Article
Molecular Dynamics Simulation of Laser Desorption of a Fragment of Protein Kinase a from Two Maldi Matrices
Journal of Physical Chemistry A
(2006)
Abstract
We have carried out molecular dynamics simulations to study the desorption of a dephosphorylated fragment of protein kinase A from two matrices, sinapic acid (SA) and 2,5-dihydroxybenzoic acid (DHB), after laser excitation. We have examined the results as a function of the laser fluence and of the burial depth of the guest peptide in the matrices. In most cases, we found that the energy transferred from the matrix to the guest peptide was not sufficiently large to fragment the peptide. Exceptions occurred when the peptide was more buried. This finding suggested that protein analytes might be less likely to break into smaller fragments if they were placed closer to the surface of the matrix. We have also examined how likely the guest peptide could form small clusters with the matrix molecules and found that the results depended on the degree of burial of the peptide, on the laser fluence, and on which matrix was used. Generally, stable clusters were more likely to be formed for guest peptides that were more buried, at a lower laser fluence, and in the SA rather than the DHB matrix. In addition, we found that the DHB matrix was broken down more easily by the laser than the SA matrix.
Disciplines
Publication Date
January 4, 2006
DOI
10.1021/jp055939r
Citation Information
Cheng Wang and Chung F. Wong. "Molecular Dynamics Simulation of Laser Desorption of a Fragment of Protein Kinase a from Two Maldi Matrices" Journal of Physical Chemistry A Vol. 110 Iss. 16 (2006) p. 5355 - 5360 Available at: http://works.bepress.com/chung-wong/34/