keyword
MENU ▼
Read by QxMD icon Read
search

Protein structure prediction

keyword
https://www.readbyqxmd.com/read/29045866/how-many-protein-sequences-fold-to-a-given-structure-a-coevolutionary-analysis
#1
Pengfei Tian, Robert B Best
Quantifying the relationship between protein sequence and structure is key to understanding the protein universe. A fundamental measure of this relationship is the total number of amino acid sequences that can fold to a target protein structure, known as the "sequence capacity," which has been suggested as a proxy for how designable a given protein fold is. Although sequence capacity has been extensively studied using lattice models and theory, numerical estimates for real protein structures are currently lacking...
October 17, 2017: Biophysical Journal
https://www.readbyqxmd.com/read/29045859/role-of-condensing-particles-in-polymer-confinement-a-model-for-virus-packed-minichromosomes
#2
Sanjin Marion, Carmen San Martín, Antonio Šiber
Confined mixtures of a polymer and nonspecifically binding particles (condensers) are studied as models for viruses containing double-stranded DNA (polymer) and condensing proteins (particles). We explore a model in which all interactions between the packed content (polymer and particles) and its confinement are purely repulsive, with only a short-range attraction between the condensers and polymer to simulate binding. In the range of physical parameters applicable to viruses, the model predicts reduction of pressure in the system effected by the condensers, despite the reduction in free volume...
October 17, 2017: Biophysical Journal
https://www.readbyqxmd.com/read/29044810/simultaneous-refinement-of-inaccurate-local-regions-and-overall-structure-in-the-casp12-protein-model-refinement-experiment
#3
Gyu Rie Lee, Lim Heo, Chaok Seok
Advances in protein model refinement techniques are required as diverse sources of protein structure information are available from low-resolution experiments or informatics-based computations such as cryo-EM, NMR, homology models, or predicted residue contacts. Given semi-reliable or incomplete structural information, structure quality of a protein model has to be improved by ab initio methods such as energy-based simulation. In this study, we describe a new automatic refinement server method designed to improve locally inaccurate regions and overall structure simultaneously...
October 16, 2017: Proteins
https://www.readbyqxmd.com/read/29044714/definition-and-classification-of-evaluation-units-for-tertiary-structure-prediction-in-casp12-facilitated-through-semi-automated-metrics
#4
Luciano A Abriata, Lisa N Kinch, Giorgio E Tamò, Bohdan Monastyrskyy, Andriy Kryshtafovych, Matteo Dal Peraro
For assessment purposes, CASP targets are split into evaluation units. We herein present the official definition of CASP12 evaluation units (EUs) and their classification into difficulty categories. Each target can be evaluated as one EU (the whole target) or/and several EUs (separate structural domains or groups of structural domains). The specific scenario for a target split is determined by the domain organization of available templates, the difference in server performance on separate domains versus combination of the domains, and visual inspection...
October 16, 2017: Proteins
https://www.readbyqxmd.com/read/29044109/apobec3h-structure-reveals-an-unusual-mechanism-of-interaction-with-duplex-rna
#5
Jennifer A Bohn, Keyur Thummar, Ashley York, Alice Raymond, W Clay Brown, Paul D Bieniasz, Theodora Hatziioannou, Janet L Smith
The APOBEC3 family of cytidine deaminases cause lethal hypermutation of retroviruses via deamination of newly reverse-transcribed viral DNA. Their ability to bind RNA is essential for virion infiltration and antiviral activity, yet the mechanisms of viral RNA recognition are unknown. By screening naturally occurring, polymorphic, non-human primate APOBEC3H variants for biological and crystallization properties, we obtained a 2.24-Å crystal structure of pig-tailed macaque APOBEC3H with bound RNA. Here, we report that APOBEC3H forms a dimer around a short RNA duplex and, despite the bound RNA, has potent cytidine deaminase activity...
October 18, 2017: Nature Communications
https://www.readbyqxmd.com/read/29043485/nitrate-assimilation-pathway-nap-role-of-structural-nit-and-transporter-ntr1-genes-in-fusarium-oxysporum-f-sp-lycopersici-growth-and-pathogenicity
#6
Lucia Gomez-Gil, Jesus Camara Almiron, Patricia Lizett Rodriguez Carrillo, Cindy Nayely Olivares Medina, Gustavo Bravo Ruiz, Pamela Romo Rodriguez, Alma Rosa Corrales Escobosa, Felix Gutierrez Corona, M Isabel Roncero
