Two-dimensional gel electrophoresis simultaneously exploits charge differences and molecular weight to separate greater than a thousand cellular proteins in highly reproducible patterns. Until recently, the large volume of data gathered from these gels was not easily manipulated. However, development of desktop computers with high computational capability and software systems designed to analyze protein pattern data has enabled detailed characterization of individual proteins against a large matrix. Complimenting these developments is the rapid accrual of protein and gene databases with analytic algorithms for using local pattern and protein sequence data for rapidly searching these burgeoning databases at several locations around the world. We have recently acquired the Melanie II 2D PAGE software package which will analyze protein patterns obtained from a Molecular Dynamics Laser Digitizing Scanner (Storm 860). We will digitize and analyze the protein patterns from our P53 complex studies and be able to discriminate which proteins have been modulated both quantitatively and qualitatively. We have already reported in the literature massive change in cellular protein patterns in p53 null mouse cells suggesting a cascade of biochemical events occur after loss of a single growth gene. Unique proteins can be searched for on SwissProt directly or, GenBank and Embl database via back-translation for identification. Using these advanced analytical systems, all protein data are permanently stored and are retrievable for detailed analysis against any other data in any genetic data bank on a worldwide basis. Once the system is established, we plan to use this technology to characterize proteins found to be complexed with p53, and ascertain their potential function in nuclear translocation and/or protection against proteolysis.
