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    556 results match your criteria BMC Structural Biology [Journal]

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    Functional insights from proteome-wide structural modeling of Treponema pallidum subspecies pallidum, the causative agent of syphilis.
    BMC Struct Biol 2018 May 16;18(1). Epub 2018 May 16.
    Department of Biochemistry and Microbiology, University of Victoria, Victoria, British Columbia, Canada.
    Background: Syphilis continues to be a major global health threat with 11 million new infections each year, and a global burden of 36 million cases. The causative agent of syphilis, Treponema pallidum subspecies pallidum, is a highly virulent bacterium, however the molecular mechanisms underlying T. pallidum pathogenesis remain to be definitively identified. Read More

    Structure activity relationship (SAR) and quantitative structure activity relationship (QSAR) studies showed plant flavonoids as potential inhibitors of dengue NS2B-NS3 protease.
    BMC Struct Biol 2018 Apr 19;18(1). Epub 2018 Apr 19.
    Virology Lab, Centre of Agricultural Biochemistry and Biotechnology, University of Agriculture, Jail road, Faisalabad, 38000, Pakistan.
    Background: Due to dengue virus disease, half of the world population is at severe health risk. Viral encoded NS2B-NS3 protease complex causes cleavage in the nonstructural region of the viral polyprotein. The cleavage is essentially required for fully functional viral protein. Read More

    Three-dimensional models of Mycobacterium tuberculosis proteins Rv1555, Rv1554 and their docking analyses with sildenafil, tadalafil, vardenafil drugs, suggest interference with quinol binding likely to affect protein's function.
    BMC Struct Biol 2018 Apr 18;18(1). Epub 2018 Apr 18.
    Kunchur Guruprasad, Bioinformatics, Centre for Cellular and Molecular Biology (CCMB), Uppal Road, Hyderabad, 500007, India.
    Background: Earlier based on bioinformatics analyses, we had predicted the Mycobacterium tuberculosis (M.tb) proteins; Rv1555 and Rv1554, among the potential new tuberculosis drug targets. According to the 'TB-drugome' the Rv1555 protein is 'druggable' with sildenafil (Viagra), tadalafil (Cialis) and vardenafil (Levitra) drugs. Read More

    re-TAMD: exploring interactions between H3 peptide and YEATS domain using enhanced sampling.
    BMC Struct Biol 2018 Apr 3;18(1). Epub 2018 Apr 3.
    Unité de Bioinformatique Structurale, UMR CNRS 3528 and Institut Pasteur, Paris, France.
    Background: Analysis of preferred binding regions of a ligand on a protein is important for detecting cryptic binding pockets and improving the ligand selectivity.

    Result: The enhanced sampling approach TAMD has been adapted to allow a ligand to unbind from its native binding site and explore the protein surface. This so-called re-TAMD procedure was then used to explore the interaction between the N terminal peptide of histone H3 and the YEATS domain. Read More

    Correction to: selected articles from Belyaev Conference 2017: structural biology.
    BMC Struct Biol 2018 Mar 21;18(1). Epub 2018 Mar 21.
    The Federal Research Center Institute of Cytology and Genetics, The Siberian Branch of the Russian Academy of Sciences, 630090, Novosibirsk, Russia.
    After publication of the article [1], it has been brought to our attention that there is a discrepancy between the publication date on the pdf and online formats. The date on the pdf is 6th February 2018 and online is 5th February 2018. The correct publication date is the one on the pdf, 6th February 2018. Read More

    A structural preview of aquaporin 8 via homology modeling of seven vertebrate isoforms.
    BMC Struct Biol 2018 Feb 17;18(1). Epub 2018 Feb 17.
    Division of Biochemistry and Structural Biology, Center for Molecular Protein Science, Department of Chemistry, Lund University, Box 124, SE-221 00, Lund, Sweden.
    Background: Aquaporins (AQPs) facilitate the passage of small neutral polar molecules across membranes of the cell. In animals there are four distinct AQP subfamilies, whereof AQP8 homologues constitute one of the smallest subfamilies with just one member in man. AQP8 conducts water, ammonia, urea, glycerol and HO through various membranes of animal cells. Read More

