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Characterization of putative proteins encoded by variable ORFs in white spot syndrome virus genome. BMC Struct. Biol. Pub Date : 2019-04-18 Cayro de Macêdo Mendes,Diego Gomes Teixeira,João Paulo Matos Santos Lima,Daniel Carlos Ferreira Lanza
BACKGROUND White Spot Syndrome Virus (WSSV) is an enveloped double-stranded DNA virus which causes mortality of several species of shrimp, being considered one of the main pathogens that affects global shrimp farming. This virus presents a complex genome of ~ 300 kb and viral isolates that present genomes with great identity. Despite this conservation, some variable regions in the WSSV genome occur
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Correction to: Classification of the human THAP protein family identifies an evolutionarily conserved coiled coil region. BMC Struct. Biol. Pub Date : 2019-03-29 Hiral M Sanghavi,Sairam S Mallajosyula,Sharmistha Majumdar
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Effect of low complexity regions within the PvMSP3α block II on the tertiary structure of the protein and implications to immune escape mechanisms. BMC Struct. Biol. Pub Date : 2019-03-27 Alebachew Messele Kebede,Fitsum Girma Tadesse,Adey Desta Feleke,Lemu Golassa,Endalamaw Gadisa
BACKGROUND Plasmodium vivax merozoite surface protein 3α (PvMSP3α) is a promising vaccine candidate which has shown strong association with immunogenicity and protectiveness. Its use is however complicated by evolutionary plasticity features which enhance immune evasion. Low complexity regions (LCRs) provide plasticity in surface proteins of Plasmodium species, but its implication in vaccine design
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QRNAS: software tool for refinement of nucleic acid structures. BMC Struct. Biol. Pub Date : 2019-03-21 Juliusz Stasiewicz,Sunandan Mukherjee,Chandran Nithin,Janusz M Bujnicki
BACKGROUND Computational models of RNA 3D structure often present various inaccuracies caused by simplifications used in structure prediction methods, such as template-based modeling or coarse-grained simulations. To obtain a high-quality model, the preliminary RNA structural model needs to be refined, taking into account atomic interactions. The goal of the refinement is not only to improve the local
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Classification of the human THAP protein family identifies an evolutionarily conserved coiled coil region. BMC Struct. Biol. Pub Date : 2019-03-05 Hiral M Sanghavi,Sairam S Mallajosyula,Sharmistha Majumdar
BACKGROUND The THAP (Thanatos Associated Proteins) protein family in humans is implicated in various important cellular processes like epigenetic regulation, maintenance of pluripotency, transposition and disorders like cancers and hemophilia. The human THAP protein family which consists of twelve members of different lengths has a well characterized amino terminal, zinc-coordinating, DNA-binding domain
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Structures of EccB1 and EccD1 from the core complex of the mycobacterial ESX-1 type VII secretion system. BMC Struct. Biol. Pub Date : 2016-02-29 Jonathan M Wagner,Sum Chan,Timothy J Evans,Sara Kahng,Jennifer Kim,Mark A Arbing,David Eisenberg,Konstantin V Korotkov
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
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Structuprint: a scalable and extensible tool for two-dimensional representation of protein surfaces. BMC Struct. Biol. Pub Date : 2016-02-26 Dimitrios Georgios Kontopoulos,Dimitrios Vlachakis,Georgia Tsiliki,Sofia Kossida
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
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Crystal structure and functional implications of the tandem-type universal stress protein UspE from Escherichia coli. BMC Struct. Biol. Pub Date : 2016-02-13 Yongbin Xu,Jianyun Guo,Xiaoling Jin,Jin-Sik Kim,Ying Ji,Shengdi Fan,Nam-Chul Ha,Chun-Shan Quan
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. It has been shown that UspA family members are survival factors during cellular
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A direct interaction between NQO1 and a chemotherapeutic dimeric naphthoquinone. BMC Struct. Biol. Pub Date : 2016-01-30 Lakshmi Swarna Mukhi Pidugu,J C Emmanuel Mbimba,Muqeet Ahmad,Edwin Pozharski,Edward A Sausville,Ashkan Emadi,Eric A Toth
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
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A new technique for predicting intrinsically disordered regions based on average distance map constructed with inter-residue average distance statistics. BMC Struct. Biol. Pub Date : 2019-02-06 Takumi Shimomura,Kohki Nishijima,Takeshi Kikuchi
BACKGROUND It had long been thought that a protein exhibits its specific function through its own specific 3D-structure under physiological conditions. However, subsequent research has shown that there are many proteins without specific 3D-structures under physiological conditions, so-called intrinsically disordered proteins (IDPs). This study presents a new technique for predicting intrinsically disordered
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Crystal structure of E. coli PRPP synthetase. BMC Struct. Biol. Pub Date : 2019-01-15 Weijie Zhou,Andrew Tsai,Devon A Dattmore,Devin P Stives,Iva Chitrakar,Alexis M D'alessandro,Shiv Patil,Katherine A Hicks,Jarrod B French
