Common Folding Mechanism of a β-Hairpin Peptide via Non-native Turn Formation Revealed by Unbiased Molecular Dynamics Simulations.
The folding of a 15-residue β-hairpin peptide (Peptide 1) is characterized using multiple unbiased, atomistic molecular dynamics (MD) simulations. Fifteen independent MD trajectories, each 2.5 μs-long for a total of 37.5 μs, are performed of the peptide in explicit solvent, at room temperature, and...
| Publicado en: | Journal of the American Chemical Society Vol. 131; no. 50; pp. 18147 - 18153 |
|---|---|
| Autores principales: | , , |
| Formato: | Artículo |
| Publicado: |
American Chemical Society
12/23/2009
|
| Materias: | |
| Acceso en línea: | Ver este registro en EBSCOhost |
| fields | @attributes: recordID: 1 pdfLink: plink: https://search.ebscohost.com/login.aspx?direct=true&db=hlh&AN=47561121&site=ehost-live header: @attributes: shortDbName: hlh uiTerm: 47561121 longDbName: Humanities International Complete uiTag: AN controlInfo: bkinfo: jinfo: jid: 00027863 ACS jtl: Journal of the American Chemical Society issn: 00027863 maglogo: N pubinfo: dt: 12/23/2009 vid: 131 iid: 50 pid: 997 pub: American Chemical Society artinfo: ui: 47561121 10.1021/ja9064365 ppf: 18147 ppct: 6 formats: tig: atl: Common Folding Mechanism of a β-Hairpin Peptide via Non-native Turn Formation Revealed by Unbiased Molecular Dynamics Simulations. aug: au: Thukral, Lipi Smith, Jeremy C. Daidone, Isabella affil: Interdisciplinary Center for Scientific Computing, University of Heidelberg, mi Neuenheimer Feld 368, 69120 Heidelberg, Germany Center for Molecular Biophysics, University of Tennesse/Oak Ridge National Laboratory, One Bethel Valley Road, Oak Ridge, Tennessee 37831 Dipartmento di Chimica ingegneria Chimica e Materiali, University of L'Aquila, Via Vetoio (Coppito 1), 67010 Coppito (AQ), Italy su: Molecular dynamics Peptides Quantum trajectories Chemical research Sampling (Process) sug: subj: Molecular dynamics Peptides Quantum trajectories Chemical research Sampling (Process) ab: The folding of a 15-residue β-hairpin peptide (Peptide 1) is characterized using multiple unbiased, atomistic molecular dynamics (MD) simulations. Fifteen independent MD trajectories, each 2.5 μs-long for a total of 37.5 μs, are performed of the peptide in explicit solvent, at room temperature, and without the use of enhanced sampling techniques. The computed folding time of 1-1.5 eμs obtained from the simulations is in good agreement with experiment [Xu, Y.; et al. J. Am. Chem. Soc. 2003, 125, 15388-15394]. A common folding mechanism is observed, in which the turn is always found to be the major determinant in initiating the folding process, followed by cooperative formation of the interstrand hydrogen bonds and the side-chain packing. Furthermore, direct transition to the folded state from fully unstructured conformations does not take place. Instead, the peptide is always observed to form partially structured conformations involving a non-native (ESYI) turn from which the native (NPDG) turn forms, triggering the folding to the β-hairpin. pubtype: Academic Journal doctype: Article src: R language: English refInfo: copyright: @attributes: flag: Y dt: @attributes: year: 2009 holdings: @attributes: islocal: N |
|---|