• Crystal structure of carbonic anhydrase CaNce103p from the pathogenic yeast Candida albicans.

    abstract:BACKGROUND:The pathogenic yeast Candida albicans can proliferate in environments with different carbon dioxide concentrations thanks to the carbonic anhydrase CaNce103p, which accelerates spontaneous conversion of carbon dioxide to bicarbonate and vice versa. Without functional CaNce103p, C. albicans cannot survive in ...

    journal_title:BMC structural biology

    pub_type: 杂志文章


    authors: Dostál J,Brynda J,Blaha J,Macháček S,Heidingsfeld O,Pichová I

    更新日期:2018-10-26 00:00:00

  • Destabilization of the TWIST1/E12 complex dimerization following the R154P point-mutation of TWIST1: an in silico approach.

    abstract: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 TWI...

    journal_title:BMC structural biology

    pub_type: 杂志文章


    authors: Bouard C,Terreux R,Tissier A,Jacqueroud L,Vigneron A,Ansieau S,Puisieux A,Payen L

    更新日期:2017-05-18 00:00:00

  • Comprehensive analysis of the Co-structures of dipeptidyl peptidase IV and its inhibitor.

    abstract: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 ...

    journal_title:BMC structural biology

    pub_type: 杂志文章


    authors: Nojima H,Kanou K,Terashi G,Takeda-Shitaka M,Inoue G,Atsuda K,Itoh C,Iguchi C,Matsubara H

    更新日期:2016-08-05 00:00:00

  • Structural determinant for inducing RORgamma specific inverse agonism triggered by a synthetic benzoxazinone ligand.

    abstract: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 modulat...

    journal_title:BMC structural biology

    pub_type: 杂志文章


    authors: Marcotte DJ,Liu Y,Little K,Jones JH,Powell NA,Wildes CP,Silvian LF,Chodaparambil JV

    更新日期:2016-06-01 00:00:00

  • Predicted binding site information improves model ranking in protein docking using experimental and computer-generated target structures.

    abstract: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 rece...

    journal_title:BMC structural biology

    pub_type: 杂志文章


    authors: Maheshwari S,Brylinski M

    更新日期:2015-11-23 00:00:00

  • The crystal structure of JNK from Drosophila melanogaster reveals an evolutionarily conserved topology with that of mammalian JNK proteins.

    abstract: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...

    journal_title:BMC structural biology

    pub_type: 杂志文章


    authors: Chimnaronk S,Sitthiroongruang J,Srisucharitpanit K,Srisaisup M,Ketterman AJ,Boonserm P

    更新日期:2015-09-16 00:00:00

  • Binding of undamaged double stranded DNA to vaccinia virus uracil-DNA Glycosylase.

    abstract: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 pr...

    journal_title:BMC structural biology

    pub_type: 杂志文章


    authors: Schormann N,Banerjee S,Ricciardi R,Chattopadhyay D

    更新日期:2015-06-02 00:00:00

  • Human coronavirus OC43 3CL protease and the potential of ML188 as a broad-spectrum lead compound: homology modelling and molecular dynamic studies.

    abstract:BACKGROUND:The coronavirus 3 chymotrypsin-like protease (3CL(pro)) is a validated target in the design of potential anticoronavirus inhibitors. The high degree of homology within the protease's active site and substrate conservation supports the identification of broad spectrum lead compounds. A previous study identifi...

    journal_title:BMC structural biology

    pub_type: 杂志文章


    authors: Berry M,Fielding B,Gamieldien J

    更新日期:2015-04-28 00:00:00

  • A three dimensional visualisation approach to protein heavy-atom structure reconstruction.

    abstract:BACKGROUND:A commonly recurring problem in structural protein studies, is the determination of all heavy atom positions from the knowledge of the central α-carbon coordinates. RESULTS:We employ advances in virtual reality to address the problem. The outcome is a 3D visualisation based technique where all the heavy bac...

    journal_title:BMC structural biology

    pub_type: 杂志文章


    authors: Peng X,Chenani A,Hu S,Zhou Y,Niemi AJ

    更新日期:2014-12-31 00:00:00

  • Crystal structure of signal regulatory protein gamma (SIRPγ) in complex with an antibody Fab fragment.

    abstract:BACKGROUND:Signal Regulatory Protein γ (SIRPγ) is a member of a closely related family of three cell surface receptors implicated in modulating immune/inflammatory responses. SIRPγ is expressed on T lymphocytes where it appears to be involved in the integrin-independent adhesion of lymphocytes to antigen-presenting cel...