BACKGROUND Ribose-phosphate pyrophosphokinase (EC 2.7.6.1) is an enzyme that catalyzes the ATP-dependent conversion of ribose-5-phosphate to phosphoribosyl pyrophosphate. The reaction product is a key precursor for the biosynthesis of purine and pyrimidine nucleotides. RESULTS We report the 2.2 Å crystal structure of the E. coli ribose-phosphate pyrophosphobinase (EcKPRS). The protein has two type
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The human transketolase-like proteins TKTL1 and TKTL2 are bona fide transketolases. BMC Struct. Biol. Pub Date : 2019-01-15 Gaurang P Deshpande,Hugh-George Patterton,M Faadiel Essop
BACKGROUND Three transketolase genes have been identified in the human genome to date: transketolase (TKT), transketolase-like 1 (TKTL1) and transketolase-like 2 (TKTL2). Altered TKT functionality is strongly implicated in the development of diabetes and various cancers, thus offering possible therapeutic utility. It will be of great value to know whether TKTL1 and TKTL2 are, similarly, potential therapeutic
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Deciphering evolution of immune recognition in antibodies. BMC Struct. Biol. Pub Date : 2018-12-19 Harmeet Kaur,Neetu Sain,Debasisa Mohanty,Dinakar M Salunke
BACKGROUND Antibody, the primary effector molecule of the immune system, evolves after initial encounter with the antigen from a precursor form to a mature one to effectively deal with the antigen. Antibodies of a lineage diverge through antigen-directed isolated pathways of maturation to exhibit distinct recognition potential. In the context of evolution in immune recognition, diversity of antigen
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Cryo-electron microscope image denoising based on the geodesic distance. BMC Struct. Biol. Pub Date : 2018-12-17 Jianquan Ouyang,Zezhi Liang,Chunyu Chen,Zhuosong Fu,Yue Zhang,Hongrong Liu
BACKGROUND To perform a three-dimensional (3-D) reconstruction of electron cryomicroscopy (cryo-EM) images of viruses, it is necessary to determine the similarity of image blocks of the two-dimensional (2-D) projections of the virus. The projections containing high resolution information are typically very noisy. Instead of the traditional Euler metric, this paper proposes a new method, based on the
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Novel features in the structure of P-glycoprotein (ABCB1) in the post-hydrolytic state as determined at 7.9 Å resolution. BMC Struct. Biol. Pub Date : 2018-12-13 Nopnithi Thonghin,Richard F Collins,Alessandro Barbieri,Talha Shafi,Alistair Siebert,Robert C Ford
BACKGROUND P-glycoprotein (ABCB1) is an ATP-binding cassette transporter that plays an important role in the clearance of drugs and xenobiotics and is associated with multi-drug resistance in cancer. Although several P-glycoprotein structures are available, these are either at low resolution, or represent mutated and/or quiescent states of the protein. RESULTS In the post-hydrolytic state the structure
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An improved protein structure evaluation using a semi-empirically derived structure property. BMC Struct. Biol. Pub Date : 2018-12-12 Manoj Kumar Pal,Tapobrata Lahiri,Garima Tanwar,Rajnish Kumar
BACKGROUND In the backdrop of challenge to obtain a protein structure under the known limitations of both experimental and theoretical techniques, the need of a fast as well as accurate protein structure evaluation method still exists to substantially reduce a huge gap between number of known sequences and structures. Among currently practiced theoretical techniques, homology modelling backed by molecular
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Comparative analysis of interactions between aryl hydrocarbon receptor ligand binding domain with its ligands: a computational study. BMC Struct. Biol. Pub Date : 2018-12-06 Kumaraswamy Naidu Chitrala,Xiaoming Yang,Prakash Nagarkatti,Mitzi Nagarkatti
BACKGROUND Aryl hydrocarbon receptor (AhR) ligands may act as potential carcinogens or anti-tumor agents. Understanding how some of the residues in AhR ligand binding domain (AhRLBD) modulate their interactions with ligands would be useful in assessing their divergent roles including toxic and beneficial effects. To this end, we have analysed the nature of AhRLBD interactions with 2,3,7,8-tetrachlorodibenzo-ρ-dioxin
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Crystal structure of carbonic anhydrase CaNce103p from the pathogenic yeast Candida albicans. BMC Struct. Biol. Pub Date : 2018-10-26 Jiří Dostál,Jiří Brynda,Jan Blaha,Stanislav Macháček,Olga Heidingsfeld,Iva Pichová
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 atmospheric air. CaNce103p falls into the β-carbonic anhydrase class, along with
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Computational analysis of the interactions of a novel cephalosporin derivative with β-lactamases. BMC Struct. Biol. Pub Date : 2018-10-04 Anna Verdino,Felicia Zollo,Margherita De Rosa,Annunziata Soriente,Miguel Ángel Hernández-Martínez,Anna Marabotti
