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Protein structure prediction

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https://www.readbyqxmd.com/read/29906639/development-of-a-machine-learning-model-to-predict-gibbs-free-energy-of-binding-for-protein-ligand-complexes
#1
Gabriela Bitencourt-Ferreira, Walter Filgueira de Azevedo
The possibility of using the atomic coordinates of protein-ligand complexes to assess binding affinity has a beneficial impact in the early stages of drug development and design. From the computational view, the creation of reliable scoring functions is still an open problem in the simulation of biological systems, and the development of a new generation machine-learning model is an active research field. In this work, we propose a novel scoring function to predict Gibbs free energy of binding (ΔG) based on the crystallographic structure of complexes involving a protein and an active ligand...
June 7, 2018: Biophysical Chemistry
https://www.readbyqxmd.com/read/29906485/deciphering-brain-specific-transcriptomic-expression-of-ezr-rad-and-msn-genes-in-the-development-of-mus-musculus
#2
Syed Aoun Ali, Deeba N Baig
Ezrin, Radixin and Moesin (ERM) are critical membranous component involved in cross-linking of actin filaments. Moesin (Msn) is recognized as a pivotal protein involved in regulation of cell signalling events associated with the maintenance of epithelial integrity, actin organization and polarity. Radixin (Rad) is known to cell-to-cell adherens junction as a barbed end-capping protein whereas ezrin (Ezr) is recognized at cell adhesion, motility, apoptosis and phagocytosis. The current study for the first time reports the transcriptional and RNA secondary structural variations among brain-specific ERM genes...
June 12, 2018: International Journal of Developmental Neuroscience
https://www.readbyqxmd.com/read/29905875/mistic2-comprehensive-server-to-study-coevolution-in-protein-families
#3
Eloy A Colell, Javier A Iserte, Franco L Simonetti, Cristina Marino-Buslje
Correlated mutations between residue pairs in evolutionarily related proteins arise from constraints needed to maintain a functional and stable protein. Identifying these inter-related positions narrows down the search for structurally or functionally important sites. MISTIC is a server designed to assist users to calculate covariation in protein families and provide them with an interactive tool to visualize the results. Here, we present MISTIC2, an update to the previous server, that allows to calculate four covariation methods (MIp, mfDCA, plmDCA and gaussianDCA)...
June 14, 2018: Nucleic Acids Research
https://www.readbyqxmd.com/read/29905873/identification-and-visualization-of-protein-binding-regions-with-the-ardock-server
#4
Sébastien Reille, Mélanie Garnier, Xavier Robert, Patrice Gouet, Juliette Martin, Guillaume Launay
ArDock (ardock.ibcp.fr) is a structural bioinformatics web server for the prediction and the visualization of potential interaction regions at protein surfaces. ArDock ranks the surface residues of a protein according to their tendency to form interfaces in a set of predefined docking experiments between the query protein and a set of arbitrary protein probes. The ArDock methodology is derived from large scale cross-docking studies where it was observed that randomly chosen proteins tend to dock in a non-random way at protein surfaces...
June 14, 2018: Nucleic Acids Research
https://www.readbyqxmd.com/read/29905574/mechanisms-leading-to-t-cell-activation-in-drug-hypersensitivity
#5
Xiaoli Meng, Daniel Yerly, Dean J Naisbitt
PURPOSE OF REVIEW: Delayed-type or nonimmediate drug hypersensitivity reactions often involve the activation of drug-specific T cells. As such, the molecular initiating event is an interaction between HLA proteins, HLA-binding peptides and the drug. For many years, the formation of covalently modified drug protein adducts was assumed to be a prerequisite for T-cell activation. The purpose of this article is to review recent studies using human PBMC, T-cell lines and clones, which show that drugs are in fact loaded onto HLA molecules in different forms to activate T cells...
June 13, 2018: Current Opinion in Allergy and Clinical Immunology
https://www.readbyqxmd.com/read/29905467/lov-domains-in-the-design-of-photoresponsive-enzymes
#6
Swantje Seifert, Susanne Brakmann
In nature, a multitude of mechanisms have emerged for regulating biological processes and, specifically, protein activity. Light as a natural regulatory element is of outstanding interest for studying and modulating protein activity because it can be precisely applied with regard to a site of action, instant of time, or intensity. Naturally occuring photoresponsive proteins, predominantly those containing a light-oxygen-voltage (LOV) domain, have been characterized structurally and mechanistically and also conjugated to various proteins of interest...
