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"protein docking"

Rajesh Durairaj, Patrick Pageat, Cécile Bienboire-Frosini
The mammalian secretoglobin (SCGB) superfamily contains functionally diverse members, among which the major cat allergen Fel d 1 and mouse salivary androgen-binding protein (ABP) display similar subunits. We searched for molecular similarities between Fel d 1 and ABP to examine the possibility that they play similar roles. We aimed to i) cluster the evolutionary relationships of the SCGB superfamily; ii) identify divergence patterns, structural overlap, and protein-protein docking between Fel d 1 and ABP dimers; and iii) explore the residual interaction between ABP dimers and steroid binding in chemical communication using computational approaches...
2018: PloS One
Logesh Mathivathanan, Guang Yang, Fenfei Leng, Raphael G Raptis
Crystal structure determination of doxorubicin nitrate, (DoxH)NO3 , systematic name (7 S ,9 S )-7-{[(2 R ,4 S ,5 S ,6 S )-4-azaniumyl-5-hy-droxy-6-methyl-oxan-2-yl]-oxy}-6,9,11-trihy-droxy-9-(2-hy-droxy-acet-yl)-4-meth-oxy-8,10-di-hydro-7 H -tetra-cen-5,12-dione nitrate, shows two formula units present in the asymmetric unit. In the crystal lattice, hydrogen-bonded pairs of (DoxH+ ) cations and segregation of the aglycone and sugar moieties are observed. Inspection of mol-ecular overlays reveals that the conformation of (DoxH)NO3 resembles that of DNA-inter-calated, but not of protein-docked (DoxH)+ ...
March 1, 2018: Acta Crystallographica. Section E, Crystallographic Communications
Pei Zhou, Bowen Jin, Hao Li, Sheng-You Huang
Protein-peptide interactions are crucial in many cellular functions. Therefore, determining the structure of protein-peptide complexes is important for understanding the molecular mechanism of related biological processes and developing peptide drugs. HPEPDOCK is a novel web server for blind protein-peptide docking through a hierarchical algorithm. Instead of running lengthy simulations to refine peptide conformations, HPEPDOCK considers the peptide flexibility through an ensemble of peptide conformations generated by our MODPEP program...
May 9, 2018: Nucleic Acids Research
Takanori Hayashi, Yuri Matsuzaki, Keisuke Yanagisawa, Masahito Ohue, Yutaka Akiyama
BACKGROUND: Protein-protein interactions (PPIs) play several roles in living cells, and computational PPI prediction is a major focus of many researchers. The three-dimensional (3D) structure and binding surface are important for the design of PPI inhibitors. Therefore, rigid body protein-protein docking calculations for two protein structures are expected to allow elucidation of PPIs different from known complexes in terms of 3D structures because known PPI information is not explicitly required...
May 8, 2018: BMC Bioinformatics
Chloé Quignot, Julien Rey, Jinchao Yu, Pierre Tufféry, Raphaël Guerois, Jessica Andreani
Computational protein docking is a powerful strategy to predict structures of protein-protein interactions and provides crucial insights for the functional characterization of macromolecular cross-talks. We previously developed InterEvDock, a server for ab initio protein docking based on rigid-body sampling followed by consensus scoring using physics-based and statistical potentials, including the InterEvScore function specifically developed to incorporate co-evolutionary information in docking. InterEvDock2 is a major evolution of InterEvDock which allows users to submit input sequences - not only structures - and multimeric inputs and to specify constraints for the pairwise docking process based on previous knowledge about the interaction...
May 8, 2018: Nucleic Acids Research
Ákos Gellért, Tímea Pósa, Attila Fábián, László Szabó, Károly Bóka, Barbara Forró, Katalin Salánki, László Drahos, Eszter Tóth, Angéla Juhász, Ervin Balázs
A previous study showed that a single amino acid difference in the cucumber mosaic virus (CMV) capsid protein (CP) elicits unusual symptoms. The wild-type strain (CMV-R) induces green mosaic symptoms and malformation while the mutant strain (CMV-R3E79R) causes chlorotic lesions on inoculated leaves and strong stunting with necrosis on systemic leaves. Virion preparations of CMV-R and CMV-R3E79R were partially purified from Nicotiana clevelandii A. Gray and analysed by two-dimensional gel electrophoresis. Their separated protein patterns showed remarkable differences at the 50-75 kDa range, both in numbers and intensity of spots, with more protein spots for the mutant CMV...
