576 results match your criteria Bmc Structural Biology[Journal]


Characterization of putative proteins encoded by variable ORFs in white spot syndrome virus genome.

BMC Struct Biol 2019 Apr 18;19(1). Epub 2019 Apr 18.

Applied Molecular Biology Lab - LAPLIC, Department of Biochemistry, Federal University of Rio Grande do Norte, Natal, RN, Brazil.

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 in coding regions, and these putative proteins may have some relationship with viral adaptation and virulence mechanisms. Read More

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1186/s12900-019-0106-yDOI Listing

Correction to: Classification of the human THAP protein family identifies an evolutionarily conserved coiled coil region.

BMC Struct Biol 2019 03 29;19(1). Epub 2019 Mar 29.

Discipline of Biological Engineering, Indian Institute of Technology Gandhinagar, Gandhinagar, India.

. Read More

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1186/s12900-019-0105-zDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6441143PMC

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 2019 03 27;19(1). Epub 2019 Mar 27.

Armauer Hansen Research Institute (AHRI), Addis Ababa, Ethiopia.

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 remain unexplored. Read More

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1186/s12900-019-0104-0DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6437935PMC

QRNAS: software tool for refinement of nucleic acid structures.

BMC Struct Biol 2019 03 21;19(1). Epub 2019 Mar 21.

Laboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology, 02-109, Warsaw, Poland.

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 quality of the model but to bring it globally closer to the true structure. Read More

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1186/s12900-019-0103-1DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6429776PMC

Classification of the human THAP protein family identifies an evolutionarily conserved coiled coil region.

BMC Struct Biol 2019 03 5;19(1). Epub 2019 Mar 5.

Discipline of Biological Engineering, Indian Institute of Technology Gandhinagar, Gandhinagar, India.

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 called the THAP domain. However, the carboxy terminus of most THAP proteins is yet to be structurally characterized. Read More

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1186/s12900-019-0102-2DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6402169PMC

A new technique for predicting intrinsically disordered regions based on average distance map constructed with inter-residue average distance statistics.

BMC Struct Biol 2019 02 6;19(1). Epub 2019 Feb 6.

Department of Bioinformatics, College of Life Sciences, Ritsumeikan University, 1-1-1 Nojihigashi, Kusatsu, Shiga, 525-8577, Japan.

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 regions in a protein, based on our average distance map (ADM) technique. Read More

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1186/s12900-019-0101-3DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6366092PMC
February 2019

Crystal structure of E. coli PRPP synthetase.

BMC Struct Biol 2019 01 15;19(1). Epub 2019 Jan 15.

Department of Chemistry, Stony Brook University, Stony Brook, NY, 11794, USA.

Background: Ribose-phosphate pyrophosphokinase (EC 2.7.6. Read More

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1186/s12900-019-0100-4DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6332680PMC
January 2019
1 Read

The human transketolase-like proteins TKTL1 and TKTL2 are bona fide transketolases.

BMC Struct Biol 2019 01 15;19(1). Epub 2019 Jan 15.

Cardio-Metabolic Research Group (CMRG), Department of Physiological Sciences, Stellenbosch University, Room 2005, Mike De Vries Building, Merriman Avenue, Stellenbosch, 7600, South Africa.

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 targets. Read More

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1186/s12900-018-0099-yDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6334435PMC
January 2019
2 Reads

Deciphering evolution of immune recognition in antibodies.

BMC Struct Biol 2018 12 19;18(1):19. Epub 2018 Dec 19.

Regional Centre for Biotechnology, Biotech Science Cluster, Faridabad, Haryana, 121001, India.

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 cannot be ignored. Read More

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1186/s12900-018-0096-1DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6299584PMC
December 2018
4 Reads

Cryo-electron microscope image denoising based on the geodesic distance.

BMC Struct Biol 2018 12 17;18(1):18. Epub 2018 Dec 17.

College of Physics and Information Science, Hunan Normal University, Changsha, 410081, Hunan, China.

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 geodesic metric, to measure the similarity of blocks. Read More

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1186/s12900-018-0094-3DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6296045PMC
December 2018
1 Read

Novel features in the structure of P-glycoprotein (ABCB1) in the post-hydrolytic state as determined at 7.9 Å resolution.

BMC Struct Biol 2018 12 13;18(1):17. Epub 2018 Dec 13.

School of Biology, Faculty of Biology Medicine and Health, Michael Smith Building, The University of Manchester, Oxford Road, Manchester, M13 9PL, UK.

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 of the wild-type protein has been resolved at about 8 Å resolution. Read More

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1186/s12900-018-0098-zDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6293506PMC
December 2018
2 Reads

An improved protein structure evaluation using a semi-empirically derived structure property.

BMC Struct Biol 2018 12 12;18(1):16. Epub 2018 Dec 12.

