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"protein docking"

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https://www.readbyqxmd.com/read/28334258/review-and-comparative-assessment-of-sequence-based-predictors-of-protein-binding-residues
#1
Jian Zhang, Lukasz Kurgan
Understanding of molecular mechanisms that govern protein-protein interactions and accurate modeling of protein-protein docking rely on accurate identification and prediction of protein-binding partners and protein-binding residues. We review over 40 methods that predict protein-protein interactions from protein sequences including methods that predict interacting protein pairs, protein-binding residues for a pair of interacting sequences and protein-binding residues in a single protein chain. We focus on the latter methods that provide residue-level annotations and that can be broadly applied to all protein sequences...
March 1, 2017: Briefings in Bioinformatics
https://www.readbyqxmd.com/read/28282269/endoa-endophilin-a-creates-docking-stations-for-autophagic-proteins-at-synapses
#2
Sandra-Fausia Soukup, Patrik Verstreken
Synapses are very specialized compartments with high metabolic demand to maintain neurotransmission, an essential step for basic brain function. Neurons are post-mitotic and synapses need to stay functional over time-sometimes over decades. Given that synapses are often at a long distance from the cell body, they must use local mechanisms to regulate protein quality control. We show that macroautophagy/autophagy is one of these local processes and found that it is under strict control of the synapse-enriched protein EndoA/Endophilin-A, previously only implicated in endocytosis...
February 15, 2017: Autophagy
https://www.readbyqxmd.com/read/28271460/structural-evaluation-and-binding-mode-analysis-of-ccl19-and-ccr7-proteins-identification-of-novel-leads-for-rheumatic-and-autoimmune-diseases-an-insilico-study
#3
Santhi Prada Vellanki, Ramasree Dulapalli, Bhargavi Kondagari, Navaneetha Nambigari, Rajender Vadija, Vishwanath Ramatenki, Rama Krishna Dumpati, Uma Vuruputuri
The Human Chemokine (C-C motif) ligand 19 (CCL19) protein plays a major role in rheumatic and autoimmune diseases. The 3D models of the CCL19 and its receptor CCR7 are generated using homology modeling and are validated using standard computational protocols. Disulfide bridges identified in 3D model of CCL19 protein give extra stability to the overall protein structure. The active site region of protein CCL19, containing N-terminal amino acid residues (Gly22 to Leu31), is predicted using in silico techniques...
March 7, 2017: Interdisciplinary Sciences, Computational Life Sciences
https://www.readbyqxmd.com/read/28263438/interpred-a-pipeline-to-identify-and-model-protein-protein-interactions
#4
Claudio Mirabello, Björn Wallner
Protein-protein interactions (PPI) are crucial for protein function. There exist many techniques to identify PPIs experimentally, but to determine the interactions in molecular detail is still difficult and very time-consuming. The fact that the number of PPIs is vastly larger than the number of individual proteins makes it practically impossible to characterize all interactions experimentally. Computational approaches that can bridge this gap and predict PPIs and model the interactions in molecular detail are greatly needed...
March 6, 2017: Proteins
https://www.readbyqxmd.com/read/28255315/in-silico-designing-of-a-new-cysteine-analogue-of-hirudin-variant-3-for-site-specific-pegylation
#5
Seyed Mehdi Sajjadi, Hamzeh Rahimi, Saeed Mohammadi, Mohammad Faranoush, Hasan Mirzahoseini, Gholamreza Toogeh
Hirudin is an anticoagulant agent of the salivary glands of the medicinal leech. Recombinant hirudin (r-Hir) displays certain drawbacks including bleeding and immunogenicity. To solve these problems, cysteine-specific PEGylation has been proposed as a successful technique. However, proper selection of the appropriate cysteine residue for substitution is a critical step. This study has, for the first time, used a computational approach aimed at identifying a single potential PEGylation site for replacement by cysteine residue in the hirudin variant 3 (HV3)...
