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Folding alphabets

Nature Structural Biology volume 6, pages 994–996 (1999)Cite this article

Abstract

A new computational approach optimizes searches for reduced protein folding alphabets that use fewer than 20 types of amino acids. The predicted optimal five-letter alphabet happens to be in agreement with the suggestive results of a recent experiment, but whether highly reduced alphabets are sufficient for truly protein-like properties remains an open experimental question.

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Figure 1: An illustration of how optimized reduced alphabets are deduced by the mismatch minimization procedure of Wang and Wang.
Figure 2: Reduced alphabets by mismatch minimization follow an approximate hydrophobicity scale.

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Acknowledgements

I am very grateful to A. R. Davidson for communicating unpublished results and for critically reading this manuscript. I also thank M. Gross, S.L. LaPorte, K.W. Plaxco,D. Thirumalai, and T. Yomo for helpful discussions.

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  1. the Department of Biochemistry, and Department of Medical Genetics and Microbiology, Faculty of Medicine, University of Toronto, 1 King's College Circle, Toronto, M5S 1A8, Ontario, Canada

    Hue Sun Chan

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Chan, H. Folding alphabets. Nat Struct Mol Biol 6, 994–996 (1999). https://doi.org/10.1038/14876

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