Incorporation of pairwise interactions into the Lifson‐Roig model for helix prediction

The helix/coil equilibrium of a peptide in solution can be modulated by a variety of side‐chain interactions that are not incorporated into the standard statistical mechanical models for prediction of peptide helical content. In this report, we describe a recursive formulation of the Lifson‐Roig mod...

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Bibliographic Details
Published in:Protein science 1995-06, Vol.4 (6), p.1161-1166
Main Authors: Shalongo, William, Stellwagen, Earle
Format: Article
Language:English
Subjects:
Amino Acid Sequence
apolar interactions
capping interactions
Computer Simulation
helical peptides
helix prediction
Lifson‐Roig model
Models, Chemical
Molecular Sequence Data
Peptides - chemistry
Protein Structure, Secondary
side‐chain interactions
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Summary:The helix/coil equilibrium of a peptide in solution can be modulated by a variety of side‐chain interactions that are not incorporated into the standard statistical mechanical models for prediction of peptide helical content. In this report, we describe a recursive formulation of the Lifson‐Roig model that facilitates incorporation of specific pairwise side‐chain interactions as well as nonspecific individual side‐chain capping interactions. Application of this extended model to a series of host/guest peptides indicates that the apparent AG value for a pairwise apolar interaction is dependent upon the spacing and orientation but not the sequential location of the participating residues. The apparent AG values for such interactions are about 40% greater than the corresponding apparent ΔΔG values obtained from difference measurements.
ISSN:0961-8368
1469-896X
DOI:10.1002/pro.5560040614