    Molecular mechanisms underlying the impact of mutations in SOD1 on its conformational properties associated with amyotrophic lateral sclerosis as revealed with molecular modelling.
    BMC Struct Biol 2018 02 5;18(Suppl 1). Epub 2018 Feb 5.
    The Federal Research Center Institute of Cytology and Genetics, The Siberian Branch of the Russian Academy of Sciences, 630090, Novosibirsk, Russia.
    Background: So far, little is known about the molecular mechanisms of amyotrophic lateral sclerosis onset and progression caused by SOD1 mutations. One of the hypotheses is based on SOD1 misfolding resulting from mutations and subsequent deposition of its cytotoxic aggregates. This hypothesis is complicated by the fact that known SOD1 mutations of similar clinical effect could be distributed over the whole protein structure. Read More

    Leishmania infantum 5'-Methylthioadenosine Phosphorylase presents relevant structural divergence to constitute a potential drug target.
    BMC Struct Biol 2017 Dec 19;17(1). Epub 2017 Dec 19.
    Laboratory of Molecular Epidemiology and Experimental Pathology (LR11IPT04/ LR16IPT04), Institut Pasteur de Tunis, Université de Tunis El Manar, Tunis, Tunisia.
    Background: The 5'-methylthioadenosine phosphorylase (MTAP), an enzyme involved in purine and polyamine metabolism and in the methionine salvage pathway, is considered as a potential drug target against cancer and trypanosomiasis. In fact, Trypanosoma and Leishmania parasites lack de novo purine pathways and rely on purine salvage pathways to meet their requirements. Herein, we propose the first comprehensive bioinformatic and structural characterization of the putative Leishmania infantum MTAP (LiMTAP), using a comparative computational approach. Read More

    Rosetta Broker for membrane protein structure prediction: concentrative nucleoside transporter 3 and corticotropin-releasing factor receptor 1 test cases.
    BMC Struct Biol 2017 Aug 3;17(1). Epub 2017 Aug 3.
    Faculty of Chemistry, University of Warsaw, Pasteur St. 1, 02-093, Warsaw, Poland.
    Background: Membrane proteins are difficult targets for structure prediction due to the limited structural data deposited in Protein Data Bank. Most computational methods for membrane protein structure prediction are based on the comparative modeling. There are only few de novo methods targeting that distinct protein family. Read More

    A computational assessment of pH-dependent differential interaction of T7 lysozyme with T7 RNA polymerase.
    BMC Struct Biol 2017 May 25;17(1). Epub 2017 May 25.
    Centre for Bioinformatics, School of Life Sciences, Pondicherry University, Puducherry, 605014, India.
    Background: T7 lysozyme (T7L), also known as N-acetylmuramoyl-L-alanine amidase, is a T7 bacteriophage gene product. It involves two functions: It can cut amide bonds in the bacterial cell wall and interacts with T7 RNA polymerase (T7RNAP) as a part of transcription inhibition. In this study, with the help of molecular dynamics (MD) calculations and computational interaction studies, we investigated the effect of varying pH conditions on conformational flexibilities of T7L and their influence on T7RNAP -T7L interactions. Read More

    Destabilization of the TWIST1/E12 complex dimerization following the R154P point-mutation of TWIST1: an in silico approach.
    BMC Struct Biol 2017 May 18;17(1). Epub 2017 May 18.
    Inserm UMR-S1052, Centre de Recherche en Cancérologie de Lyon, Lyon, 69373, France.
    Background: The bHLH transcription factor TWIST1 plays a key role in the embryonic development and in tumorigenesis. Some loss-of-function mutations of the TWIST1 gene have been shown to cause an autosomal dominant craniosynostosis, known as the Saethre-Chotzen syndrome (SCS). Although the functional impacts of many TWIST1 mutations have been experimentally reported, little is known on the molecular mechanisms underlying their loss-of-function. Read More

    Molecular dynamics simulation of the opposite-base preference and interactions in the active site of formamidopyrimidine-DNA glycosylase.
    BMC Struct Biol 2017 May 8;17(1). Epub 2017 May 8.
    SB RAS Institute of Chemical Biology and Fundamental Medicine, 8 Lavrentieva Ave., Novosibirsk, 630090, Russia.
    Background: Formamidopyrimidine-DNA glycosylase (Fpg) removes abundant pre-mutagenic 8-oxoguanine (oxoG) bases from DNA through nucleophilic attack of its N-terminal proline at C1' of the damaged nucleotide. Since oxoG efficiently pairs with both C and A, Fpg must excise oxoG from pairs with C but not with A, otherwise a mutation occurs. The crystal structures of several Fpg-DNA complexes have been solved, yet no structure with A opposite the lesion is available. Read More