May 3, 2018: Virus Research
Dasari Ankaiah, Esakkiraj Palanichamy, Christian Bharathi Antonyraj, Repally Ayyanna, Syed Ibrahim Basheer Ahamed, Venkatesan Arul
The bacteriocin enterocin-B contains broad anti-microbial spectrum against several gram positive, negative pathogenic bacteria was cloned, overexpressed and purified from Enterococcus faecium por1. The molecular weight of the bacteriocin enterocin-B was observed around 7.2 kDa and interacting, formation of heterodimer with another bacteriocin enterocin-A from the same organism by protein-protein docking and molecular dynamics simulation studies. The heterodimer of bacteriocin enterocin-A + B exhibited potential anti-bacterial, anti-biofilm activity against Staphylococcus aureus, Listeria monocytogenes, Escherichia coli and S...
May 2, 2018: International Journal of Biological Macromolecules
Nicholas A Marze, Shourya S Roy Burman, William Sheffler, Jeffrey J Gray
Motivation: Binding-induced conformational changes challenge current computational docking algorithms by exponentially increasing the conformational space to be explored. To restrict this search to relevant space, some computational docking algorithms exploit the inherent flexibility of the protein monomers to simulate conformational selection from pre-generated ensembles. As the ensemble size expands with increased flexibility, these methods struggle with efficiency and high false positive rates...
April 30, 2018: Bioinformatics
Mohd Aamir, Vinay Kumar Singh, Manish Kumar Dubey, Sarvesh Pratap Kashyap, Andleeb Zehra, Ram Sanmukh Upadhyay, Surendra Singh
The WRKY transcription factors have indispensable role in plant growth, development and defense responses. The differential expression of WRKY genes following the stress conditions has been well demonstrated. We investigated the temporal and tissue-specific (root and leaf tissues) differential expression of plant defense-related WRKY genes, following the infection of Fusarium oxysporum f. sp. lycopersici (Fol) in tomato. The genome-wide computational analysis revealed that during the Fol infection in tomato, 16 different members of WRKY gene superfamily were found to be involved, of which only three WRKYs (SolyWRKY4, SolyWRKY33, and SolyWRKY37) were shown to have clear-cut differential gene expression...
2018: PloS One
A A Igolkina, Yu B Porozov, E P Chizhevskaya, E E Andronov
Sandwich-like docking configurations of the heterodimeric complex of NFR5 and K1 Vicia sativa receptor-like kinases together with the putative ligand, Nod factor (NF) of Rhizobium leguminosarum bv. viciae , were modeled and two of the most probable configurations were assessed through the analysis of the mutual polymorphisms and conservatism. We carried out this analysis based on the hypothesis that in a contact zone of two docked components (proteins or ligands) the population polymorphism or conservatism is mutual, i...
2018: Frontiers in Plant Science
Thom Vreven, Devin K Schweppe, Juan D Chavez, Chad R Weisbrod, Sayaka Shibata, Chunxiang Zheng, James E Bruce, Zhiping Weng
Ab initio protein-protein docking algorithms often rely on experimental data to identify the most likely complex structure. We integrated protein-protein docking with the experimental data of chemical cross-linking followed by mass spectrometry. We tested our approach using 19 cases that resulted from an exhaustive search of the Protein Data Bank for protein complexes with cross-links identified in our experiments. We implemented cross-links as constraints based on Euclidean distance or void-volume distance...
April 14, 2018: Journal of Molecular Biology
Shahrooz Zarbafian, Mohammad Moghadasi, Athar Roshandelpoor, Feng Nan, Keyong Li, Pirooz Vakli, Sandor Vajda, Dima Kozakov, Ioannis Ch Paschalidis
We propose a novel stochastic global optimization algorithm with applications to the refinement stage of protein docking prediction methods. Our approach can process conformations sampled from multiple clusters, each roughly corresponding to a different binding energy funnel. These clusters are obtained using a density-based clustering method. In each cluster, we identify a smooth "permissive" subspace which avoids high-energy barriers and then underestimate the binding energy function using general convex polynomials in this subspace...
April 12, 2018: Scientific Reports
Mikhail Ignatov, Andrey Kazennov, Dima Kozakov
We have recently demonstrated that incorporation of SAXS-based filtering in our heavily used docking server ClusPro improves docking results. However, the filtering step is time consuming, since ≈105 conformations have to be sequentially processed. At the same time we have demonstrated the possibility of ultra-fast systematic energy evaluation for all rigid body orientations of two proteins, by sampling using Fast Manifold Fourier Transform (FMFT), if energies are represented as a combination of convolution-like expressions...