Department of Applied Science, Indian Institute of Information Technology, Biomedical Informatics Lab, Room no 4302, CC2 Building, Allahabad, UP, 211012, India.

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 dynamics based optimization appears to be the most popular one. However it suffers from contradictory indications of different validation parameters generated from a set of protein models which are predicted against a particular target protein. Read More

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1186/s12900-018-0097-0DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6291994PMC
December 2018
13 Reads
1.178 Impact Factor

Comparative analysis of interactions between aryl hydrocarbon receptor ligand binding domain with its ligands: a computational study.

BMC Struct Biol 2018 12 6;18(1):15. Epub 2018 Dec 6.

Department of Pathology, Microbiology and Immunology, University of South Carolina, School of Medicine, Columbia, SC, 29208, USA.

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 (TCDD), 6-formylindolo[3,2-b]carbazole (FICZ), indole-3-carbinol (I3C) and its degradation product, 3,3'-diindolylmethane (DIM), Resveratrol (RES) and its analogue, Piceatannol (PTL) using molecular modeling approach followed by molecular dynamic simulations. Read More

View Article

Download full-text PDF

Source
https://bmcstructbiol.biomedcentral.com/articles/10.1186/s12
Publisher Site
http://dx.doi.org/10.1186/s12900-018-0095-2DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6282305PMC
December 2018
15 Reads

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

BMC Struct Biol 2018 10 26;18(1):14. Epub 2018 Oct 26.

Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Flemingovo náměstí 2, 166 10, Prague, Czech Republic.

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. Read More

View Article

Download full-text PDF

Source
https://bmcstructbiol.biomedcentral.com/articles/10.1186/s12
Publisher Site
http://dx.doi.org/10.1186/s12900-018-0093-4DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6203986PMC
October 2018
28 Reads

Computational analysis of the interactions of a novel cephalosporin derivative with β-lactamases.

BMC Struct Biol 2018 10 4;18(1):13. Epub 2018 Oct 4.

Department of Chemistry and Biology "A. Zambelli", University of Salerno, Via Giovanni Paolo II, 132, 84084, Fisciano, SA, Italy.

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 between a new cephalosporin derivative containing an additional β-lactam ring with different substituents, and several serine β-lactamases representative of the different classes of this family of enzymes. Read More

View Article

Download full-text PDF

Source
https://bmcstructbiol.biomedcentral.com/articles/10.1186/s12
Publisher Site
http://dx.doi.org/10.1186/s12900-018-0092-5DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6389238PMC
October 2018
2 Reads

Accurate flexible refinement of atomic models against medium-resolution cryo-EM maps using damped dynamics.

BMC Struct Biol 2018 09 15;18(1):12. Epub 2018 Sep 15.

Department of Mechanical and Aerospace Engineering, Old Dominion University, Norfolk, VA, USA.

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 of such medium-resolution refinement methods. Read More

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1186/s12900-018-0089-0DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6139150PMC
September 2018
2 Reads

Comparative sequence and structure analysis of eIF1A and eIF1AD.

BMC Struct Biol 2018 09 4;18(1):11. Epub 2018 Sep 4.

Department of Physiology and Biophysics, Boston University School of Medicine, Boston, MA, USA.

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. Read More

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1186/s12900-018-0091-6DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6122471PMC
September 2018
1 Read

Crystal structure of duck egg lysozyme isoform II (DEL-II).

BMC Struct Biol 2018 08 22;18(1):10. Epub 2018 Aug 22.

Immunology Division, Garvan Institute of Medical Research, 384 Victoria Road, Darlinghurst, Sydney, NSW, 2010, Australia.

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 of all three isoforms by mass spectrometry. Read More

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1186/s12900-018-0090-7DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6103880PMC
August 2018
24 Reads

In silico prediction of novel residues involved in amyloid primary nucleation of human I56T and D67H lysozyme.

BMC Struct Biol 2018 07 20;18(1). Epub 2018 Jul 20.

Department of Biomedical Sciences, Quillen College of Medicine, East Tennessee State University, Johnson City, TN, 37614, USA.

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 the process of amyloid formation of lysozyme tend to focus on partial unfolding of the native state due to the relative instability of mutant amyloidogenic variants. Read More

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1186/s12900-018-0088-1DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6053722PMC
July 2018
3 Reads

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 2018 06 25;18(1). Epub 2018 Jun 25.

Faculty of Biochemistry and Molecular Medicine, University of Oulu, Oulu, Finland.

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 Charcot-Marie-Tooth disease. Read More

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1186/s12900-018-0087-2DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6020228PMC
June 2018
6 Reads

Functional insights from proteome-wide structural modeling of Treponema pallidum subspecies pallidum, the causative agent of syphilis.

