Amino acid propensities are position-dependent throughout the length of alpha-helices.
The 20 commonly occurring amino acids have been shown to have distinct position-dependent, helix-forming propensities near the ends of alpha-helices. Here, we show that the amino acids also have very strong position-dependent propensities throughout the length of a helix. Most helices are amphiphilic, and they have a strong tendency to both begin and end on the solvent-inaccessible face of the helix. These position-specific propensities should provide valuable parameters to guide de novo protein design, and should allow more precise prediction of helical topology in natural proteins.
Engel
Donald E
DE
Department of Physics, University of Pennsylvania, Philadelphia, PA 19104, USA.
DeGrado
William F
WF
D000595:Amino Acid Sequence; D000596:Amino Acids / Q000737:chemistry; D030562:Databases, Protein; D057927:Hydrophobic and Hydrophilic Interactions; D008958:Models, Molecular; D017433:Protein Structure, Secondary; D011506:Proteins / Q000737:chemistry*
D000596:Amino Acids; D011506:Proteins