endo/lysosomal cysteine proteases, our understanding of the specific endocytic pathways co-opted by filoviruses remains limited. This review addresses the current knowledge on cellular endocytic pathways implicated in filovirus entry, highlights the consensus as well as controversies, and discusses important remaining questions.

  17. BioMagResBank databases DOCR and FRED containing converted and filtered sets of experimental NMR restraints and coordinates from over 500 protein PDB structures

    We present two new databases of NMR-derived distance and dihedral angle restraints: the Database Of Converted Restraints (DOCR) and the Filtered Restraints Database (FRED). These databases currently correspond to 545 proteins with NMR structures deposited in the Protein Databank (PDB). The criteria for inclusion were that these should be unique, monomeric proteins with author-provided experimental NMR data and coordinates available from the PDB capable of being parsed and prepared in a consistent manner. The Wattos program was used to parse the files, and the CcpNmr FormatConverter program was used to prepare them semi-automatically. New modules, including a new implementation of Aqua in the BioMagResBank (BMRB) software Wattos were used to analyze the sets of distance restraints (DRs) for inconsistencies, redundancies, NOE completeness, classification and violations with respect to the original coordinates. Restraints that could not be associated with a known nomenclature were flagged. The coordinates of hydrogen atoms were recalculated from the positions of heavy atoms to allow for a full restraint analysis. The DOCR database contains restraint and coordinate data that is made consistent with each other and with IUPAC conventions. The FRED database is based on the DOCR data but is filtered for use by test calculation protocols and longitudinal analyses and validations. These two databases are available from websites of the BMRB and the Macromolecular Structure Database (MSD) in various formats: NMR-STAR, CCPN XML, and in formats suitable for direct use in the software packages CNS and CYANA

  18. Entry Strategies, Welfare Analysis and Firms’ Behaviors

    Wang Xun; Luo Ting

    2007-01-01

    Before serving a new market, a multinational enterprise (MNE) has several entry strategies, which include foreign direct investment (FDI), joint venture (JV) and exclusive licensing (EL). Entry cost, market size of the host country, and the discount rate are the main determinants when the MNE chooses its optimal entry strategy. At a certain level of ownership share that the MNE holds, JV will generate the highest social welfare. If firms can choose between competition and collusion, at differ...

  19. Who Benefits from Store Brand Entry?

    Koen Pauwels; Shuba Srinivasan

    2004-01-01

    Store brand entry has become a key issue in marketing as it may structurally change the performance of and the interactions among all market players. Based on their multivariate time-series analysis, the authors demonstrate permanent performance effects of store brand entry, typically benefiting the retailer, the consumers, and premium-brand manufacturers, while harming second-tier brand manufacturers. For the , they consistently find two of store brand entry: . This increase in unit margins ...

  20. Foreign market entry strategies and post-entry growth: Acquisitions vs greenfield investments

    Danchi Tan

    2009-01-01

    We examine the relationship between the foreign market entry strategy and the subsequent growth of a subsidiary. We build upon the Penrose theory of firm growth, and on the organizational economics, international management, and foreign market entry strategy literatures. We hypothesize that the post-entry growth of acquisitions is positively associated with weak and codifiable interdependence within the multinational enterprise network, whereas the post-entry growth of greenfield investments ...

  1. Entry Mode and Performance of Nordic Firms

    Wulff, Jesper

    2015-01-01

    market entries made by Norwegian, Danish and Swedish firms suggests that the association between equity mode choice and non-location bound international experience diminishes in the presence of higher levels of multinational experience. Furthermore, firms whose entry mode choice is predicted by the model...

  2. Specification of the Model 3 Entry Lexicon.

    Rhode, Mary

    The Model 3 communication skills lexicon consists of three lists of words developed by the Southwest Regional Laboratory (SWRL) for use in communication skills instruction in K-6. This report documents the procedures followed in compiling the entry lexicon, the first component of the Model 3 communication skills lexicon. The entry lexicon is…

  3. 19 CFR 141.91 - Entry without required invoice.

    2010-04-01

    ... 19 Customs Duties 2 2010-04-01 2010-04-01 false Entry without required invoice. 141.91 Section 141... THE TREASURY (CONTINUED) ENTRY OF MERCHANDISE Invoices § 141.91 Entry without required invoice. If a required invoice is not available in proper form at the time the entry or entry summary documentation...