BMC Struct Biol 2018 05 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

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1186/s12900-018-0086-3DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5956850PMC
May 2018
40 Reads

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 04 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

View Article

Download full-text PDF

Source
https://bmcstructbiol.biomedcentral.com/articles/10.1186/s12
Publisher Site
http://dx.doi.org/10.1186/s12900-018-0084-5DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5909242PMC
April 2018
13 Reads

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 04 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

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1186/s12900-018-0085-4DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5907181PMC
April 2018
6 Reads

re-TAMD: exploring interactions between H3 peptide and YEATS domain using enhanced sampling.

BMC Struct Biol 2018 04 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

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1186/s12900-018-0083-6DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5883362PMC
April 2018
4 Reads

Correction to: selected articles from Belyaev Conference 2017: structural biology.

BMC Struct Biol 2018 03 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

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1186/s12900-018-0082-7DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5863448PMC
March 2018
11 Reads

A structural preview of aquaporin 8 via homology modeling of seven vertebrate isoforms.

BMC Struct Biol 2018 02 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

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1186/s12900-018-0081-8DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5816522PMC
February 2018
3 Reads

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

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1186/s12900-018-0080-9DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5808480PMC
February 2018
10 Reads

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

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1186/s12900-017-0079-7DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5738077PMC
December 2017
4 Reads

Rosetta Broker for membrane protein structure prediction: concentrative nucleoside transporter 3 and corticotropin-releasing factor receptor 1 test cases.

Authors:
Dorota Latek

BMC Struct Biol 2017 08 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

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1186/s12900-017-0078-8DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5543540PMC
August 2017
21 Reads

A computational assessment of pH-dependent differential interaction of T7 lysozyme with T7 RNA polymerase.

BMC Struct Biol 2017 05 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

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1186/s12900-017-0077-9DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5445346PMC
May 2017
12 Reads

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

BMC Struct Biol 2017 05 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

View Article

Download full-text PDF

Source
http://link.springer.com/content/pdf/10.1186%2Fs12900-017-00
Web Search
http://bmcstructbiol.biomedcentral.com/articles/10.1186/s129
Publisher Site
http://dx.doi.org/10.1186/s12900-017-0076-xDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5437649PMC
May 2017
17 Reads

Molecular dynamics simulation of the opposite-base preference and interactions in the active site of formamidopyrimidine-DNA glycosylase.

BMC Struct Biol 2017 05 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

View Article

Download full-text PDF

Source
http://bmcstructbiol.biomedcentral.com/articles/10.1186/s129
Publisher Site
http://dx.doi.org/10.1186/s12900-017-0075-yDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5422863PMC
May 2017
22 Reads

REFOLDdb: a new and sustainable gateway to experimental protocols for protein refolding.

BMC Struct Biol 2017 04 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

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1186/s12900-017-0074-zDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5402662PMC
April 2017
39 Reads

A comparative analysis of the foamy and ortho virus capsid structures reveals an ancient domain duplication.

BMC Struct Biol 2017 04 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

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1186/s12900-017-0073-0DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5379526PMC
April 2017
9 Reads

DynaDom: structure-based prediction of T cell receptor inter-domain and T cell receptor-peptide-MHC (class I) association angles.

BMC Struct Biol 2017 02 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

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1186/s12900-016-0071-7DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5289058PMC
February 2017
8 Reads

Prokaryotic ubiquitin-like protein remains intrinsically disordered when covalently attached to proteasomal target proteins.

BMC Struct Biol 2017 02 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

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1186/s12900-017-0072-1DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5286830PMC
February 2017
6 Reads

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

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1186/s12900-016-0069-1DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5093936PMC
November 2016
9 Reads

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

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1186/s12900-016-0068-2DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5081678PMC
October 2016
9 Reads

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

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1186/s12900-016-0070-8DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5080731PMC
October 2016
7 Reads
2 Citations
1.180 Impact Factor

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

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1186/s12900-016-0067-3DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5056528PMC
September 2016
12 Reads
2 Citations
1.180 Impact Factor

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

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1186/s12900-016-0066-4DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5056466PMC
September 2016
16 Reads
1.180 Impact Factor

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

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1186/s12900-016-0065-5DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5020537PMC
September 2016
7 Reads

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

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1186/s12900-016-0064-6DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5006420PMC
August 2016
7 Reads

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

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1186/s12900-016-0063-7DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4989538PMC
August 2016
15 Reads

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

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1186/s12900-016-0062-8DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4974693PMC
August 2016
16 Reads

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

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1186/s12900-016-0061-9DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4930610PMC
July 2016
17 Reads

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

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1186/s12900-016-0060-xDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4930595PMC
July 2016
9 Reads

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

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1186/s12900-016-0058-4DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4888247PMC
June 2016
13 Reads

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

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1186/s12900-016-0059-3DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4888278PMC
June 2016
52 Reads

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.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1186/s12900-016-0057-5DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4788825PMC
March 2016
6 Reads