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Protein interface prediction

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https://www.readbyqxmd.com/read/28319831/structure-based-prediction-of-host-pathogen-protein-interactions
#1
REVIEW
Rachelle Mariano, Stefan Wuchty
The discovery, validation, and characterization of protein-based interactions from different species are crucial for translational research regarding a variety of pathogens, ranging from the malaria parasite Plasmodium falciparum to HIV-1. Here, we review recent advances in the prediction of host-pathogen protein interfaces using structural information. In particular, we observe that current methods chiefly perform machine learning on sequence and domain information to produce large sets of candidate interactions that are further assessed and pruned to generate final, highly probable sets...
March 16, 2017: Current Opinion in Structural Biology
https://www.readbyqxmd.com/read/28303031/a-biologically-validated-hcv-e1e2-heterodimer-structural-model
#2
Matteo Castelli, Nicola Clementi, Jennifer Pfaff, Giuseppe A Sautto, Roberta A Diotti, Roberto Burioni, Benjamin J Doranz, Matteo Dal Peraro, Massimo Clementi, Nicasio Mancini
The design of vaccine strategies and the development of drugs targeting the early stages of Hepatitis C virus (HCV) infection are hampered by the lack of structural information about its surface glycoproteins E1 and E2, the two constituents of HCV entry machinery. Despite the recent crystal resolution of limited versions of both proteins in truncated form, a complete picture of the E1E2 complex is still missing. Here we combined deep computational analysis of E1E2 secondary, tertiary and quaternary structure with functional and immunological mutational analysis across E1E2 in order to propose an in silico model for the ectodomain of the E1E2 heterodimer...
March 16, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28289744/adsorption-of-the-natural-protein-surfactant-rsn-2-onto-liquid-interfaces
#3
Giovanni B Brandani, Steven J Vance, Marieke Schor, Alan Cooper, Malcolm W Kennedy, Brian O Smith, Cait E MacPhee, David L Cheung
To stabilize foams, droplets and films at liquid interfaces a range of protein biosurfactants have evolved in nature. Compared to synthetic surfactants, these combine surface activity with biocompatibility and low solution aggregation. One recently studied example is Rsn-2, a component of the foam nest of the frog Engystomops pustulosus, which has been predicted to undergo a clamshell-like opening transition at the air-water interface. Using atomistic molecular dynamics simulations and surface tension measurements we study the adsorption of Rsn-2 onto air-water and cyclohexane-water interfaces...
March 14, 2017: Physical Chemistry Chemical Physics: PCCP
https://www.readbyqxmd.com/read/28289198/large-scale-identification-of-coevolution-signals-across-homo-oligomeric-protein-interfaces-by-direct-coupling-analysis
#4
Guido Uguzzoni, Shalini John Lovis, Francesco Oteri, Alexander Schug, Hendrik Szurmant, Martin Weigt
Proteins have evolved to perform diverse cellular functions, from serving as reaction catalysts to coordinating cellular propagation and development. Frequently, proteins do not exert their full potential as monomers but rather undergo concerted interactions as either homo-oligomers or with other proteins as hetero-oligomers. The experimental study of such protein complexes and interactions has been arduous. Theoretical structure prediction methods are an attractive alternative. Here, we investigate homo-oligomeric interfaces by tracing residue coevolution via the global statistical direct coupling analysis (DCA)...
March 13, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/28277940/a-single-structurally-conserved-sumoylation-site-in-crmp2-controls-nav1-7-function
#5
Erik Thomas Dustrude, Samantha Perez-Miller, Liberty François-Moutal, Aubin Moutal, May Khanna, Rajesh Khanna
The neuronal collapsin response mediator protein 2 (CRMP2) undergoes several posttranslational modifications that codify its functions. Most recently, CRMP2 SUMOylation (addition of small ubiquitin like modifier (SUMO)) was identified as a key regulatory step within a modification program that codes for CRMP2 interaction with, and trafficking of, voltage-gated sodium channel NaV1.7. In this addendum, we illustrate the utility of combining sequence alignment within protein families with structural analysis to identify, from a number of putative SUMOylation sites, those that are most likely to be biologically relevant...
