keyword
MENU ▼
Read by QxMD icon Read
search

Protein interface prediction

keyword
https://www.readbyqxmd.com/read/27908641/free-energy-perturbation-calculation-of-relative-binding-free-energy-between-broadly-neutralizing-antibodies-and-the-gp120-glycoprotein-of-hiv-1
#1
Anthony J Clark, Tatyana Gindin, Baoshan Zhang, Lingle Wang, Robert Abel, Colleen S Murret, Fang Xu, Amy Bao, Nina J Lu, Tongqing Zhou, Peter D Kwong, Lawrence Shapiro, Barry Honig, Richard A Friesner
Direct calculation of relative binding affinities between antibodies and antigens is a long-sought goal. However, despite substantial efforts, no generally applicable computational method has been described. Here we describe a systematic free energy perturbation (FEP) protocol and calculate the binding affinities between the gp120 envelope glycoprotein of HIV-1 and three broadly neutralizing antibodies (bNAbs) of the VRC01 class. The protocol has been adapted from successful studies of small molecules to address the challenges associated with modeling protein-protein interactions...
November 28, 2016: Journal of Molecular Biology
https://www.readbyqxmd.com/read/27905545/on-the-ability-of-molecular-dynamics-simulation-and-continuum-electrostatics-to-treat-interfacial-water-molecules-in-protein-protein-complexes
#2
Guillaume Copie, Fabrizio Cleri, Ralf Blossey, Marc F Lensink
Interfacial waters are increasingly appreciated as playing a key role in protein-protein interactions. We report on a study of the prediction of interfacial water positions by both Molecular Dynamics and explicit solvent-continuum electrostatics based on the Dipolar Poisson-Boltzmann Langevin (DPBL) model, for three test cases: (i) the barnase/barstar complex (ii) the complex between the DNase domain of colicin E2 and its cognate Im2 immunity protein and (iii) the highly unusual anti-freeze protein Maxi which contains a large number of waters in its interior...
December 1, 2016: Scientific Reports
https://www.readbyqxmd.com/read/27899675/jet2-viewer-a-database-of-predicted-multiple-possibly-overlapping-protein-protein-interaction-sites-for-pdb-structures
#3
Hughes Ripoche, Elodie Laine, Nicoletta Ceres, Alessandra Carbone
The database JET2 Viewer, openly accessible at http://www.jet2viewer.upmc.fr/, reports putative protein binding sites for all three-dimensional (3D) structures available in the Protein Data Bank (PDB). This knowledge base was generated by applying the computational method JET(2) at large-scale on more than 20 000 chains. JET(2) strategy yields very precise predictions of interacting surfaces and unravels their evolutionary process and complexity. JET2 Viewer provides an online intelligent display, including interactive 3D visualization of the binding sites mapped onto PDB structures and suitable files recording JET(2) analyses...
November 28, 2016: Nucleic Acids Research
https://www.readbyqxmd.com/read/27899624/microscope-in-2017-an-expanding-and-evolving-integrated-resource-for-community-expertise-of-microbial-genomes
#4
David Vallenet, Alexandra Calteau, Stéphane Cruveiller, Mathieu Gachet, Aurélie Lajus, Adrien Josso, Jonathan Mercier, Alexandre Renaux, Johan Rollin, Zoe Rouy, David Roche, Claude Scarpelli, Claudine Médigue
The annotation of genomes from NGS platforms needs to be automated and fully integrated. However, maintaining consistency and accuracy in genome annotation is a challenging problem because millions of protein database entries are not assigned reliable functions. This shortcoming limits the knowledge that can be extracted from genomes and metabolic models. Launched in 2005, the MicroScope platform (http://www.genoscope.cns.fr/agc/microscope) is an integrative resource that supports systematic and efficient revision of microbial genome annotation, data management and comparative analysis...
November 29, 2016: Nucleic Acids Research
https://www.readbyqxmd.com/read/27899614/suba4-the-interactive-data-analysis-centre-for-arabidopsis-subcellular-protein-locations
#5
Cornelia M Hooper, Ian R Castleden, Sandra K Tanz, Nader Aryamanesh, A Harvey Millar
The SUBcellular location database for Arabidopsis proteins (SUBA4, http://suba.live) is a comprehensive collection of manually curated published data sets of large-scale subcellular proteomics, fluorescent protein visualization, protein-protein interaction (PPI) as well as subcellular targeting calls from 22 prediction programs. SUBA4 contains an additional 35 568 localizations totalling more than 60 000 experimental protein location claims as well as 37 new suborganellar localization categories. The experimental PPI data has been expanded to 26 327 PPI pairs including 856 PPI localizations from experimental fluorescent visualizations...
