Education Template

Selected References

The below list is a useful starting point for investigating co-evolution further, and formed the basis of much of my own research into the subject.

[1] M.A. Stiffler, F.J. Poelwijk, K.P. Brock, R.R. Stein, A. Riesselman, J. Teyra, et al., Protein Structure from Experimental Evolution, Cell Syst. (2019). doi:10.1016/j.cels.2019.11.008.

[2] S. de Oliveira, C. Deane, Co-evolution techniques are reshaping the way we do structural bioinformatics., F1000Research. 6 (2017) 1224. doi:10.12688/f1000research.11543.1.

[3] S. Mallik, S. Kundu, Co-evolutionary constraints of globular proteins correlate with their folding rates, FEBS Lett. 589 (2015) 2179–2185. doi:10.1016/j.febslet.2015.06.032.

[4] D.S. Marks, L.J. Colwell, R. Sheridan, T.A. Hopf, A. Pagnani, Protein 3D Structure Computed from Evolutionary Sequence Variation, PLoS One. 6 (2011) 28766. doi:10.1371/journal.pone.0028766.

[5] D.S. Marks, L.J. Colwell, R. Sheridan, T.A. Hopf, A. Pagnani, R. Zecchina, et al., Protein 3D Structure Computed from Evolutionary Sequence Variation, PLoS One. 6 (2011) e28766. doi:10.1371/journal.pone.0028766.

[6] D.H. Ardell, S.G.E. Andersson, TFAM detects co-evolution of tRNA identity rules with lateral transfer of histidyl-tRNA synthetase, Nucleic Acids Res. 34 (2006) 893–904. doi:10.1093/nar/gkj449.

[7] D. de Juan, F. Pazos, A. Valencia, Emerging methods in protein co-evolution., Nat. Rev. Genet. 14 (2013) 249–61. doi:10.1038/nrg3414.

[8] T.A. Hopf, J.B. Ingraham, F.J. Poelwijk, C.P.I. Schärfe, M. Springer, C. Sander, et al., Mutation effects predicted from sequence co-variation, Nat. Biotechnol. 35 (2017) 128–135. doi:10.1038/nbt.3769.

[9] I. Sandler, N. Zigdon, E. Levy, A. Aharoni, The functional importance of co-evolving residues in proteins, Cell. Mol. Life Sci. 71 (2014) 673–682. doi:10.1007/s00018-013-1458-2.

[10] C.K. Sruthi, M. Prakash, Amino acid impact factor., PLoS One. 13 (2018) e0198645. doi:10.1371/journal.pone.0198645.

[11] S.H. Ackerman, E.R. Tillier, D.L. Gatti, Accurate simulation and detection of coevolution signals in multiple sequence alignments., PLoS One. 7 (2012) e47108. doi:10.1371/journal.pone.0047108.

[12] C.A. Brown, K.S. Brown, Validation of coevolving residue algorithms via pipeline sensitivity analysis: ELSC and OMES and ZNMI, oh my!, PLoS One. 5 (2010) e10779. doi:10.1371/journal.pone.0010779.

[13] S.H. Ackerman, E.R. Tillier, D.L. Gatti, Accurate Simulation and Detection of Coevolution Signals in Multiple Sequence Alignments, PLoS One. 7 (2012) e47108. doi:10.1371/journal.pone.0047108.

[14] L.C. Martin, G.B. Gloor, S.D. Dunn, L.M. Wahl, Using information theory to search for co-evolving residues in proteins., Bioinformatics. 21 (2005) 4116–24. doi:10.1093/bioinformatics/bti671.

[15] F.L. Simonetti, E. Teppa, A. Chernomoretz, M. Nielsen, C. Marino Buslje, MISTIC: Mutual information server to infer coevolution., Nucleic Acids Res. 41 (2013). doi:10.1093/nar/gkt427.

[16] G. Uguzzoni, S. John Lovis, F. Oteri, A. Schug, H. Szurmant, M. Weigt, Large-scale identification of coevolution signals across homo-oligomeric protein interfaces by direct coupling analysis., Proc. Natl. Acad. Sci. U. S. A. 114 (2017) E2662–E2671. doi:10.1073/pnas.1615068114.