February 28, 2017: Channels
https://www.readbyqxmd.com/read/28276299/immunohistochemical-analysis-of-the-stem-cell-marker-lgr5-in-pediatric-liver-disease
#6
Zahida Khan, Anne Orr, George K Michalopoulos, Sarangarajan Ranganathan
Aims In regenerating liver, hepatic progenitor cells (HPCs) are recruited in response to injury; however, few highly specific human HPC markers exist for the hepatocyte lineage. Leucine-rich repeat-containing G-protein coupled receptor 5 (LGR5), a Wnt-associated stem cell marker, has been extensively studied in intestinal stem cells, but little is known about its expression in human liver. We hypothesized that LGR5+ HPCs are induced in the regenerative response to pediatric liver injury. Methods and results Immunohistochemistry was used to characterize LGR5 expression in pediatric liver explants (n = 36)...
January 2017: Pediatric and Developmental Pathology
https://www.readbyqxmd.com/read/28270517/mcm10-regulates-dna-replication-elongation-by-stimulating-the-cmg-replicative-helicase
#7
Marko Lõoke, Michael F Maloney, Stephen P Bell
Activation of the Mcm2-7 replicative DNA helicase is the committed step in eukaryotic DNA replication initiation. Although Mcm2-7 activation requires binding of the helicase-activating proteins Cdc45 and GINS (forming the CMG complex), an additional protein, Mcm10, drives initial origin DNA unwinding by an unknown mechanism. We show that Mcm10 binds a conserved motif located between the oligonucleotide/oligosaccharide fold (OB-fold) and A subdomain of Mcm2. Although buried in the interface between these domains in Mcm2-7 structures, mutations predicted to separate the domains and expose this motif restore growth to conditional-lethal MCM10 mutant cells...
February 1, 2017: Genes & Development
https://www.readbyqxmd.com/read/28264645/systematic-substitutions-at-blip-position-50-result-in-changes-in-binding-specificity-for-class-a-%C3%AE-lactamases
#8
Carolyn J Adamski, Timothy Palzkill
BACKGROUND: The production of β-lactamases by bacteria is the most common mechanism of resistance to the widely prescribed β-lactam antibiotics. β-lactamase inhibitory protein (BLIP) competitively inhibits class A β-lactamases via two binding loops that occlude the active site. It has been shown that BLIP Tyr50 is a specificity determinant in that substitutions at this position result in large differential changes in the relative affinity of BLIP for class A β-lactamases. RESULTS: In this study, the effect of systematic substitutions at BLIP position 50 on binding to class A β-lactamases was examined to further explore the role of BLIP Tyr50 in modulating specificity...
March 6, 2017: BMC Biochemistry
https://www.readbyqxmd.com/read/28257595/aggregation-propensity-of-human-proteome-insights-from-large-scale-data-analyses
#9
Prabakaran Ramakrishnan, Dhruv Goel, Sandeep Kumar, M Michael Gromiha
Protein aggregation leads to several burdensome human maladies, but a molecular level understanding of how human proteome has tackled the threat of aggregation is currently lacking. In this work, we survey the human proteome for incidence of aggregation prone regions (APRs), by using sequences of experimentally validated amyloid-fibril forming peptides and via computational predictions. While approximately 30 human proteins are currently known to be amyloidogenic, we found that 260 proteins (∼1% of human proteome) contain at least one experimentally validated amyloid-fibril forming segment...
March 3, 2017: Proteins
https://www.readbyqxmd.com/read/28254726/ionic-tethering-contributes-to-the-conformational-stability-and-function-of-complement-c3b
#10
Andrés López-Perrote, Reed E S Harrison, Marta Subías, Martín Alcorlo, Santiago Rodríguez de Córdoba, Dimitrios Morikis, Oscar Llorca
C3b, the central component of the alternative pathway (AP) of the complement system, coexists as a mixture of conformations in solution. These conformational changes can affect interactions with other proteins and complement regulators. Here we combine a computational model for electrostatic interactions within C3b with molecular imaging to study the conformation of C3b. The computational analysis shows that the TED domain in C3b is tethered ionically to the macroglobulin (MG) ring. Monovalent counterion concentration affects the magnitude of electrostatic forces anchoring the TED domain to the rest of the C3b molecule in a thermodynamic model...