February 2017: Research in Pharmaceutical Sciences
https://www.readbyqxmd.com/read/28236233/application-of-the-attract-coarse-grained-docking-and-atomistic-refinement-for-predicting-peptide-protein-interactions
#6
Christina Schindler, Martin Zacharias
Peptide-protein interactions are abundant in the cell and form an important part of the interactome. Large-scale modeling of peptide-protein complexes requires a fully blind approach; i.e., simultaneously predicting the peptide-binding site and the peptide conformation to high accuracy. Here, we present one of the first fully blind peptide-protein docking protocols, pepATTRACT. It combines a coarse-grained ensemble docking search of the entire protein surface with two stages of atomistic flexible refinement...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28235665/an-in-silico-approach-to-find-a-peptidomimetic-targeting-extracellular-domain-of-her3-from-a-her3-nanobody
#7
Z Pourhashem, M Mehrpouya, N Yardehnavi, A Eslamparast, F Kazemi-Lomedasht
HER3 is an important therapeutic target in cancer treatments. HER3 Nanobodies (Nbs) are a novel class of antibodies with several competitive advantages over conventional antibodies. A peptidomimetic derived from these Nbs can be considered to be a small peptide mimicking some of the molecular recognition interactions of a natural peptide or protein in a three-dimensional (3D) space, with a receptor that has improved properties. In this study, we introduce a new approach to design a peptidomimetic derived from HER3 Nb through an in silico analysis...
February 10, 2017: Computational Biology and Chemistry
https://www.readbyqxmd.com/read/28193857/mass-spectrometry-based-cross-linking-study-shows-that-the-psb28-protein-binds-to-cytochrome-b559-in-photosystem-ii
#8
Daniel A Weisz, Haijun Liu, Hao Zhang, Sundarapandian Thangapandian, Emad Tajkhorshid, Michael L Gross, Himadri B Pakrasi
Photosystem II (PSII), a large pigment protein complex, undergoes rapid turnover under natural conditions. During assembly of PSII, oxidative damage to vulnerable assembly intermediate complexes must be prevented. Psb28, the only cytoplasmic extrinsic protein in PSII, protects the RC47 assembly intermediate of PSII and assists its efficient conversion into functional PSII. Its role is particularly important under stress conditions when PSII damage occurs frequently. Psb28 is not found, however, in any PSII crystal structure, and its structural location has remained unknown...
February 28, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/28185054/identification-of-new-lead-molecules-against-ube2nl-enzyme-for-cancer-therapy
#9
Vishwanath Ramatenki, Ramakrishna Dumpati, Rajender Vadija, Santhiprada Vellanki, Sarita Rajender Potlapally, Rohini Rondla, Uma Vuruputuri
Cancer is characterized by abnormal growth of cells. Targeting ubiquitin proteins in the discovery of new anticancer therapeutics is an attractive strategy. The present study uses the structure-based drug discovery methods to identify new lead structures, which are selective to the putative ubiquitin-conjugating enzyme E2N-like (UBE2NL). The 3D structure of the UBE2NL was evaluated using homology modeling techniques. The model was validated using standard in silico methods. The hydrophobic pocket of UBE2NL that aids in binding with its natural receptor ubiquitin-conjugating enzyme E2 variant (UBE2V) was identified through protein-protein docking study...
February 9, 2017: Applied Biochemistry and Biotechnology
https://www.readbyqxmd.com/read/28174118/molecular-and-structural-characterization-of-novel-cystatins-from-the-taiga-tick-ixodes-persulcatus
#10
Carolina K Rangel, Luís F Parizi, Gabriela A Sabadin, Evenilton P Costa, Nelilma C Romeiro, Masayoshi Isezaki, Naftaly W Githaka, Adriana Seixas, Carlos Logullo, Satoru Konnai, Kazuhiko Ohashi, Itabajara da Silva Vaz
Cystatins are cysteine peptidase inhibitors that in ticks mediate processes such as blood feeding and digestion. The ixodid tick Ixodes persulcatus is endemic to the Eurasia, where it is the principal vector of Lyme borreliosis. To date, no I. persulcatus cystatin has been characterized. In the present work, we describe three novel cystatins from I. persulcatus, named JpIpcys2a, JpIpcys2b and JpIpcys2c. In addition, the potential of tick cystatins as cross-protective antigens was evaluated by vaccination of hamsters using BrBmcys2c, a cystatin from Rhipicephalus microplus, against I...
