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Protein contact prediction

Claire Marks, Jaroslaw Nowak, Stefan Klostermann, Guy Georges, James Dunbar, Jiye Shi, Sebastian Kelm, Charlotte M Deane
MOTIVATION: Loops are often vital for protein function, however their irregular structures make them difficult to model accurately. Current loop modelling algorithms can mostly be divided into two categories: knowledge-based, where databases of fragments are searched to find suitable conformations; and ab initio, where conformations are generated computationally. Existing knowledge-based methods only use fragments that are the same length as the target, even though loops of slightly different lengths may adopt similar conformations...
January 16, 2017: Bioinformatics
Avisek Das, Huan Rui, Robert Nakamoto, Benoît Roux
Ion pumps are integral membrane proteins responsible for transporting ions against concentration gradients across biological membranes. Sarco/endoplasmic reticulum Ca(2+)-ATPase (SERCA), a member of the P-type ATPases family, transports two calcium ions per hydrolyzed ATP molecule via an "alternating-access" mechanism. High-resolution crystallographic structures provide invaluable insight on the structural mechanism of the ion pumping process. However, to understand the molecular details of how ATP hydrolysis is coupled to calcium transport, it is necessary to gain knowledge about the conformational transition pathways connecting the crystallographically resolved conformations...
January 13, 2017: Journal of Molecular Biology
Andreas Natsch, Roger Emter
The publication by the OECD of the adverse outcome pathway (AOP) for skin sensitization has accelerated the development and validation of mechanistic tests and testing strategies to assess the potential of new molecules to trigger skin allergies. The molecular initiating event (MIE) in the AOP is reaction with skin peptides/proteins. It is followed by a number of cellular events. Currently, only one in chemico test to characterize the MIE was proposed to and underwent adoption by the OECD, while two cell-based assays have completed the process...
January 17, 2017: Chemical Research in Toxicology
Govardhan Reddy, Dave Thirumalai
The folding of small protein Ubiquitin (Ub), which plays an indispensable role in targeting proteins for degradation and DNA damage response is complex. A number of experiments on Ub folding have reached differing conclusions regarding the relation between collapse and folding, and whether intermediates are populated. In order to resolve these vexing issues, we elucidate the denaturant-dependent thermodynamics and kinetics of Ub folding at low and neutral pH as a function of Guanidinium chloride and Urea using coarse-grained molecular simulations...
January 11, 2017: Journal of Physical Chemistry. B
Surendra S Negi, Werner Braun
: The phenomenon of cross-reactivity between allergenic proteins plays an important role to understand how the immune system recognizes different antigen proteins. Allergen proteins are known to cross-react if their sequence comparison shows a high sequence identity which also implies that the proteins have a similar 3D fold. In such cases, linear sequence alignment methods are frequently used to predict cross-reactivity between allergenic proteins. However, the prediction of cross-reactivity between distantly related allergens continues to be a challenging task...
January 5, 2017: Bioinformatics
Surendra K Sharma, Richa Vashishtha, L S Chauhan, V Sreenivas, Divya Seth
BACKGROUND: There are currently two tests for diagnosing latent tuberculosis infection (LTBI); TST and IGRA. However, it is still unclear that which one of these tests performs better in high TB-burden settings. METHODS: 1511 household contacts of pulmonary TB patients were enrolled to compare the performance of TST and IGRA for LTBI. At baseline all participant underwent testing for IGRA [QuantiFERON-TB® Gold In-tube (QFT-GIT) assay] and TST [2 tuberculin unit (TU), purified protein derivative (PPD), RT23, Staten Serum Institute (SSI), Copenhagen, Denmark]...
2017: PloS One
Andrzej Zielezinski, Michal Dziubek, Jan Sliski, Wojciech M Karlowski
: ORCAN (ORtholog sCANner) is a web-based meta-server for one-click evolutionary and functional annotation of protein sequences. The server combines information from the most popular orthology-prediction resources, including 4 tools and 4 online databases. Functional annotation utilizes 5 additional comparisons between the query and identified homologs, including: sequence similarity, protein domain architectures, functional motifs, Gene Ontology term assignments, and a list of associated articles...
