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Stress and strain in staphylococcal nuclease
A Hodel1, R A Kautz, M D Jacobs
1Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut 06511.
Summary
Staphylococcal nuclease A exhibits a cis peptide bond at Lys116-Pro117. Replacing Lys116 with Glycine relieves backbone strain, favoring a trans peptide bond and altering protein conformation.
Area of Science:
- Biochemistry
- Structural Biology
- Protein Folding
Background:
- Proteins typically adopt stable tertiary structures.
- Locally strained geometries, like cis peptide bonds, can occur in protein structures.
- Staphylococcal nuclease A features a cis peptide bond at Lys116-Pro117 within a beta-turn.
Purpose of the Study:
- Investigate the role of the Lys116-Pro117 peptide bond in staphylococcal nuclease A structure and stability.
- Analyze the impact of mutations at residue 116 on peptide bond conformation and protein fold.
Main Methods:
- Nuclear Magnetic Resonance (NMR) spectroscopy to detect cis/trans isomers and alternative folded forms.
- X-ray crystallography to determine high-resolution protein structures.
- Analysis of nuclease variants K116G and K116A.
Main Results:
- The K116A variant structure is identical to wild-type nuclease A, with a predominantly cis 116-117 peptide bond (92%).
- The K116G variant structure is similar, but features a predominantly trans 116-117 Gly116-Pro117 peptide bond (80%).
- Steric clashes restrict backbone conformations for Lys116 and Ala116, favoring cis peptide bonds, while Gly116's absence reduces this strain.
Conclusions:
- Backbone strain in the trans conformation of the 116-117 peptide bond is compensated by the energetic cost of a cis X-Pro bond in wild-type nuclease.
- Removal of side chain steric hindrance at residue 116 (K116G) reduces backbone strain, making the trans conformation energetically favorable over the cis conformation.