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BMC Structural Biology

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 regions in a protein, based on our average distance map (ADM) technique. The ADM technique was developed to predict compact regions or structural domains in a protein...
February 6, 2019: BMC Structural Biology
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 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 I phosphoribosyltransferase folds, related by 2-fold pseudosymmetry...
January 15, 2019: BMC Structural Biology
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 targets. However, it remains unclear whether TKTL1 and TKTL2 are functional transketolases...
January 15, 2019: BMC Structural Biology
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 cannot be ignored. While there are reports on antibody lineage, structural perspective with respect to diverse recognition potential in a lineage has never been studied...
December 19, 2018: BMC Structural Biology
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 geodesic metric, to measure the similarity of blocks. RESULTS: Our method is a 2-D image denoising approach...
December 17, 2018: BMC Structural Biology
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 of the wild-type protein has been resolved at about 8 Å resolution...
December 13, 2018: BMC Structural Biology
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 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...
December 12, 2018: BMC Structural Biology
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 (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...
December 6, 2018: BMC Structural Biology
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 its ortholog ScNce103p from Saccharomyces cerevisiae. The crystal structure of CaNce103p is of interest because this enzyme is a potential target for surface disinfectants...
October 26, 2018: BMC Structural Biology
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 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...
October 4, 2018: BMC Structural Biology
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 of such medium-resolution refinement methods. These algorithms aim to automatically optimize the parameters that define the density shape of the flexibly fitted model, as well as the time-dependent damper cutoff distance...
September 15, 2018: BMC Structural Biology
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 of an eIF1A homolog, the eIF1A domain-containing protein (eIF1AD) was recently determined but its biological functions are unknown...
September 4, 2018: BMC Structural Biology
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 of all three isoforms by mass spectrometry. Here we present the crystal structure of isoform II (DEL-II)...
August 22, 2018: BMC Structural Biology
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 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...
July 20, 2018: BMC Structural Biology
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 Charcot-Marie-Tooth disease. A conserved residue that has been proposed to participate in membrane and fatty acid binding and conformational changes in FABPs is Phe57...
June 25, 2018: BMC Structural Biology
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 is currently uncultivatable, inherently fragile and thus difficult to work with, and phylogenetically distinct with no conventional virulence factor homologs found in other pathogens...
May 16, 2018: BMC Structural Biology
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, the NS2B-NS3 is a well-characterized target for designing antiviral drug. RESULTS: In this study docking analysis was performed with active site of dengue NS2B-NS3 protein with selected plant flavonoids...
April 19, 2018: BMC Structural Biology
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, how the above drugs are likely to inhibit the M.tb protein's function. RESULTS: The three-dimensional computer models for M...
April 18, 2018: BMC Structural Biology
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 terminal peptide of histone H3 and the YEATS domain. Depending on the length of the peptide, several regions of the protein surface were explored...
April 3, 2018: BMC Structural Biology
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.
March 21, 2018: BMC Structural Biology
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