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Molecular Biology and Evolution, Vol 13, 666-673, Copyright © 1996 by Society for Molecular Biology and Evolution

ORIGINAL ARTICLE

Combining protein evolution and secondary structure

JL Thorne, N Goldman and DT Jones
Statistics Department, North Carolina State University, Raleigh 27695- 8203, USA. thorne@stat.ncsu.edu

An evolutionary model that combines protein secondary structure and amino acid replacement is introduced. It allows likelihood analysis of aligned protein sequences and does not require the underlying secondary (or tertiary) structures of these sequences to be known. One component of the model describes the organization of secondary structure along a protein sequence and another specifies the evolutionary process for each category of secondary structure. A database of proteins with known secondary structures is used to estimate model parameters representing these two components. Phylogeny, the third component of the model, can be estimated from the data set of interest. As an example, we employ our model to analyze a set of sucrose synthase sequences. For the evolution of sucrose synthase, a parametric bootstrap approach indicates that our model is statistically preferable to one that ignores secondary structure.
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