November 28, 2016: Nucleic Acids Research
https://www.readbyqxmd.com/read/27899586/r-loopdb-a-database-for-r-loop-forming-sequences-rlfs-and-r-loops
#6
Piroon Jenjaroenpun, Thidathip Wongsurawat, Sawannee Sutheeworapong, Vladimir A Kuznetsov
R-loopDB (http://rloop.bii.a-star.edu.sg) was originally constructed as a collection of computationally predicted R-loop forming sequences (RLFSs) in the human genic regions. The renewed R-loopDB provides updates, improvements and new options, including access to recent experimental data. It includes genome-scale prediction of RLFSs for humans, six other animals and yeast. Using the extended quantitative model of RLFSs (QmRLFS), we significantly increased the number of RLFSs predicted in the human genes and identified RLFSs in other organism genomes...
November 28, 2016: Nucleic Acids Research
https://www.readbyqxmd.com/read/27899282/bindprofx-assessing-mutation-induced-binding-affinity-change-by-protein-interface-profiles-with-pseudo-counts
#7
Peng Xiong, Chengxin Zhang, Wei Zheng, Yang Zhang
Understanding how gene-level mutations affect the binding affinity of protein-protein interactions is a key issue of protein engineering. Due to the complexity of the problem, using physical force field to predict the mutation-induced binding free-energy change remains challenging. In this work, we present a renewed approach to calculate the impact of gene mutations on the binding affinity through the structure-based profiling of protein-protein interfaces, where the binding free-energy change (ΔΔG) is counted as the logarithm of relative probability of mutant amino acids over wild-type ones in the interface alignment matrix; three pseudo counts are introduced to alleviate the limit of the current interface library...
November 26, 2016: Journal of Molecular Biology
https://www.readbyqxmd.com/read/27890784/identifying-residues-that-determine-scf-molecular-level-interactions-through-a-combination-of-experimental-and-in-silico-analyses
#8
Eitan Rabinovich, Michael Heyne, Anna Bakhman, Mickey Kosloff, Julia M Shifman, Niv Papo
The stem cell factor (SCF)/c-Kit receptor tyrosine kinase complex - with its significant roles in hematopoiesis and angiogenesis - is an attractive target for rational drug design. There is thus a need to map, in detail, the SCF/c-Kit interaction sites and the mechanisms that modulate this interaction. While most residues in the direct SCF/c-Kit binding interface can be identified from the existing crystal structure of the complex, other residues that affect binding through protein unfolding, intermolecular interactions, or allosteric or long-distance electrostatic effects cannot be directly inferred...
November 24, 2016: Journal of Molecular Biology
https://www.readbyqxmd.com/read/27875310/extending-halogen-based-medicinal-chemistry-to-proteins-iodo-insulin-as-a-case-study
#9
Krystel El Hage, Vijay Pandyarajan, Nelson B Phillips, Brian J Smith, John G Menting, Jonathan Whittaker, Michael C Lawrence, Markus Meuwly, Michael A Weiss
Insulin, a protein critical for metabolic homeostasis, provides a classical model for protein design with application to human health. Recent efforts to improve its pharmaceutical formulation demonstrated that iodination of a conserved tyrosine (Tyr(B26)) enhances key properties of a rapid-acting clinical analog. Moreover, the broad utility of halogens in medicinal chemistry has motivated use of hybrid quantum- and molecular-mechanical methods to study proteins. Here, we (i) undertook quantitative atomic-level simulations of 3-I-Tyr(B26)-insulin to predict its structural features and (ii) tested these predictions by X-ray crystallography...
November 14, 2016: Journal of Biological Chemistry
https://www.readbyqxmd.com/read/27862345/predicting-protein-conformational-changes-for-unbound-and-homology-docking-learning-from-intrinsic-and-induced-flexibility
#10
Haoran Chen, Yuanfei Sun, Yang Shen
Predicting protein conformational changes from unbound structures or even homology models to bound structures remains a critical challenge for protein docking. Here we present a study directly addressing the challenge by reducing the dimensionality and narrowing the range of the corresponding conformational space. The study builds on cNMA - our new framework of partner- and contact-specific normal mode analysis that exploits encounter complexes and considers both intrinsic and induced flexibility. First, we established over a CAPRI (Critical Assessment of PRedicted Interactions) target set that the direction of conformational changes from unbound structures and homology models can be reproduced to a great extent by a small set of cNMA modes...
