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Protein contact prediction

Stefan A P Lenz, Stacey D Wetmore
Human alkyladenine DNA glycosylase (AAG) functions as part of the base excision repair pathway to excise structurally diverse oxidized and alkylated DNA purines. Specifically, AAG uses a water molecule activated by a general base and a non-specific active site lined with aromatic residues to cleave the N-glycosidic bond. Despite broad substrate specificity, AAG does not target the natural purines (adenine (A) and guanine (G)). Using the ONIOM(QM:MM) methodology, we provide fundamental atomic level details of AAG bound to DNA-containing a neutral substrate (hypoxanthine (Hx)), a non-substrate (G), or a cationic substrate (7-methylguanine (7MeG)), and probe changes in the reaction pathway that occur when AAG targets different nucleotides...
November 17, 2017: Journal of Physical Chemistry. B
Andrés Bustamante, Juan Sotelo-Campos, Daniel G Guerra, Martin Floor, Christian M A Wilson, Carlos Bustamante, Mauricio Báez
Knots are natural topologies of chains. Yet, little is known about spontaneous knot formation in a polypeptide chain-an event that can potentially impair its folding-and about the effect of a knot on the stability and folding kinetics of a protein. Here we used optical tweezers to show that the free energy cost to form a trefoil knot in the denatured state of a polypeptide chain of 120 residues is 5.8 ± 1 kcal mol(-1). Monte Carlo dynamics of random chains predict this value, indicating that the free energy cost of knot formation is of entropic origin...
November 17, 2017: Nature Communications
Samantha Barrick, Jing Li, Xinyu Kong, Alokananda Ray, Emad Tajkhorshid, Deborah Leckband
Cadherin complexes transduce force fluctuations at junctions to activate signals that reinforce stressed intercellular contacts. α-Catenin is an identified force transducer within cadherin complexes that is autoinhibited under low tension. Increased force triggers a conformational change that exposes a cryptic site for the actin-binding protein vinculin. This study tested predictions that salt bridges within the force-sensing core modulate α-catenin activation. Studies with a fluorescence resonance energy transfer (FRET)-based α-catenin conformation sensor demonstrated that the salt-bridge mutations R551A and D503N each enhance α-catenin activation in live cells, but R551A has a greater impact...
November 15, 2017: Molecular Biology of the Cell
Christian Herzmann, Martin Ernst, Christoph Lange, Steffen Stenger, Stefan H E Kaufmann, Norbert Reiling, Tom Schaberg, Lize van der Merwe, Jeroen Maertzdorf
BACKGROUND: Blood based Interferon-(IFN)-γ release assays (IGRAs) have a poor predictive value for the development of tuberculosis. This study aimed to investigate the correlation between IGRAs and pulmonary immune responses in tuberculosis contacts in Germany. METHODS: IGRAs were performed on bronchoalveolar lavage (BAL) cells and peripheral blood from close healthy contacts of patients with culturally confirmed tuberculosis. Cellular BAL composition was determined by flow cytometry...
2017: PloS One
Alexandra J Weisberg, Gunjune Kim, James H Westwood, John G Jelesko
Contact with poison ivy plants is widely dreaded because they produce a natural product called urushiol that is responsible for allergenic contact delayed-dermatitis symptoms lasting for weeks. For this reason, the catchphrase most associated with poison ivy is "leaves of three, let it be", which serves the purpose of both identification and an appeal for avoidance. Ironically, despite this notoriety, there is a dearth of specific knowledge about nearly all other aspects of poison ivy physiology and ecology...
November 10, 2017: Genes
Sergey Antipov, Sergey Turishchev, Yuriy Purtov, Uliana Shvyreva, Alexander Sinelnikov, Yuriy Semov, Elena Preobrazhenskaya, Andrey Berezhnoy, Natalia Shusharina, Natalia Novolokina, Viktor Vakhtel, Valeriy Artyukhov, Olga Ozoline
The Dps protein of Escherichia coli, which combines ferroxidase activity and the ability to bind DNA, is effectively used by bacteria to protect their genomes from damage. Both activities depend on the integrity of this multi-subunit protein, which has an inner cavity for iron oxides; however, the diversity of its oligomeric forms has only been studied fragmentarily. Here, we show that iron ions stabilize the dodecameric form of Dps. This was found by electrophoretic fractionation and size exclusion chromatography, which revealed several oligomers in highly purified protein samples and demonstrated their conversion to dodecamers in the presence of 1 mM Mohr's salt...
November 5, 2017: Molecules: a Journal of Synthetic Chemistry and Natural Product Chemistry
Anastasia K Atabekova, Ekaterina A Lazareva, Olga S Strelkova, Andrey G Solovyev, Sergey Y Morozov
The Nicotiana tabacum 4/1 protein (Nt-4/1) of unknown function expressed in plant vasculature has been shown to localize to cytoplasmic bodies associated with endoplasmic reticulum. Here, we analyzed molecular interactions of an Nt-4/1 mutant with a deletion of 90 N-terminal amino acid residues (Nt-4/1d90) having a diffuse GFP-like localization. Upon transient co-expression with VAP27, a membrane protein known to localize to the ER, ER-plasma membrane contact sites and plasmodesmata, Nt-4/1d90 was concentrated around the cortical ER tubules, forming a network matching the shape of the cortical ER...
