In conclusion, I believe that the concept of coevolution, and the non-independence of posi- tions within a protein family, is just as important to the understanding of a protein family as is the concept of conservation. The comparative popularity of conservation can be simply attributed to the relative simplicity of conservation as a concept. In order to improve the col- lective understanding of protein coevolution, and increase our ability to generalize it across major databases of protein families, I demonstrated the implicit link between the quality of co- evolution predictions and the fundamental biochemical assumptions implicit in such analyses. I investigated the relationship between multiple sequence alignment methodologies and their effect on coevolution inference. This work led to an innovation in sequence alignment methods in the form of local covariation [7], and a user-friendly sofware tool, LoCo [6], which provides an interface for curating protein family alignments based on local covariation. With this new ability to generate high-quality sequence alignments for input into the coevolution inference analysis pipeline, new statistics with greater coevolution prediction accuracy and greater re- sistance to alignment errors were produced. These new innovations have been applied to the LAGLIDADG Homing Endonuclease protein family, andin vivoandin vitroexperimentation supports the hypothesis that a coevolving network of residues constrains the variation of the family’s active site. The advances in sequence alignment and coevolutionary inference pre- sented here have the potential to provide new exciting insights into the evolution, structure,
[1] W R Atchley, K R Wollenberg, W M Fitch, W Terhalle, and A W Dress. Correlations among amino acid sites in bHLH protein domains: an information theoretic analysis.Mol Biol Evol, 17(1):164–178, January 2000.
[2] Lukas Burger and Erik van Nimwegen. Disentangling direct from indirect co-evolution of residues in protein alignments. PLoS Computational Biology, 6(1):e1000633, January 2010.
[3] J Z Dalgaard, A J Klar, M J Moser, W R Holley, A Chatterjee, and I S Mian. Statistical modeling and analysis of the LAGLIDADG family of site-specific endonucleases and identification of an intein that encodes a site-specific endonuclease of the HNH family.
Nucleic Acids Research, 25(22):4626–4638, November 1997.
[4] R J Dickson and G B Gloor. The MIp Toolset: an efficient algorithm for calculating Mutual Information in protein alignments. arXiv.org, 2013.
[5] RJ Dickson, LM Wahl, AD Fernandes, and GB Gloor. Identifying and seeing beyond multiple sequence alignment errors using intra-molecular protein covariation.PLoS ONE, 5(6):e11082, 2010.
[6] Russell J Dickson and Gregory B Gloor. Protein sequence alignment analysis by lo- cal covariation: coevolution statistics detect benchmark alignment errors. PLoS ONE, 7(6):e37645, 2012.
[7] Russell J Dickson, Lindi M Wahl, Andrew D Fernandes, and Gregory B Gloor. Identify- ing and seeing beyond multiple sequence alignment errors using intra-molecular protein covariation. PLoS ONE, 5(6):e11082, 2010.
[8] S D Dunn, L M Wahl, and G B Gloor. Mutual information without the influence of phylogeny or entropy dramatically improves residue contact prediction. Bioinformatics, 24(3):333–340, January 2008.
[9] RC Edgar. Quality measures for protein alignment benchmarks. Nucleic Acids Research, 38(7):2145, 2010.
[10] Robert C Edgar. MUSCLE: a multiple sequence alignment method with reduced time and space complexity. BMC Bioinformatics, 5:113, August 2004.
[11] W M Fitch and E Markowitz. An improved method for determining codon variability in a gene and its application to the rate of fixation of mutations in evolution. Biochem Genet, 4(5):579–593, 1970.
[12] Anthony A Fodor and Richard W Aldrich. On evolutionary conservation of thermody- namic coupling in proteins. 279(18):19046–19050, 2004.
[13] GB Gloor, G Tyagi, DM Abrassart, AJ Kingston, AD Fernandes, SD Dunn, and CJ Brandl. Functionally Compensating Coevolving Positions Are Neither Homoplasic Nor Conserved in Clades. Molecular Biology and Evolution, 27(5):1181, 2010.
[14] Gregory B Gloor, Louise C Martin, Lindi M Wahl, and Stanley D Dunn. Mutual informa- tion in protein multiple sequence alignments reveals two classes of coevolving positions.
Biochemistry, 44(19):7156–7165, May 2005.
[15] Xun Gu. Functional divergence in protein (family) sequence evolution. Genetica, 118(2- 3):133–141, July 2003.
