Coevolutionary signals across protein lineages help capture multiple protein conformations

By Faruck Morcos, Biman Jana, Terence Hwa, José N. Onuchic. 2013

174 citations recorded by the source corpus.

Subfields: Materials Chemistry, Molecular Biology

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Citations in the corpus

Predicting multiple conformations via sequence clustering and AlphaFold2 (2023, positive): “As previous studies have identified evolutionary couplings corresponding to multiple states of domain-based conformational changes 15,16,20 , we speculate that clustering-based MSA preprocessing methods will offer improvements over existing methods 14 and, importantly, insights into the evolution…”
Robust and accurate prediction of residue–residue interactions across protein interfaces using evolutionary information (2014, background): “…already a structure of a family member from which comparative models could be built, limiting the utility of the predicted contacts in structure prediction (Though predicted contacts can be useful in modeling allosteric changes in protein structures [ Hopf et al., 2012 ; Morcos et al., 2013 ]).”
Evolutionary Conserved Positions Define Protein Conformational Diversity (2016, background): “Previous works found that sequence evolutionary conservation results from multiple factors such as structural, dynamics, and/or functional features [62,63,64,65].”
Structured states of disordered proteins from genomic sequences (2016, unknown): “…on recent successful attempts to predict 3D structures from natural sequence variation (Hopf et al., 2012; Hopf et al., 2014; Marks et al., 2011; Morcos et al., 2013; Ovchinnikov et al., 2014; Weinreb et al., 2016) and here we develop statistical methods crucial for the applicability to…”
Coevolutionary Analysis of Protein Subfamilies by Sequence Reweighting (2019, background): “Beyond the de-novo prediction of novel folds [5,7,8], coevolution-based analysis has also allowed the structural characterization of homo [2,9–11] and hetero-oligomeric [4,12,13] complexes and the determination of conformational ensembles [10,14,15].”
Connecting the Sequence-Space of Bacterial Signaling Proteins to Phenotypes Using Coevolutionary Landscapes (2016, background): “…Sutto et al. 2015), including repeat proteins (Espada et al. 2015), as well as identify additional functionally relevant conformational states (Morcos et al. 2013; Malinverni et al. 2015; Sutto et al. 2015) and multi-meric states (Schug et al. 2009; Weigt et al. 2009; Morcos et al. 2011; dos…”
Prediction of multiple conformational states by combining sequence clustering with AlphaFold2 (2022, methodology): “Additionally, older coevolutionary-based methods 19-22 were able to extract multiple states of proteins with conformational changes, including ion channels 19 , ligand-induced conformational changes 23 , and multimerization-induced conformational changes 24 .”
Large-Scale Conformational Transitions and Dimerization Are Encoded in the Amino-Acid Sequences of Hsp70 Chaperones (2015, unknown): “However since DCA analysis is expected to capture contacts present in all the functionally relevant conformers [48,59], the most appropriate strategy is to compare DCA predictions with a contact map corresponding to the union of those relative to single-states.”
Coevolution‐derived native and non‐native contacts determine the emergence of a novel fold in a universally conserved family of transcription factors (2022, background): “Given that spatially proximate residues in the native state of a given protein family tend to coevolve,(21) these methods have been widely successful in inferring the structural proximity of coevolving residue pairs that are fundamental for folding, function, and dynamics from sequence information a”
Large-scale identification of coevolution signals across homo-oligomeric protein interfaces by direct coupling analysis (2017, background): “Such information has proven useful in the prediction of tertiary protein structures (10-13), conformational transitions (14-16), and similarly RNA structures (17, 18).”
The challenge of modeling protein assemblies: the CASP12‐CAPRI experiment (2018, result): “Progress in this endeavor will likely come from charting conformational changes in families or related proteins(50) and exploiting information on co-evolution.(51,52) The latter approach is already making important headways in predicting the structures of protein monomers, as witnessed by results ob”