    journal_title:BMC structural biology

    pub_type: 杂志文章


    authors: Nettleship JE,Ren J,Scott DJ,Rahman N,Hatherley D,Zhao Y,Stuart DI,Barclay AN,Owens RJ

    更新日期:2013-07-04 00:00:00

  • Disturbance of DNA conformation by the binding of testosterone-based platinum drugs via groove-face and intercalative interactions: a molecular dynamics simulation study.

    abstract:BACKGROUND:To explore novel platinum-based anticancer agents that are distinct from the structure and interaction mode of the traditional cisplatin by forming the bifunctional intrastrand 1,2 GpG adduct, the monofunctional platinum+DNA adducts with extensive non-covalent interactions had been studied. It was reported t...

    journal_title:BMC structural biology

    pub_type: 杂志文章


    authors: Cui S,Wang Y,Chen G

    更新日期:2013-03-22 00:00:00

  • A population-based evolutionary search approach to the multiple minima problem in de novo protein structure prediction.

    abstract:BACKGROUND:Elucidating the native structure of a protein molecule from its sequence of amino acids, a problem known as de novo structure prediction, is a long standing challenge in computational structural biology. Difficulties in silico arise due to the high dimensionality of the protein conformational space and the r...

    journal_title:BMC structural biology

    pub_type: 杂志文章


    authors: Saleh S,Olson B,Shehu A

    更新日期:2013-01-01 00:00:00

  • The possible mechanisms of CYP2E1 interactions with HSP90 and the influence of ethanol on them.

    abstract:BACKGROUND:Microsomal CYP2E1 metabolizes about 160 hydrophobic exogens, many of which are environmental pollutants. While metabolising xenobiotics CYP2E1 on one hand facilitates in their excretion and on the other hand activates them into the cytotoxins, which may damage the cell. Thus the CYP2E1 activity level signifi...

    journal_title:BMC structural biology

    pub_type: 杂志文章


    authors: Kitam VO,Maksymchuk OV,Chashchyn MO

    更新日期:2012-12-17 00:00:00

  • MTMDAT-HADDOCK: high-throughput, protein complex structure modeling based on limited proteolysis and mass spectrometry.

    abstract:BACKGROUND:MTMDAT is a program designed to facilitate analysis of mass spectrometry data of proteins and biomolecular complexes that are probed structurally by limited proteolysis. This approach can provide information about stable fragments of multidomain proteins, yield tertiary and quaternary structure data, and hel...

    journal_title:BMC structural biology

    pub_type: 杂志文章


    authors: Hennig J,de Vries SJ,Hennig KD,Randles L,Walters KJ,Sunnerhagen M,Bonvin AM

    更新日期:2012-11-15 00:00:00

  • Evolutionarily consistent families in SCOP: sequence, structure and function.

    abstract:BACKGROUND:SCOP is a hierarchical domain classification system for proteins of known structure. The superfamily level has a clear definition: Protein domains belong to the same superfamily if there is structural, functional and sequence evidence for a common evolutionary ancestor. Superfamilies are sub-classified into ...

    journal_title:BMC structural biology

    pub_type: 杂志文章


    authors: Pethica RB,Levitt M,Gough J

    更新日期:2012-10-18 00:00:00

  • Dependence of α-helical and β-sheet amino acid propensities on the overall protein fold type.

    abstract:BACKGROUND:A large number of studies have been carried out to obtain amino acid propensities for α-helices and β-sheets. The obtained propensities for α-helices are consistent with each other, and the pair-wise correlation coefficient is frequently high. On the other hand, the β-sheet propensities obtained by several s...

    journal_title:BMC structural biology

    pub_type: 杂志文章


    authors: Fujiwara K,Toda H,Ikeguchi M

    更新日期:2012-08-02 00:00:00

  • The host-pathogen interaction of human cyclophilin A and HIV-1 Vpr requires specific N-terminal and novel C-terminal domains.

    abstract:BACKGROUND:Cyclophilin A (CypA) represents a potential key molecule in future antiretroviral therapy since inhibition of CypA suppresses human immunodeficiency virus type 1 (HIV-1) replication. CypA interacts with the virus proteins Capsid (CA) and Vpr, however, the mechanism through which CypA influences HIV-1 infecti...

    journal_title:BMC structural biology

    pub_type: 杂志文章


    authors: Solbak SM,Wray V,Horvli O,Raae AJ,Flydal MI,Henklein P,Henklein P,Nimtz M,Schubert U,Fossen T

    更新日期:2011-12-20 00:00:00

  • Computational analysis of a novel mutation in ETFDH gene highlights its long-range effects on the FAD-binding motif.

