Molecular dynamics and ion mobility spectrometry study of model -hairpin peptide, trpzip1. Academic Article

abstract

• Here, we explore the conformations of gas phase, protonated tryptophan zipper 1 (trpzip1) ions and its six derivatives by an enhanced sampling molecular dynamics, specially the integrated tempering sampling molecular dynamics simulation (ITS-MDS). The structural distributions obtained from ITS-MDS are compared with results obtained from matrix-assisted laser desorption ionization (MALDI)-ion mobility-mass spectrometry (IM-MS). The IM-MS measured collision cross-section (CCS) profiles compare well with the calculated CCS profiles obtained from ITS-MDS. Although -turn structures are preferred for solution phase species, the ITS-MDS and IM-MS structural analysis suggests that the -turn structures are preferred for gas-phase, unsolvated trpzip1 [M + H](+) ions. In addition, the data suggests that the energy landscape of the gas phase peptide ions is sensitive to the site of protonation as well as intramolecular interactions involving the lysine side chain.

authors

• Russell, David

published proceedings

• J Phys Chem A

author list (cited authors)

• Chen, L., Shao, Q., Gao, Y., & Russell, D. H.

citation count

• 22

complete list of authors

• Chen, Liuxi||Shao, Qiang||Gao, Yi-Qin||Russell, David H

publication date

• May 2011

publisher

• American Chemical Society (ACS)  Publisher

published in

• The Journal of Physical Chemistry A: Isolated Molecules, Clusters, Radicals, and Ions; Environmental Chemistry, Geochemistry, and Astrochemistry; Theory  Journal

keywords

• Ions
• Mass Spectrometry
• Models, Molecular
• Molecular Dynamics Simulation
• Protein Conformation
• Tryptophan

PubMed Central ID

• 21476523

Digital Object Identifier (DOI)

• 10.1021/jp110014j

start page

• 4427

end page

• 4435

volume

• 115

issue

• 17

URL

• http://dx.doi.org/10.1021/jp110014j