Hydrogen-bond cooperativity, vibrational coupling, and dependence of helix stability on changes in amino acid sequence in small 3 10-helical peptides. A density functional theory study.
Five pentapeptides, GGGGG, GAGGG, GVGGG, GLGGG, and GIGGG, have been completely optimized in the 3(10)-helical and open beta-strand conformations at the B3LYP/D95 level. The energies of the helices relative to the beta-strands vary from -2.1 to -3.6 kcal and depend on the amino acid residue sequence. The energies of substituting A, V, L, or I for G in the second position are also presented. Vibrational analyses were performed on the optimized structures. Vibrational coupling through the individual H-bond chains of the helices is confirmed to be stronger than that through space or through the covalent bonds. The cooperative interactions of the H-bonds are evident from both the structures and the coupling of the amide I, amide II, and N-H vibrations.
Wieczorek
Robert
R
Department of Chemistry, City University of New York, Hunter College and the Graduate School, 695 Park Avenue, New York, NY 10021, USA.
Dannenberg
J J
JJ
D000409:Alanine / Q000737:chemistry; D000596:Amino Acids / Q000737:chemistry*; D003198:Computer Simulation; D007532:Isoleucine / Q000737:chemistry; D007930:Leucine / Q000737:chemistry; D008958:Models, Molecular; D009842:Oligopeptides / Q000737:chemistry*; D010455:Peptides / Q000737:chemistry*; D017433:Protein Structure, Secondary; D013816:Thermodynamics; D014633:Valine / Q000737:chemistry
D000596:Amino Acids; D009842:Oligopeptides; D010455:Peptides; D007532:Isoleucine; C011080:polyglycine; D007930:Leucine; D014633:Valine; D000409:Alanine