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Selection of organisms for the co-evolution-based study of protein interactions

Dorota Herman, David Ochoa, David Juan, Daniel Lopez, Alfonso Valencia, Florencio Pazos
2011 BMC Bioinformatics  
The prediction and study of protein interactions and functional relationships based on similarity of phylogenetic trees, exemplified by the mirrortree and related methodologies, is being widely used.  ...  This relationship between type of interaction and optimal set of organism for detecting them makes sense in the light of the phylogenetic distribution of the organisms and the nature of the interactions  ...  This work was partially funded by projects BIO2009-11966 and BIO2010-22109 from the Spanish Ministry for Science and Innovation, and project KBBE-2007-3-2-08 from the 7FP of the EU.  ... 
doi:10.1186/1471-2105-12-363 pmid:21910884 pmcid:PMC3179974 fatcat:n33kxd6vnzbbrjrpntgpxlqlbe

Studying the co-evolution of protein families with the Mirrortree web server

David Ochoa, Florencio Pazos
2010 Computer applications in the biosciences : CABIOS  
The Mirrortree server allows to graphically and interactively study the co-evolution of two protein families, and investigate their possible interactions and functional relationships in a taxonomic context  ...  Adobe Flash Player is required at the client side to perform the interactive assessment of co-evolution.  ...  ACKNOWLEDGEMENTS We want to thank Octavio Diaz-Pines and the members of the CTI-CSIC for computer support.  ... 
doi:10.1093/bioinformatics/btq137 pmid:20363731 fatcat:gyh4jhjikjhfhea3f6ig3ra5oi

Practical aspects of protein co-evolution

David Ochoa, Florencio Pazos
2014 Frontiers in Cell and Developmental Biology  
At the molecular level, co-evolutionary linkages between protein families have been used as indicators of protein interactions and functional relationships from long ago.  ...  Co-evolution is a fundamental aspect of Evolutionary Theory.  ...  ACKNOWLEDGMENTS We thank Alfonso Valencia and David Juan (CNIO) and the members of the Computational System Biology Group (CNB-CSIC) for interesting discussions.  ... 
doi:10.3389/fcell.2014.00014 pmid:25364721 pmcid:PMC4207036 fatcat:dgsepmbscrga5ansj2gkp3v7dy

Protein co-evolution, co-adaptation and interactions

Florencio Pazos, Alfonso Valencia
2008 EMBO Journal  
protein interactions through the characteristics of co-evolution.  ...  The extrapolation of the concepts and methodologies developed for the study of species co-evolution at the molecular level has prompted the development of a variety of computational methods able to predict  ...  Acknowledgements We sincerely thank David Juan (CNIO, Madrid) for interesting discussions and earlier contributions to some of the topics reviewed here.  ... 
doi:10.1038/emboj.2008.189 pmid:18818697 pmcid:PMC2556093 fatcat:pcnqhpkkj5c4fc2g3a6d3eaiam

Co Evolution of Man and Microbial Pathogenic Genome

Ambreen Ayub, Yasra Sarwar, Waseem Akhtar shamshari
2015 Molecular Biology  
Co-evolution of human and microbial genome is of fundamental interest. It allows both the human and pathogens to adapt themselves in the changing environment.  ...  Purpose: The present study is focus on the currently evolved pathogens and availability of vaccines; that work against the pathogens to protect human population.  ...  The study of co-evolution at molecular level is the most recent trend basically depends upon the evolution of protein families and protein-protein interaction.  ... 
doi:10.4172/2168-9547.1000141 fatcat:ykxel67nk5cbpoelurqzdsths4

Co-evolution and co-adaptation in protein networks

David Juan, Florencio Pazos, Alfonso Valencia
2008 FEBS Letters  
The other states that the tree similarity may be an indirect consequence of the involvement of the two proteins in similar cellular process, which in turn would be reflected by similar evolutionary pressure  ...  Interacting or functionally related proteins have been repeatedly shown to have similar phylogenetic trees. Two main hypotheses have been proposed to explain this fact.  ...  For example, knowing what is behind the process would speed up the development and improvement of the co-evolution based methods for predicting interactions, since they would be designed in a more rational  ... 
doi:10.1016/j.febslet.2008.02.017 pmid:18282476 fatcat:tdpnqzx7endpnpxuteokl5bwme

The Biochemical Evolution of Protein Complexes

Todd M. Greco, Ileana M. Cristea
2016 TIBS -Trends in Biochemical Sciences. Regular ed  
Here, we discuss a recent study by Wan and colleagues, which highlights the significance of protein complexes by studying their conservation in organisms separated by up to a billion years of evolution  ...  Over the past decade, it became evident that proteins perform critical functions as components of specialized macromolecular complexes.  ...  Acknowledgments Many scientists have contributed to protein interaction studies, and we apologize for not being able to give credit because of citation limits.  ... 
doi:10.1016/j.tibs.2015.11.007 pmid:26682499 pmcid:PMC4706493 fatcat:ulslmucggfdwhgums3unbfgvae

Integrative Approaches for Studying Mitochondrial and Nuclear Genome Co-evolution in Oxidative Phosphorylation

Paul Sunnucks, Hernán E. Morales, Annika M. Lamb, Alexandra Pavlova, Chris Greening
2017 Frontiers in Genetics  
In this perspective, we present principles and approaches to understanding the co-evolution of these interactions, with a novel focus on how genomic architecture might facilitate it.  ...  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  ...  The comments of Dan Mishmar and Alan Brelsford helped improve the manuscript.  ... 
doi:10.3389/fgene.2017.00025 pmid:28316610 pmcid:PMC5334354 fatcat:q5i2qjyvmzhl7dqghvbh7f63fi