    REFOLDdb: a new and sustainable gateway to experimental protocols for protein refolding.
    BMC Struct Biol 2017 Apr 24;17(1). Epub 2017 Apr 24.
    Center for Information Biology, National Institute of Genetics, 1111 Yata Mishima, Shizuoka, 411-8540, Japan.
    Background: More than 7000 papers related to "protein refolding" have been published to date, with approximately 300 reports each year during the last decade. Whilst some of these papers provide experimental protocols for protein refolding, a survey in the structural life science communities showed a necessity for a comprehensive database for refolding techniques. We therefore have developed a new resource - "REFOLDdb" that collects refolding techniques into a single, searchable repository to help researchers develop refolding protocols for proteins of interest. Read More

    A comparative analysis of the foamy and ortho virus capsid structures reveals an ancient domain duplication.
    BMC Struct Biol 2017 Apr 4;17(1). Epub 2017 Apr 4.
    Macromolecular Structure Laboratory, Francis Crick Institute, Midland Road, London, NW1 1AT, UK.
    Background: The Spumaretrovirinae (foamy viruses) and the Orthoretrovirinae (e.g. HIV) share many similarities both in genome structure and the sequences of the core viral encoded proteins, such as the aspartyl protease and reverse transcriptase. Read More

    DynaDom: structure-based prediction of T cell receptor inter-domain and T cell receptor-peptide-MHC (class I) association angles.
    BMC Struct Biol 2017 Feb 2;17(1). Epub 2017 Feb 2.
    Department of Biosciences and Center for Integrated Protein Science Munich, Technische Universität München, Emil-Erlenmeyer-Forum 8, 85354, Freising, Germany.
    Background: T cell receptor (TCR) molecules are involved in the adaptive immune response as they distinguish between self- and foreign-peptides, presented in major histocompatibility complex molecules (pMHC). Former studies showed that the association angles of the TCR variable domains (Vα/Vβ) can differ significantly and change upon binding to the pMHC complex. These changes can be described as a rotation of the domains around a general Center of Rotation, characterized by the interaction of two highly conserved glutamine residues. Read More

    Prokaryotic ubiquitin-like protein remains intrinsically disordered when covalently attached to proteasomal target proteins.
    BMC Struct Biol 2017 Feb 1;17(1). Epub 2017 Feb 1.
    ETH Zurich, Institute of Molecular Biology & Biophysics, Zürich, CH-8093, Switzerland.
    Background: The post-translational modification pathway referred to as pupylation marks proteins for proteasomal degradation in Mycobacterium tuberculosis and other actinobacteria by covalently attaching the small protein Pup (prokaryotic ubiquitin-like protein) to target lysine residues. In contrast to the functionally analogous eukaryotic ubiquitin, Pup is intrinsically disordered in its free form. Its unfolded state allows Pup to adopt different structures upon interaction with different binding partners like the Pup ligase PafA and the proteasomal ATPase Mpa. Read More

    Controlled dehydration improves the diffraction quality of two RNA crystals.
    BMC Struct Biol 2016 11 3;16(1):19. Epub 2016 Nov 3.
    Department of Chemistry, The Scripps Research Institute, Scripps Florida, 130 Scripps Way, Jupiter, FL, 33458, USA.
    Background: Post-crystallization dehydration methods, applying either vapor diffusion or humidity control devices, have been widely used to improve the diffraction quality of protein crystals. Despite the fact that RNA crystals tend to diffract poorly, there is a dearth of reports on the application of dehydration methods to improve the diffraction quality of RNA crystals.

    Results: We use dehydration techniques with a Free Mounting System (FMS, a humidity control device) to recover the poor diffraction quality of RNA crystals. Read More

    Combined small angle X-ray solution scattering with atomic force microscopy for characterizing radiation damage on biological macromolecules.
    BMC Struct Biol 2016 10 27;16(1):18. Epub 2016 Oct 27.
    European Molecular Biology Laboratory, 71 Avenue des Martyrs, Grenoble, 38000, France.
    Background: Synchrotron radiation facilities are pillars of modern structural biology. Small-Angle X-ray scattering performed at synchrotron sources is often used to characterize the shape of biological macromolecules. A major challenge with high-energy X-ray beam on such macromolecules is the perturbation of sample due to radiation damage. Read More

    The C-terminal domain of TPX2 is made of alpha-helical tandem repeats.
    BMC Struct Biol 2016 10 26;16(1):17. Epub 2016 Oct 26.
    Faculty of Biology, Johannes-Gutenberg University, Gresemundweg 2, 55128, Mainz, Germany.
    Background: TPX2 (Targeting Protein for Xklp2) is essential for spindle assembly, activation of the mitotic kinase Aurora A and for triggering microtubule nucleation. Homologs of TPX2 in Chordata and plants were previously identified. Currently, proteins of the TPX2 family have little structural information and only small parts are covered by defined protein domains. Read More

