NDLI: How are model protein structures distributed in sequence space?

Content Provider	PubMed Central
Author	Bornberg-bauer, E.
Abstract	The figure-to-structure maps for all uniquely folding sequences of short hydrophobic polar (HP) model proteins on a square lattice is analyzed to investigate aspects considered relevant to evolution. By ranking structures by their frequencies, few very frequent and many rare structures are found. The distribution can be empirically described by a generalized Zipf's law. All structures are relatively compact, yet the most compact ones are rare. Most sequences falling to the same structure belong to "neutral nets." These graphs in sequence space are connected by point mutations and centered around prototype sequences, which tolerate the largest number (up to 55%) of neutral mutations. Profiles have been derived from these homologous sequences. Frequent structures conserve hydrophobic cores only while rare ones are sensitive to surface mutations as well. Shape space covering, i.e., the ability to transform any structure into most others with few point mutations, is very unlikely. It is concluded that many characteristic features of the sequence-to-structure map of real proteins, such as the dominance of few folds, can be explained by the simple HP model. In analogy to protein families, nets are dense and well separated in sequence space. Potential implications in better understanding the evolution of proteins and applications to improving database searches are discussed.
Related Links	http://dx.doi.org/10.1016/s0006-3495(97)78268-7
Ending Page	2403
Page Count	11
Starting Page	2393
File Format	PDF
ISSN	00063495
e-ISSN	15420086
Journal	Biophysical Journal
Issue Number	5
Volume Number	73
Language	English
Publisher Date	1997-11-01
Access Restriction	Open
Subject Keyword	Biophysics Research in Higher Education
Content Type	Text
Resource Type	Article
Subject	Biophysics

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