    abstract:BACKGROUND:Multiple acyl-coenzyme A dehydrogenase deficiency (MADD) is an autosomal recessive disease caused by the defects in the mitochondrial electron transfer system and the metabolism of fatty acids. Recently, mutations in electron transfer flavoprotein dehydrogenase (ETFDH) gene, encoding electron transfer flavop...

    journal_title:BMC structural biology

    pub_type: 杂志文章


    authors: Er TK,Chen CC,Liu YY,Chang HC,Chien YH,Chang JG,Hwang JK,Jong YJ

    更新日期:2011-10-21 00:00:00

  • Hydration studies on the archaeal protein Sso7d using NMR measurements and MD simulations.

    abstract:BACKGROUND:How proteins approach surrounding molecules is fundamental to our understanding of the specific interactions that occur at the surface of proteins. The enhanced surface accessibility of small molecules such as organic solvents and paramagnetic probes to protein binding sites has been observed; however, the m...

    journal_title:BMC structural biology

    pub_type: 杂志文章


    authors: Bernini A,Spiga O,Consonni R,Arosio I,Fusi P,Cirri S,Guagliardi A,Niccolai N

    更新日期:2011-10-21 00:00:00

  • Hydration sites of unpaired RNA bases: a statistical analysis of the PDB structures.

    abstract:BACKGROUND:Hydration is crucial for RNA structure and function. X-ray crystallography is the most commonly used method to determine RNA structures and hydration and, therefore, statistical surveys are based on crystallographic results, the number of which is quickly increasing. RESULTS:A statistical analysis of the wa...

    journal_title:BMC structural biology

    pub_type: 杂志文章


    authors: Kirillova S,Carugo O

    更新日期:2011-10-19 00:00:00

  • Evolutionary traces decode molecular mechanism behind fast pace of myosin XI.

    abstract:BACKGROUND:Cytoplasmic class XI myosins are the fastest processive motors known. This class functions in high-velocity cytoplasmic streaming in various plant cells from algae to angiosperms. The velocities at which they process are ten times faster than its closest class V homologues. RESULTS:To provide sequence deter...

    journal_title:BMC structural biology

    pub_type: 杂志文章


    authors: Syamaladevi DP,Sowdhamini R

    更新日期:2011-09-26 00:00:00

  • Secondary structure of protamine in sperm nuclei: an infrared spectroscopy study.

    abstract:BACKGROUND:Protamines are small basic proteins that condense the DNA in mature spermatozoa. Typical protamines are of simple composition and very arginine-rich, usually in the range of 60-80%. Arginine residues are distributed in a number of stretches separated by neutral amino acids. We have used Fourier transform inf...

    journal_title:BMC structural biology

    pub_type: 杂志文章


    authors: Roque A,Ponte I,Suau P

    更新日期:2011-03-24 00:00:00

  • Analysis of electric moments of RNA-binding proteins: implications for mechanism and prediction.

    abstract:BACKGROUND:Protein-RNA interactions play important role in many biological processes such as gene regulation, replication, protein synthesis and virus assembly. Although many structures of various types of protein-RNA complexes have been determined, the mechanism of protein-RNA recognition remains elusive. We have earl...

    journal_title:BMC structural biology

    pub_type: 杂志文章


    authors: Ahmad S,Sarai A

    更新日期:2011-02-01 00:00:00

  • Differential molecular information of maurotoxin peptide recognizing IK(Ca) and Kv1.2 channels explored by computational simulation.

    abstract:BACKGROUND:Scorpion toxins are invaluable tools for ion channel research and are potential drugs for human channelopathies. However, it is still an open task to determine the molecular basis underlying the diverse interactions between toxin peptides and ion channels. The inhibitory peptide Maurotoxin (MTX) recognized t...

    journal_title:BMC structural biology

    pub_type: 杂志文章


    authors: Yi H,Qiu S,Wu Y,Li W,Wang B

    更新日期:2011-01-25 00:00:00

  • Prediction of protein motions from amino acid sequence and its application to protein-protein interaction.

    abstract:BACKGROUND:Structural flexibility is an important characteristic of proteins because it is often associated with their function. The movement of a polypeptide segment in a protein can be broken down into two types of motions: internal and external ones. The former is deformation of the segment itself, but the latter in...

    journal_title:BMC structural biology

    pub_type: 杂志文章


    authors: Hirose S,Yokota K,Kuroda Y,Wako H,Endo S,Kanai S,Noguchi T

    更新日期:2010-07-13 00:00:00

  • Structural definition and substrate specificity of the S28 protease family: the crystal structure of human prolylcarboxypeptidase.

