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Experimentally observed conformation-dependent geometry and hidden strain in proteins
1Section of Biochemistry, Molecular and Cell Biology, Cornell University, Ithaca, New York 14853, USA. pak4@cornell.edu
Summary
Protein peptide geometry is conformation-dependent, showing fine structure in distributions and deviations from standard values. These findings, based on empirical data, offer insights into protein strain and thermostability.
Area of Science:
- Structural Biology
- Computational Biology
- Biophysics
Background:
- Peptide bond geometry is typically considered rigid.
- Protein structures exhibit diverse conformations.
- Understanding peptide geometry's dependence on conformation is crucial for predicting protein behavior.
Purpose of the Study:
- To create a database of peptide conformations and geometries from high-resolution protein structures.
- To analyze the fine structure of phi, psi-distributions in well-ordered protein residues.
- To investigate the relationship between peptide covalent geometry and protein conformation.
Main Methods:
- Compiled a database of peptide conformations and geometries from 70 diverse proteins.
- Analyzed well-ordered residues to determine phi, psi-distributions.
- Examined variations in the interpeptide N-C alpha-C bond angle.
Main Results:
- Observed finer structure in phi, psi-distributions than previously reported.
- Demonstrated that peptide covalent geometry, specifically the N-C alpha-C bond angle, varies with conformation by up to +/-5 degrees.
- Found that deviations from standard geometry are greatest at the edges of populated regions, suggesting strain.
Conclusions:
- Peptide geometry is not fixed but depends on protein conformation.
- Hidden strain in proteins, indicated by geometric deviations, may influence thermostability.
- Empirical data confirm and extend quantum mechanics calculations, aiding protein structure analysis.