January 31, 2017: Ticks and Tick-borne Diseases
https://www.readbyqxmd.com/read/28168752/monte-carlo-replica-exchange-based-ensemble-docking-of-protein-conformations
#11
Zhe Zhang, Uwe Ehmann, Martin Zacharias
A Replica-exchange Monte Carlo (REMC) ensemble docking approach has been developed that allows efficient exploration of protein-protein docking geometries. In addition to Monte Carlo steps in translation and orientation of binding partners, possible conformational changes upon binding are included based on Monte Carlo selection of protein conformations stored as ordered pre-generated conformational ensembles. The conformational ensembles of each binding partner protein were generated by three different approaches starting from the unbound partner protein structure with a range spanning a root mean square deviation of 1-2...
February 7, 2017: Proteins
https://www.readbyqxmd.com/read/28166455/structural-and-mechanistic-insights-into-nuclear-transport-and-delivery-of-the-critical-pluripotency-factor-oct4-to-dna
#12
Takahide Okuyama, Ryosuke Yamagishi, Jiro Shimada, Masaaki Ikeda, Yayoi Maruoka, Hiroki Kaneko
Oct4 is a master regulator of the induction and maintenance of cellular pluripotency, and has crucial roles in early stages of differentiation. It is the only factor that cannot be substituted by other members of the same protein family to induce pluripotency. However, although Oct4 nuclear transport and delivery to target DNA are critical events for reprogramming to pluripotency, little is known about the molecular mechanism. Oct4 is imported to the nucleus by the classical nuclear transport mechanism, which requires importin α as an adaptor to bind the nuclear localization signal (NLS)...
February 17, 2017: Journal of Biomolecular Structure & Dynamics
https://www.readbyqxmd.com/read/28132614/insight-into-the-intermolecular-recognition-mechanism-involved-in-complement-component-4-activation-through-serine-protease-trypsin
#13
Vikrant Kumar Sinha, Om Prakash Sharma, Muthuvel Suresh Kumar
Serine protease cleaved-complement component 4 (C4) at sessile loop, which is significant for completion of lectin and classical complement pathways at the time of infections. The co-crystalized structure of C4 with Mannose-binding protein-associated serine protease 2 (MASP2) provided the structural and functional aspects of its interaction and underlined the C4 activation by MASP2. The same study also revealed the significance of complement control protein (CCP) domain through mutational study, where mutated CCP domain led to the inhibition of C4 activation...
February 13, 2017: Journal of Biomolecular Structure & Dynamics
https://www.readbyqxmd.com/read/28130547/mitochondrial-protein-interactome-elucidated-by-chemical-cross-linking-mass-spectrometry
#14
Devin K Schweppe, Juan D Chavez, Chi Fung Lee, Arianne Caudal, Shane E Kruse, Rudy Stuppard, David J Marcinek, Gerald S Shadel, Rong Tian, James E Bruce
Mitochondrial protein interactions and complexes facilitate mitochondrial function. These complexes range from simple dimers to the respirasome supercomplex consisting of oxidative phosphorylation complexes I, III, and IV. To improve understanding of mitochondrial function, we used chemical cross-linking mass spectrometry to identify 2,427 cross-linked peptide pairs from 327 mitochondrial proteins in whole, respiring murine mitochondria. In situ interactions were observed in proteins throughout the electron transport chain membrane complexes, ATP synthase, and the mitochondrial contact site and cristae organizing system (MICOS) complex...
February 14, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/28129657/physiological-characterization-of-a-novel-ppar-pan-agonist-2-4-5-6-methylenedioxybenzo-d-thiazol-2-yl-2-methylphenoxy-2-methylpropanoic-acid-mhy2013
#15
Hye Jin An, Bonggi Lee, Dae Hyun Kim, Eun Kyeong Lee, Ki Wung Chung, Min Hi Park, Hyoung Oh Jeong, Sung Min Kim, Kyoung Mi Moon, Ye Ra Kim, Seong Jin Kim, Hwi Young Yun, Pusoon Chun, Byung Pal Yu, Hyung Ryong Moon, Hae Young Chung
Recently, agonists targeting multiple peroxisome proliferator-activated receptors (PPARs) have been developed to improve metabolic disorders and minimize the side effects of selective PPAR agonists such as weight gain and dyslipidemia. We newly synthesized six 2-methyl-2-(o-tolyloxy)propanoic acid derivatives based on the structure of a well-known PPAR pan agonist, bezafibrate. Of six compounds, MHY2013 was screened as the strongest activator of three PPAR subtypes based on protein docking simulation and luciferase assays...