    Human sex hormone-binding globulin as a potential target of alternate plasticizers: an in silico study.
    BMC Struct Biol 2016 09 30;16(Suppl 1):15. Epub 2016 Sep 30.
    King Fahd Medical Research Center, King Abdulaziz University, PO Box 80216, 21589, Jeddah, Kingdom of Saudi Arabia.
    Background: Currently, alternate plasticizers are used to replace phthalate plasticizers in children's toys, medical equipments and food packaging, due to the adverse effects of phthalate compounds on human health and laws prohibiting their use. Current information regarding the safety and potential adverse effects of alternate plasticizers is limited and recent studies have found alternate plasticizers to display similar characteristics to those observed in phthalate plasticizers. This study was undertaken to evaluate and predict the potential endocrine disrupting activity of the three most commonly used alternate plasticizers: di(2-ethylhexyl)terephthalate (DEHT), tris(2-ethylhexyl)trimellitate (TOTM), and diisononyl hexahydrophthalate (DINCH) against human sex hormone-binding globulin (SHBG) using in silico approaches. Read More

    Endocrine disruption: In silico perspectives of interactions of di-(2-ethylhexyl)phthalate and its five major metabolites with progesterone receptor.
    BMC Struct Biol 2016 09 30;16(Suppl 1):16. Epub 2016 Sep 30.
    Centre of Excellence in Genomic Medicine Research, King Abdulaziz University, Jeddah, Kingdom of Saudi Arabia.
    Background: Di-(2-ethylhexyl)phthalate (DEHP) is a common endocrine disrupting compound (EDC) present in the environment as a result of industrial activity and leaching from polyvinyl products. DEHP is used as a plasticizer in medical devices and many commercial and household items. Exposure occurs through inhalation, ingestion, and skin contact. Read More

    A lack of peptide binding and decreased thermostability suggests that the CASKIN2 scaffolding protein SH3 domain may be vestigial.
    BMC Struct Biol 2016 09 13;16:14. Epub 2016 Sep 13.
    Department of Biology, York University, 4700 Keele Street, Toronto, ON, M3J 1P3, Canada.
    Background: CASKIN2 is a neuronal signaling scaffolding protein comprised of multiple ankyrin repeats, two SAM domains, and one SH3 domain. The CASKIN2 SH3 domain for an NMR structural determination because its peptide-binding cleft appeared to deviate from the repertoire of aromatic enriched amino acids that typically bind polyproline-rich sequences.

    Results: The structure demonstrated that two non-canonical basic amino acids (K290/R319) in the binding cleft were accommodated well in the SH3 fold. Read More

    Conservation of the C-type lectin fold for accommodating massive sequence variation in archaeal diversity-generating retroelements.
    BMC Struct Biol 2016 08 31;16(1):13. Epub 2016 Aug 31.
    Department of Chemistry & Biochemistry, University of California, San Diego, La Jolla, CA, 92093, USA.
    Background: Diversity-generating retroelements (DGRs) provide organisms with a unique means for adaptation to a dynamic environment through massive protein sequence variation. The potential scope of this variation exceeds that of the vertebrate adaptive immune system. DGRs were known to exist only in viruses and bacteria until their recent discovery in archaea belonging to the 'microbial dark matter', specifically in organisms closely related to Nanoarchaeota. Read More

    3D QSAR, pharmacophore and molecular docking studies of known inhibitors and designing of novel inhibitors for M18 aspartyl aminopeptidase of Plasmodium falciparum.
    BMC Struct Biol 2016 08 17;16:12. Epub 2016 Aug 17.
    School of Computational and Integrative Sciences, Jawaharlal Nehru University, New Delhi, 110067, India.
    Background: The Plasmodium falciparum M18 Aspartyl Aminopeptidase (PfM18AAP) is only aspartyl aminopeptidase which is found in the genome of P. falciparum and is essential for its survival. The PfM18AAP enzyme performs various functions in the parasite and the erythrocytic host such as hemoglobin digestion, erythrocyte invasion, parasite growth and parasite escape from the host cell. Read More

    Comprehensive analysis of the Co-structures of dipeptidyl peptidase IV and its inhibitor.
    BMC Struct Biol 2016 08 5;16:11. Epub 2016 Aug 5.
    School of Pharmacy, Kitasato University, 5-9-1 Shirokane, Minato-ku, Tokyo, 108-8641, Japan.
    Background: We comprehensively analyzed X-ray cocrystal structures of dipeptidyl peptidase IV (DPP-4) and its inhibitor to clarify whether DPP-4 alters its general or partial structure according to the inhibitor used and whether DPP-4 has a common rule for inhibitor binding.

