Title | Designability of alpha-helical proteins. |
Publication Type | Journal Article |
Year of Publication | 2002 |
Authors | Emberly, EG, Wingreen, NS, Tang, C |
Journal | Proc Natl Acad Sci U S A |
Volume | 99 |
Issue | 17 |
Pagination | 11163-8 |
Date Published | 2002 Aug 20 |
Keywords | Amino Acid Sequence, Databases, Protein, Drug Design, Models, Molecular, Protein Structure, Secondary, Protein Structure, Tertiary, Proteins |
Abstract | A typical protein structure is a compact packing of connected alpha-helices and/or beta-strands. We have developed a method for generating the ensemble of compact structures a given set of helices and strands can form. The method is tested on structures composed of four alpha-helices connected by short turns. All such natural four-helix bundles that are connected by short turns seen in nature are reproduced to closer than 3.6 A per residue within the ensemble. Because structures with no natural counterpart may be targets for ab initio structure design, the designability of each structure in the ensemble-defined as the number of sequences with that structure as their lowest-energy state-is evaluated using a hydrophobic energy. For the case of four alpha-helices, a small set of highly designable structures emerges, most of which have an analog among the known four-helix fold families; however, several packings and topologies with no analogs in protein database are identified. |
Alternate Journal | Proc. Natl. Acad. Sci. U.S.A. |