February 27, 2017: Molecular Immunology
https://www.readbyqxmd.com/read/28236233/application-of-the-attract-coarse-grained-docking-and-atomistic-refinement-for-predicting-peptide-protein-interactions
#11
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/28235382/can-f%C3%A3-rster-theory-describe-stereoselective-energy-transfer-dynamics-in-a-protein-ligand-complex
#12
Silvana Pinheiro, Carles Curutchet
Förster resonance energy transfer (FRET) reactions involving ligands and aromatic amino acids can substantially impact the fluorescence properties of a protein-ligand complex, an impact intimately related to the corresponding binding mode. Structural characterization of such binding events in terms of intermolecular distances can be done through the well-known R(-6) distance-dependent Förster rate expression. However, such an interpretation suffers from uncertainties underlying Förster theory in the description of the electronic coupling that promotes FRET, mostly related to the dipole-dipole orientation factor, dielectric screening effects, and deviations from the ideal dipole approximation...
March 8, 2017: Journal of Physical Chemistry. B
https://www.readbyqxmd.com/read/28228527/activation-mechanism-of-the-g-protein-coupled-sweet-receptor-heterodimer-with-sweeteners-and-allosteric-agonists
#13
Soo-Kyung Kim, Yalu Chen, Ravinder Abrol, William A Goddard, Brian Guthrie
The sweet taste in humans is mediated by the TAS1R2/TAS1R3 G protein-coupled receptor (GPCR), which belongs to the class C family that also includes the metabotropic glutamate and γ-aminobutyric acid receptors. We report here the predicted 3D structure of the full-length TAS1R2/TAS1R3 heterodimer, including the Venus Flytrap Domains (VFDs) [in the closed-open (co) active conformation], the cysteine-rich domains (CRDs), and the transmembrane domains (TMDs) at the TM56/TM56 interface. We observe that binding of agonists to VFD2 of TAS1R2 leads to major conformational changes to form a TM6/TM6 interface between TMDs of TAS1R2 and TAS1R3, which is consistent with the activation process observed biophysically on the metabotropic glutamate receptor 2 homodimer...
March 7, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/28217262/the-effects-of-shared-information-on-semantic-calculations-in-the-gene%C3%A2-ontology
#14
Paul W Bible, Hong-Wei Sun, Maria I Morasso, Rasiah Loganantharaj, Lai Wei
The structured vocabulary that describes gene function, the gene ontology (GO), serves as a powerful tool in biological research. One application of GO in computational biology calculates semantic similarity between two concepts to make inferences about the functional similarity of genes. A class of term similarity algorithms explicitly calculates the shared information (SI) between concepts then substitutes this calculation into traditional term similarity measures such as Resnik, Lin, and Jiang-Conrath. Alternative SI approaches, when combined with ontology choice and term similarity type, lead to many gene-to-gene similarity measures...
2017: Computational and Structural Biotechnology Journal
https://www.readbyqxmd.com/read/28212602/happi-2-a-comprehensive-and-high-quality-map-of-human-annotated-and-predicted-protein-interactions
#15
Jake Y Chen, Ragini Pandey, Thanh M Nguyen
BACKGROUND: Human protein-protein interaction (PPI) data is essential to network and systems biology studies. PPI data can help biochemists hypothesize how proteins form complexes by binding to each other, how extracellular signals propagate through post-translational modification of de-activated signaling molecules, and how chemical reactions are coupled by enzymes involved in a complex biological process. Our capability to develop good public database resources for human PPI data has a direct impact on the quality of future research on genome biology and medicine...