BACKGROUND One of the main concerns of the modern medicine is the frightening spread of antimicrobial resistance caused mainly by the misuse of antibiotics. The researchers worldwide are actively involved in the search for new classes of antibiotics, and for the modification of known molecules in order to face this threatening problem. We have applied a computational approach to predict the interactions
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Accurate flexible refinement of atomic models against medium-resolution cryo-EM maps using damped dynamics. BMC Struct. Biol. Pub Date : 2018-09-15 Julio A Kovacs,Vitold E Galkin,Willy Wriggers
BACKGROUND Dramatic progress has recently been made in cryo-electron microscopy technologies, which now make possible the reconstruction of a growing number of biomolecular structures to near-atomic resolution. However, the need persists for fitting and refinement approaches that address those cases that require modeling assistance. METHODS In this paper, we describe algorithms to optimize the performance
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Comparative sequence and structure analysis of eIF1A and eIF1AD. BMC Struct. Biol. Pub Date : 2018-09-04 Jielin Yu,Assen Marintchev
BACKGROUND Eukaryotic translation initiation factor 1A (eIF1A) is universally conserved in all organisms. It has multiple functions in translation initiation, including assembly of the ribosomal pre-initiation complexes, mRNA binding, scanning, and ribosomal subunit joining. eIF1A binds directly to the small ribosomal subunit, as well as to several other translation initiation factors. The structure
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Crystal structure of duck egg lysozyme isoform II (DEL-II). BMC Struct. Biol. Pub Date : 2018-08-22 David B Langley,Daniel Christ
BACKGROUND Lysozyme purified from duck eggs (DEL) has long been used as a model antigen as a counterpoint to the enzyme purified from hen eggs (HEL). However, unlike the single C-type variant found in hen eggs, duck eggs contain multiple isoforms: I, II and III. We recently reported the structures of isoforms I and III from Pekin duck (Anas platyrhynchos) and unequivocally determined the sequences
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In silico prediction of novel residues involved in amyloid primary nucleation of human I56T and D67H lysozyme. BMC Struct. Biol. Pub Date : 2018-07-20 Jeddidiah W D Griffin,Patrick C Bradshaw
BACKGROUND Amyloidogenic proteins are most often associated with neurodegenerative diseases such as Alzheimer's disease, Parkinson's disease, and Huntington's disease, but there are more than two dozen human proteins known to form amyloid fibrils associated with disease. Lysozyme is an antimicrobial protein that is used as a general model to study amyloid fibril formation. Studies aimed at elucidating
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Structure and dynamics of a human myelin protein P2 portal region mutant indicate opening of the β barrel in fatty acid binding proteins. BMC Struct. Biol. Pub Date : 2018-06-25 Saara Laulumaa,Tuomo Nieminen,Arne Raasakka,Oda C Krokengen,Anushik Safaryan,Erik I Hallin,Guillaume Brysbaert,Marc F Lensink,Salla Ruskamo,Ilpo Vattulainen,Petri Kursula
BACKGROUND Myelin is a multilayered proteolipid sheath wrapped around selected axons in the nervous system. Its constituent proteins play major roles in forming of the highly regular membrane structure. P2 is a myelin-specific protein of the fatty acid binding protein (FABP) superfamily, which is able to stack lipid bilayers together, and it is a target for mutations in the human inherited neuropathy
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Functional insights from proteome-wide structural modeling of Treponema pallidum subspecies pallidum, the causative agent of syphilis. BMC Struct. Biol. Pub Date : 2018-05-16 Simon Houston,Karen Vivien Lithgow,Kara Krista Osbak,Chris Richard Kenyon,Caroline E Cameron
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. This is due to the fact that T. pallidum
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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. Pub Date : 2018-04-19 Muhammad Waseem Sarwar,Adeel Riaz,Syed Muhammad Raihan Dilshad,Ahmed Al-Qahtani,Muhammad Shah Nawaz-Ul-Rehman,Muhammad Mubin
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. It has already been reported that if function of NS2B-NS3 complex is disrupted, viral replication is inhibited. Therefore,
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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. Pub Date : 2018-04-18 Pallabini Dash,M Bala Divya,Lalitha Guruprasad,Kunchur Guruprasad
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. In the present work, we intended to understand via computer modeling studies
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re-TAMD: exploring interactions between H3 peptide and YEATS domain using enhanced sampling. BMC Struct. Biol. Pub Date : 2018-04-03 Gilles Lamothe,Thérèse E Malliavin
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
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Correction to: selected articles from Belyaev Conference 2017: structural biology. BMC Struct. Biol. Pub Date : 2018-03-21 Nikolay A Alemasov,Nikita V Ivanisenko,Srinivasan Ramachandran,Vladimir A Ivanisenko
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.