  4. Modeling late entry bias in survival analysis.

    Matsuura, Masaaki; Eguchi, Shinto

    2005-06-01

    In a failure time analysis, we sometimes observe additional study subjects who enter during the study period. These late entries are treated as left-truncated data in the statistical literature. However, with real data, there is a substantial possibility that the delayed entries may have extremely different hazards compared to the other standard subjects. We focus on a situation in which such entry bias might arise in the analysis of survival data. The purpose of the present article is to develop an appropriate methodology for making inference about data including late entries. We construct a model that includes parameters for the effect of delayed entry bias having no specification for the distribution of entry time. We also discuss likelihood inference based on this model and derive the asymptotic behavior of estimates. A simulation study is conducted for a finite sample size in order to compare the analysis results using our method with those using the standard method, where independence between entry time and failure time is assumed. We apply this method to mortality analysis among atomic bomb survivors defined in a geographical study region. PMID:16011705

  5. Optimal firm growth under the threat of entry

    Peter M. Kort; Wrzaczek, Stefan

    2015-01-01

    The paper studies the incumbent-entrant problem in a fully dynamic setting. We find that under an open-loop information structure the incumbent anticipates entry by overinvesting, whereas in the Markov perfect equilibrium the incumbent slightly underinvests in the period before the entry. The entry cost level where entry accommodation passes into entry deterrence is lower in the Markov perfect equilibrium. Further we find that the incumbent’s capital stock level needed to deter entry is hump ...

  6. Advances in spacecraft atmospheric entry guidance

    Benito Manrique, Joel

    In order to advance entry guidance technology two different research areas have been explored with the objective of increasing the reachable landing area and the landing accuracy for future Mars missions. Currently only the northern hemisphere of Mars is available for landing due to its low elevation. Only low elevation landing sites have the necessary atmospheric density to allow landing using current Entry, Descent and Landing (EDL) technology. In order to reach most of the Ancient Highlands, the majority of the southern hemisphere, advanced EDL technology is needed in multiple fields, including entry guidance. The first research area is the definition and applications of reachable and controllable sets for entry. The definition of the reachable and controllable sets provides a framework for the study of the capabilities of an entry vehicle in a given planet. Reachable and controllable sets can be used to comprehensively characterize the envelope of trajectories that a vehicle can fly, the sites it can reach and the entry states that can be accommodated. The sets can also be used for the evaluation of trajectory planning algorithms and to assist in the selection of the entry or landing sites. In essence, the reachable and controllable sets offer a powerful vehicle and trajectory analysis and design framework that allows for better mission design choices. In order to illustrate the use of the sets, they are computed for a representative Mars mission using two different vehicle configurations. The sets characterize the impact of the vehicle configuration on the entry capability. Furthermore, the sets are used to find the best skip-entry trajectory for a return from the Moon mission, highlighting the utility of the sets in atmospheric maneuvers other than entry. The second research area is the development of the components of an entry guidance algorithm that allow high elevation landing and provide as well high landing accuracy. The approach taken follows the

  7. Foreign Entry and Heterogeneous Growth of Firms

    Deng, Paul Duo; Jefferson, Gary H.

    We adopt the framework of Schumpeterian creative destruction formalized by Aghion et al. (2009) to analyze the impact of foreign entry on the productivity growth of domestic firms. In the face of foreign entry, domestic firms exhibit heterogeneous patterns of growth depending on their technological...... distance from foreign firms. Domestic firms with smaller technological distance from their foreign counterparts tend to experience faster productivity growth, while firms with larger technological distance tend to lag further behind. We test this hypothesis using a unique firm-level data of Chinese...... manufacturing. Our empirical results confirm that foreign entry indeed generates strong heterogeneous growth patterns among domestic firms....

  8. Physical security workshop summary: entry control

    Entry control hardware has been used extensively in the past to assist security forces in separating the authorized from the unauthorized at the plant perimeter. As more attention is being focused on the insider threat, these entry control elements are being used to extend the security inspectors' presence into the plant by compartmentalizing access and monitoring vital components. This paper summarizes the experiences expressed by the participants at the March 16 to 19, 1982 INMM Physical Protection Workshop in utilizing access control and contraband detection hardware for plant wide entry control applications

  9. Entry Regulation under Asymmetric Information about Demand

    Paula Sarmento

    2010-01-01

    Full Text Available We investigate how an incumbent firm can use the regulatory policy about entry and the informational advantage to protect his market position. This question is studied through the construction of a signalling game where we assume that the regulator has less information about demand than the firms. We conclude that there is a pooling equilibrium and partially separating equilibria in which entry is deterred and, if demand is high, there will be insufficient entry. The final effect on welfare depends on the tradeoff between short-run benefits (lower price and long-run losses (weaker competition.

