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Protein structure prediction

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https://www.readbyqxmd.com/read/29232711/dependence-of-prevalence-of-contiguous-pathways-in-proteins-on-structural-complexity
#1
Kelly M Thayer, Jesse C Galganov, Avram J Stein
Allostery is a regulatory mechanism in proteins where an effector molecule binds distal from an active site to modulate its activity. Allosteric signaling may occur via a continuous path of residues linking the active and allosteric sites, which has been suggested by large conformational changes evident in crystal structures. An alternate possibility is that the signal occurs in the realm of ensemble dynamics via an energy landscape change. While the latter was first proposed on theoretical grounds, increasing evidence suggests that such a control mechanism is plausible...
2017: PloS One
https://www.readbyqxmd.com/read/29232602/cooperative-protein-unfolding-a-statistical-mechanical-model-for-the-action-of-denaturants
#2
J Seelig
Knowledge of protein stability is of utmost importance in various fields of biotechnology. Protein stability can be assessed in solution by increasing the concentration of denaturant and recording the structural changes with spectroscopic or thermodynamic methods. The standard interpretation of the experimental data is to assume a 2-state equilibrium between completely folded and completely unfolded protein molecules. Here we propose a cooperative model based on the statistical-mechanical Zimm-Bragg theory...
December 5, 2017: Biophysical Chemistry
https://www.readbyqxmd.com/read/29232197/dna-based-construction-at-the-nanoscale-emerging-trends-and-applications
#3
Lourdu Xavier Paulraj, Arun Richard Chandrasekaran
The field of structural DNA nanotechnology has reached adolescence - starting with the creation of artificial immobile junctions leading to the recent DNA-protein hybrid nanoscale shapes - in a span of about 35 years. It is now possible to create complex DNA-based nanoscale shapes and assemblies with greater stability and predictability, thanks to the development of computational tools and advances in experimental techniques. Although started with the original goal of DNA-assisted structure determination of difficult-to-crystallize molecules, DNA nanotechnology has found its applications in a myriad of fields...
December 12, 2017: Nanotechnology
https://www.readbyqxmd.com/read/29231944/stability-of-plant-virus-based-nanocarriers-in-gastrointestinal-fluids
#4
Alberto Berardi, David J Evans, Francesca Baldelli Bombelli, George P Lomonossoff
Cowpea mosaic virus (CPMV) is a plant virus which is being extensively investigated as a drug delivery and vaccine nanocarrier for parenteral administration. However, to date little is known about the suitability of plant-based nanocarriers for oral delivery. In this study, the colloidal (i.e. aggregation), physical (i.e. denaturation) and chemical (i.e. digestion of the polypeptides) stability of CPMV and its empty virus-like particles (eVLPs) in conditions resembling the gastrointestinal fluids were evaluated...
December 12, 2017: Nanoscale
https://www.readbyqxmd.com/read/29231195/hsd3b1-status-as-a-biomarker-of-androgen-deprivation-resistance-and-implications-for-prostate-cancer
#5
REVIEW
Daniel Hettel, Nima Sharifi
Patients with advanced prostate cancer who receive androgen deprivation therapy (ADT) almost invariably develop castration-resistant disease. The mechanism of resistance is largely based on synthesis of intratumoral androgens from adrenal precursors, requiring enzymatic action of 3β-hydroxysteroid dehydrogenase/Δ5→4 isomerase 1 (3β-HSD1), encoded by HSD3B1. A nucleotide polymorphism (1245A>C) in HSD3B1 results in a protein variant with increased steady-state levels and subsequently increased androgen synthesis from extragonadal precursors...
December 12, 2017: Nature Reviews. Urology
https://www.readbyqxmd.com/read/29231176/tensorcalculator-exploring-the-evolution-of-mechanical-stress-in-the-ccmv-capsid
#6
Olga Kononova, Farkhad Maksudov, Kenneth A Marx, Valeri Barsegov
A new computational methodology for accurate numerical calculation of the Cauchy stress tensor, stress invariants, principal stress components, von Mises and Tresca tensors is developed. The methodology is based on the atomic stress approach which permits the calculation of stress tensors, widely used in continuum mechanics modeling of materials properties, using the output from the MD simulations of discrete atomic and Cα-based coarse-grained structural models of biological particles. The methodology mapped into software package TensorCalculator was successfully applied to the empty Cowpea Chlorotic Mottle virus (CCMV) shell to explore the evolution of mechanical stress in this mechanically-tested specific example of a soft virus capsid...