The tomato pathogen Fusarium oxysporum f.sp. lycopersici possesses the capability to use nitrate as the only nitrogen source under aerobic and anaerobic conditions and to activate virulence-related functions when cultivated in the presence of nitrate, but not in ammonium. The genome of F. oxysporum f.sp. lycopersici encodes three paralogs nitrate reductase (NR) genes (nit1, nit2 and nit3) and one predicted ortholog of the Aspergillus nidulans high-affinity nitrate/nitrite transporters NtrA and NtrB, named ntr1...
October 17, 2017: Current Genetics
https://www.readbyqxmd.com/read/29042212/morfpred-plus-computational-identification-of-morfs-in-protein-sequences-using-physicochemical-properties-and-hmm-profiles
#7
Ronesh Sharma, Maitsetseg Bayarjargal, Tatsuhiko Tsunoda, Ashwini Patil, Alok Sharma
Motivation Intrinsically Disordered Proteins (IDPs) lack stable tertiary structure and they actively participate in performing various biological functions. These IDPs expose short binding regions called Molecular Recognition Features (MoRFs) that permit interaction with structured protein regions. Upon interaction they undergo a disorder-to-order transition as a result of which their functionality arises. Predicting these MoRFs in disordered protein sequences is a challenging task. Method In this study, we present MoRFpred-plus, an improved predictor over our previous proposed predictor to identify MoRFs in disordered protein sequences...
October 14, 2017: Journal of Theoretical Biology
https://www.readbyqxmd.com/read/29040952/design-synthesis-kinetic-mechanism-and-molecular-docking-studies-of-novel-1-pentanoyl-3-arylthioureas-as-inhibitors-of-mushroom-tyrosinase-and-free-radical-scavengers
#8
Fayaz Ali Larik, Aamer Saeed, Pervaiz Ali Channar, Urooj Muqadar, Qamar Abbas, Mubashir Hassan, Sung-Yum Seo, Michael Bolte
A series of novel 1-pentanoyl-3-arylthioureas was designed as new mushroom tyrosinase inhibitors and free radical scavengers. The title compounds were obtained in excellent yield and characterized by FTIR, (1)H NMR, (13)C NMR and X-ray crystallography in case of compound (4a). The inhibitory effects on mushroom tyrosinase and DPPH were evaluated and it was observed that 1-Pentanoyl-3-(4-methoxyphenyl) thiourea (4f) showed tyrosinase inhibitory activity (IC50 1.568 ± 0.01 mM) comparable to Kojic acid (IC50 16...
September 29, 2017: European Journal of Medicinal Chemistry
https://www.readbyqxmd.com/read/29040752/expansion-of-the-dehydrin-gene-family-in-the-pinaceae-is-associated-with-considerable-structural-diversity-and-drought-responsive-expression
#9
Juliana Stival Sena, Isabelle Giguère, Philippe Rigault, Jean Bousquet, John Mackay
Temperatures are expected to increase over the next century in all terrestrial biomes and particularly in boreal forests, where drought-induced mortality has been predicted to rise. Genomics research is helping to develop hypotheses regarding the molecular basis of drought tolerance and recent work proposed that the osmo-protecting dehydrin proteins have undergone a clade-specific expansion in the Pinaceae, a major group of conifer trees. The objectives of this study were to identify all of the putative members of the gene family, trace their evolutionary origin, examine their structural diversity and test for drought-responsive expression...
October 13, 2017: Tree Physiology
https://www.readbyqxmd.com/read/29040720/genome-wide-prediction-of-minor-groove-electrostatic-potential-enables-biophysical-modeling-of-protein-dna-binding
#10
Tsu-Pei Chiu, Satyanarayan Rao, Richard S Mann, Barry Honig, Remo Rohs
Protein-DNA binding is a fundamental component of gene regulatory processes, but it is still not completely understood how proteins recognize their target sites in the genome. Besides hydrogen bonding in the major groove (base readout), proteins recognize minor-groove geometry using positively charged amino acids (shape readout). The underlying mechanism of DNA shape readout involves the correlation between minor-groove width and electrostatic potential (EP). To probe this biophysical effect directly, rather than using minor-groove width as an indirect measure for shape readout, we developed a methodology, DNAphi, for predicting EP in the minor groove and confirmed the direct role of EP in protein-DNA binding using massive sequencing data...
October 11, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/29040693/amypro-a-database-of-proteins-with-validated-amyloidogenic-regions
#11
Mihaly Varadi, Greet De Baets, Wim F Vranken, Peter Tompa, Rita Pancsa