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A structural preview of aquaporin 8 via homology modeling of seven vertebrate isoforms. BMC Struct. Biol. Pub Date : 2018-02-17 Andreas Kirscht,Yonathan Sonntag,Per Kjellbom,Urban Johanson
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 H2O2 through various membranes of animal cells. This passive channel has been connected to
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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. Pub Date : 2018-02-05 Nikolay A Alemasov,Nikita V Ivanisenko,Srinivasan Ramachandran,Vladimir A Ivanisenko
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
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Leishmania infantum 5'-Methylthioadenosine Phosphorylase presents relevant structural divergence to constitute a potential drug target. BMC Struct. Biol. Pub Date : 2017-12-19 Hela Abid,Emna Harigua-Souiai,Thouraya Mejri,Mourad Barhoumi,Ikram Guizani
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
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Rosetta Broker for membrane protein structure prediction: concentrative nucleoside transporter 3 and corticotropin-releasing factor receptor 1 test cases. BMC Struct. Biol. Pub Date : 2017-08-03 Dorota Latek
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. In this work an example of such de novo method was used to structurally and
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A computational assessment of pH-dependent differential interaction of T7 lysozyme with T7 RNA polymerase. BMC Struct. Biol. Pub Date : 2017-05-25 Subhomoi Borkotoky,Ayaluru Murali
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
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Destabilization of the TWIST1/E12 complex dimerization following the R154P point-mutation of TWIST1: an in silico approach. BMC Struct. Biol. Pub Date : 2017-05-18 Charlotte Bouard,Raphael Terreux,Agnès Tissier,Laurent Jacqueroud,Arnaud Vigneron,Stéphane Ansieau,Alain Puisieux,Léa Payen
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
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Molecular dynamics simulation of the opposite-base preference and interactions in the active site of formamidopyrimidine-DNA glycosylase. BMC Struct. Biol. Pub Date : 2017-05-08 Alexander V Popov,Anton V Endutkin,Yuri N Vorobjev,Dmitry O Zharkov
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
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REFOLDdb: a new and sustainable gateway to experimental protocols for protein refolding. BMC Struct. Biol. Pub Date : 2017-04-24 Hisashi Mizutani,Hideaki Sugawara,Ashley M Buckle,Takeshi Sangawa,Ken-Ichi Miyazono,Jun Ohtsuka,Koji Nagata,Tomoki Shojima,Shohei Nosaki,Yuqun Xu,Delong Wang,Xiao Hu,Masaru Tanokura,Kei Yura
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
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A comparative analysis of the foamy and ortho virus capsid structures reveals an ancient domain duplication. BMC Struct. Biol. Pub Date : 2017-04-04 William R Taylor,Jonathan P Stoye,Ian A Taylor
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. Similarity in the gag region of the genome is less obvious at the sequence level but has been illuminated by the recent solution of the foamy virus capsid
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DynaDom: structure-based prediction of T cell receptor inter-domain and T cell receptor-peptide-MHC (class I) association angles. BMC Struct. Biol. Pub Date : 2017-02-02 Thomas Hoffmann,Antoine Marion,Iris Antes
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
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Prokaryotic ubiquitin-like protein remains intrinsically disordered when covalently attached to proteasomal target proteins. BMC Struct. Biol. Pub Date : 2017-02-01 Jonas Barandun,Fred F Damberger,Cyrille L Delley,Juerg Laederach,Frédéric H T Allain,Eilika Weber-Ban
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
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Controlled dehydration improves the diffraction quality of two RNA crystals. BMC Struct. Biol. Pub Date : 2016-11-03 HaJeung Park,Tuan Tran,Jun Hyuck Lee,Hyun Park,Matthew D Disney
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
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Combined small angle X-ray solution scattering with atomic force microscopy for characterizing radiation damage on biological macromolecules. BMC Struct. Biol. Pub Date : 2016-10-27 Luca Costa,Alexander Andriatis,Martha Brennich,Jean-Marie Teulon,Shu-Wen W Chen,Jean-Luc Pellequer,Adam Round
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. RESULTS By employing atomic force microscopy, another common
