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Stereochemistry of residues in turning regions of helical proteins

  • John J. Kozak
  • Harry B. GrayEmail author
Original Paper
Part of the following topical collections:
  1. Joan Broderick: Papers in Celebration of Her 2019 ACS Alfred Bader Award in Bioinorganic or Bioorganic Chemistry

Abstract

We have developed a geometrical approach to quantify differences in the stereochemistry of α-helical and turning regions in four iron proteins. Two spatial signatures are used to analyze residue coordinate data for each protein; and a third is employed to analyze amino-acid molecular volume data. The residue-by-residue analysis of the results, taken together with the finding that two major factors stabilize an α-helix (minimization of side-chain steric interference and intrachain H-bonding), lead to the conclusion that certain residues are preferentially selected for α-helix formation. In the sequential, de novo synthesis of a turning region, residues are preferentially selected such that the overall molecular volume profile (representing purely repulsive, excluded-volume effects) spans a small range Δ of values (Δ = 39.1 Å3) relative to the total range that could be spanned (Δ = 167.7 Å3). It follows that excluded-volume effects are of enormous importance for residues in helical regions as well as those in adjacent turning regions. Once steric effects are taken into account, down-range attractive interactions between residues come into play in the formation of α-helical regions. The geometry of α-helices can be accommodated by conformational changes in less-structured turning regions of a polypeptide, thereby producing a globally optimized (native) protein structure.

Keywords

Cytochrome Heme Protein folding 

Notes

Acknowledgments

Work at Caltech was supported by the National Institutes of Health (DK-019038 to HBG).

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Copyright information

© Society for Biological Inorganic Chemistry (SBIC) 2019

Authors and Affiliations

  1. 1.Department of ChemistryDePaul UniversityChicagoUSA
  2. 2.Beckman Institute, California Institute of TechnologyPasadenaUSA

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