[16] Xun Gu. A simple statistical method for estimating type-II (cluster-specific) functional divergence of protein sequences. Mol Biol Evol, 23(10):1937–1945, October 2006. [17] Kazuharu Misawa Kei-ichi Kuma Takashi Miyata Kazutaka Katoh. MAFFT: a novel
method for rapid multiple sequence alignment based on fast Fourier transform. Nucleic Acids Research, 30(14):3059, July 2002.
[18] Ying Liu and Ivet Bahar. Sequence Evolution Correlates with Structural Dynamics.
Molecular Biology and Evolution, April 2012.
[19] P Lucas, C Otis, JP Mercier, M Turmel, and C Lemieux. Rapid evolution of the DNA- binding site in LAGLIDADG homing endonucleases.Nucleic Acids Research, 29(4):960, 2001.
[20] Thomas A McMurrough, Russell J Dickson, Stephanie M F Thibert, Gregory B Gloor, and David R Edgell. A co-evolutionary barrier constrains active site variation in LAGLI- DADG homing endonucleases .
[21] Faruck Morcos, Andrea Pagnani, Bryan Lunt, Arianna Bertolino, Debora S Marks, Chris Sander, Riccardo Zecchina, Jos´e N Onuchic, Terence Hwa, and Martin Weigt. Direct- coupling analysis of residue coevolution captures native contacts across many protein families. Proceedings of the National Academy of Sciences, 108(49):E1293–301, De- cember 2011.
[22] John Moult, Krzysztof Fidelis, Andriy Kryshtafovych, and Anna Tramontano. Criti- cal assessment of methods of protein structure prediction (CASP)—round IX. Proteins: Structure, Function, and Bioinformatics, 79(S10):1–5, 2011.
[23] Marco Punta, Penny C Coggill, Ruth Y Eberhardt, Jaina Mistry, John Tate, Chris Boursnell, Ningze Pang, Kristoffer Forslund, Goran Ceric, Jody Clements, Andreas Heger, Liisa Holm, Erik L L Sonnhammer, Sean R Eddy, Alex Bateman, and Robert D
Finn. The Pfam protein families database. Nucleic Acids Res, 40(Database issue):D290– 301, January 2012.
[24] Ryo Takeuchi, Abigail R Lambert, Amanda Nga-Sze Mak, Kyle Jacoby, Russell J Dick- son, Gregory B Gloor, Andrew M Scharenberg, David R Edgell, and Barry L Stoddard. Tapping natural reservoirs of homing endonucleases for targeted gene modification. Pro- ceedings of the National Academy of Sciences, 108(32):13077–13082, August 2011. [25] G Talavera and J Castresana. Improvement of phylogenies after removing divergent
and ambiguously aligned blocks from protein sequence alignments. Systematic biology, 56(4):564, 2007.
[26] JD Thompson, F Plewniak, and O Poch. BAliBASE: a benchmark alignment database for the evaluation of multiple alignment programs. Bioinformatics, 15(1):87, 1999. [27] Andrew M Waterhouse, James B Procter, David M A Martin, Mich`ele Clamp, and Ge-
offrey J Barton. Jalview Version 2–a multiple sequence alignment editor and analysis workbench. Bioinformatics, 25(9):1189–1191, May 2009.
[28] C Yanofsky, V Horn, and D Thorpe. PROTEIN STRUCTURE RELATIONSHIPS RE- VEALED BY MUTATIONAL ANALYSIS. Science, 146(3651):1593–1594, December 1964.
[29] C Yanofsky, V Horn, and D Thorpe. Protein structure relationships revealed by mutational analysis. Science, 146:1593–1594, 1964.
Reprint permissions
A.1
Chapter 2
http://www.elsevier.com/journals/journal-of-molecular-biology/0022-2836/guide-for-authors Authors can use their articles for a wide range of scholarly, non-commercial purposes as outlined below. These rights apply for all Elsevier authors who publish their article as either a subscription article or an open access article.
We require that all Elsevier authors always include a full acknowledgement and, if appro- priate, a link to the final published version hosted on Science Direct.
For open access articles these rights are separate from how readers can reuse your article as defined by the author’s choice of Creative Commons user license options.
Authors can use either their accepted author manuscript or final published article for: Use at a conference, meeting or for teaching purposes
Internal training by their company
Sharing individual articles with colleagues for their research use* (also known as ’scholarly sharing’)
Use in a subsequent compilation of the author’s works
Inclusion in a thesis or dissertation
Reuse of portions or extracts from the article in other works
Preparation of derivative works (other than for commercial purposes)