January 5, 2017: Bioinformatics
Sheng Wang, Siqi Sun, Zhen Li, Renyu Zhang, Jinbo Xu
MOTIVATION: Protein contacts contain key information for the understanding of protein structure and function and thus, contact prediction from sequence is an important problem. Recently exciting progress has been made on this problem, but the predicted contacts for proteins without many sequence homologs is still of low quality and not very useful for de novo structure prediction. METHOD: This paper presents a new deep learning method that predicts contacts by integrating both evolutionary coupling (EC) and sequence conservation information through an ultra-deep neural network formed by two deep residual neural networks...
January 5, 2017: PLoS Computational Biology
Jeremy Adams, Michael J Mansfield, Daniel J Richard, Andrew C Doxey
MOTIVATION: Spatially clustered mutations within specific regions of protein structure are thought to result from strong positive selection for altered protein functions and are a common feature of oncoproteins in cancer. Although previous studies have used spatial substitution clustering to identify positive selection between pairs of proteins, the ability of this approach to identify functional shifts in protein phylogenies has not been explored. RESULTS: We implemented a previous measure of spatial substitution clustering (the P3D statistic) and extended it to detect spatially clustered substitutions at specific branches of phylogenetic trees...
January 3, 2017: Bioinformatics
Jordane Preto
Almost five decades ago, H. Fröhlich [H. Fröhlich, "Long-range coherence and energy storage in biological systems," Int. J. Quantum Chem. 2(5), 641-649 (1968)] reported, on a theoretical basis, that the excitation of quantum modes of vibration in contact with a thermal reservoir may lead to steady states, where under high enough rate of energy supply, only specific low-frequency modes of vibration are strongly excited. This nonlinear phenomenon was predicted to occur in biomolecular systems, which are known to exhibit complex vibrational spectral properties, especially in the terahertz frequency domain...
December 2016: Chaos
Jiaqi Xia, Zhenling Peng, Dawei Qi, Hongbo Mu, Jianyi Yang
MOTIVATION: Protein fold classification is a critical step in protein structure prediction. There are two possible ways to classify protein folds. One is through template-based fold assignment and the other is ab-initio prediction using machine learning algorithms. Combination of both solutions to improve the prediction accuracy was never explored before. RESULTS: We developed two algorithms, HH-fold and SVM-fold for protein fold classification. HH-fold is a template-based fold assignment algorithm using the HHsearch program...
December 30, 2016: Bioinformatics
Renzhi Cao, Badri Adhikari, Debswapna Bhattacharya, Miao Sun, Jie Hou, Jianlin Cheng
MOTIVATION: Protein model quality assessment (QA) plays a very important role in protein structure prediction. It can be divided into two groups of methods: single model and consensus QA method. The consensus QA methods may fail when there is a large portion of low quality models in the model pool. RESULTS: In this paper, we develop a novel single-model quality assessment method QAcon utilizing structural features, physicochemical properties, and residue contact predictions...
December 28, 2016: Bioinformatics
Marcel Ooms, Michael Letko, Viviana Simon
: Human APOBEC3H (A3H) is a cytidine deaminase that inhibits HIV-1 replication. To evade this restriction, the HIV-1 Vif protein binds A3H and mediates its proteasomal degradation. To date, little information on the Vif-A3H interface is available. To decipher how both proteins interact we first mapped the Vif-binding site on A3H by functionally testing a large set of A3H mutants in single cycle infectivity and replication assays. Our data show that the two A3H α-helixes α3 and α4 represent the Vif-binding site of A3H...
