Designability of alpha-helical proteins. Author Eldon Emberly, Ned Wingreen, Chao Tang Publication Year 2002 Type Journal Article 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. Keywords Proteins, Models, Molecular, Amino Acid Sequence, Protein Structure, Tertiary, Databases, Protein, Protein Structure, Secondary, Drug Design Journal Proc Natl Acad Sci U S A Volume 99 Issue 17 Pages 11163-8 Date Published 08/2002 Alternate Journal Proc. Natl. Acad. Sci. U.S.A. Google ScholarBibTeXEndNote X3 XML