    Results: All the main and side chains in the inhibitor binding area were minimally altered, except for a few side chains, despite binding to inhibitors of various shapes. Some residues (Arg125, Glu205, Glu206, Tyr662 and Asn710) in the area had binding modes to fix a specific atom of inhibitor to a particular spatial position in DPP-4. Read More

    Investigation of allosteric coupling in human β2-adrenergic receptor in the presence of intracellular loop 3.
    BMC Struct Biol 2016 07 2;16(1). Epub 2016 Jul 2.
    Department of Bioinformatics and Genetics, Faculty of Natural Sciences and Engineering, Kadir Has University, Cibali, 34083, Istanbul, Turkey.
    Background: This study investigates the allosteric coupling that exists between the intra- and extracellular parts of human β2-adrenergic receptor (β2-AR), in the presence of the intracellular loop 3 (ICL3), which is missing in all crystallographic experiments and most of the simulation studies reported so far. Our recent 1 μs long MD run has revealed a transition to the so-called very inactive state of the receptor, in which ICL3 packed under the G protein's binding cavity and completely blocked its accessibility to G protein. Simultaneously, an outward tilt of transmembrane helix 5 (TM5) caused an expansion of the extracellular ligand-binding site. Read More

    Comparison of human and mouse E-selectin binding to Sialyl-Lewis(x).
    BMC Struct Biol 2016 07 2;16(1):10. Epub 2016 Jul 2.
    Meinig School of Biomedical Engineering, Cornell University, Ithaca, NY, USA.
    Background: During inflammation, leukocytes are captured by the selectin family of adhesion receptors lining blood vessels to facilitate exit from the bloodstream. E-selectin is upregulated on stimulated endothelial cells and binds to several ligands on the surface of leukocytes. Selectin:ligand interactions are mediated in part by the interaction between the lectin domain and Sialyl-Lewis x (sLe(x)), a tetrasaccharide common to selectin ligands. Read More

    Crystal structure of human S100A8 in complex with zinc and calcium.
    BMC Struct Biol 2016 06 1;16(1). Epub 2016 Jun 1.
    Department of Molecular Biology and Genetics, Aarhus University, Gustav Wieds Vej 10C, DK-8000, Aarhus, Denmark.
    Background: S100 proteins are a large family of calcium binding proteins present only in vertebrates. They function intra- and extracellularly both as regulators of homeostatic processes and as potent effectors during inflammation. Among these, S100A8 and S100A9 are two major constituents of neutrophils that can assemble into homodimers, heterodimers and higher oligomeric species, including fibrillary structures found in the ageing prostate. Read More

    Structural determinant for inducing RORgamma specific inverse agonism triggered by a synthetic benzoxazinone ligand.
    BMC Struct Biol 2016 06 1;16(1). Epub 2016 Jun 1.
    Chemical and Molecular Therapeutics, Biogen Inc, 250 Binney Street, Cambridge, MA, 02142, USA.
    Background: The nuclear hormone receptor RORγ regulates transcriptional genes involved in the production of the pro-inflammatory interleukin IL-17 which has been linked to autoimmune diseases such as rheumatoid arthritis, multiple sclerosis and inflammatory bowel disease. This transcriptional activity of RORγ is modulated through a protein-protein interaction involving the activation function 2 (AF2) helix on the ligand binding domain of RORγ and a conserved LXXLL helix motif on coactivator proteins. Our goal was to develop a RORγ specific inverse agonist that would help down regulate pro-inflammatory gene transcription by disrupting the protein protein interaction with coactivator proteins as a therapeutic agent. Read More

    Erratum to: Structuprint: a scalable and extensible tool for two-dimensional representation of protein surfaces.
    BMC Struct Biol 2016 Mar 11;16. Epub 2016 Mar 11.
    IMGT®, The International ImMunoGeneTics Information System®, Université de Montpellier, Laboratoire d'ImmunoGénétique Moléculaire LIGM, UPR CNRS 1142, Institut de Génétique Humaine, Montpellier, France.