June 15, 2018: ACS Chemical Biology
https://www.readbyqxmd.com/read/29902657/effect-of-cao-2-addition-on-anaerobic-digestion-of-waste-activated-sludge-at-different-temperatures-and-the-promotion-of-valuable-carbon-source-production-under-ambient-condition
#7
Qian Ping, Xiao Lu, Ming Zheng, Yongmei Li
The effect of calcium peroxide (CaO2 ) addition on anaerobic digestion (AD) of waste activated sludge (WAS) at different temperatures (20 °C, 35 °C, and 55 °C) were investigated. The results show that CaO2 addition had significant positive effect on short-chain fatty acids (SCFAs) production under ambient and mesophilic conditions. Polysaccharides and proteins embedded in extracellular polymeric substances (EPS) were effectively released from inner fraction to outer fraction, and non-biodegradable humic-like substances were decreased while easily biodegradable tryptophan-like proteins increased...
June 6, 2018: Bioresource Technology
https://www.readbyqxmd.com/read/29902495/gonococcal-mtre-and-its-surface-expressed-loop-2-are-immunogenic-and-elicit-bactericidal-antibodies
#8
Shuyi Wang, Juan Xue, Ping Lu, Chunshan Ni, Hao Cheng, Rui Han, Stijn van der Veen
OBJECTIVES: The rise in multidrug resistant Neisseria gonorrhoeae poses a threat to healthcare, while the development of an effective vaccine has remained elusive due to antigenic and phase variability of surface-expressed proteins. In the current study, we identified a fully conserved surface expressed protein and characterized its suitability as a vaccine antigen. METHODS: An in silico approach was used to predict surface-expressed proteins and analyze sequence conservation and phase variability...
June 11, 2018: Journal of Infection
https://www.readbyqxmd.com/read/29902242/effects-of-low-dose-silver-nanoparticle-treatment-on-the-structure-and-community-composition-of-bacterial-freshwater-biofilms
#9
Alexandra Y Grün, Constantin B App, Andreas Breidenbach, Jutta Meier, George Metreveli, Gabriele E Schaumann, Werner Manz
The application of engineered silver nanoparticles (AgNPs) in a considerable amount of registered commercial products inevitably will result in the continuous release of AgNPs into the natural aquatic environment. Therefore, native biofilms, as the prominent life form of microorganisms in almost all known ecosystems, will be subjected to AgNP exposure. Despite the exponentially growing research activities worldwide, it is still difficult to assess nanoparticle-mediated toxicity in natural environments. In order to obtain an ecotoxicologically relevant exposure scenario, we performed experiments with artificial stream mesocosm systems approaching low dose AgNP concentrations close to predicted environmental concentrations...
2018: PloS One
https://www.readbyqxmd.com/read/29901984/modulating-enzyme-activity-by-altering-protein-dynamics-with-solvent
#10
Michael R Duff, Jose M Borreguero, Matthew Cuneo, Arvind Ramanathan, Junhong He, Ganesh Kamath, Chakra S Chennubhotla, Flora Meilleur, Elizabeth E Howell, Kenneth W Herwig, Dean A A Myles, Pratul K Agarwal
Optimal enzyme activity depends on a number of factors, including structure and dynamics. The role of enzyme structure is well recognized, however, the linkage between protein dynamics and enzyme activity has given rise to a contentious debate. We have developed an approach that uses an aqueous mixture of organic solvent to control the functionally relevant enzyme dynamics (without changing the structure), which in turn modulates the enzyme activity. Using this approach, we predicted that the hydride transfer reaction catalyzed by the enzyme dihydrofolate reductase (DHFR) from Escherichia coli in aqueous mixtures of isopropanol (IPA) with water will decrease by ~3 fold at 20% (v/v) IPA concentration...
June 14, 2018: Biochemistry
https://www.readbyqxmd.com/read/29901188/differences-in-the-expression-profiles-of-claudin-proteins-in-human-gastric-carcinoma-compared-with-non%C3%A2-neoplastic-mucosa
#11
Luoluo Yang, Xun Sun, Xiangwei Meng
Numerous genetic alterations associated with cancer progression have the potential to serve as biomarkers for the early diagnosis of cancer. Numerous studies have suggested that claudin proteins, which are the primary components of tight junction structures, are associated with the regulation of cell polarity and cell differentiation. To investigate the expression profiles of the tight junction proteins claudin‑2, ‑5, ‑7 and ‑8 in gastric carcinoma, immunohistochemical analysis, western blotting and reverse transcription‑quantitative polymerase chain reaction analysis was used to detect the expression profiles of these claudin proteins in gastric carcinoma tissues and in homologous non‑neoplastic mucosal tissues...
