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Local interactions in bends of proteins.

S S Zimmerman, H A Scheraga

Proceedings of the National Academy of Sciences of the United States of America

|October 1, 1977

Summary

Local interactions influence protein bend formation in many dipeptide sequences. However, long-range, solvent, and specific amino acid interactions, like glycine, significantly impact protein structure and conformational preferences.

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Area of Science:

Protein structure and conformation
Biophysics
Computational biology

Background:

Understanding protein folding and stability is crucial in molecular biology.
Dipeptide sequences play a fundamental role in protein secondary structure formation.
Conformational preferences of amino acid sequences influence protein tertiary structure.

Purpose of the Study:

To compare calculated bend formation probabilities with observed bend fractions in dipeptides.
To investigate the influence of local versus long-range interactions on protein conformational preferences.
To identify amino acid sequence characteristics that correlate with observed bend formation in globular proteins.

Main Methods:

Statistical mechanical analysis of N-acetyl-N'-methylamide dipeptides.
Empirical conformational energy calculations.
Comparison with X-ray crystallographic data of 20 globular proteins.

Main Results:

Agreement between calculated and observed bend fractions for 26 dipeptides indicates local interaction dominance.
Seven Glycine-containing dipeptides showed higher calculated than observed bend preference, suggesting long-range/solvent influence.
13 of 14 sequences with lower calculated than observed bend fractions contained polar or aromatic residues, implying solvent effects.

Conclusions:

Local interactions are primary drivers of conformational preference in many dipeptide sequences.
Long-range, solvent interactions, and specific residues (e.g., Gly, polar, aromatic) significantly modulate protein bend formation.
The 4-to-1 hydrogen bond is not a dominant bend stabilizer; diverse bend conformations are possible for most dipeptides.

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