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The flexibility in the proline ring couples to the protein backbone
Bosco K Ho1, Evangelos A Coutsias, Chaok Seok
1Department of Pharmaceutical Chemistry, University of California-San Francisco, 600 16th Street, San Francisco, CA 94148, USA. bosco@maxwell.ucsf.edu
Protein Science : a Publication of the Protein Society
|March 18, 2005
Summary
Proline rings in proteins exhibit flexibility, coupled to backbone conformation. A geometric model accurately predicts this coupling, identifying angle strain as key to proline ring conformations.
Area of Science:
- Protein structure and dynamics
- Computational biology
- Biophysics
Background:
- Proline residues in proteins typically adopt one of two main ring conformations.
- High-resolution protein structures reveal subtle flexibility within the proline ring.
- This proline ring flexibility is intrinsically linked to the protein backbone's conformation.
Purpose of the Study:
- To investigate the coupling between proline side-chain and backbone conformations.
- To develop a predictive model for proline ring flexibility based on geometric principles.
- To elucidate the factors governing transitions between different proline ring states.
Main Methods:
- Development of a computational model based solely on geometric and steric factors.
- Application of an analytic equation derived from Bricard (1897) to describe proline torsion coupling.
- Implementation of a computer algorithm to apply the geometric model.
Main Results:
- The geometric model successfully predicts the observed coupling between proline's phi and chi1 torsion angles.
- The model demonstrates strong agreement with experimental data from high-resolution protein structures.
- Analysis identified strain in the C(gamma)-C(delta)-N angle as the primary determinant of UP and DOWN puckering states.
Conclusions:
- Geometric and steric factors are sufficient to explain the coupling between proline ring and backbone conformations.
- Angle strain in the proline ring is the main energetic barrier for puckering state transitions.
- Relaxation of this strain facilitates the rare planar conformation of the proline ring.