    Structures of EccB1 and EccD1 from the core complex of the mycobacterial ESX-1 type VII secretion system.
    BMC Struct Biol 2016 Feb 27;16. Epub 2016 Feb 27.
    Department of Molecular & Cellular Biochemistry and Center for Structural Biology, University of Kentucky, 741 South Limestone, Lexington, KY, 40536, USA.
    Background: The ESX-1 type VII secretion system is an important determinant of virulence in pathogenic mycobacteria, including Mycobacterium tuberculosis. This complicated molecular machine secretes folded proteins through the mycobacterial cell envelope to subvert the host immune response. Despite its important role in disease very little is known about the molecular architecture of the ESX-1 secretion system. Read More

    Structuprint: a scalable and extensible tool for two-dimensional representation of protein surfaces.
    BMC Struct Biol 2016 Feb 24;16. Epub 2016 Feb 24.
    IMGT®, The International ImMunoGeneTics Information System®, Université de Montpellier, Laboratoire d'ImmunoGénétique Moléculaire LIGM, UPR CNRS 1142, Institut de Génétique Humaine, Montpellier, France.
    Background: The term 'molecular cartography' encompasses a family of computational methods for two-dimensional transformation of protein structures and analysis of their physicochemical properties. The underlying algorithms comprise multiple manual steps, whereas the few existing implementations typically restrict the user to a very limited set of molecular descriptors.

    Results: We present Structuprint, a free standalone software that fully automates the rendering of protein surface maps, given - at the very least - a directory with a PDB file and an amino acid property. Read More

    Crystal structure and functional implications of the tandem-type universal stress protein UspE from Escherichia coli.
    BMC Struct Biol 2016 Feb 11;16. Epub 2016 Feb 11.
    Department of Bioengineering, College of Life Science, Dalian Nationalities University, Dalian, 116600, Liaoning, China.
    Background: The universal stress proteins (USP) family member UspE is a tandem-type USP that consists of two Usp domains. The UspE expression levels of the Escherichia coli (E. coli) become elevated in response to oxidative stress and DNA damaging agents, including exposure to mitomycin C, cadmium, and hydrogen peroxide. Read More

    A direct interaction between NQO1 and a chemotherapeutic dimeric naphthoquinone.
    BMC Struct Biol 2016 Jan 28;16. Epub 2016 Jan 28.
    Department of Biochemistry and Molecular Biology, University of Maryland School of Medicine, Baltimore, MD, 21201, USA.
    Background: Multimeric naphthoquinones are redox-active compounds that exhibit antineoplastic, antiprotozoal, and antiviral activities. Due to their multimodal effect on perturbation of cellular oxidative state, these compounds hold great potential as therapeutic agents against highly proliferative neoplastic cells. In our previous work, we developed a series of novel dimeric naphthoquinones and showed that they were selectively cytotoxic to human acute myeloid leukemia (AML), breast and prostate cancer cell lines. Read More

    The crystal structure of the Hazara virus nucleocapsid protein.
    BMC Struct Biol 2015 Dec 29;15:24. Epub 2015 Dec 29.
    School of Molecular and Cellular Biology, Faculty of Biological Sciences, and Astbury Centre for Molecular and Structural Biology, University of Leeds, Leeds, LS2 9JT, UK.
    Background: Hazara virus (HAZV) is a member of the Bunyaviridae family of segmented negative stranded RNA viruses, and shares the same serogroup as Crimean-Congo haemorrhagic fever virus (CCHFV). CCHFV is responsible for fatal human disease with a mortality rate approaching 30 %, which has an increased recent incidence within southern Europe. There are no preventative or therapeutic treatments for CCHFV-mediated disease, and thus CCHFV is classified as a hazard group 4 pathogen. Read More

    Predicted binding site information improves model ranking in protein docking using experimental and computer-generated target structures.
    BMC Struct Biol 2015 Nov 23;15:23. Epub 2015 Nov 23.
    Department of Biological Sciences, Louisiana State University, Baton Rouge, LA, 70803, USA.
    Background: Protein-protein interactions (PPIs) mediate the vast majority of biological processes, therefore, significant efforts have been directed to investigate PPIs to fully comprehend cellular functions. Predicting complex structures is critical to reveal molecular mechanisms by which proteins operate. Despite recent advances in the development of new methods to model macromolecular assemblies, most current methodologies are designed to work with experimentally determined protein structures. Read More

    Clustering and percolation in protein loop structures.
    BMC Struct Biol 2015 Oct 29;15:22. Epub 2015 Oct 29.
    Department of Physics and Astronomy, Uppsala University, P.O. Box 803, Uppsala, S-75108, Sweden.
    Background: High precision protein loop modelling remains a challenge, both in template based and template independent approaches to protein structure prediction.