    abstract:BACKGROUND:The unique S28 family of proteases is comprised of the carboxypeptidase PRCP and the aminopeptidase DPP7. The structural basis of the different substrate specificities of the two enzymes is not understood nor has the structure of the S28 fold been described. RESULTS:The experimentally phased 2.8 A crystal s...

    journal_title:BMC structural biology

    pub_type: 杂志文章


    authors: Soisson SM,Patel SB,Abeywickrema PD,Byrne NJ,Diehl RE,Hall DL,Ford RE,Reid JC,Rickert KW,Shipman JM,Sharma S,Lumb KJ

    更新日期:2010-06-11 00:00:00

  • Novel structural features in two ZHX homeodomains derived from a systematic study of single and multiple domains.

    abstract:BACKGROUND:Zhx1 to 3 (zinc-fingers and homeoboxes) form a set of paralogous genes encoding multi-domain proteins. ZHX proteins consist of two zinc fingers followed by five homeodomains. ZHXs have biological roles in cell cycle control by acting as co-repressors of the transcriptional regulator Nuclear Factor Y. As part...

    journal_title:BMC structural biology

    pub_type: 杂志文章


    authors: Bird LE,Ren J,Nettleship JE,Folkers GE,Owens RJ,Stammers DK

    更新日期:2010-05-28 00:00:00

  • Generalized spring tensor models for protein fluctuation dynamics and conformation changes.

    abstract:BACKGROUND:In the last decade, various coarse-grained elastic network models have been developed to study the large-scale motions of proteins and protein complexes where computer simulations using detailed all-atom models are not feasible. Among these models, the Gaussian Network Model (GNM) and Anisotropic Network Mod...

    journal_title:BMC structural biology

    pub_type: 杂志文章


    authors: Lin TL,Song G

    更新日期:2010-05-17 00:00:00

  • Analysis of the role of PCNA-DNA contacts during clamp loading.

    abstract:BACKGROUND:Sliding clamps, such as Proliferating Cell Nuclear Antigen (PCNA) in eukaryotes, are ring-shaped protein complexes that encircle DNA and enable highly processive DNA replication by serving as docking sites for DNA polymerases. In an ATP-dependent reaction, clamp loader complexes, such as the Replication Fact...

    journal_title:BMC structural biology

    pub_type: 杂志文章


    authors: McNally R,Bowman GD,Goedken ER,O'Donnell M,Kuriyan J

    更新日期:2010-01-30 00:00:00

  • Structural and functional characteristics of xenavidin, the first frog avidin from Xenopus tropicalis.

    abstract:BACKGROUND:Avidins are proteins with extraordinarily high ligand-binding affinity, a property which is used in a wide array of life science applications. Even though useful for biotechnology and nanotechnology, the biological function of avidins is not fully understood. Here we structurally and functionally characteris...

    journal_title:BMC structural biology

    pub_type: 杂志文章


    authors: Määttä JA,Helppolainen SH,Hytönen VP,Johnson MS,Kulomaa MS,Airenne TT,Nordlund HR

    更新日期:2009-09-29 00:00:00

  • Hydrogen bonding and packing density are factors most strongly connected to limiting sites of high flexibility in the 16S rRNA in the 30S ribosome.

    abstract:BACKGROUND:Conformational flexibility in structured RNA frequently is critical to function. The 30S ribosomal subunit exists in different conformations in different functional states due to changes in the central part of the 16S rRNA. We are interested in evaluating the factors that might be responsible for restricting...

    journal_title:BMC structural biology

    pub_type: 杂志文章


    authors: Huggins W,Ghosh SK,Wollenzien P

    更新日期:2009-07-30 00:00:00

  • Conservation of structure and activity in Plasmodium purine nucleoside phosphorylases.

    abstract:BACKGROUND:Purine nucleoside phosphorylase (PNP) is central to purine salvage mechanisms in Plasmodium parasites, the causative agents of malaria. Most human malaria results from infection either by Plasmodium falciparum (Pf), the deadliest form of the parasite, or by the widespread Plasmodium vivax (Pv). Whereas the P...

    journal_title:BMC structural biology

    pub_type: 杂志文章


    authors: Chaikuad A,Brady RL

    更新日期:2009-07-03 00:00:00

  • Analysis of the impact of solvent on contacts prediction in proteins.