October 30, 2017: Biochimie
John Moult, Krzysztof Fidelis, Andriy Kryshtafovych, Torsten Schwede, Anna Tramontano
This paper reports the outcome of the 12th round of Critical Assessment of Structure Prediction (CASP12), held in 2016. CASP is a community experiment to determine the state of the art in modeling protein structure from amino acid sequence. Participants are provided sequence information and in turn provide protein structure models and related information. Analysis of the submitted structures by independent assessors provides a comprehensive picture of the capabilities of current methods, and allows progress to be identified...
October 30, 2017: Proteins
Chengxin Zhang, S M Mortuza, Baoji He, Yanting Wang, Yang Zhang
We develop two complementary pipelines, "Zhang-Server" and "QUARK", based on I-TASSER and QUARK pipelines for template-based modeling (TBM) and free modeling (FM), and test them in the CASP12 experiment. The combination of I-TASSER and QUARK successfully folds three medium-size FM targets that have more than 150 residues, even though the interplay between the two pipelines still awaits further optimization. Newly developed sequence-based contact prediction by NeBcon plays a critical role to enhance the quality of models, particularly for FM targets, by the new pipelines...
October 30, 2017: Proteins
Mayra A Machuca, Kevin S Johnson, Yu C Liu, David L Steer, Karen M Ottemann, Anna Roujeinikova
It is recently appreciated that many bacterial chemoreceptors have ligand-binding domains (LBD) of the dCACHE family, a structure with two PAS-like subdomains, one membrane-proximal and the other membrane-distal. Previous studies had implicated only the membrane-distal subdomain in ligand recognition. Here, we report the 2.2 Å resolution crystal structure of dCACHE LBD of the Helicobacter pylori chemoreceptor TlpC. H. pylori tlpC mutants are outcompeted by wild type during stomach colonisation, but no ligands had been mapped to this receptor...
October 26, 2017: Scientific Reports
Keisuke Kawata, Leah H Rubin, Leroy Wesley, Jong Lee, Thomas Sim, Masahiro Takahagi, Al Bellamy, Ryan Tierney, Dianne Langford
Athletes in contact sports sustain repetitive subconcussive head impacts in a brief window, yet neurophysiological sequelae from repetitive subconcussion remain unclear. This prospective longitudinal study examined a relationship between changes in plasma Tau protein levels and subconcussive impact kinematic data in 23 Division-I collegiate football players during a series of pre-season practices. Plasma measures for Tau and S100β proteins, symptom scores, and near point of convergence were obtained at preseason baseline and pre-post practices...
October 26, 2017: Journal of Neurotrauma
Aleix Lafita, Spencer Bliven, Andriy Kryshtafovych, Martino Bertoni, Bohdan Monastyrskyy, Jose M Duarte, Torsten Schwede, Guido Capitani
We present the results of the first independent assessment of protein assemblies in CASP. A total of 1,624 oligomeric models were submitted by 108 predictor groups for the 30 oligomeric targets in the CASP12 edition. The target assemblies were of diverse topology, composition and prediction difficulty, including eight heteromeric complexes, five viral fibre heads, four dihedral homomers and two membrane dimers. We evaluated the accuracy of oligomeric predictions by comparison to their experimentally determined reference structures at the interface patch and residue contact levels...
October 26, 2017: Proteins
D M Lesovoy, K S Mineev, P E Bragin, O V Bocharova, E V Bocharov, A S Arseniev
In the case of soluble proteins, chemical shift mapping is used to identify the intermolecular interfaces when the NOE-based calculations of spatial structure of the molecular assembly are impossible or impracticable. However, the reliability of the membrane protein interface mapping based on chemical shifts or other relevant parameters was never assessed. In the present work, we investigate the predictive power of various NMR parameters that can be used for mapping of helix-helix interfaces in dimeric TM domains...
October 23, 2017: Journal of Biomolecular NMR
Badri Adhikari, Jie Hou, Jianlin Cheng
In this work, we report the evaluation of the residue-residue contacts predicted by our three different methods in the CASP12 experiment, focusing on studying the impact of multiple sequence alignment, residue coevolution and machine learning on contact prediction. The first method (MULTICOM-NOVEL) uses only traditional features (sequence profile, secondary structure and solvent accessibility) with deep learning to predict contacts and serves as a baseline. The second method (MULTICOM-CONSTRUCT) uses our new alignment algorithm to generate deep multiple sequence alignment to derive coevolution-based features, which are integrated by a neural network method to predict contacts...
October 19, 2017: Proteins
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
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
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
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
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...
November 1, 2017: Bioinformatics
Francesca Nadalin, Alessandra Carbone
Motivation: Large-scale computational docking will be increasingly used in future years to discriminate protein-protein interactions at the residue resolution. Complete cross-docking experiments make in silico reconstruction of protein-protein interaction networks a feasible goal. They ask for efficient and accurate screening of the millions structural conformations issued by the calculations. Results: We propose CIPS (Combined Interface Propensity for decoy Scoring), a new pair potential combining interface composition with residue-residue contact preference...
September 22, 2017: Bioinformatics
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