November 15, 2016: Proteins
https://www.readbyqxmd.com/read/27859766/structural-and-molecular-analysis-of-a-protective-epitope-of-lyme-disease-antigen-ospa-and-antibody-interactions
#11
Shivender Shandilya, Nese Kurt Yilmaz, Andrew Sadowski, Ejemel Monir, Zachary A Schiller, William D Thomas, Mark S Klempner, Celia A Schiffer, Yang Wang
The murine monoclonal antibody LA-2 recognizes a clinically protective epitope on outer surface protein (OspA) of Borrelia burgdorferi, the causative agent of Lyme disease in North America. Human antibody equivalence to LA-2 is the best serologic correlate of protective antibody responses following OspA vaccination. Understanding the structural and functional basis of the LA-2 protective epitope is important for developing OspA-based vaccines and discovering prophylactic antibodies against Lyme disease. Here, we present a detailed structure-based analysis of the LA-2/OspA interaction interface and identification of residues mediating antibody recognition...
November 16, 2016: Journal of Molecular Recognition: JMR
https://www.readbyqxmd.com/read/27855192/primo-an-interactive-homology-modeling-pipeline
#12
Rowan Hatherley, David K Brown, Michael Glenister, Özlem Tastan Bishop
The development of automated servers to predict the three-dimensional structure of proteins has seen much progress over the years. These servers make calculations simpler, but largely exclude users from the process. In this study, we present the PRotein Interactive MOdeling (PRIMO) pipeline for homology modeling of protein monomers. The pipeline eases the multi-step modeling process, and reduces the workload required by the user, while still allowing engagement from the user during every step. Default parameters are given for each step, which can either be modified or supplemented with additional external input...
2016: PloS One
https://www.readbyqxmd.com/read/27846259/introducing-a-clustering-step-in-a-consensus-approach-for-the-scoring-of-protein-protein-docking-models
#13
Edrisse Chermak, Renato De Donato, Marc F Lensink, Andrea Petta, Luigi Serra, Vittorio Scarano, Luigi Cavallo, Romina Oliva
Correctly scoring protein-protein docking models to single out native-like ones is an open challenge. It is also an object of assessment in CAPRI (Critical Assessment of PRedicted Interactions), the community-wide blind docking experiment. We introduced in the field the first pure consensus method, CONSRANK, which ranks models based on their ability to match the most conserved contacts in the ensemble they belong to. In CAPRI, scorers are asked to evaluate a set of available models and select the top ten ones, based on their own scoring approach...
2016: PloS One
https://www.readbyqxmd.com/read/27845431/ligand-mediated-changes-in-conformational-dynamics-of-npma-implications-for-ribosomal-interactions
#14
Nilofer Husain, Nikhil Kumar Tulsian, Wang Loo Chien, Sushant Suresh, Ganesh Srinivasan Anand, J Sivaraman
Aminoglycosides are broad-spectrum antibiotics that bind to the 30S ribosomal subunit (30S) of bacteria and disrupt protein translation. NpmA, a structurally well-characterized methyltransferase identified in an E. coli clinical isolate, catalyzes methylation of 30S at A1408 of the 16S rRNA and confers aminoglycoside resistance. Using sucrose cushion centrifugation and isothermal titration calorimetry, we first confirmed the binding between NpmA and 30S. Next, we performed amide Hydrogen/Deuterium Exchange Mass Spectrometry (HDXMS) of apo NpmA and in the presence and absence of SAM/SAH...
November 15, 2016: Scientific Reports
https://www.readbyqxmd.com/read/27836975/a-conserved-tripeptide-sequence-at-the-c-terminus-of-the-poxvirus-dna-processivity-factor-d4-is-essential-for-protein-integrity-and-function
#15
Manunya Nuth, Hancheng Guan, Robert P Ricciardi
Vaccinia virus (VACV) is a poxvirus member, and the VACV D4 protein serves both as a uracil-DNA glycosylase (UDG) and as an essential component required for processive DNA synthesis. The VACV A20 protein has no known catalytic function itself, but associates with D4 to form the D4-A20 heterodimer that functions as the poxvirus DNA processivity factor. The heterodimer enables the DNA polymerase to efficiently synthesize extended strands of DNA. Upon characterizing the interaction between D4 and A20, we observed that the C-terminus of D4 is susceptible to perturbation...
