Biophysical and structural considerations for protein sequence evolution
Genre
Journal ArticleDate
2011-12-19Author
Grahnen, JANandakumar, P
Kubelka, J
Liberles, DA
Subject
Amino Acid SequenceBiophysics
Computer Simulation
Evolution, Molecular
Models, Molecular
Molecular Sequence Data
Protein Conformation
Protein Folding
Proteins
Thermodynamics
Permanent link to this record
http://hdl.handle.net/20.500.12613/5489
Metadata
Show full item recordDOI
10.1186/1471-2148-11-361Abstract
Background: Protein sequence evolution is constrained by the biophysics of folding and function, causing interdependence between interacting sites in the sequence. However, current site-independent models of sequence evolutions do not take this into account. Recent attempts to integrate the influence of structure and biophysics into phylogenetic models via statistical/informational approaches have not resulted in expected improvements in model performance. This suggests that further innovations are needed for progress in this field. Results: Here we develop a coarse-grained physics-based model of protein folding and binding function, and compare it to a popular informational model. We find that both models violate the assumption of the native sequence being close to a thermodynamic optimum, causing directional selection away from the native state. Sampling and simulation show that the physics-based model is more specific for fold-defining interactions that vary less among residue type. The informational model diffuses further in sequence space with fewer barriers and tends to provide less support for an invariant sites model, although amino acid substitutions are generally conservative. Both approaches produce sequences with natural features like dN/dS < 1 and gamma-distributed rates across sites. Conclusions: Simple coarse-grained models of protein folding can describe some natural features of evolving proteins but are currently not accurate enough to use in evolutionary inference. This is partly due to improper packing of the hydrophobic core. We suggest possible improvements on the representation of structure, folding energy, and binding function, as regards both native and non-native conformations, and describe a large number of possible applications for such a model. © 2011 Grahnen et al; licensee BioMed Central Ltd.Citation to related work
Springer Science and Business Media LLCHas part
BMC Evolutionary BiologyADA compliance
For Americans with Disabilities Act (ADA) accommodation, including help with reading this content, please contact scholarshare@temple.eduae974a485f413a2113503eed53cd6c53
http://dx.doi.org/10.34944/dspace/5471