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The C-terminal domain of TPX2 is made of alpha-helical tandem repeats. BMC Struct. Biol. Pub Date : 2016-10-26 Luis Sanchez-Pulido,Laurent Perez,Steffen Kuhn,Isabelle Vernos,Miguel A Andrade-Navarro
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. METHODS We have used computational
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Human sex hormone-binding globulin as a potential target of alternate plasticizers: an in silico study. BMC Struct. Biol. Pub Date : 2016-09-30 Ishfaq A Sheikh,Muhammad Yasir,Muhammad Abu-Elmagd,Tanveer A Dar,Adel M Abuzenadah,Ghazi A Damanhouri,Mohammed Al-Qahtani,Mohd A Beg
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
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Endocrine disruption: In silico perspectives of interactions of di-(2-ethylhexyl)phthalate and its five major metabolites with progesterone receptor. BMC Struct. Biol. Pub Date : 2016-09-30 Ishfaq A Sheikh,Muhammad Abu-Elmagd,Rola F Turki,Ghazi A Damanhouri,Mohd A Beg,Mohammed Al-Qahtani
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. DEHP is metabolized to a primary metabolite mono-(2-
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A lack of peptide binding and decreased thermostability suggests that the CASKIN2 scaffolding protein SH3 domain may be vestigial. BMC Struct. Biol. Pub Date : 2016-09-13 Jamie J Kwan,Logan W Donaldson
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
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Conservation of the C-type lectin fold for accommodating massive sequence variation in archaeal diversity-generating retroelements. BMC Struct. Biol. Pub Date : 2016-08-31 Sumit Handa,Blair G Paul,Jeffery F Miller,David L Valentine,Partho Ghosh
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'
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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. Pub Date : 2016-08-17 Madhulata Kumari,Subhash Chandra,Neeraj Tiwari,Naidu Subbarao
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. It is a valid target
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Comprehensive analysis of the Co-structures of dipeptidyl peptidase IV and its inhibitor. BMC Struct. Biol. Pub Date : 2016-08-05 Hiroyuki Nojima,Kazuhiko Kanou,Genki Terashi,Mayuko Takeda-Shitaka,Gaku Inoue,Koichiro Atsuda,Chihiro Itoh,Chie Iguchi,Hajime Matsubara
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
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Investigation of allosteric coupling in human β2-adrenergic receptor in the presence of intracellular loop 3. BMC Struct. Biol. Pub Date : 2016-07-02 Canan Ozgur,Pemra Doruker,E Demet Akten
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
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Comparison of human and mouse E-selectin binding to Sialyl-Lewis(x). BMC Struct. Biol. Pub Date : 2016-07-02 Anne D Rocheleau,Thong M Cao,Tait Takitani,Michael R King
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))
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Structural determinant for inducing RORgamma specific inverse agonism triggered by a synthetic benzoxazinone ligand. BMC Struct. Biol. Pub Date : 2016-06-01 Douglas J Marcotte,YuTing Liu,Kevin Little,John H Jones,Noel A Powell,Craig P Wildes,Laura F Silvian,Jayanth V Chodaparambil
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)
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Crystal structure of human S100A8 in complex with zinc and calcium. BMC Struct. Biol. Pub Date : 2016-06-01 Haili Lin,Gregers Rom Andersen,Laure Yatime
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
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Erratum to: Structuprint: a scalable and extensible tool for two-dimensional representation of protein surfaces. BMC Struct. Biol. Pub Date : 2016-03-11 Dimitrios Georgios Kontopoulos,Dimitrios Vlachakis,Georgia Tsiliki,Sofia Kossida
Due to a formatting error during the production process of this article [1], equations 4 and 5 were published incorrectly in the PDF of the article [1]. The equations were, however, correctly presented in the HTML version of the article. Equations 4 and 5 are correctly included in this erratum. The publisher takes full responsibility for the errors which occurred and sincerely apologises for the inconvenience
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BMC Structural Biology reviewer acknowledgement 2015 BMC Struct. Biol. Pub Date : 2016-02-09 Julia Simundza
The editors of BMC Structural Biology would like to thank all our reviewers who have contributed to the journal in Volume 15 (2015).