    Method: We introduce the concepts of protein loop clustering and percolation, to develop a quantitative approach to systematically classify the modular building blocks of loops in crystallographic folded proteins. These fragments are all different parameterisations of a unique kink solution to a generalised discrete nonlinear Schrödinger (DNLS) equation. Read More

    The origin of β-strand bending in globular proteins.
    BMC Struct Biol 2015 Oct 22;15:21. Epub 2015 Oct 22.
    Department of Bioinformatics, Soka University, 1-236 Tangi-cho, Hachioji, Tokyo, 192-8577, Japan.
    Background: Many β-strands are not flat but bend and/or twist. However, although almost all β-strands have a twist, not all have a bend, suggesting that the underlying force(s) driving β-strand bending is distinct from that for the twist. We, therefore, investigated the physical origin(s) of β-strand bends. Read More

    Three-dimensional structure model and predicted ATP interaction rewiring of a deviant RNA ligase 2.
    BMC Struct Biol 2015 Oct 9;15:20. Epub 2015 Oct 9.
    Department of Biochemistry and Robert-Cedergren Centre for Bioinformatics and Genomics, Université de Montréal, Montreal, QC, Canada.
    Background: RNA ligases 2 are scarce and scattered across the tree of life. Two members of this family are well studied: the mitochondrial RNA editing ligase from the parasitic trypanosomes (Kinetoplastea), a promising drug target, and bacteriophage T4 RNA ligase 2, a workhorse in molecular biology. Here we report the identification of a divergent RNA ligase 2 (DpRNL) from Diplonema papillatum (Diplonemea), a member of the kinetoplastids' sister group. Read More

    The crystal structure of JNK from Drosophila melanogaster reveals an evolutionarily conserved topology with that of mammalian JNK proteins.
    BMC Struct Biol 2015 Sep 16;15:17. Epub 2015 Sep 16.
    Institute of Molecular Biosciences, Mahidol University, Salaya, Phuttamonthon, Nakhon Pathom, 73170, Thailand.
    Background: The c-Jun N-terminal kinases (JNKs), members of the mitogen-activated protein kinase (MAPK) family, engage in diverse cellular responses to signals produced under normal development and stress conditions. In Drosophila, only one JNK member is present, whereas ten isoforms from three JNK genes (JNK1, 2, and 3) are present in mammalian cells. To date, several mammalian JNK structures have been determined, however, there has been no report of any insect JNK structure. Read More

    An intact helical domain is required for Gα14 to stimulate phospholipase Cβ.
    BMC Struct Biol 2015 Sep 16;15:18. Epub 2015 Sep 16.
    Division of Life Science and the Biotechnology Research Institute, Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong.
    Background: Stimulation of phospholipase Cβ (PLCβ) by the activated α-subunit of Gq (Gαq) constitutes a major signaling pathway for cellular regulation, and structural studies have recently revealed the molecular interactions between PLCβ and Gαq. Yet, most of the PLCβ-interacting residues identified on Gαq are not unique to members of the Gαq family. Molecular modeling predicts that the core PLCβ-interacting residues located on the switch regions of Gαq are similarly positioned in Gαz which does not stimulate PLCβ. Read More

    Free fatty acid receptors: structural models and elucidation of ligand binding interactions.
    BMC Struct Biol 2015 Sep 7;15:16. Epub 2015 Sep 7.
    Molecular Therapeutics, School of Pharmacy, Medical Biology Centre, Queen's University Belfast, Belfast, BT9 7BL, Northern Ireland, UK.
    Background: The free fatty acid receptors (FFAs), including FFA1 (orphan name: GPR40), FFA2 (GPR43) and FFA3 (GPR41) are G protein-coupled receptors (GPCRs) involved in energy and metabolic homeostasis. Understanding the structural basis of ligand binding at FFAs is an essential step toward designing potent and selective small molecule modulators.

