Literature DB >> 29101847

Inter-residue, inter-protein and inter-family coevolution: bridging the scales.

Hendrik Szurmant1, Martin Weigt2.   

Abstract

Interacting proteins coevolve at multiple but interconnected scales, from the residue-residue over the protein-protein up to the family-family level. The recent accumulation of enormous amounts of sequence data allows for the development of novel, data-driven computational approaches. Notably, these approaches can bridge scales within a single statistical framework. Although being currently applied mostly to isolated problems on single scales, their immense potential for an evolutionary informed, structural systems biology is steadily emerging.
Copyright © 2017 Elsevier Ltd. All rights reserved.

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Year:  2017        PMID: 29101847      PMCID: PMC5940578          DOI: 10.1016/j.sbi.2017.10.014

Source DB:  PubMed          Journal:  Curr Opin Struct Biol        ISSN: 0959-440X            Impact factor:   6.809


  47 in total

1.  Assigning protein functions by comparative genome analysis: protein phylogenetic profiles.

Authors:  M Pellegrini; E M Marcotte; M J Thompson; D Eisenberg; T O Yeates
Journal:  Proc Natl Acad Sci U S A       Date:  1999-04-13       Impact factor: 11.205

2.  Direct-coupling analysis of residue coevolution captures native contacts across many protein families.

Authors:  Faruck Morcos; Andrea Pagnani; Bryan Lunt; Arianna Bertolino; Debora S Marks; Chris Sander; Riccardo Zecchina; José N Onuchic; Terence Hwa; Martin Weigt
Journal:  Proc Natl Acad Sci U S A       Date:  2011-11-21       Impact factor: 11.205

3.  Features of protein-protein interactions in two-component signaling deduced from genomic libraries.

Authors:  Robert A White; Hendrik Szurmant; James A Hoch; Terence Hwa
Journal:  Methods Enzymol       Date:  2007       Impact factor: 1.600

4.  Origins of coevolution between residues distant in protein 3D structures.

Authors:  Ivan Anishchenko; Sergey Ovchinnikov; Hetunandan Kamisetty; David Baker
Journal:  Proc Natl Acad Sci U S A       Date:  2017-08-07       Impact factor: 11.205

5.  Protein-protein interactions essentials: key concepts to building and analyzing interactome networks.

Authors:  Javier De Las Rivas; Celia Fontanillo
Journal:  PLoS Comput Biol       Date:  2010-06-24       Impact factor: 4.475

6.  Dissecting the specificity of protein-protein interaction in bacterial two-component signaling: orphans and crosstalks.

Authors:  Andrea Procaccini; Bryan Lunt; Hendrik Szurmant; Terence Hwa; Martin Weigt
Journal:  PLoS One       Date:  2011-05-09       Impact factor: 3.240

7.  Robust and accurate prediction of residue-residue interactions across protein interfaces using evolutionary information.

Authors:  Sergey Ovchinnikov; Hetunandan Kamisetty; David Baker
Journal:  Elife       Date:  2014-05-01       Impact factor: 8.140

8.  Modeling Hsp70/Hsp40 interaction by multi-scale molecular simulations and coevolutionary sequence analysis.

Authors:  Duccio Malinverni; Alfredo Jost Lopez; Paolo De Los Rios; Gerhard Hummer; Alessandro Barducci
Journal:  Elife       Date:  2017-05-12       Impact factor: 8.140

9.  Dimeric interactions and complex formation using direct coevolutionary couplings.

Authors:  Ricardo N dos Santos; Faruck Morcos; Biman Jana; Adriano D Andricopulo; José N Onuchic
Journal:  Sci Rep       Date:  2015-09-04       Impact factor: 4.379

10.  iPfam: a database of protein family and domain interactions found in the Protein Data Bank.

Authors:  Robert D Finn; Benjamin L Miller; Jody Clements; Alex Bateman
Journal:  Nucleic Acids Res       Date:  2013-12-01       Impact factor: 16.971

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  17 in total

1.  Evolutionary couplings of amino acid residues reveal structure and function of bacterial signaling proteins.

Authors:  Hendrik Szurmant
Journal:  Mol Microbiol       Date:  2019-07-03       Impact factor: 3.501

Review 2.  Co-evolution in the Jungle: From Leafcutter Ant Colonies to Chromosomal Ends.

Authors:  Ľubomír Tomáška; Jozef Nosek
Journal:  J Mol Evol       Date:  2020-03-10       Impact factor: 2.395

3.  Probing pathways of adaptation with continuous evolution.

Authors:  Ziwei Zhong; Chang C Liu
Journal:  Curr Opin Syst Biol       Date:  2019-02-13

4.  Machine-learning of complex evolutionary signals improves classification of SNVs.

Authors:  Sapir Labes; Doron Stupp; Naama Wagner; Idit Bloch; Michal Lotem; Ephrat L Lahad; Paz Polak; Tal Pupko; Yuval Tabach
Journal:  NAR Genom Bioinform       Date:  2022-04-07

5.  AF2Complex predicts direct physical interactions in multimeric proteins with deep learning.

Authors:  Mu Gao; Davi Nakajima An; Jerry M Parks; Jeffrey Skolnick
Journal:  Nat Commun       Date:  2022-04-01       Impact factor: 14.919

6.  Deciphering polymorphism in 61,157 Escherichia coli genomes via epistatic sequence landscapes.

Authors:  Lucile Vigué; Giancarlo Croce; Marie Petitjean; Etienne Ruppé; Olivier Tenaillon; Martin Weigt
Journal:  Nat Commun       Date:  2022-07-12       Impact factor: 17.694

7.  Role of Position K+4 in the Phosphorylation and Dephosphorylation Reaction Kinetics of the CheY Response Regulator.

Authors:  Clay A Foster; Ruth E Silversmith; Robert M Immormino; Luke R Vass; Emily N Kennedy; Yael Pazy; Edward J Collins; Robert B Bourret
Journal:  Biochemistry       Date:  2021-06-24       Impact factor: 3.321

8.  Size and structure of the sequence space of repeat proteins.

Authors:  Jacopo Marchi; Ezequiel A Galpern; Rocio Espada; Diego U Ferreiro; Aleksandra M Walczak; Thierry Mora
Journal:  PLoS Comput Biol       Date:  2019-08-15       Impact factor: 4.475

9.  Modeling of protein complexes in CASP14 with emphasis on the interaction interface prediction.

Authors:  Justas Dapkūnas; Kliment Olechnovič; Česlovas Venclovas
Journal:  Proteins       Date:  2021-07-05

Review 10.  Combined approaches from physics, statistics, and computer science for ab initio protein structure prediction: ex unitate vires (unity is strength)?

Authors:  Marc Delarue; Patrice Koehl
Journal:  F1000Res       Date:  2018-07-24
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