Identification of high affinity displacers for proteomic applications using high throughput screening and quantitative structure-efficacy relationship models

BIOT 257

Jia Liu, liuj2@rpi.edu1, Asif Ladiwala1, Kaushal Rege, regek@rpi.edu1, Curt M. Breneman, brenec@rpi.edu2, and Steven M. Cramer, crames@rpi.edu1. (1) Department of Chemical and Biological Engineering, Rensselaer Polytechnic Institute, 110 8th Street, Troy, NY 12180, (2) Department of Chemistry and Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, 110 8th Street, Troy, NY 12180-3590
One of the major challenges in proteomics is the identification of trace proteins in complex protein mixture. Since displacement chromatography has the ability to carry out simultaneous concentration and high resolution separations, it is uniquely well suited for proteomic applications. In this work, high affinity displacers for ion exchange systems were identified using parallel batch experiments to determine the concentration of displacer required to displace 50% of the adsorbed biomolecules (DC-50). Using this approach, a large number of high affinity displacers were identified that could displace the adsorbed biomolecules at relatively low concentrations. In addition, the DC-50 data were employed in concert with molecular structural information of the displacers to produce predictive quantitative structure-efficacy relationship (QSER) models based on a support vector machine (SVM) regression approach. Several of the high affinity displacers were then employed for concentration and purification of peptides from complex protein digests and the ability of this technique to identify trace components was demonstrated. Furthermore, the ability to use these high affinity displacers at relatively low displacer concentrations in order to produce wider displaced zones, higher purities and improved trace component detection was demonstrated.

Poster Session
5:30 PM-7:30 PM, Wednesday, 16 March 2005 Convention Center -- Sails Pavilion, Poster

Division of Biochemical Technology

The 229th ACS National Meeting, in San Diego, CA, March 13-17, 2005