December 12, 2017: Journal of Physics. Condensed Matter: An Institute of Physics Journal
https://www.readbyqxmd.com/read/29231144/qsar-of-natural-sesquiterpene-lactones-as-inhibitors-of-myb-dependent-gene-expression
#7
Gloria Castellano, Lucia Redondo, Francisco Torrens
Protein c-Myb is a therapeutic target. Some sesquiterpene lactones suppress Myb-dependent gene expression, which results in a mechanism for their potential anti-cancer activity. Database ChEMBL is representative of lactones for physicochemical and physiochemical properties. Data presented for 31 natural lactones are discussed in terms of quantitative structure-activity relationships, which objective is to predict inhibitors of Myb-induced gene expression. Several constitutional descriptors are related to structure-activity...
December 11, 2017: Current Topics in Medicinal Chemistry
https://www.readbyqxmd.com/read/29230368/stem-loop-structure-preference-for-site-specific-rna-editing-by-apobec3a-and-apobec3g
#8
Shraddha Sharma, Bora E Baysal
APOBEC3A and APOBEC3G cytidine deaminases inhibit viruses and endogenous retrotransposons. We recently demonstrated the novel cellular C-to-U RNA editing function of APOBEC3A and APOBEC3G. Both enzymes deaminate single-stranded DNAs at multiple TC or CC nucleotide sequences, but edit only a select set of RNAs, often at a single TC or CC nucleotide sequence. To examine the specific site preference for APOBEC3A and -3G-mediated RNA editing, we performed mutagenesis studies of the endogenous cellular RNA substrates of both proteins...
2017: PeerJ
https://www.readbyqxmd.com/read/29230365/identification-and-characterization-of-a-novel-zebrafish-danio-rerio-pentraxin-carbonic-anhydrase
#9
Maarit S Patrikainen, Martti E E Tolvanen, Ashok Aspatwar, Harlan R Barker, Csaba Ortutay, Janne Jänis, Mikko Laitaoja, Vesa P Hytönen, Latifeh Azizi, Prajwol Manandhar, Edit Jáger, Daniela Vullo, Sampo Kukkurainen, Mika Hilvo, Claudiu T Supuran, Seppo Parkkila
Background: Carbonic anhydrases (CAs) are ubiquitous, essential enzymes which catalyze the conversion of carbon dioxide and water to bicarbonate and H+ ions. Vertebrate genomes generally contain gene loci for 15-21 different CA isoforms, three of which are enzymatically inactive. CA VI is the only secretory protein of the enzymatically active isoforms. We discovered that non-mammalian CA VI contains a C-terminal pentraxin (PTX) domain, a novel combination for both CAs and PTXs. Methods: We isolated and sequenced zebrafish (Danio rerio) CA VI cDNA, complete with the sequence coding for the PTX domain, and produced the recombinant CA VI-PTX protein...
2017: PeerJ
https://www.readbyqxmd.com/read/29229851/structure-based-prediction-of-ligand-protein-interactions-on-a-genome-wide-scale
#10
Howook Hwang, Fabian Dey, Donald Petrey, Barry Honig
We report a template-based method, LT-scanner, which scans the human proteome using protein structural alignment to identify proteins that are likely to bind ligands that are present in experimentally determined complexes. A scoring function that rapidly accounts for binding site similarities between the template and the proteins being scanned is a crucial feature of the method. The overall approach is first tested based on its ability to predict the residues on the surface of a protein that are likely to bind small-molecule ligands...
December 11, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/29229843/machine-learning-shows-association-between-genetic-variability-in-pparg-and-cerebral-connectivity-in-preterm-infants
#11
Michelle L Krishnan, Zi Wang, Paul Aljabar, Gareth Ball, Ghazala Mirza, Alka Saxena, Serena J Counsell, Joseph V Hajnal, Giovanni Montana, A David Edwards
Preterm infants show abnormal structural and functional brain development, and have a high risk of long-term neurocognitive problems. The molecular and cellular mechanisms involved are poorly understood, but novel methods now make it possible to address them by examining the relationship between common genetic variability and brain endophenotype. We addressed the hypothesis that variability in the Peroxisome Proliferator Activated Receptor (PPAR) pathway would be related to brain development. We employed machine learning in an unsupervised, unbiased, combined analysis of whole-brain diffusion tractography together with genomewide, single-nucleotide polymorphism (SNP)-based genotypes from a cohort of 272 preterm infants, using Sparse Reduced Rank Regression (sRRR) and correcting for ethnicity and age at birth and imaging...
