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Protein evolution, protein co-evolution, protein structure prediction, protein structures

Baoji He, S M Mortuza, Yanting Wang, Hong-Bin Shen, Yang Zhang
Motivation: Recent CASP experiments have witnessed exciting progress on folding large-size non-humongous proteins with the assistance of co-evolution based contact predictions. The success is however anecdotal due to the requirement of the contact prediction methods for the high volume of sequence homologs that are not available to most of the non-humongous protein targets. Development of efficient methods that can generate balanced and reliable contact maps for different type of protein targets is essential to enhance the success rate of the ab initio protein structure prediction...
March 28, 2017: Bioinformatics
Paul Sunnucks, Hernán E Morales, Annika M Lamb, Alexandra Pavlova, Chris Greening
In animals, interactions among gene products of mitochondrial and nuclear genomes (mitonuclear interactions) are of profound fitness, evolutionary, and ecological significance. Most fundamentally, the oxidative phosphorylation (OXPHOS) complexes responsible for cellular bioenergetics are formed by the direct interactions of 13 mitochondrial-encoded and ∼80 nuclear-encoded protein subunits in most animals. It is expected that organisms will develop genomic architecture that facilitates co-adaptation of these mitonuclear interactions and enhances biochemical efficiency of OXPHOS complexes...
2017: Frontiers in Genetics
Saulo Henrique Pires de Oliveira, Jiye Shi, Charlotte M Deane
No abstract text is available yet for this article.
February 1, 2017: Bioinformatics
Sebastian John, Rashmi Mishra
Background: Galectins, a family of non-classically secreted, β-galactoside binding proteins is involved in several brain disorders; however, no systematic knowledge on the normal neuroanatomical distribution and functions of galectins exits. Hence, the major purpose of this study was to understand spatial distribution and predict functions of galectins in brain and also compare the degree of conservation vs. divergence between mouse and human species. The latter objective was required to determine the relevance and appropriateness of studying galectins in mouse brain which may ultimately enable us to extrapolate the findings to human brain physiology and pathologies...
2016: Frontiers in Molecular Neuroscience
Dominik Sammer, Katrin Krause, Matthias Gube, Katharina Wagner, Erika Kothe
Hydrophobins-secreted small cysteine-rich, amphipathic proteins-foster interactions of fungal hyphae with hydrophobic surfaces, and are involved in the formation of aerial hyphae. Phylogenetic analyses of Tricholoma vaccinum hydrophobins showed a grouping with hydrophobins of other ectomycorrhizal fungi, which might be a result of co-evolution. Further analyses indicate angiosperms as likely host trees for the last common ancestor of the genus Tricholoma. The nine hydrophobin genes in the T. vaccinum genome were investigated to infer their individual roles in different stages of the life cycle, host interaction, asexual and sexual development, and with respect to different stresses...
2016: PloS One
Felicity Alcock, Phillip J Stansfeld, Hajra Basit, Johann Habersetzer, Matthew Ab Baker, Tracy Palmer, Mark I Wallace, Ben C Berks
The twin-arginine protein translocation system (Tat) transports folded proteins across the bacterial cytoplasmic membrane and the thylakoid membranes of plant chloroplasts. The Tat transporter is assembled from multiple copies of the membrane proteins TatA, TatB, and TatC. We combine sequence co-evolution analysis, molecular simulations, and experimentation to define the interactions between the Tat proteins of Escherichia coli at molecular-level resolution. In the TatBC receptor complex the transmembrane helix of each TatB molecule is sandwiched between two TatC molecules, with one of the inter-subunit interfaces incorporating a functionally important cluster of interacting polar residues...
December 3, 2016: ELife
Ronald M Levy, Allan Haldane, William F Flynn
Potts Hamiltonian models of protein sequence co-variation are statistical models constructed from the pair correlations observed in a multiple sequence alignment (MSA) of a protein family. These models are powerful because they capture higher order correlations induced by mutations evolving under constraints and help quantify the connections between protein sequence, structure, and function maintained through evolution. We review recent work with Potts models to predict protein structure and sequence-dependent conformational free energy landscapes, to survey protein fitness landscapes and to explore the effects of epistasis on fitness...