April 4, 2018: Journal of Molecular Biology
Dina Schneidman-Duhovny, Michal Hammel
Small-angle X-ray scattering (SAXS) is an increasingly common and useful technique for structural characterization of molecules in solution. A SAXS experiment determines the scattering intensity of a molecule as a function of spatial frequency, termed SAXS profile. SAXS profiles can be utilized in a variety of molecular modeling applications, such as comparing solution and crystal structures, structural characterization of flexible proteins, assembly of multi-protein complexes, and modeling of missing regions in the high-resolution structure...
2018: Methods in Molecular Biology
Aravindan Arun Nadaradjane, Raphael Guerois, Jessica Andreani
The structural modeling of protein complexes by docking simulations has been attracting increasing interest with the rise of proteomics and of the number of experimentally identified binary interactions. Structures of unbound partners, either modeled or experimentally determined, can be used as input to sample as extensively as possible all putative binding modes and single out the most plausible ones. At the scoring step, evolutionary information contained in the joint multiple sequence alignments of both partners can provide key insights to recognize correct interfaces...
2018: Methods in Molecular Biology
Iain H Moal, Raphael A G Chaleil, Paul A Bates
The atomic structures of protein complexes can provide useful information for drug design, protein engineering, systems biology, and understanding pathology. Obtaining this information experimentally can be challenging. However, if the structures of the subunits are known, then it is often possible to model the complex computationally. This chapter provide practical guidelines for docking proteins using the SwarmDock flexible protein-protein docking method, providing an overview of the factors that need to be considered when deciding whether docking is likely to be successful, the preparation of structural input, generation of docked poses, analysis and ranking of docked poses, and the validation of models using external data...
2018: Methods in Molecular Biology
Agnieszka A Kaczor, Damian Bartuzi, Tomasz Maciej Stępniewski, Dariusz Matosiuk, Jana Selent
Protein-protein interactions (PPIs) are responsible for a number of key physiological processes in the living cells and underlie the pathomechanism of many diseases. Nowadays, along with the concept of so-called "hot spots" in protein-protein interactions, which are well-defined interface regions responsible for most of the binding energy, these interfaces can be targeted with modulators. In order to apply structure-based design techniques to design PPIs modulators, a three-dimensional structure of protein complex has to be available...
2018: Methods in Molecular Biology
Diego Sbardella, Grazia R Tundo, Andrea Coletta, Julien Marcoux, Efthymia Ioanna Koufogeorgou, Chiara Ciaccio, Anna M Santoro, Danilo Milardi, Giuseppe Grasso, Paola Cozza, Marie-Pierre Bousquet-Dubouch, Stefano Marini, Massimo Coletta
The interaction of insulin-degrading enzyme (IDE) with the main intracellular proteasome assemblies (i.e, 30S, 26S and 20S) was analyzed by enzymatic activity, mass spectrometry and native gel electrophoresis. IDE was mainly detected in association with assemblies with at least one free 20S end and biochemical investigations suggest that IDE competes with the 19S in vitro. IDE directly binds the 20S and affects its proteolytic activities in a bimodal fashion, very similar in human and yeast 20S, inhibiting at (IDE) ≤ 30 nM and activating at (IDE) ≥ 30 nM...
March 28, 2018: Cellular and Molecular Life Sciences: CMLS
Mahesh Chandra Patra, Hyuk-Kwon Kwon, Maria Batool, Sangdun Choi
Toll-like receptors (TLRs) are a unique category of pattern recognition receptors that recognize distinct pathogenic components, often utilizing the same set of downstream adaptors. Specific molecular features of extracellular, transmembrane (TM), and cytoplasmic domains of TLRs are crucial for coordinating the complex, innate immune signaling pathway. Here, we constructed a full-length structural model of TLR4-a widely studied member of the interleukin-1 receptor/TLR superfamily-using homology modeling, protein-protein docking, and molecular dynamics simulations to understand the differential domain organization of TLR4 in a membrane-aqueous environment...
2018: Frontiers in Immunology
Kazuhiro Takemura, Nobuyuki Matubayasi, Akio Kitao
To aid the evaluation of protein-protein complex model structures generated by protein docking prediction (decoys), we previously developed a method to calculate the binding free energies for complexes. The method combines a short (2 ns) all-atom molecular dynamics simulation with explicit solvent and solution theory in the energy representation (ER). We showed that this method successfully selected structures similar to the native complex structure (near-native decoys) as the lowest binding free energy structures...
March 14, 2018: Journal of Chemical Physics
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