Wang Cheng, Wong Chung F
Department of Chemistry and Biochemistry, University of Missouri, One University Boulevard, St. Louis, Missouri 63121, USA.
J Phys Chem A. 2006 Apr 27;110(16):5355-60. doi: 10.1021/jp055939r.
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.
我们进行了分子动力学模拟，以研究蛋白激酶A的去磷酸化片段在激光激发后从两种基质（芥子酸（SA）和2,5-二羟基苯甲酸（DHB））上的解吸情况。我们研究了结果与激光能量密度以及客体肽在基质中的埋藏深度之间的关系。在大多数情况下，我们发现从基质转移到客体肽的能量不足以使肽片段化。当肽埋藏更深时会出现例外情况。这一发现表明，如果蛋白质分析物放置在更靠近基质表面的位置，则它们分裂成较小片段的可能性可能较小。我们还研究了客体肽与基质分子形成小聚集体的可能性，发现结果取决于肽的埋藏程度、激光能量密度以及使用的基质。一般来说，对于埋藏更深、激光能量密度较低且处于SA基质而非DHB基质中的客体肽，更有可能形成稳定的聚集体。此外，我们发现DHB基质比SA基质更容易被激光分解。