June 1, 2018: Molecular Medicine Reports
https://www.readbyqxmd.com/read/29899746/bgtep-an-antiprotease-involved-in-innate-immune-sensing-in-biomphalaria-glabrata
#12
Anaïs Portet, Richard Galinier, Silvain Pinaud, Julien Portela, Fanny Nowacki, Benjamin Gourbal, David Duval
Insect thioester-containing protein (iTEP) is the most recently defined group among the thioester-containing protein (TEP) superfamily. TEPs are key components of the immune system, and iTEPs from flies and mosquitoes were shown to be major immune weapons. Initially characterized from insects, TEP genes homologous to iTEP were further described from several other invertebrates including arthropods, cniderians, and mollusks albeit with few functional characterizations. In the freshwater snail Biomphalaria glabrata , a vector of the schistosomiasis disease, the presence of a TEP protein (BgTEP) was previously described in a well-defined immune complex involving snail lectins (fibrinogen-related proteins) and schistosome parasite mucins (SmPoMuc)...
2018: Frontiers in Immunology
https://www.readbyqxmd.com/read/29899369/network-biology-discovers-pathogen-contact-points-in-host-protein-protein-interactomes
#13
Hadia Ahmed, T C Howton, Yali Sun, Natascha Weinberger, Youssef Belkhadir, M Shahid Mukhtar
In all organisms, major biological processes are controlled by complex protein-protein interactions networks (interactomes), yet their structural complexity presents major analytical challenges. Here, we integrate a compendium of over 4300 phenotypes with Arabidopsis interactome (AI-1MAIN ). We show that nodes with high connectivity and betweenness are enriched and depleted in conditional and essential phenotypes, respectively. Such nodes are located in the innermost layers of AI-1MAIN and are preferential targets of pathogen effectors...
June 13, 2018: Nature Communications
https://www.readbyqxmd.com/read/29898867/differential-proteomics-research-of-bacillus-amyloliquefaciens-and-its-genome-shuffled-saltant-for-improving-fengycin-production
#14
Junfeng Zhao, Chong Zhang, Zhaoxin Lu
In the previous study, we used genome shuffling to improve fengycin production of the original strain Bacillus amyloliquefaciens ES-2-4. After two rounds of genome shuffling, a high-yield recombinant FMB72 strain that exhibited 8.30-fold increase in fengycin production was obtained. In this study, comparative proteomic analysis of the parental ES-2-4 and genome-shuffled FMB72 strains was conducted to examine the differentially expressed proteins. In the shuffled strain FMB72, 50 differently expressed spots (p<0...
May 19, 2018: Brazilian Journal of Microbiology: [publication of the Brazilian Society for Microbiology]
https://www.readbyqxmd.com/read/29897877/a-predicted-mannoprotein-participates-in-cryptococcus-gattii-capsular-structure
#15
Julia Catarina Vieira Reuwsaat, Heryk Motta, Ane Wichine Acosta Garcia, Carolina Bettker Vasconcelos, Bárbara Machado Marques, Natália Kronbauer Oliveira, Jéssica Rodrigues, Patrícia Aline Gröhns Ferrareze, Susana Frases, William Lopes, Vanessa Abreu Barcellos, Eamim Daidrê Squizani, Jorge André Horta, Augusto Schrank, Marcio Lourenço Rodrigues, Charley Christian Staats, Marilene Henning Vainstein, Lívia Kmetzsch
The yeast-like pathogen Cryptococcus gattii is an etiological agent of cryptococcosis. The major cryptococcal virulence factor is the polysaccharide capsule, which is composed of glucuronoxylomannan (GXM), galactoxylomannan (GalXM), and mannoproteins (MPs). The GXM and GalXM polysaccharides have been extensively characterized; however, there is little information about the role of mannoproteins in capsule assembly and their participation in yeast pathogenicity. The present study characterized the function of a predicted mannoprotein from C...
April 25, 2018: MSphere
https://www.readbyqxmd.com/read/29897777/computational-design-to-reduce-conformational-flexibility-and-aggregation-rates-of-an-antibody-fab-fragment
#16
Cheng Zhang, Maariyah Samad, Haoran Yu, Nesrine Chakroun, David Hilton, Paul A Dalby
Computationally-guided semi-rational design has significant potential for improving the aggregation kinetics of protein biopharmaceuticals. While improvement in the global conformational stability can stabilise proteins to aggregation under some conditions, previous studies suggest that such an approach is limited because thermal transition temperatures (Tm) and the fraction of protein unfolded (fT) tend to only correlate with aggregation kinetics where the protein is incubated at temperatures approaching the Tm...
