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The flexibility in the proline ring couples to the protein backbone

¹ Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, California 94148, USA² Department of Mathematics and Statistics, University of New Mexico, Albuquerque, New Mexico 87131, USA³ School of Chemistry, College of Natural Sciences, Seoul National University, Seoul 151-747, Republic of Korea

(RECEIVED October 4, 2004; FINAL REVISION December 20, 2004; ACCEPTED December 21, 2004)

In proteins, the proline ring exists predominantly in two discrete states. However, there is also a small but significant amount of flexibility in the proline ring of high-resolution protein structures. We have found that this side-chain flexibility is coupled to the backbone conformation. To study this coupling, we have developed a model that is simply based on geometric and steric factors and not on energetics. We show that the coupling between and 1 torsions in the proline ring can be described by an analytic equation that was developed by Bricard in 1897, and we describe a computer algorithm that implements the equation. The model predicts the observed coupling very well. The strain in the C-C-N angle appears to be the principal barrier between the UP and DOWN pucker. This strain is relaxed to allow the proline ring to flatten in the rare PLANAR conformation.

Keywords: proline; pucker; backbone; cyclic ring

Article and publication date are at http://www.proteinscience.org/cgi/doi/10.1110/ps.041156905.

Reprint requests to: Bosco K. Ho, Department of Pharmaceutical Chemistry, University of California San Francisco, 600 16th Street, San Francisco, CA 94148, USA; e-mail: bosco{at}maxwell.ucsf.edu; fax: (415) 502-4222.

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