November 11, 2016: Journal of Biological Chemistry
https://www.readbyqxmd.com/read/27835934/the-conformational-feasibility-for-the-formation-of-reaching-dimer-in-asv-and-hiv-integrase-a-molecular-dynamics-study
#16
Sangeetha Balasubramanian, Muthukumaran Rajagopalan, Ravi Shankar Bojja, Anna Marie Skalka, Mark D Andrake, Amutha Ramaswamy
Retroviral integrases are reported to form alternate dimer assemblies like the core-core dimer and reaching dimer. The core-core dimer is stabilized predominantly by an extensive interface between two catalytic core domains. The reaching dimer is stabilized by N-terminal domains (NTD) that reach to form intermolecular interfaces with the other subunit's core and C-terminal domains (CTD), as well as CTD-CTD interactions. In this study, molecular dynamics (MD), Brownian dynamics (BD) simulations, and free energy analyses, were performed to elucidate determinants for the stability of the reaching dimer forms of full-length ASV and HIV IN, and to examine the role of the C-tails (the last ~16-18 residues at the C-termini) in their structural dynamics...
November 11, 2016: Journal of Biomolecular Structure & Dynamics
https://www.readbyqxmd.com/read/27835840/correlation-between-the-number-of-pro-ala-repeats-in-the-emra-homologue-of-acinetobacter-baumannii-and-resistance-to-netilmicin-tobramycin-imipenem-and-ceftazidime
#17
Alicja Nowak-Zaleska, Miłosz Wieczór, Jacek Czub, Łukasz Nierzwicki, Roman Kotłowski, Agnieszka Mikucka, Eugenia Gospodarek
Acinetobacter baumannii coccobacilli are dangerous to patients in intensive care units because of their multidrug resistance to antibiotics, developed mainly in the past decade. This study aimed to examine whether there is a significant correlation between the number of Pro-Ala repeats in the CAP01997 protein, the EmrA homologue of A. baumannii, and resistance to antibiotics. A total of 79 multidrug-resistant A. baumannii strains isolated from patients were analysed. Resistance to antibiotics was determined on Mueller-Hinton agar plates using the Kirby-Bauer disk diffusion method...
December 2016: Journal of Global Antimicrobial Resistance
https://www.readbyqxmd.com/read/27834201/identification-of-ybey-protein-interactions-involved-in-16s-rrna-maturation-and-stress-regulation-in-escherichia-coli
#18
Maarten Vercruysse, Caroline Köhrer, Yang Shen, Sandra Proulx, Anubrata Ghosal, Bryan W Davies, Uttam L RajBhandary, Graham C Walker
: YbeY is part of a core set of RNases in Escherichia coli and other bacteria. This highly conserved endoribonuclease has been implicated in several important processes such as 16S rRNA 3' end maturation, 70S ribosome quality control, and regulation of mRNAs and small noncoding RNAs, thereby affecting cellular viability, stress tolerance, and pathogenic and symbiotic behavior of bacteria. Thus, YbeY likely interacts with numerous protein or RNA partners that are involved in various aspects of cellular physiology...
November 8, 2016: MBio
https://www.readbyqxmd.com/read/27830221/kinetics-of-liquid-liquid-phase-separation-in-protein-solutions-exhibiting-lcst-phase-behavior-studied-by-time-resolved-usaxs-and-vsans
#19
Stefano Da Vela, Michal K Braun, Andreas Dörr, Alessandro Greco, Johannes Möller, Zhendong Fu, Fajun Zhang, Frank Schreiber
We study the kinetics of the liquid-liquid phase separation (LLPS) and its arrest in protein solutions exhibiting a lower critical solution temperature (LCST) phase behavior using the combination of ultra-small angle X-ray scattering (USAXS) and very-small angle neutron scattering (VSANS). We employ a previously established model system consisting of bovine serum albumin (BSA) solutions with YCl3. We follow the phase transition from sub-second to 10(4) s upon an off-critical temperature jump. After a temperature jump, the USAXS profiles exhibit a peak that grows in intensity and shifts to lower q values with time...
November 10, 2016: Soft Matter
https://www.readbyqxmd.com/read/27816523/structural-and-energy-determinants-in-protein-rna-docking
#20
Laura Pérez-Cano, Miguel Romero-Durana, Juan Fernández-Recio
Deciphering the structural and energetic determinants of protein-RNA interactions harbors the potential to understand key cell processes at molecular level, such as gene expression and regulation. With this purpose, computational methods like docking aim to complement current biophysical and structural biology efforts. However, the few reported docking algorithms for protein-RNA interactions show limited predictive success rates, mainly due to incomplete sampling of the conformational space of both the protein and the RNA molecules, as well as to the difficulties of the scoring function in identifying the correct docking models...
November 2, 2016: Methods: a Companion to Methods in Enzymology
keyword
keyword
13118
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"