    abstract:BACKGROUND:The correlated mutations concept is based on the assumption that interacting protein residues coevolve, so that a mutation in one of the interacting counterparts is compensated by a mutation in the other. Approaches based on this concept have been widely used for protein contacts prediction since the 90s. Pr...

    journal_title:BMC structural biology

    pub_type: 杂志文章


    authors: Samsonov SA,Teyra J,Anders G,Pisabarro MT

    更新日期:2009-04-15 00:00:00

  • ProteinShader: illustrative rendering of macromolecules.

    abstract:BACKGROUND:Cartoon-style illustrative renderings of proteins can help clarify structural features that are obscured by space filling or balls and sticks style models, and recent advances in programmable graphics cards offer many new opportunities for improving illustrative renderings. RESULTS:The ProteinShader program...

    journal_title:BMC structural biology

    pub_type: 杂志文章


    authors: Weber JR

    更新日期:2009-03-30 00:00:00

  • The glycine brace: a component of Rab, Rho, and Ran GTPases associated with hinge regions of guanine- and phosphate-binding loops.

    abstract:BACKGROUND:Ras-like GTPases function as on-off switches in intracellular signalling pathways and include the Rab, Rho/Rac, Ran, Ras, Arf, Sar and G alpha families. How these families have evolutionarily diverged from each other at the sequence level provides clues to underlying mechanisms associated with their function...

    journal_title:BMC structural biology

    pub_type: 杂志文章


    authors: Neuwald AF

    更新日期:2009-03-05 00:00:00

  • Residue contact-count potentials are as effective as residue-residue contact-type potentials for ranking protein decoys.

    abstract:BACKGROUND:For over 30 years potentials of mean force have been used to evaluate the relative energy of protein structures. The most commonly used potentials define the energy of residue-residue interactions and are derived from the empirical analysis of the known protein structures. However, single-body residue 'envir...

    journal_title:BMC structural biology

    pub_type: 杂志文章


    authors: Bolser DM,Filippis I,Stehr H,Duarte J,Lappe M

    更新日期:2008-12-08 00:00:00

  • PDBalert: automatic, recurrent remote homology tracking and protein structure prediction.

    abstract:BACKGROUND:During the last years, methods for remote homology detection have grown more and more sensitive and reliable. Automatic structure prediction servers relying on these methods can generate useful 3D models even below 20% sequence identity between the protein of interest and the known structure (template). When...

    journal_title:BMC structural biology

    pub_type: 杂志文章


    authors: Agarwal V,Remmert M,Biegert A,Söding J

    更新日期:2008-11-25 00:00:00

  • Statistical analysis of the Bacterial Carbohydrate Structure Data Base (BCSDB): characteristics and diversity of bacterial carbohydrates in comparison with mammalian glycans.

    abstract:BACKGROUND:There are considerable differences between bacterial and mammalian glycans. In contrast to most eukaryotic carbohydrates, bacterial glycans are often composed of repeating units with diverse functions ranging from structural reinforcement to adhesion, colonization and camouflage. Since bacterial glycans are ...

    journal_title:BMC structural biology

    pub_type: 杂志文章


    authors: Herget S,Toukach PV,Ranzinger R,Hull WE,Knirel YA,von der Lieth CW

    更新日期:2008-08-11 00:00:00

  • Structure of Arabidopsis thaliana 5-methylthioribose kinase reveals a more occluded active site than its bacterial homolog.

    abstract:BACKGROUND:Metabolic variations exist between the methionine salvage pathway of humans and a number of plants and microbial pathogens. 5-Methylthioribose (MTR) kinase is a key enzyme required for methionine salvage in plants and many bacteria. The absence of a mammalian homolog suggests that MTR kinase is a good target...

    journal_title:BMC structural biology

    pub_type: 杂志文章


    authors: Ku SY,Cornell KA,Howell PL

    更新日期:2007-10-25 00:00:00

  • Crystal structures of Leptospira interrogans FAD-containing ferredoxin-NADP+ reductase and its complex with NADP+.

    abstract:BACKGROUND:Ferredoxin-NADP(H) reductases (FNRs) are flavoenzymes that catalyze the electron transfer between NADP(H) and the proteins ferredoxin or flavodoxin. A number of structural features distinguish plant and bacterial FNRs, one of which is the mode of the cofactor FAD binding. Leptospira interrogans is a spirocha...

    journal_title:BMC structural biology

    pub_type: 杂志文章


    authors: Nascimento AS,Catalano-Dupuy DL,Bernardes A,Neto Mde O,Santos MA,Ceccarelli EA,Polikarpov I

    更新日期:2007-10-24 00:00:00

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