  10. Texting while driving: is speech-based text entry less risky than handheld text entry?

    He, J; Chaparro, A; Nguyen, B; Burge, R J; Crandall, J; Chaparro, B; Ni, R; Cao, S

    2014-11-01

    Research indicates that using a cell phone to talk or text while maneuvering a vehicle impairs driving performance. However, few published studies directly compare the distracting effects of texting using a hands-free (i.e., speech-based interface) versus handheld cell phone, which is an important issue for legislation, automotive interface design and driving safety training. This study compared the effect of speech-based versus handheld text entries on simulated driving performance by asking participants to perform a car following task while controlling the duration of a secondary text-entry task. Results showed that both speech-based and handheld text entries impaired driving performance relative to the drive-only condition by causing more variation in speed and lane position. Handheld text entry also increased the brake response time and increased variation in headway distance. Text entry using a speech-based cell phone was less detrimental to driving performance than handheld text entry. Nevertheless, the speech-based text entry task still significantly impaired driving compared to the drive-only condition. These results suggest that speech-based text entry disrupts driving, but reduces the level of performance interference compared to text entry with a handheld device. In addition, the difference in the distraction effect caused by speech-based and handheld text entry is not simply due to the difference in task duration. PMID:25089769

  11. Market entry strategies into the BRIC countries

    Boyd, Britta; Dyhr Ulrich, Anna Marie

    2014-01-01

    Based on a sample of 177 exporting SMEs, this study investigates what market entry strategy is used by Danish family and non-family businesses. From a resource-based view, three critical internal factors (risk, flexibility and control) affecting the entry mode choice into the BRIC markets...... compared to non-family firms. Furthermore, the Danish exporters regarded China as being the most established of the four BRIC markets which could be seen in their willingness to use high control entry modes in China. Finally, non-family firms are more concerned about higher flexibility and lower control...... when entering the BRIC markets. In contrast, family firms choose high commitment entry modes which involve high risk and low flexibility when entering the BRIC markets. Further implications discuss the suitability of export strategies to BRIC markets for managers of Danish family and non-family firms....

  12. Adaptive Text Entry for Mobile Devices

    Proschowsky, Morten Smidt

    for mobile devices and a framework for adaptive context-aware language models. Based on analysis of current text entry methods, the requirements to the new text entry methods are established. Transparent User guided Prediction (TUP) is a text entry method for devices with one dimensional touch input....... It can be touch sensitive wheels, sliders or similar input devices. The interaction design of TUP is done with a combination of high level task models and low level models of human motor behaviour. Three prototypes of TUP are designed and evaluated by more than 30 users. Observations from the...... evaluations are used to improve the models of human motor behaviour. TUP-Key is a variant of TUP, designed for 12 key phone keyboards. It is introduced in the thesis but has not been implemented or evaluated. Both text entry methods support adaptive context-aware language models. YourText is a framework for...

  13. The Effects of Entry in Bilateral Oligopoly

    Alex Dickson

    2013-06-01

    Full Text Available The purpose of this paper is to study the effects of entry into the market for a single commodity in which both sellers and buyers are permitted to interact strategically. With the inclusion of an additional seller, the market is quasi-competitive: the price falls and volume of trade increases, as expected. However, contrary to the conventional wisdom, existing sellers’ payoffs may increase. The conditions under which entry by new sellers raises the equilibrium payoffs of existing sellers are derived. These depend in an intuitive way on the elasticity of a strategic analog of demand and the market share of existing sellers, and encompass entirely standard economic environments. Similar results are derived relating to the entry of additional buyers and the effects of entry on both sides of the market are investigated.

  14. Entry tank calibration in TOR pilot plant

    The objective of this communication is the description of calibration measurements used for determining the uranium and plutonium mass entry in the fast neutron fuel reprocessing pilot plant (TOR) of Marcoule

  15. Aerocapture Inflatable Decelerator for Planetary Entry

    Reza, Sajjad; Hund, Richard; Kustas, Frank; Willcockson, William; Songer, Jarvis; Brown, Glen

    2007-01-01

    Forward Attached Inflatable Decelerators, more commonly known as inflatable aeroshells, provide an effective, cost efficient means of decelerating spacecrafts by using atmospheric drag for aerocapture or planetary entry instead of conventional liquid propulsion deceleration systems. Entry into planetary atmospheres results in significant heating and aerodynamic pressures which stress aeroshell systems to their useful limits. Incorporation of lightweight inflatable decelerator surfaces with increased surface-area footprints provides the opportunity to reduce heat flux and induced temperatures, while increasing the payload mass fraction. Furthermore, inflatable aeroshell decelerators provide the needed deceleration at considerably higher altitudes and Mach numbers when compared with conventional rigid aeroshell entry systems. Inflatable aeroshells also provide for stowage in a compact space, with subsequent deployment of a large-area, lightweight heatshield to survive entry heating. Use of a deployable heatshield decelerator enables an increase in the spacecraft payload mass fraction and may eliminate the need for a spacecraft backshell.