December 11, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/29229841/predicting-glycosaminoglycan-surface-protein-interactions-and-implications-for-studying-axonal-growth
#12
Adam R Griffith, Claude J Rogers, Gregory M Miller, Ravinder Abrol, Linda C Hsieh-Wilson, William A Goddard
Cell-surface carbohydrates play important roles in numerous biological processes through their interactions with various protein-binding partners. These interactions are made possible by the vast structural diversity of carbohydrates and the diverse array of carbohydrate presentations on the cell surface. Among the most complex and important carbohydrates are glycosaminoglycans (GAGs), which display varied stereochemistry, chain lengths, and patterns of sulfation. GAG-protein interactions participate in neuronal development, angiogenesis, spinal cord injury, viral invasion, and immune response...
December 11, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/29229831/clinical-genetic-and-structural-basis-of-apparent-mineralocorticoid-excess-due-to-11%C3%AE-hydroxysteroid-dehydrogenase-type-2-deficiency
#13
Mabel Yau, Shozeb Haider, Ahmed Khattab, Chen Ling, Mehr Mathew, Samir Zaidi, Madison Bloch, Monica Patel, Sinead Ewert, Wafa Abdullah, Aysenur Toygar, Vitalii Mudryi, Maryam Al Badi, Mouch Alzubdi, Robert C Wilson, Hanan Said Al Azkawi, Hatice Nur Ozdemir, Wahid Abu-Amer, Jozef Hertecant, Maryam Razzaghy-Azar, John W Funder, Aisha Al Senani, Li Sun, Se-Min Kim, Tony Yuen, Mone Zaidi, Maria I New
Mutations in 11β-hydroxysteroid dehydrogenase type 2 gene (HSD11B2) cause an extraordinarily rare autosomal recessive disorder, apparent mineralocorticoid excess (AME). AME is a form of low renin hypertension that is potentially fatal if untreated. Mutations in the HSD11B2 gene result either in severe AME or a milder phenotype (type 2 AME). To date, ∼40 causative mutations have been identified. As part of the International Consortium for Rare Steroid Disorders, we have diagnosed and followed the largest single worldwide cohort of 36 AME patients...
December 11, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/29229819/discovery-of-the-leinamycin-family-of-natural-products-by-mining-actinobacterial-genomes
#14
Guohui Pan, Zhengren Xu, Zhikai Guo, Hindra, Ming Ma, Dong Yang, Hao Zhou, Yannick Gansemans, Xiangcheng Zhu, Yong Huang, Li-Xing Zhao, Yi Jiang, Jinhua Cheng, Filip Van Nieuwerburgh, Joo-Won Suh, Yanwen Duan, Ben Shen
Nature's ability to generate diverse natural products from simple building blocks has inspired combinatorial biosynthesis. The knowledge-based approach to combinatorial biosynthesis has allowed the production of designer analogs by rational metabolic pathway engineering. While successful, structural alterations are limited, with designer analogs often produced in compromised titers. The discovery-based approach to combinatorial biosynthesis complements the knowledge-based approach by exploring the vast combinatorial biosynthesis repertoire found in Nature...
December 11, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/29229761/an-unusual-diphosphatase-from-the-phnp-family-cleaves-reactive-fad-photoproducts
#15
Guillaume Aw Beaudoin, Qiang Li, Steven D Bruner, Andrew D Hanson
Flavins are notoriously photolabile, but while the photoproducts derived from the iso -alloxazine ring are well known the other photoproducts are not. In the case of FAD, typically the main cellular flavin, the other photoproducts are predicted to include four- and five-carbon sugars linked to ADP. These FAD photoproducts were shown to be potent glycating agents, more so than ADP-ribose. Such toxic compounds would require disposal via an ADP-sugar diphosphatase or other route. Comparative analysis of bacterial genomes uncovered a candidate disposal gene that is chromosomally clustered with genes for FAD synthesis or transport and is predicted to encode a protein of the PhnP cyclic phosphodiesterase family...