Slow Co-Evolution of the MAGO and Y14 Protein Families Is Required for the Maintenance of Their Obligate Heterodimerization Mode

Pichang Gong, Man Zhao, Chaoying He, Alistair P. McGregor
2014 PLoS ONE  
In turn, the obliged heterodimerization in an organism serves as a strong functional constraint for the co-evolution of the MAGO and Y14 families.  ...  Such a co-evolution allows maintaining the interaction between the proteins through large evolutionary time scales.  ...  S Ge and XQ Wang for their valuable comments on interpretation of phylogenetic analyses during preparation of the manuscript.  ... 
doi:10.1371/journal.pone.0084842 pmid:24416299 pmcid:PMC3885619 fatcat:fqfvfdxsgngtvaficwvr4k7waa

Protein evolution in yeast transcription factor subnetworks

Yong Wang, Eric A. Franzosa, Xiang-Sun Zhang, Yu Xia
2010 Nucleic Acids Research  
Most importantly, the correlations between evolutionary rate (K A /K S ) and degrees for TFs are significantly more positive than those for generic proteins within the same global protein-protein interaction  ...  This result holds for all four major types of TF hubs: interaction hubs, regulatory in-degree and outdegree hubs, as well as co-regulatory hubs that jointly regulate target genes with many TFs.  ...  RESULTS Significantly different evolutionary trends for TF hubs and generic protein hubs in the protein-protein interaction network We studied protein evolution among TFs in the genome-wide protein networks  ... 
doi:10.1093/nar/gkq353 pmid:20466810 pmcid:PMC2952844 fatcat:knslj6ffbbex3ibqlkpvo2hqna

Key transitions during the evolution of animal phototransduction: novelty, "tree-thinking," co-option, and co-duplication

D. C. Plachetzki, T. H. Oakley
2007 Integrative and Comparative Biology  
Second, we review two case studies in photoreceptor evolution-one suggesting a role for duplication plus divergence, the other exemplifying how co-option can shape evolutionary change.  ...  Synopsis Biologists are amazed by the intricacy and complexity of biological interactions between molecules, cells, organisms, and ecosystems.  ...  Acknowledgments We are grateful to Bernd Schierwater and Rob DeSalle for organizing the symposium ''Key transitions in animal evolution'' at the 2007 SICB meeting.  ... 
doi:10.1093/icb/icm050 pmid:21669757 fatcat:um2wuyxierdbjixgjbtcivm6cq

The Nature of Protein Domain Evolution: Shaping the Interaction Network

Christoph P. Bagowski, Wouter Bruins, Aartjan J.W. te Velthuis
2010 Current Genomics  
Additionally, these studies can be used for the design of new and optimized protein domains for therapy.  ...  The proteomes that make up the collection of proteins in contemporary organisms evolved through recombination and duplication of a limited set of domains.  ...  Evolutionary models for protein-protein interactions. The evolution of protein networks is tightly coupled to the addition or deletion of nodes.  ... 
doi:10.2174/138920210791616725 pmid:21286315 pmcid:PMC2945003 fatcat:s55tr4iidvap3o44nlnn72zcoa

Towards a Dynamic Interaction Network of Life to unify and expand the evolutionary theory

Eric Bapteste, Philippe Huneman
2018 BMC Biology  
The classic Darwinian theory and the Synthetic evolutionary theory and their linear models, while invaluable to study the origins and evolution of species, are not primarily designed to model the evolution  ...  Inclusive network-based analyses of dynamic systems could retrace interactions between (related or unrelated) components.  ...  Acknowledgements This manuscript is dedicated to the memory of Jean Gayon, a great historian and philosopher of biology, and a great friend. We thank Ford Doolittle, P. Lopez, G.  ... 
doi:10.1186/s12915-018-0531-6 pmid:29843714 pmcid:PMC5972403 fatcat:vcx3tz7jbbft3pwtc2e54kphvu

Plasmodium phylogenetic profile: an assessment of a predictive tool for protein-protein interactions

G Sferra, D Santoni, E Pizzi
2012 EMBnet journal  
One of the computational tools mostly used for this aim is the phylogenetic profiling, based on the co-conserved proteins identification by local alignments.  ...  Motivations Prediction of protein-protein interactions (PPIs) is a crucial goal for bioinformatics and the increasing availability of sequenced genomes support this challenge.  ...  One of the computational tools mostly used for this aim is the phylogenetic profiling, based on the co-conserved proteins identification by local alignments.  ... 
doi:10.14806/ej.18.a.427 fatcat:vubuqmmhanfmrhijn6j44iv4pu

Co-evolutionary Landscape at the Interface and Non-Interface Regions of Protein-Protein Interaction Complexes [article]

Ishita Mukherjee, Saikat Chakrabarti
2021 bioRxiv   pre-print
Proteins involved in interactions throughout the course of evolution tend to co-evolve and compensatory or coordinated changes may occur in interacting proteins to maintain or refine interactions between  ...  The physiological relevance of these predictions suggests that Co-Var can predict residues that could be crucial for preserving functional protein-protein interactions.  ...  Acknowledgments Authors would like to acknowledge the initial contribution of Abhijit Chakraborty in the project.  ... 
doi:10.1101/2021.01.09.426046 fatcat:7nqabx32fbanzcicybjdokyxlu
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