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BMC Structural Biology

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https://www.readbyqxmd.com/read/30367660/crystal-structure-of-carbonic-anhydrase-cance103p-from-the-pathogenic-yeast-candida-albicans
#1
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
https://www.readbyqxmd.com/read/30286754/computational-analysis-of-the-interactions-of-a-novel-cephalosporin-derivative-with-%C3%AE-lactamases
#2
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
https://www.readbyqxmd.com/read/30219048/accurate-flexible-refinement-of-atomic-models-against-medium-resolution-cryo-em-maps-using-damped-dynamics
#3
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
https://www.readbyqxmd.com/read/30180896/comparative-sequence-and-structure-analysis-of-eif1a-and-eif1ad
#4
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
https://www.readbyqxmd.com/read/30134879/crystal-structure-of-duck-egg-lysozyme-isoform-ii-del-ii
#5
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
https://www.readbyqxmd.com/read/30029603/in-silico-prediction-of-novel-residues-involved-in-amyloid-primary-nucleation-of-human-i56t-and-d67h-lysozyme
#6
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
https://www.readbyqxmd.com/read/29940944/structure-and-dynamics-of-a-human-myelin-protein-p2-portal-region-mutant-indicate-opening-of-the-%C3%AE-barrel-in-fatty-acid-binding-proteins
#7
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
https://www.readbyqxmd.com/read/29769048/functional-insights-from-proteome-wide-structural-modeling-of-treponema-pallidum-subspecies-pallidum-the-causative-agent-of-syphilis
#8
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
https://www.readbyqxmd.com/read/29673347/structure-activity-relationship-sar-and-quantitative-structure-activity-relationship-qsar-studies-showed-plant-flavonoids-as-potential-inhibitors-of-dengue-ns2b-ns3-protease
#9
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
https://www.readbyqxmd.com/read/29669541/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
#10
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
https://www.readbyqxmd.com/read/29615024/re-tamd-exploring-interactions-between-h3-peptide-and-yeats-domain-using-enhanced-sampling
#11
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
https://www.readbyqxmd.com/read/29562896/correction-to-selected-articles-from-belyaev-conference-2017-structural-biology
#12
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
https://www.readbyqxmd.com/read/29454339/a-structural-preview-of-aquaporin-8-via-homology-modeling-of-seven-vertebrate-isoforms
#13
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 H2 O2 through various membranes of animal cells. This passive channel has been connected to a number of phenomena, such as volume change of mitochondria, ammonia neurotoxicity, and mitochondrial dysfunction related to oxidative stress...
February 17, 2018: BMC Structural Biology
https://www.readbyqxmd.com/read/29431095/molecular-mechanisms-underlying-the-impact-of-mutations-in-sod1-on-its-conformational-properties-associated-with-amyotrophic-lateral-sclerosis-as-revealed-with-molecular-modelling
#14
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 whole protein structure. RESULTS: In this work, a measure of hydrogen bond stability in conformational states was studied with elastic network analysis of 35 SOD1 mutants...
February 5, 2018: BMC Structural Biology
https://www.readbyqxmd.com/read/29258562/leishmania-infantum-5-methylthioadenosine-phosphorylase-presents-relevant-structural-divergence-to-constitute-a-potential-drug-target
#15
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 bioinformatic and structural characterization of the putative Leishmania infantum MTAP (LiMTAP), using a comparative computational approach...
December 19, 2017: BMC Structural Biology
https://www.readbyqxmd.com/read/28774292/rosetta-broker-for-membrane-protein-structure-prediction-concentrative-nucleoside-transporter-3-and-corticotropin-releasing-factor-receptor-1-test-cases
#16
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 functionally characterize two representatives of distinct membrane proteins families of solute carrier transporters and G protein-coupled receptors...
August 3, 2017: BMC Structural Biology
https://www.readbyqxmd.com/read/28545576/a-computational-assessment-of-ph-dependent-differential-interaction-of-t7-lysozyme-with-t7-rna-polymerase
#17
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 the effect of varying pH conditions on conformational flexibilities of T7L and their influence on T7RNAP -T7L interactions...
May 25, 2017: BMC Structural Biology
https://www.readbyqxmd.com/read/28521820/destabilization-of-the-twist1-e12-complex-dimerization-following-the-r154p-point-mutation-of-twist1-an-in-silico-approach
#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 mechanisms underlying their loss-of-function. In a previous study, we highlighted the predictive value of in silico molecular dynamics (MD) simulations in deciphering the molecular function of TWIST1 residues...
May 18, 2017: BMC Structural Biology
https://www.readbyqxmd.com/read/28482831/molecular-dynamics-simulation-of-the-opposite-base-preference-and-interactions-in-the-active-site-of-formamidopyrimidine-dna-glycosylase
#19
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 solved, yet no structure with A opposite the lesion is available. RESULTS: Here we use molecular dynamic simulation to model interactions in the pre-catalytic complex of Lactococcus lactis Fpg with DNA containing oxoG opposite C or A, the latter in either syn or anti conformation...
May 8, 2017: BMC Structural Biology
https://www.readbyqxmd.com/read/28438161/refolddb-a-new-and-sustainable-gateway-to-experimental-protocols-for-protein-refolding
#20
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 - "REFOLDdb" that collects refolding techniques into a single, searchable repository to help researchers develop refolding protocols for proteins of interest...
April 24, 2017: BMC Structural Biology
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