Soluble functional proteins may transform into insoluble amyloid fibrils that deposit in a variety of tissues. Amyloid formation is a hallmark of age-related degenerative disorders. Perhaps surprisingly, amyloid fibrils can also be beneficial and are frequently exploited for diverse functional roles in organisms. Here we introduce AmyPro, an open-access database providing a comprehensive, carefully curated collection of validated amyloid fibril-forming proteins from all kingdoms of life classified into broad functional categories (http://amypro...
October 13, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/29040665/systematic-classification-of-the-his-me-finger-superfamily
#12
Jagoda Jablonska, Dorota Matelska, Kamil Steczkiewicz, Krzysztof Ginalski
The His-Me finger endonucleases, also known as HNH or ββα-metal endonucleases, form a large and diverse protein superfamily. The His-Me finger domain can be found in proteins that play an essential role in cells, including genome maintenance, intron homing, host defense and target offense. Its overall structural compactness and non-specificity make it a perfectly-tailored pathogenic module that participates on both sides of inter- and intra-organismal competition. An extremely low sequence similarity across the superfamily makes it difficult to identify and classify new His-Me fingers...
October 10, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/29040432/machine-learning-accelerates-md-based-binding-pose-prediction-between-ligands-and-proteins
#13
Kei Terayama, Hiroaki Iwata, Mitsugu Araki, Yasushi Okuno, Koji Tsuda
Motivation: Fast and accurate prediction of protein-ligand binding structures is indispensable for structure-based drug design (SBDD) and accurate estimation of binding free energy of drug candidate molecules in drug discovery. Recently, accurate pose prediction methods based on short-MD simulations such as MM-PBSA and MM-GBSA among generated docking poses have been used. Since molecular structures obtained from MD simulation depends on the initial condition, taking the average over different initial conditions leads to better accuracy...
October 11, 2017: Bioinformatics
https://www.readbyqxmd.com/read/29039523/analysis-of-men1-c-482g-a-p-gly161asp-mutation-in-a-pedigree-with-familial-multiple-endocrine-neoplasia-type-1
#14
Yuanyuan Luo, Yongxiang Sun, Xiaofan Zhu, Xialian Li
Multiple endocrine neoplasia type 1 (MEN1) is an autosomal dominant disorder characterized by the development of neuroendocrine tumors, which in turn are caused by mutations in the MEN1 gene. In the present study, a case of a 46‑year‑old woman who was clinically diagnosed with MEN1 based on the presence of prolactinoma and bilateral parathyroid adenoma was reported. The patient's serum prolactin (PRL) levels were successfully controlled via bromocriptine therapy, and the serum levels of calcium and intact parathyroid hormone (PTH) reduced one day following parathyroidectomy...
October 10, 2017: Molecular Medicine Reports
https://www.readbyqxmd.com/read/29039460/characterization-of-tree-shrew-tupaia-belangeri-interleukin-6-and-its-expression-pattern-in-response-to-exogenous-challenge
#15
Yuanyuan Han, Xiaomei Sun, Dexuan Kuang, Pinfen Tong, Caixia Lu, Wenguang Wang, Na Li, Yang Chen, Xiaoping Wang, Jiejie Dai, Huatang Zhang
Tree shrews, one of the closest relatives of primates, have attracted increasing attention as a model of human diseases, particularly for viral infections. As the first line of defense against microbial pathogens, the innate immune system is crucial in tree shrews. Interleukin-6 (IL-6) is important in the pathophysiology of infection, inflammation and cancer, where it promotes disease development or sustains immune reactions. The present study aimed to obtain further insight into the tree shrew IL-6 (tsIL-6) system, and the function of tsIL-6 in the antiviral and antibacterial response...
October 2, 2017: International Journal of Molecular Medicine
https://www.readbyqxmd.com/read/29039067/in-silico-system-pharmacology-for-the-potential-bioactive-ingredients-contained-in-xingnaojing-injection-and-its-material-basis-for-sepsis-treatment
#16
Shi-Tang Ma, Cheng-Tao Feng, You-Xi Xiong, Xiao-Lin Zhang, Cheng-Gui Miao, Hao Yu
OBJECTIVE: To elucidate the action mechanism of Xingnaojing Injection (, XNJI) for sepsis, and to target screen the potential bioactive ingredients. METHODS: An integrated protocol that combines in silico target screen (molecular docking) and database mapping was employed to find the potential inhibitors from XNJI for the sepsis-related targets and to establish the compound-target (C-T) interaction network. The XNJI's bioactive components database was investigated and the sepsis-associated targets were comprehensively constructed; the 3D structure of adenosine receptor A2a and 5-lipoxygenase proteins were established and evaluated with homology modeling method; system network pharmacology for sepsis treatment was studied between the bioactive ingredients and the sepsis targets using computational biology methods to distinguish inhibitors from non inhibitors for the selected sepsis-related targets and C-T network construction...