[17] S. Ovchinnikov, H. Kamisetty, D. Baker, Robust and accurate prediction of residue-residue interactions across protein interfaces using evolutionary information, Elife. 2014 (2014) 1–21. doi:10.7554/eLife.02030.

[18] D. Petrović, V.A. Risso, S.C.L. Kamerlin, J.M. Sanchez-Ruiz, Conformational dynamics and enzyme evolution, J. R. Soc. Interface. 15 (2018) 20180330. doi:10.1098/rsif.2018.0330.

[19] F. Morcos, A. Pagnani, B. Lunt, A. Bertolino, D.S. Marks, C. Sander, et al., Direct-coupling analysis of residue coevolution captures native contacts across many protein families., Proc. Natl. Acad. Sci. U. S. A. 108 (2011) E1293-301. doi:10.1073/pnas.1111471108.

[20] B. Adhikari, J. Cheng, Protein Residue Contacts and Prediction Methods., Methods Mol. Biol. 1415 (2016) 463–76. doi:10.1007/978-1-4939-3572-7_24.

[21] M.A. Fares, S.A.A. Travers, P.H. Degnan, J.J. Wernegreen, A novel method for detecting intramolecular coevolution: adding a further dimension to selective constraints analyses., Genetics. 173 (2006) 9–23. doi:10.1534/genetics.105.053249.

[22] D. Talavera, S.C. Lovell, S. Whelan, Covariation Is a Poor Measure of Molecular Coevolution., Mol. Biol. Evol. 32 (2015) 2456–68. doi:10.1093/molbev/msv109.

[23] C.M. Buslje, E. Teppa, T. Di Doménico, J.M. Delfino, M. Nielsen, Networks of high mutual information define the structural proximity of catalytic sites: Implications for catalytic residue identification, PLoS Comput. Biol. 6 (2010). doi:10.1371/journal.pcbi.1000978.

[24] H. Kamisetty, S. Ovchinnikov, D. Baker, Assessing the utility of coevolution-based residue-residue contact predictions in a sequence- and structure-rich era., Proc. Natl. Acad. Sci. U. S. A. 110 (2013) 15674–9. doi:10.1073/pnas.1314045110.

[25] J.M. Nicoludis, R. Gaudet, Applications of sequence coevolution in membrane protein biochemistry, Biochim. Biophys. Acta - Biomembr. 1860 (2018) 895–908. doi:10.1016/J.BBAMEM.2017.10.004.

[26] *,‡ Gregory B. Gloor, § Louise C. Martin, § and Lindi M. Wahl, S.D. Dunn‡, Mutual Information in Protein Multiple Sequence Alignments Reveals Two Classes of Coevolving Positions†, (2005). doi:10.1021/BI050293E.

[27] G.W. Clark, S.H. Ackerman, E.R. Tillier, D.L. Gatti, Multidimensional mutual information methods for the analysis of covariation in multiple sequence alignments., BMC Bioinformatics. 15 (2014) 157. doi:10.1186/1471-2105-15-157.

[28] J. Franceus, T. Verhaeghe, T. Desmet, Correlated positions in protein evolution and engineering, J. Ind. Microbiol. Biotechnol. 44 (2017) 687–695. doi:10.1007/s10295-016-1811-1.

[29] J. Iserte, F.L. Simonetti, D.J. Zea, E. Teppa, C. Marino-Buslje, I-COMS: Interprotein-COrrelated Mutations Server., Nucleic Acids Res. 43 (2015) W320-5. doi:10.1093/nar/gkv572.

[30] I. Anishchenko, S. Ovchinnikov, H. Kamisetty, D. Baker, Origins of coevolution between residues distant in protein 3D structures, Proc. Natl. Acad. Sci. U. S. A. 114 (2017) 9122. doi:10.1073/PNAS.1702664114.

[31] F. Morcos, J.N. Onuchic, The role of coevolutionary signatures in protein interaction dynamics, complex inference, molecular recognition, and mutational landscapes, Curr. Opin. Struct. Biol. 56 (2019) 179–186. doi:10.1016/J.SBI.2019.03.024.

[32] F.M. Codoñer, M.A. Fares, Why should we care about molecular coevolution?, Evol. Bioinform. Online. 4 (2008) 29–38. (accessed August 21, 2019).