June 13, 2018: Molecular Pharmaceutics
https://www.readbyqxmd.com/read/29896744/-mutation-analysis-of-fbn1-gene-in-a-child-with-marfan-syndrome
#17
Linxin Jiang, Dingding Zhang, Ying Xiao, Qi Wang, Bo Gong, Xiaoxin Guo, Maomin Huang, Zhenglin Yang
OBJECTIVE: To detect potential mutations of fibrillin-1 (FBN1) gene in a child with Marfan syndrome (MFS) and explore its molecular pathogenesis. METHODS: The 66 exons of the FBN1 gene were analyzed by direct sequencing. SIFT and PolyPhen-2 were used to predict the structural and functional changes at the protein level. RESULTS: A novel heterozygous mutation c.3998 G>A (p.Cys1333Tyr) was found in exon 32 in the child. The same mutation was not found among his unaffected family members and 683 healthy controls...
June 10, 2018: Zhonghua Yi Xue Yi Chuan Xue za Zhi, Zhonghua Yixue Yichuanxue Zazhi, Chinese Journal of Medical Genetics
https://www.readbyqxmd.com/read/29896723/-analysis-of-smpd1-gene-mutations-in-chinese-patients-with-parkinson-s-disease
#18
Na Song, Wei Wang, Chao Chen, Jianyi Niu, Yuxuan Guojin, Cunju Guo, Fabin Han
OBJECTIVE: To explore the role of sphingomyedlin phosphodiesterase 1 (SMPD1) gene mutations in the pathogenesis of Parkinson's disease (PD). METHODS: For 110 Chinese patients with PD, all exons of the SMPD1 gene were sequenced, and the results were compared with reference sequence from GenBank to identify possible mutations. RESULTS: A novel heterozygous mutation Ex2:c.677C>A/p.P226Q (likely pathogenic) was identified in a patient, which resulted in substitution of Glutamic acid by Proline at position 226...
June 10, 2018: Zhonghua Yi Xue Yi Chuan Xue za Zhi, Zhonghua Yixue Yichuanxue Zazhi, Chinese Journal of Medical Genetics
https://www.readbyqxmd.com/read/29896472/quantum-chemical-approaches-in-structure-based-virtual-screening-and-lead-optimization
#19
REVIEW
Claudio N Cavasotto, Natalia S Adler, Maria G Aucar
Today computational chemistry is a consolidated tool in drug lead discovery endeavors. Due to methodological developments and to the enormous advance in computer hardware, methods based on quantum mechanics (QM) have gained great attention in the last 10 years, and calculations on biomacromolecules are becoming increasingly explored, aiming to provide better accuracy in the description of protein-ligand interactions and the prediction of binding affinities. In principle, the QM formulation includes all contributions to the energy, accounting for terms usually missing in molecular mechanics force-fields, such as electronic polarization effects, metal coordination, and covalent binding; moreover, QM methods are systematically improvable, and provide a greater degree of transferability...
2018: Frontiers in Chemistry
https://www.readbyqxmd.com/read/29895642/sequence-variation-of-rare-outer-membrane-protein-%C3%AE-barrel-domains-in-clinical-strains-provides-insights-into-the-evolution-of-treponema-pallidum-subsp-pallidum-the-syphilis-spirochete
#20
Sanjiv Kumar, Melissa J Caimano, Arvind Anand, Abhishek Dey, Kelly L Hawley, Morgan E LeDoyt, Carson J La Vake, Adriana R Cruz, Lady G Ramirez, Lenka Paštěková, Irina Bezsonova, David Šmajs, Juan C Salazar, Justin D Radolf
In recent years, considerable progress has been made in topologically and functionally characterizing integral outer membrane proteins (OMPs) of Treponema pallidum subspecies pallidum , the syphilis spirochete, and identifying its surface-exposed β-barrel domains. Extracellular loops in OMPs of Gram-negative bacteria are known to be highly variable. We examined the sequence diversity of β-barrel-encoding regions of tprC , tprD , and bamA in 31 specimens from Cali, Colombia; San Francisco, California; and the Czech Republic and compared them to allelic variants in the 41 reference genomes in the NCBI database...
June 12, 2018: MBio
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