  16. Border Crossing/Entry Data - Boarder Crossing

    Department of Transportation — Border Crossing/Entry Data provides summary statistics for incoming crossings at the U.S.-Canadian and the U.S.-Mexican border at the port level. Data are available...

  17. Developing Quantitative Models for Auditing Journal Entries

    Argyrou, Argyris

    2013-01-01

    The thesis examines how the auditing of journal entries can detect and prevent financial statement fraud. Financial statement fraud occurs when an intentional act causes financial statements to be materially misstated. Although it is not a new phenomenon, financial statement fraud has attracted much publicity in the wake of numerous cases of financial malfeasance (e.g. ENRON, WorldCom). Existing literature has provided limited empirical evidence on the link between auditing journal entrie...

  18. Entry and exit decisions under uncertainty

    Kongsted, Hans Christian

    1996-01-01

    This paper establishes the general deterministic limit that corresponds to Dixit's model of entry and exit decisions under uncertainty. The interlinked nature of decisions is shown to be essential also in the deterministic limit. A numerical example illustrates the result......This paper establishes the general deterministic limit that corresponds to Dixit's model of entry and exit decisions under uncertainty. The interlinked nature of decisions is shown to be essential also in the deterministic limit. A numerical example illustrates the result...

  19. Market Structure and Entry: Where's the Beef?.

    Toivanen, O.; Waterson, M

    2001-01-01

    We study the effects of market structure on entry using data from the UK fast food (counter-service burger)industry over the years 1991-1995. Over this period, the market can be characterized as a duopoly. We find that market structure matters greatly: for both firms, rival presence increases the probability of entry. We control for market specific time-invariant unobservable and their correlation with existing outlets of both firms through a variety of methods.

  20. Entry Modes for British MNCs into China

    Phillips, Alexander

    2013-01-01

    China has undergone massive economic reforms and institutional changes over the last 3 decades. Increasingly liberalized government regulations and the opening up of the Chinese market have attracted British MNCs to enter into this ‘dream market’. This paper seeks to primarily explore the factors that affect the entry mode selection of British MNCs. It will also seek to investigate how the current institutional environment affects entry mode selection. This paper uses a case study method to a...

  1. Entry modes of European firms in Vietnam

    Daniel Simonet

    2012-01-01

    Purpose: The purpose of the paper is to explore the entry modes of EU firms setting up operations in Vietnam. Design/methodology/approach: we use a case study approach on Haymarket, Cadbury, Creative Education, Fairchild, Aventis and Artemisinin and Farming International using interviews from managerial professionals in Vietnam. Findings: Despite the fact that Vietnam has been opening up for more than 20 years, licensing is the preferred entry mode because of the risks involved in ventur...

  2. Predecessors of Double-Entry Accounting

    Mykhaylo Kuter; Maryna Gurskaya; Artem Musaelyan

    2013-01-01

    The article covers analysis of some historically significant issues of accounting development in the home-country of contemporary accounting made with reference to the archived materials found in Italy. In particular, the issue of purpose and order of taking entries in the book titled 'RICORDANZE' ('Memorials') has been considered. Resulting from the analysis done, the significance has been grounded for keeping accounting records which do not subject to double-entry principle thus being busin...

  3. Double Entry in Accounting of Small Businesses

    Gogol Tatyana A.

    2013-01-01

    The article states that a separate category of small businesses (starting from 2011) acquired the right to conduct simplified accounting of income and expenses without application of the plan of accounts and method of double entry. Analysis of literature sources allowed drawing a conclusion that it is impossible to imagine development of accounting without the use of the method of double entry and appearance of various theories regarding the reasons of its appearance. Having analysed methods ...

  4. Global Strategy and Multinationals' Entry Mode Choice

    W. Chan Kim; Peter Hwang

    1992-01-01

    This paper makes a case directed towards establishing the importance of global strategic considerations in choosing multinationals' entry mode. Specifically, it is our contention that beyond the environmental and transaction-specific factors well established in the literature to affect the entry mode decision, we should also consider the strategic relationship a multinational envisages between its operations across borders in reaching this decision. After incorporating various global strategi...

