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

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https://www.readbyqxmd.com/read/28683816/uncovering-missing-pieces-duplication-and-deletion-history-of-arrestins-in-deuterostomes
#1
Henrike Indrischek, Sonja J Prohaska, Vsevolod V Gurevich, Eugenia V Gurevich, Peter F Stadler
BACKGROUND: The cytosolic arrestin proteins mediate desensitization of activated G protein-coupled receptors (GPCRs) via competition with G proteins for the active phosphorylated receptors. Arrestins in active, including receptor-bound, conformation are also transducers of signaling. Therefore, this protein family is an attractive therapeutic target. The signaling outcome is believed to be a result of structural and sequence-dependent interactions of arrestins with GPCRs and other protein partners...
July 6, 2017: BMC Evolutionary Biology
https://www.readbyqxmd.com/read/28683440/genetics-of-cerebellar-and-neocortical-expansion-in-anthropoid-primates-a-comparative-approach
#2
Peter W Harrison, Stephen H Montgomery
What adaptive changes in brain structure and function underpin the evolution of increased cognitive performance in humans and our close relatives? Identifying the genetic basis of brain evolution has become a major tool in answering this question. Numerous cases of positive selection, altered gene expression or gene duplication have been identified that may contribute to the evolution of the neocortex, which is widely assumed to play a predominant role in cognitive evolution. However, the components of the neocortex co-evolve with other functionally interdependent regions of the brain, most notably in the cerebellum...
July 6, 2017: Brain, Behavior and Evolution
https://www.readbyqxmd.com/read/28578020/pathogenicity-analysis-of-novel-variations-in-chinese-han-patients-with-polycystic-kidney-disease
#3
Zishui Fang, Shiyan Xu, Yonghua Wang, Liwei Sun, Yi Feng, Yibin Guo, Hongyi Li, Weiying Jiang
OBJECTIVE: Locus and allellic heterogeneity in polycystic kidney disease (PKD) is a great challenge in precision diagnosis. We aim to establish comprehensive methods to distinguish the pathogenic mutations from the variations in PKD1, PKD2 and PKHD1 genes in a limited time and lay the foundation for precisely prenatal diagnosis, preimplantation genetic diagnosis and presymptom diagnosis of PKD. METHODS: Nested PCR combined with direct DNA sequencing were used to screen variations in PKD1, PKD2 and PKHD1 genes...
May 31, 2017: Gene
https://www.readbyqxmd.com/read/28542325/membrane-protein-contact-and-structure-prediction-using-co-evolution-in-conjunction-with-machine-learning
#4
Pedro L Teixeira, Jeff L Mendenhall, Sten Heinze, Brian Weiner, Marcin J Skwark, Jens Meiler
De novo membrane protein structure prediction is limited to small proteins due to the conformational search space quickly expanding with length. Long-range contacts (24+ amino acid separation)-residue positions distant in sequence, but in close proximity in the structure, are arguably the most effective way to restrict this conformational space. Inverse methods for co-evolutionary analysis predict a global set of position-pair couplings that best explain the observed amino acid co-occurrences, thus distinguishing between evolutionarily explained co-variances and these arising from spurious transitive effects...
2017: PloS One
https://www.readbyqxmd.com/read/28369334/nebcon-protein-contact-map-prediction-using-neural-network-training-coupled-with-na%C3%A3-ve-bayes-classifiers
#5
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
https://www.readbyqxmd.com/read/28316610/integrative-approaches-for-studying-mitochondrial-and-nuclear-genome-co-evolution-in-oxidative-phosphorylation
#6
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
https://www.readbyqxmd.com/read/28171606/comparing-co-evolution-methods-and-their-application-to-template-free-protein-structure-prediction
#7
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 ∼3500 proteins and found that metaPSICOV stage 2 produces, on average, the most precise predictions...
February 1, 2017: Bioinformatics
https://www.readbyqxmd.com/read/28018170/mrna-transcriptomics-of-galectins-unveils-heterogeneous-organization-in-mouse-and-human-brain
#8
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
https://www.readbyqxmd.com/read/27936063/hydrophobins-in-the-life-cycle-of-the-ectomycorrhizal-basidiomycete-tricholoma-vaccinum
#9
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
https://www.readbyqxmd.com/read/27914200/assembling-the-tat-protein-translocase
#10
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
https://www.readbyqxmd.com/read/27870991/potts-hamiltonian-models-of-protein-co-variation-free-energy-landscapes-and-evolutionary-fitness
#11
REVIEW
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...
April 2017: Current Opinion in Structural Biology
https://www.readbyqxmd.com/read/27832945/protein-protein-interactions-can-be-predicted-using-coiled-coil-co-evolution-patterns
#12
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
https://www.readbyqxmd.com/read/27701780/lessons-from-co-evolution-in-the-docking-of-proteins-and-peptides-for-capri-rounds-28-35
#13
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...
March 2017: Proteins
https://www.readbyqxmd.com/read/27682254/comparing-co-evolution-methods-and-their-application-to-template-free-protein-structure-prediction
#14
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
https://www.readbyqxmd.com/read/27334580/distinct-viral-lineages-from-fish-and-amphibians-reveal-the-complex-evolutionary-history-of-hepadnaviruses
#15
COMPARATIVE STUDY
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
https://www.readbyqxmd.com/read/26892075/generation-and-characterization-of-novel-dna-aptamers-against-coat-protein-of-grouper-nervous-necrosis-virus-gnnv-with-antiviral-activities-and-delivery-potential-in-grouper-cells
#16
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
https://www.readbyqxmd.com/read/26851352/accurate-prediction-of-helix-interactions-and-residue-contacts-in-membrane-proteins
#17
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
https://www.readbyqxmd.com/read/26737780/modeling-hpv-early-promoter-regulation
#18
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
https://www.readbyqxmd.com/read/26677056/improved-de-novo-structure-prediction-in-casp11-by-incorporating-coevolution-information-into-rosetta
#19
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
https://www.readbyqxmd.com/read/26335199/large-scale-determination-of-previously-unsolved-protein-structures-using-evolutionary-information
#20
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
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