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The role of α-, 310-, and π-helix in helix→coil transitions

Armen, Roger; Alonso, Darwin O.V.; Daggett, Valerie
Fonte: Cold Spring Harbor Laboratory Press Publicador: Cold Spring Harbor Laboratory Press
Tipo: Artigo de Revista Científica
Publicado em /06/2003 EN
Relevância na Pesquisa
26.98%
The conformational equilibrium between 310- and α-helical structure has been studied via high-resolution NMR spectroscopy by Millhauser and coworkers using the MW peptide Ac-AMAAKAWAAKA AAARA-NH2. Their 750-MHz nuclear Overhauser effect spectroscopy (NOESY) spectra were interpreted to reflect appreciable populations of 310-helix throughout the peptide, with the greatest contribution at the N and C termini. The presence of simultaneous αN(i,i + 2) and αN(i,i + 4) NOE cross-peaks was proposed to represent conformational averaging between 310- and α-helical structures. In this study, we describe 25-nsec molecular dynamics simulations of the MW peptide at 298 K, using both an 8 Å and a 10 Å force-shifted nonbonded cutoff. The ensemble averages of both simulations are in reasonable agreement with the experimental helical content from circular dichroism (CD), the 3JHNα coupling constants, and the 57 observed NOEs. Analysis of the structures from both simulations revealed very little formation of contiguous i → i + 3 hydrogen bonds (310-helix); however, there was a large population of bifurcated i → i + 3 and i → i + 4 α-helical hydrogen bonds. In addition, both simulations contained considerable populations of π-helix (i → i + 5 hydrogen bonds). Individual turns formed over residues 1–9...

Energy landscape of a peptide consisting of α-helix, 310-helix, β-turn, β-hairpin, and other disordered conformations

Higo, Junichi; Ito, Nobutoshi; Kuroda, Masataka; Ono, Satoshi; Nakajima, Nobuyuki; Nakamura, Haruki
Fonte: Cold Spring Harbor Laboratory Press Publicador: Cold Spring Harbor Laboratory Press
Tipo: Artigo de Revista Científica
Publicado em /06/2001 EN
Relevância na Pesquisa
26.75%
The energy landscape of a peptide [Ace-Lys-Gln-Cys-Arg-Glu-Arg-Ala-Nme] in explicit water was studied with a multicanonical molecular dynamics simulation, and the AMBER parm96 force field was used for the energy calculation. The peptide was taken from the recognition helix of the DNA-binding protein, c-Myb. A rugged energy landscape was obtained, in which the random-coil conformations were dominant at room temperature. The CD spectra of the synthesized peptide revealed that it is in the random state at room temperature. However, the 300 K canonical ensemble, Q(300K), contained α-helix, 310-helix, β-turn, and β-hairpin structures with small but notable probabilities of existence. The complete α-helix, imperfect α-helix, and random-coil conformations were separated from one another in the conformational space. This means that the peptide must overcome energy barriers to form the α-helix. The overcoming process may correspond to the hydrogen-bond rearrangements from peptide–water to peptide–peptide interactions. The β-turn, imperfect 310-helix, and β-hairpin structures, among which there are no energy barriers at 300 K, were embedded in the ensemble of the random-coil conformations. Two types of β-hairpin with different β-turn regions were observed in Q(300K). The two β-hairpin structures may have different mechanisms for the β-hairpin formation. The current study proposes a scheme that the random state of this peptide consists of both ordered and disordered conformations. In contrast...