December 28, 2016: Journal of Virology
Gui-Min Qin, Rui-Yi Li, Xing-Ming Zhao
MOTIVATION: Identifying the kinase-substrate relationships is vital to understanding the phosphorylation events and various biological processes, especially signal transductions. Although large amount of phosphorylation sites have been detected, unfortunately, it is rarely known which kinases activate those sites. Despite distinct computational approaches have been proposed to predict the kinase-substrate interactions, the prediction accuracy still needs to be improved. RESULTS: In this paper, we propose a novel probabilistic model named as PhosD to predict kinase-substrate relationships based on protein domains with the assumption that kinase-substrate interactions are accomplished with kinase-domain interactions...
December 28, 2016: Bioinformatics
Li-Na Wang, Shao-Ping Shi, Hao-Dong Xu, Ping-Ping Wen, Jian-Ding Qiu
MOTIVATION: Protein malonylation is a novel post-translational modification (PTM) which orchestrates a variety of biological processes. Annotation of malonylation in proteomics is the first-crucial step to decipher its physiological roles which are implicated in the pathological processes. Comparing with the expensive and laborious experimental research, computational prediction can provide an accurate and effective approach to the identification of many types of PTMs sites. However, there is still no online predictor for lysine malonylation...
December 23, 2016: Bioinformatics
L A Uroshlev, I V Kulakovskiy, N G Esipova, V G Tumanyan, S V Rahmanov, V J Makeev
: Structures of many metal-binding proteins are often obtained without structural cations, in their apoprotein forms. Missing cation coordinates are usually updated from structural templates constructed from many holoprotein structures. Such templates usually do not include structural water, the important contributor to the ion binding energy. Structural templates are also inconvenient for taking into account structural modifications around the binding site at apo-/holo- transitions. An approach based upon statistical potentials readily takes into account structural modifications associated with binding as well as contribution of structural water molecules...
December 26, 2016: Journal of Biomolecular Structure & Dynamics
Shibiao Wan, Man-Wai Mak, Sun-Yuan Kung
: Although many web-servers for predicting protein subcellular localization have been developed, they often have the following drawbacks: (i) lack of interpretability or interpreting results with heterogenous information which may confuse users; (ii) ignoring multi-location proteins and (iii) only focusing on specific organism. To tackle these problems, we present an interpretable and efficient web-server, namely FUEL-mLoc, using F: eature- U: nified prediction and E: xplanation of multi- L: ocalization of cellular proteins in multiple organisms...
December 23, 2016: Bioinformatics
Julia Koehler Leman, Benjamin K Mueller, Jeffrey J Gray
MOTIVATION: A range of membrane protein modeling tools has been developed in the past 5-10 years, yet few of these tools are integrated and make use of existing functionality for soluble proteins. To extend existing methods in the Rosetta biomolecular modeling suite for membrane proteins, we recently implemented RosettaMP, a general framework for membrane protein modeling. While RosettaMP facilitates implementation of new methods, addressing real-world biological problems also requires a set of accessory tools that are used to carry out standard modeling tasks...
December 22, 2016: Bioinformatics
Jack Hanson, Yuedong Yang, Kuldip Paliwal, Yaoqi Zhou
MOTIVATION: Capturing long-range interactions between structural but not sequence neighbors of proteins is a long-standing challenging problem in bioinformatics. Recently, long short-term memory (LSTM) networks have significantly improved the accuracy of speech and image classification problems by remembering useful past information in long sequential events. Here, we have implemented deep bidirectional LSTM recurrent neural networks in the problem of protein intrinsic disorder prediction...
December 22, 2016: Bioinformatics
Io Nam Wong, Jon R Sayers, Cyril M Sanders
Helicases catalyze the unwinding of double-stranded nucleic acids where structure and phosphate backbone contacts, rather than nucleobase sequence, usually determines substrate specificity. We have expressed and purified a putative helicase encoded by the D10 gene of bacteriophage T5. Here we report that this hitherto uncharacterized protein possesses branch migration and DNA unwinding activity. The initiation of substrate unwinding showed some sequence dependency, while DNA binding and DNA-dependent ATPase activity did not...
December 23, 2016: Scientific Reports
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