February 17, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28205569/heteroaryldihydropyrimidine-hap-and-sulfamoylbenzamide-sba-inhibit-hepatitis-b-virus-replication-by-different-molecular-mechanisms
#16
Zheng Zhou, Taishan Hu, Xue Zhou, Steffen Wildum, Fernando Garcia-Alcalde, Zhiheng Xu, Daitze Wu, Yi Mao, Xiaojun Tian, Yuan Zhou, Fang Shen, Zhisen Zhang, Guozhi Tang, Isabel Najera, Guang Yang, Hong C Shen, John A T Young, Ning Qin
Heteroaryldihydropyrimidine (HAP) and sulfamoylbenzamide (SBA) are promising non-nucleos(t)ide HBV replication inhibitors. HAPs are known to promote core protein mis-assembly, but the molecular mechanism of abnormal assembly is still elusive. Likewise, the assembly status of core protein induced by SBA remains unknown. Here we show that SBA, unlike HAP, does not promote core protein mis-assembly. Interestingly, two reference compounds HAP_R01 and SBA_R01 bind to the same pocket at the dimer-dimer interface in the crystal structures of core protein Y132A hexamer...
February 13, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28182405/blip-ii-employs-differential-hotspot-residues-to-bind-structurally-similar-staphylococcus-aureus-pbp2a-and-class-a-%C3%AE-lactamases
#17
Carolyn J Adamski, Timothy Palzkill
The interaction of β-lactamase inhibitory protein II (BLIP-II) with β-lactamases serves as a model system to investigate the principles underlying protein-protein interactions. Previous studies have focused on identifying the determinants of binding affinity and specificity between BLIP-II and class A β-lactamases. However, interactions between BLIP-II and other bacterial proteins have yet to be explored. Here, we provide evidence that BLIP-II binds penicillin binding protein 2a (PBP2a) from methicillin-resistant Staphylococcus aureus (MRSA) with a KD in the low micromolar range...
February 16, 2017: Biochemistry
https://www.readbyqxmd.com/read/28174738/microgeographic-proteomic-networks-of-the-human-colonic-mucosa-and-their-association-with-inflammatory-bowel-disease
#18
Xiaoxiao Li, James LeBlanc, David Elashoff, Ian McHardy, Maomeng Tong, Bennett Roth, Andrew Ippoliti, Gildardo Barron, Dermot McGovern, Keely McDonald, Rodney Newberry, Thomas Graeber, Steve Horvath, Lee Goodglick, Jonathan Braun
BACKGROUND & AIMS: Interactions between mucosal cell types, environmental stressors, and intestinal microbiota contribute to pathogenesis in inflammatory bowel disease (IBD). Here, we applied metaproteomics of the mucosal-luminal interface to study the disease-related biology of the human colonic mucosa. METHODS: We recruited a discovery cohort of 51 IBD and non-IBD subjects endoscopically sampled by mucosal lavage at 6 colonic regions, and a validation cohort of 38 no-IBD subjects...
September 2016: Cellular and Molecular Gastroenterology and Hepatology
https://www.readbyqxmd.com/read/28168669/multiscale-modelling-of-bionano-interface
#19
Hender Lopez, Erik G Brandt, Alexander Mirzoev, Dmitry Zhurkin, Alexander Lyubartsev, Vladimir Lobaskin
We present a framework for coarse-grained modelling of the interface between foreign nanoparticles (NP) and biological fluids and membranes. Our model includes united-atom presentations of membrane lipids and globular proteins in implicit solvent, which are based on all-atom structures of the corresponding molecules and parameterised using experimental data or atomistic simulation results. The NPs are modelled by homogeneous spheres that interact with the beads of biomolecules via a central force that depends on the NP size...
2017: Advances in Experimental Medicine and Biology
https://www.readbyqxmd.com/read/28166227/improving-protein-protein-interaction-prediction-using-evolutionary-information-from-low-quality-msas
#20
Csilla Várnai, Nikolas S Burkoff, David L Wild
Evolutionary information stored in multiple sequence alignments (MSAs) has been used to identify the interaction interface of protein complexes, by measuring either co-conservation or co-mutation of amino acid residues across the interface. Recently, maximum entropy related correlated mutation measures (CMMs) such as direct information, decoupling direct from indirect interactions, have been developed to identify residue pairs interacting across the protein complex interface. These studies have focussed on carefully selected protein complexes with large, good-quality MSAs...
2017: PloS One
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