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Protein Engineering vol. 16 no. 12 pp. 971-977, 2003
© 2003 Oxford University Press

Probabilistic approach to the design of symmetric protein quaternary structures

Xiaoran Fu1, Hidetoshi Kono2 and Jeffery G. Saven1,3

1Makineni Theoretical Laboratories, Department of Chemistry, University of Pennsylvania, 231 South 34th Street, Philadelphia, PA 19104, USA and 2Neutron Science Center and Center for Promotion of Computational Science and Engineering, Japan Atomic Energy Research Institiute, 8-1, Umemidai, Kizu-cho, Souraku-gun, Kyoto 619-0215, Japan

3 To whom correspondence should be addressed. e-mail: saven{at}sas.upenn.edu

Probabilistic methods have been developed that estimate the site-specific probabilities of the amino acids in sequences likely to fold to a particular target structure, and such information can be used to guide the de novo design of proteins and to probe sequence variability. An extension of these methods for the design of symmetric homo-oligomeric quaternary structures is presented. The theory is in excellent agreement with the results of studies on exactly solvable lattice models. Application to an atomically detailed representation of proteins verifies the utility of a symmetry assumption, which greatly simplifies and accelerates the calculations. The method may be applied to a wide variety of symmetric and periodic protein structures.

Received August 20, 2003; revised October 24, 2003; accepted October 28, 2003


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