November 18, 2016: Current Opinion in Structural Biology
Pablo Mier, Gregorio Alanis-Lobato, Miguel A Andrade-Navarro
Protein-protein interactions are sometimes mediated by coiled coil structures. The evolutionary conservation of interacting orthologs in different species, along with the presence or absence of coiled coils in them, may help in the prediction of interacting pairs. Here, we illustrate how the presence of coiled coils in a protein can be exploited as a potential indicator for its interaction with another protein with coiled coils. The prediction capability of our strategy improves when restricting our dataset to highly reliable, known protein-protein interactions...
January 7, 2017: Journal of Theoretical Biology
Jinchao Yu, Jessica Andreani, Françoise Ochsenbein, Raphaël Guerois
Computational protein-protein docking is of great importance for understanding protein interactions at the structural level. Critical assessment of prediction of interactions (CAPRI) experiments provide the protein docking community with a unique opportunity to blindly test methods based on real-life cases and help accelerate methodology development. For CAPRI Rounds 28-35, we used an automatic docking pipeline integrating the coarse-grained co-evolution-based potential InterEvScore. This score was developed to exploit the information contained in the multiple sequence alignments of binding partners and selectively recognize co-evolved interfaces...
October 4, 2016: Proteins
Saulo Henrique Pires de Oliveira, Jiye Shi, Charlotte M Deane
MOTIVATION: Co-evolution methods have been used as contact predictors to identify pairs of residues that share spatial proximity. Such contact predictors have been compared in terms of the precision of their predictions, but there is no study that compares their usefulness to model generation. RESULTS: We compared eight different co-evolution methods for a set of ~3,500 proteins and found that metaPSICOV stage 2 produces, on average, the most precise predictions...
September 27, 2016: Bioinformatics
Jennifer A Dill, Alvin C Camus, John H Leary, Francesca Di Giallonardo, Edward C Holmes, Terry Fei Fan Ng
UNLABELLED: Hepadnaviruses (hepatitis B viruses [HBVs]) are the only animal viruses that replicate their DNA by reverse transcription of an RNA intermediate. Until recently, the known host range of hepadnaviruses was limited to mammals and birds. We obtained and analyzed the first amphibian HBV genome, as well as several prototype fish HBVs, which allow the first comprehensive comparative genomic analysis of hepadnaviruses from four classes of vertebrates. Bluegill hepadnavirus (BGHBV) was characterized from in-house viral metagenomic sequencing...
September 1, 2016: Journal of Virology
Lingli Zhou, Pengfei Li, Min Yang, Yepin Yu, Youhua Huang, Jingguang Wei, Shina Wei, Qiwei Qin
Nervous necrosis virus (NNV) infected larvae and juveniles of more than 50 fish species, resulting in mortality rates of greater than 95%. However, there is no efficient method to control NNV infections. Aptamers generated by selective evolution of ligands by exponential enrichment (SELEX) are short, single-stranded nucleic acid oligomers. They display a high degree of affinity and specificity for many targets, such as viruses and viral proteins. In this study, three novel DNA aptamers (A5, A10, and B11) that specifically target the coat protein (CP) of grouper nervous necrosis virus (GNNV) were selected using SELEX...
May 2016: Antiviral Research
Peter Hönigschmid, Dmitrij Frishman
Accurate prediction of intra-molecular interactions from amino acid sequence is an important pre-requisite for obtaining high-quality protein models. Over the recent years, remarkable progress in this area has been achieved through the application of novel co-variation algorithms, which eliminate transitive evolutionary connections between residues. In this work we present a new contact prediction method for α-helical transmembrane proteins, MemConP, in which evolutionary couplings are combined with a machine learning approach...
April 2016: Journal of Structural Biology
A Giaretta, B Di Camillo, L Barzon, G M Toffolo
In high risk forms, human papillomaviruses (HPV) can either induce or promote cancerous lesions, especially cervical cancer which is considered the second most common cancer in the women worldwide. HPV life cycle is tightly linked to the infected cell differentiation program and its evolution is strictly joined to the switch between the early and the late viral polycistronic promoters.The aim of this study is to develop a novel mathematical model which collects and structures the available biologic knowledge on the early promoter regulation for HPV in episomal form...