January 25, 2017: Oncotarget
https://www.readbyqxmd.com/read/28118389/rapid-design-of-knowledge-based-scoring-potentials-for-enrichment-of-near-native-geometries-in-protein-protein-docking
#16
Alexander Sasse, Sjoerd J de Vries, Christina E M Schindler, Isaure Chauvot de Beauchêne, Martin Zacharias
Protein-protein docking protocols aim to predict the structures of protein-protein complexes based on the structure of individual partners. Docking protocols usually include several steps of sampling, clustering, refinement and re-scoring. The scoring step is one of the bottlenecks in the performance of many state-of-the-art protocols. The performance of scoring functions depends on the quality of the generated structures and its coupling to the sampling algorithm. A tool kit, GRADSCOPT (GRid Accelerated Directly SCoring OPTimizing), was designed to allow rapid development and optimization of different knowledge-based scoring potentials for specific objectives in protein-protein docking...
2017: PloS One
https://www.readbyqxmd.com/read/28079879/the-cluspro-web-server-for-protein-protein-docking
#17
Dima Kozakov, David R Hall, Bing Xia, Kathryn A Porter, Dzmitry Padhorny, Christine Yueh, Dmitri Beglov, Sandor Vajda
The ClusPro server (https://cluspro.org) is a widely used tool for protein-protein docking. The server provides a simple home page for basic use, requiring only two files in Protein Data Bank (PDB) format. However, ClusPro also offers a number of advanced options to modify the search; these include the removal of unstructured protein regions, application of attraction or repulsion, accounting for pairwise distance restraints, construction of homo-multimers, consideration of small-angle X-ray scattering (SAXS) data, and location of heparin-binding sites...
February 2017: Nature Protocols
https://www.readbyqxmd.com/read/28078551/the-proteolysis-adaptor-nbla-binds-to-the-n-terminus-of-%C3%AE-phycocyanin-implications-for-the-mechanism-of-phycobilisome-degradation
#18
Amelia Y Nguyen, William P Bricker, Hao Zhang, Daniel A Weisz, Michael L Gross, Himadri B Pakrasi
Phycobilisome (PBS) complexes are massive light-harvesting apparati in cyanobacteria that capture and funnel light energy to the photosystem. PBS complexes are dynamically degraded during nutrient deprivation, which causes severe chlorosis, and resynthesized during nutrient repletion. PBS degradation occurs rapidly after nutrient step down, and is specifically triggered by non-bleaching protein A (NblA), a small proteolysis adaptor that facilitates interactions between a Clp chaperone and phycobiliproteins...
January 11, 2017: Photosynthesis Research
https://www.readbyqxmd.com/read/28067274/computational-and-biochemical-characterization-of-two-partially-overlapping-interfaces-and-multiple-weak-affinity-k-ras-dimers
#19
Priyanka Prakash, Abdallah Sayyed-Ahmad, Kwang-Jin Cho, Drew M Dolino, Wei Chen, Hongyang Li, Barry J Grant, John F Hancock, Alemayehu A Gorfe
Recent studies found that membrane-bound K-Ras dimers are important for biological function. However, the structure and thermodynamic stability of these complexes remained unknown because they are hard to probe by conventional approaches. Combining data from a wide range of computational and experimental approaches, here we describe the structure, dynamics, energetics and mechanism of assembly of multiple K-Ras dimers. Utilizing a range of techniques for the detection of reactive surfaces, protein-protein docking and molecular simulations, we found that two largely polar and partially overlapping surfaces underlie the formation of multiple K-Ras dimers...
January 9, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28063347/disruption-of-redox-catalytic-functions-of-peroxiredoxin-thioredoxin-complex-in-mycobacterium-tuberculosis-h37rv-using-small-interface-binding-molecules
#20
Arun Bahadur Gurung, Amit Kumar Das, Atanu Bhattacharjee
Mycobacterium tuberculosis has distinctive ability to detoxify various microbicidal superoxides and hydroperoxides via a redox catalytic cycle involving thiol reductants of peroxiredoxin (Prx) and thioredoxin (Trx) systems which has conferred on it resistance against oxidative killing and survivability within host. We have used computational approach to disrupt catalytic functions of Prx-Trx complex which can possibly render the pathogen vulnerable to oxidative killing in the host. Using protein-protein docking method, we have successfully constructed the Prx-Trx complex...
December 31, 2016: Computational Biology and Chemistry
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