Transitions from to Helix Observed in Molecular Dynamics Simulati
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- 作者：Kyung-Hoon Lee ; David R. Benson ; and Krzysztof Kuczera
- 刊名：Biochemistry
- 出版年：2000
- 出版时间：November 14, 2000
- 年：2000
- 卷：39
- 期：45
- 页码：13737 - 13747
- 全文大小：176K
- 年卷期：v.39,no.45(November 14, 2000)
- ISSN：1520-4995
文摘
Molecular dynamics simulations were carried out for three 13-residue peptides of the formAcNH-A-A-E-X-A-E-A-H-A-A-E-K-A-CONH2 with X = A, F, and W. All three peptides exhibitedunexpected dynamical behavior, undergoing a transition from an 
-helical to a 
-helical structure in thecourse of 5-ns trajectories in aqueous solution. Analysis of peptide length, accessible surface, interactionenergies, hydrogen bonding, and dihedral angles was consistent with 
transitions at 2800, 500, and800 ps for X = A, F and W, respectively. The transitions occurred sequentially and cooperatively,propagating from the C- to the N-terminus for X = A and W and from the center toward both termini forX = F. The time scale of the overall transition ranged from 300 to 500 ps. For all three peptides thebackbone structural transition was accompanied by a concerted rearrangement of the charged side chains,including a 3 Å increase in the distance between carboxylate groups of Glu-3 and Glu-6. During thetransition the peptide backbone hydrogen-bonding patterns were disrupted at the interface between the-helical and nascent -helical regions, with peptide groups forming water-bridged hydrogen bonds. Thepeptide structures exhibited significant fluidity, with individual residues sampling -, -, and 310-helicalconformations, as well as a "coil" state, without any intramolecular hydrogen bonds. The studied peptideshave been designed to form -helices when incorporated in novel hemoprotein model compounds, peptide-sandwiched mesohemes, which consist of two identical peptides covalently attached to an Fe(III)mesoporphyrin [Liu, D., Williamson, D. A., Kennedy, M. L., Williams, T. D., Morton, M. M., and Benson,D. R. (1999) J. Am. Chem. Soc. 121, 11798-11812]. The possibility of adopting -helical structures bythe constituent peptides may influence the properties of the hemoprotein models.
-helical to a -helical structure in thecourse of 5-ns trajectories in aqueous solution. Analysis of peptide length, accessible surface, interactionenergies, hydrogen bonding, and dihedral angles was consistent with transitions at 2800, 500, and800 ps for X = A, F and W, respectively. The transitions occurred sequentially and cooperatively,propagating from the C- to the N-terminus for X = A and W and from the center toward both termini forX = F. The time scale of the overall transition ranged from 300 to 500 ps. For all three peptides thebackbone structural transition was accompanied by a concerted rearrangement of the charged side chains,including a 3 Å increase in the distance between carboxylate groups of Glu-3 and Glu-6. During thetransition the peptide backbone hydrogen-bonding patterns were disrupted at the interface between the-helical and nascent -helical regions, with peptide groups forming water-bridged hydrogen bonds. Thepeptide structures exhibited significant fluidity, with individual residues sampling -, -, and 310-helicalconformations, as well as a "coil" state, without any intramolecular hydrogen bonds. The studied peptideshave been designed to form -helices when incorporated in novel hemoprotein model compounds, peptide-sandwiched mesohemes, which consist of two identical peptides covalently attached to an Fe(III)mesoporphyrin [Liu, D., Williamson, D. A., Kennedy, M. L., Williams, T. D., Morton, M. M., and Benson,D. R. (1999) J. Am. Chem. Soc. 121, 11798-11812]. The possibility of adopting -helical structures bythe constituent peptides may influence the properties of the hemoprotein models.