October 17, 2017: Chinese Journal of Integrative Medicine
https://www.readbyqxmd.com/read/29038656/unveiling-a-drift-resistant-cryptotope-within-marburgvirus-nucleoprotein-recognized-by-llama-single-domain-antibodies
#17
John Anthony Garza, Alexander Bryan Taylor, Laura Jo Sherwood, Peter John Hart, Andrew Hayhurst
Marburg virus (MARV) is a highly lethal hemorrhagic fever virus that is increasingly re-emerging in Africa, has been imported to both Europe and the US, and is also a Tier 1 bioterror threat. As a negative sense RNA virus, MARV has error prone replication which can yield progeny capable of evading countermeasures. To evaluate this vulnerability, we sought to determine the epitopes of 4 llama single-domain antibodies (sdAbs or VHH) specific for nucleoprotein (NP), each capable of forming MARV monoclonal affinity reagent sandwich assays...
2017: Frontiers in Immunology
https://www.readbyqxmd.com/read/29038601/a-structural-model-of-flagellar-filament-switching-across-multiple-bacterial-species
#18
Fengbin Wang, Andrew M Burrage, Sandra Postel, Reece E Clark, Albina Orlova, Eric J Sundberg, Daniel B Kearns, Edward H Egelman
The bacterial flagellar filament has long been studied to understand how a polymer composed of a single protein can switch between different supercoiled states with high cooperativity. Here we present near-atomic resolution cryo-EM structures for flagellar filaments from both Gram-positive Bacillus subtilis and Gram-negative Pseudomonas aeruginosa. Seven mutant flagellar filaments in B. subtilis and two in P. aeruginosa capture two different states of the filament. These reliable atomic models of both states reveal conserved molecular interactions in the interior of the filament among B...
October 16, 2017: Nature Communications
https://www.readbyqxmd.com/read/29037121/predicting-injury-severity-and-neurologic-recovery-after-acute-cervical-spinal-cord-injury-a-comparison-of-cerebrospinal-fluid-and-magnetic-resonance-imaging-biomarkers
#19
Turker Dalkilic, Nader Fallah, Vanessa K Noonan, Sanam Salimi Elizei, Kevin Dong, Lise M Belanger, Leanna Ritchie, Angela Tsang, Etienne Bourassa-Moreau, Manraj K S Heran, Scott J Paquette, Tamir Ailon, Nicolas Dea, John Street, Charles G Fisher, Marcel F Dvorak, Brian K Kwon
Biomarkers of acute human spinal cord injury (SCI) could provide a more objective measure of spinal cord damage and a better predictor of neurologic outcome than the current functional neurologic assessments. There has been growing interest in establishing neurochemical biomarkers using cerebrospinal fluid (CSF) and also imaging biomarkers using measurable features on MRI. In this study, we took the opportunity to compare CSF biomarkers and MRI biomarkers in a cohort of acute cervical SCI patients who had undergone both CSF sampling and pre-operative MRI scanning...
October 17, 2017: Journal of Neurotrauma
https://www.readbyqxmd.com/read/29036497/forecasting-residue-residue-contact-prediction-accuracy
#20
P P Wozniak, B M Konopka, J Xu, G Vriend, M Kotulska
Motivation: Apart from meta-predictors, most of today's methods for residue-residue contact prediction are based entirely on Direct Coupling Analysis (DCA) of correlated mutations in multiple sequence alignments (MSAs). These methods are on average ∼40% correct for the 100 strongest predicted contacts in each protein. The end-user who works on a single protein of interest will not know if predictions are either much more or much less correct than 40%, which is especially a problem if contacts are predicted to steer experimental research on that protein...
June 26, 2017: Bioinformatics
keyword
keyword
59622
1
2
Fetch more papers »
Fetching more papers... Fetching...
Read by QxMD. Sign in or create an account to discover new knowledge that matter to you.
Remove bar
Read by QxMD icon Read
×

Search Tips

Use Boolean operators: AND/OR

diabetic AND foot
diabetes OR diabetic

Exclude a word using the 'minus' sign

Virchow -triad

Use Parentheses

water AND (cup OR glass)

Add an asterisk (*) at end of a word to include word stems

Neuro* will search for Neurology, Neuroscientist, Neurological, and so on

Use quotes to search for an exact phrase

"primary prevention of cancer"
(heart or cardiac or cardio*) AND arrest -"American Heart Association"