Beta-sheet preferences from first principles.
The natural amino acids have different preferences of occurring in specific types of secondary protein structure. Simulations are performed on periodic model beta-sheets of 14 different amino acids, at the level of density functional theory, employing the generalized gradient approximation. We find that the statistically observed beta-sheet propensities correlate very well with the calculated binding energies. Analysis of the calculations shows that the beta-sheet propensities are determined by the local flexibility of the individual polypeptide strands.
Rossmeisl
Jan
J
Center for Atomic-scale Materials Physics, Technical University of Denmark, DK-2800 Lyngby, Denmark.
Kristensen
Iben
I
Gregersen
Misha
M
Jacobsen
Karsten W
KW
Nørskov
Jens K
JK
D000596:Amino Acids / Q000737:chemistry*; D003198:Computer Simulation; D008956:Models, Chemical; D017433:Protein Structure, Secondary; D011506:Proteins / Q000737:chemistry*; D013816:Thermodynamics
D000596:Amino Acids; D011506:Proteins