August 2015: Conference Proceedings: Annual International Conference of the IEEE Engineering in Medicine and Biology Society
Sergey Ovchinnikov, David E Kim, Ray Yu-Ruei Wang, Yuan Liu, Frank DiMaio, David Baker
We describe CASP11 de novo blind structure predictions made using the Rosetta structure prediction methodology with both automatic and human assisted protocols. Model accuracy was generally improved using coevolution derived residue-residue contact information as restraints during Rosetta conformational sampling and refinement, particularly when the number of sequences in the family was more than three times the length of the protein. The highlight was the human assisted prediction of T0806, a large and topologically complex target with no homologs of known structure, which had unprecedented accuracy-<3...
September 2016: Proteins
Sergey Ovchinnikov, Lisa Kinch, Hahnbeom Park, Yuxing Liao, Jimin Pei, David E Kim, Hetunandan Kamisetty, Nick V Grishin, David Baker
The prediction of the structures of proteins without detectable sequence similarity to any protein of known structure remains an outstanding scientific challenge. Here we report significant progress in this area. We first describe de novo blind structure predictions of unprecendented accuracy we made for two proteins in large families in the recent CASP11 blind test of protein structure prediction methods by incorporating residue-residue co-evolution information in the Rosetta structure prediction program. We then describe the use of this method to generate structure models for 58 of the 121 large protein families in prokaryotes for which three-dimensional structures are not available...
2015: ELife
Fei Guo, Yijie Ding, Zhao Li, Jijun Tang
Protein-protein interactions play key roles in a multitude of biological processes, such as de novo drug design, immune response, and enzymatic activity. It is of great interest to understand how proteins in a complex interact with each other. Here, we present a novel method for identifying protein-protein interactions, based on typical co-evolutionary information. Correlated mutation analysis can be used to predict interface residues. In this paper, we propose a non-redundant database to detect correlated mutation at the interface...
September 28, 2015: Journal of Chemical Information and Modeling
Jianzhu Ma, Sheng Wang, Zhiyong Wang, Jinbo Xu
MOTIVATION: Protein contact prediction is important for protein structure and functional study. Both evolutionary coupling (EC) analysis and supervised machine learning methods have been developed, making use of different information sources. However, contact prediction is still challenging especially for proteins without a large number of sequence homologs. RESULTS: This article presents a group graphical lasso (GGL) method for contact prediction that integrates joint multi-family EC analysis and supervised learning to improve accuracy on proteins without many sequence homologs...
November 1, 2015: Bioinformatics
David Kerk, Dylan Silver, R Glen Uhrig, Greg B G Moorhead
Mg+2/Mn+2-dependent type 2C protein phosphatases (PP2Cs) are ubiquitous in eukaryotes, mediating diverse cellular signaling processes through metal ion catalyzed dephosphorylation of target proteins. We have identified a distinct PP2C sequence class ("PP2C7s") which is nearly universally distributed in Eukaryotes, and therefore apparently ancient. PP2C7s are by far most prominent and diverse in plants and green algae. Combining phylogenetic analysis, subcellular localization predictions, and a distillation of publically available gene expression data, we have traced the evolutionary trajectory of this gene family in photosynthetic eukaryotes, demonstrating two major sequence assemblages featuring a succession of increasingly derived sub-clades...
2015: PloS One
Libia Catalina Salinas Castellanos, Jacques Chomilier, Jorge Hernández-Torres
BACKGROUND: The co-chaperone Hop [heat shock protein (HSP) organizing protein] has been shown to act as an adaptor for protein folding and maturation, in concert with Hsp70 and Hsp90. The hop gene is of eukaryotic origin. Likewise, the chloroplast elongation factor G (cEF-G) catalyzes the translocation step in chloroplast protein synthesis. The chl-fus gene, which encodes the cEF-G protein, is of plastid origin. Both proteins, Hop and cEF-G, derived from domain duplications. It was demonstrated that the nuclear chl-fus gene locates in opposite orientation to a hop gene in Glycine max...
2015: BMC Genomics
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