    Results: We analyse earlier homology models of FFAs in light of the newly published FFA1 crystal structure co-crystallized with TAK-875, an ago-allosteric ligand, focusing on the architecture of the extracellular binding cavity and agonist-receptor interactions. Read More

    Structural characterization of the carbohydrate-binding module of NanA sialidase, a pneumococcal virulence factor.
    BMC Struct Biol 2015 Aug 20;15:15. Epub 2015 Aug 20.
    Biomedical Sciences Research Complex, University of St Andrews, St Andrews, Fife, KY16 9ST, UK.
    Background: Streptococcus pneumoniae Neuraminidase A (NanA) is a multi-domain protein anchored to the bacterial surface. Upstream of the catalytic domain of NanA is a domain that conforms to the sialic acid-recognising CBM40 family of the CAZY (carbohydrate-active enzymes) database. This domain has been identified to play a critical role in allowing the bacterium to promote adhesion and invasion of human brain microvascular endothelial cells, and hence may play a key role in promoting bacterial meningitis. Read More

    New insights into the molecular mechanism of the Rab GTPase Sec4p activation.
    BMC Struct Biol 2015 Aug 12;15:14. Epub 2015 Aug 12.
    Department of Molecular Medicine, Cornell University, Ithaca, NY, 14853, USA.
    Background: Sec4p is a small monomeric Ras-related GTP-binding protein (23 kDa) that regulates polarized exocytosis in S. cerevisiae. In this study we examine the structural effects of a conserved serine residue in the P-loop corresponding to G12 in Ras. Read More

    Crystal structure of O-methyltransferase CalO6 from the calicheamicin biosynthetic pathway: a case of challenging structure determination at low resolution.
    BMC Struct Biol 2015 Jul 15;15:13. Epub 2015 Jul 15.
    Department of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky, 789 South Limestone Street, 40536-0596, Lexington, KY, USA.
    Background: Calicheamicins (CAL) are enedyine natural products with potent antibiotic and cytotoxic activity, used in anticancer therapy. The O-methyltransferase CalO6 is proposed to catalyze methylation of the hydroxyl moiety at the C2 position of the orsellinic acid group of CAL.

    Results: Crystals of CalO6 diffracted non-isotropically, with the usable data extending to 3. Read More

    Structure of the stationary phase survival protein YuiC from B.subtilis.
    BMC Struct Biol 2015 Jul 11;15:12. Epub 2015 Jul 11.
    Institute for Structural and Molecular Biology, Crystallography, Department of Biological Sciences, Birkbeck University of London, Malet Street, London, WC1E 7HX, UK.
    Background: Stationary phase survival proteins (Sps) were found in Firmicutes as having analogous domain compositions, and in some cases genome context, as the resuscitation promoting factors of Actinobacteria, but with a different putative peptidoglycan cleaving domain.

    Results: The first structure of a Firmicute Sps protein YuiC from B. subtilis, is found to be a stripped down version of the cell-wall peptidoglycan hydrolase MltA. Read More

    Variations in periplasmic loop interactions determine the pH-dependent activity of the hexameric urea transporter UreI from Helicobacter pylori: a molecular dynamics study.
    BMC Struct Biol 2015 Jun 26;15:11. Epub 2015 Jun 26.
    Department of Pharmacology, School of Sciences, University of Concepción, Concepción, Chile.
    Background: Helicobacter pylori is an important factor in the development of diseases such as ulcer and gastric cancer. This bacterium uses a periplasmic transporter, UreI, to deliver urea to the intracelullar space, where later it is transformed into ammonia by the cytoplasmic enzyme urease to survive the acidic condition of the human stomach. The UreI transporter presents a pH-dependent activity, where this pH-dependence remains unknown at a structural level. Read More

    Binding of undamaged double stranded DNA to vaccinia virus uracil-DNA Glycosylase.
    BMC Struct Biol 2015 Jun 2;15:10. Epub 2015 Jun 2.
    Department of Medicine, University of Alabama at Birmingham, Birmingham, AL, 35294, USA.
    Background: Uracil-DNA glycosylases are evolutionarily conserved DNA repair enzymes. However, vaccinia virus uracil-DNA glycosylase (known as D4), also serves as an intrinsic and essential component of the processive DNA polymerase complex during DNA replication. In this complex D4 binds to a unique poxvirus specific protein A20 which tethers it to the DNA polymerase. Read More

    Modeling of the OX1R-orexin-A complex suggests two alternative binding modes.
    BMC Struct Biol 2015 May 9;15. Epub 2015 May 9.
    Division of Pharmaceutical Chemistry and Technology, Faculty of Pharmacy, University of Helsinki, P.O. Box 56, 00014, Helsinki, Finland.
    Background: Interactions between the orexin peptides and their cognate OX1 and OX2 receptors remain poorly characterized. Site-directed mutagenesis studies on orexin peptides and receptors have indicated amino acids important for ligand binding and receptor activation. However, a better understanding of specific pairwise interactions would benefit small molecule discovery. Read More

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