December 11, 2017: Biochemical Journal
https://www.readbyqxmd.com/read/29228598/analysis-of-molecular-evolution-of-nucleocapsid-protein-in-newcastle-disease-virus
#16
Wentao Fan, Yuliang Xu, Pu Zhang, Peng Chen, Yiran Zhu, Ziqiang Cheng, Xiaona Zhao, Yongxia Liu, Jianzhu Liu
The present study investigated the molecular evolution of nucleocapsid protein (NP) in different Newcastle disease virus (NDV) genotypes. The evolutionary timescale and rate were estimated using the Bayesian Markov chain Monte Carlo (MCMC) method. The p-distance, Bayesian skyline plot (BSP), and positively selected sites were also analyzed. The MCMC tree indicated that NDV diverged about 250 years ago with a rapid evolution rate (1.059 × 10-2 substitutions/site/year) and that different NDV genotypes formed three lineages...
November 14, 2017: Oncotarget
https://www.readbyqxmd.com/read/29228193/deepsf-deep-convolutional-neural-network-for-mapping-protein-sequences-to-folds
#17
Jie Hou, Badri Adhikari, Jianlin Cheng
Motivation: Protein fold recognition is an important problem in structural bioinformatics. Almost all traditional fold recognition methods use sequence (homology) comparison to indirectly predict the fold of a target protein based on the fold of a template protein with known structure, which cannot explain the relationship between sequence and fold. Only a few methods had been developed to classify protein sequences into a small number of folds due to methodological limitations, which are not generally useful in practice...
December 8, 2017: Bioinformatics
https://www.readbyqxmd.com/read/29228185/dncon2-improved-protein-contact-prediction-using-two-level-deep-convolutional-neural-networks
#18
Badri Adhikari, Jie Hou, Jianlin Cheng
Motivation: Significant improvements in the prediction of protein residue-residue contacts are observed in the recent years. These contacts, predicted using a variety of coevolution-based and machine learning methods, are the key contributors to the recent progress in ab initio protein structure prediction, as demonstrated in the recent CASP experiments. Continuing the development of new methods to reliably predict contact maps is essential to further improve ab initio structure prediction...
December 8, 2017: Bioinformatics
https://www.readbyqxmd.com/read/29227673/crystal-structure-of-cleaved-serp-1-a-myxomavirus-derived-immune-modulating-serpin-structural-design-of-serpin-reactive-center-loop-rcl-peptides-with-improved-therapeutic-function
#19
Brian P Mahon, Sriram Ambadapadi, Jordan R Yaron, Carrie L Lomelino, Melissa A Pinard, Shahar Keinan, Igor Kurnikov, Colin Macaulay, Liqiang Zhang, Westley Reeves, Grant McFadden, Scott Tibbetts, Robert McKenna, Alexandra Lucas
The Myxomavirus-derived protein Serp-1 has potent anti-inflammatory activity in models of vasculitis, lupus, viral sepsis, and transplant. Serp-1 has also been tested successfully in a Phase IIa clinical trial in unstable angina, representing a 'first-in-class' therapeutic. Recently, peptides derived from the reactive center loop (RCL) have been developed as stand-alone therapeutics for reducing vasculitis and improving survival in MHV68-infected mice. However, both Serp-1 and the RCL peptides lose activity in MHV68-infected mice after antibiotic suppression of intestinal microbiota...
December 11, 2017: Biochemistry
https://www.readbyqxmd.com/read/29227473/structure-inspired-design-of-%C3%AE-arrestin-biased-ligands-for-aminergic-gpcrs
#20
John D McCorvy, Kyle V Butler, Brendan Kelly, Katie Rechsteiner, Joel Karpiak, Robin M Betz, Bethany L Kormos, Brian K Shoichet, Ron O Dror, Jian Jin, Bryan L Roth
Development of biased ligands targeting G protein-coupled receptors (GPCRs) is a promising approach for current drug discovery. Although structure-based drug design of biased agonists remains challenging even with an abundance of GPCR crystal structures, we present an approach for translating GPCR structural data into β-arrestin-biased ligands for aminergic GPCRs. We identified specific amino acid-ligand contacts at transmembrane helix 5 (TM5) and extracellular loop 2 (EL2) responsible for Gi/o and β-arrestin signaling, respectively, and targeted those residues to develop biased ligands...
December 11, 2017: Nature Chemical Biology
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