  5. Entry and Exit in a Liberalised Market

    Maria José Gil-Moltó; Claudio A. Piga

    2007-01-01

    We analyse the entry and exit activity in the UK airline markets in the post-liberalisation period and study the differential traits between traditional and low cost carriers. Alongside with the characteristics traditionally highlighted as determinants of entry (e.g., airport presence and network economies), we find that the existence of charter or seasonal operators, product differentiation opportunities and the level of quality provided by the incumbents are also relevant in explaining entr...

  6. Setting up a large set of protein-ligand PDB complexes for the development and validation of knowledge-based docking algorithms

    Aguilera Longendri

    2007-08-01

    Full Text Available Abstract Background The number of algorithms available to predict ligand-protein interactions is large and ever-increasing. The number of test cases used to validate these methods is usually small and problem dependent. Recently, several databases have been released for further understanding of protein-ligand interactions, having the Protein Data Bank as backend support. Nevertheless, it appears to be difficult to test docking methods on a large variety of complexes. In this paper we report the development of a new database of protein-ligand complexes tailored for testing of docking algorithms. Methods Using a new definition of molecular contact, small ligands contained in the 2005 PDB edition were identified and processed. The database was enriched in molecular properties. In particular, an automated typing of ligand atoms was performed. A filtering procedure was applied to select a non-redundant dataset of complexes. Data mining was performed to obtain information on the frequencies of different types of atomic contacts. Docking simulations were run with the program DOCK. Results We compiled a large database of small ligand-protein complexes, enriched with different calculated properties, that currently contains more than 6000 non-redundant structures. As an example to demonstrate the value of the new database, we derived a new set of chemical matching rules to be used in the context of the program DOCK, based on contact frequencies between ligand atoms and points representing the protein surface, and proved their enhanced efficiency with respect to the default set of rules included in that program. Conclusion The new database constitutes a valuable resource for the development of knowledge-based docking algorithms and for testing docking programs on large sets of protein-ligand complexes. The new chemical matching rules proposed in this work significantly increase the success rate in DOCKing simulations. The database developed in this work is

  7. “Fuzzy oil drop” model applied to individual small proteins built of 70 amino acids

    Prymula, Katarzyna; Sałapa, Kinga; Roterman, Irena

    2010-01-01

    Abstract The proteins composed of short polypeptides (about 70 amino acid residues) representing the following functional groups (according to PDB notation): growth hormones, serine protease inhibitors, antifreeze proteins, chaperones and proteins of unknown function, were selected for structural and functional analysis. Classification based on the distribution of hydrophobicity in terms of deficiency/excess as the measure of structural and functional specificity is presented. The ...

  8. Fatty acid induced remodeling within the human liver fatty acid-binding protein.

    Sharma, Ashwani; Sharma, Amit

    2011-09-01

    We crystallized human liver fatty acid-binding protein (LFABP) in apo, holo, and intermediate states of palmitic acid engagement. Structural snapshots of fatty acid recognition, entry, and docking within LFABP support a heads-in mechanism for ligand entry. Apo-LFABP undergoes structural remodeling, where the first palmitate ingress creates the atomic environment for placement of the second palmitate. These new mechanistic insights will facilitate development of pharmacological agents against LFABP. PMID:21757748

  9. Fatty Acid Induced Remodeling within the Human Liver Fatty Acid-binding Protein*

    Sharma, Ashwani; Sharma, Amit

    2011-01-01

    We crystallized human liver fatty acid-binding protein (LFABP) in apo, holo, and intermediate states of palmitic acid engagement. Structural snapshots of fatty acid recognition, entry, and docking within LFABP support a heads-in mechanism for ligand entry. Apo-LFABP undergoes structural remodeling, where the first palmitate ingress creates the atomic environment for placement of the second palmitate. These new mechanistic insights will facilitate development of pharmacological agents against ...

  10. Role of endocytosis and cathepsin-mediated activation in Nipah virus entry

    The recent discovery that the Nipah virus (NiV) fusion protein (F) is activated by endosomal cathepsin L raised the question if NiV utilize pH- and protease-dependent mechanisms of entry. We show here that the NiV receptor ephrin B2, virus-like particles and infectious NiV are internalized from the cell surface. However, endocytosis, acidic pH and cathepsin-mediated cleavage are not necessary for the initiation of infection of new host cells. Our data clearly demonstrate that proteolytic activation of the NiV F protein is required before incorporation into budding virions but not after virus entry