CSH Protocols publishes cutting-edge methods for analyzing complex molecular interactions

October 05, 2006 -- With the genomes of hundreds of organisms now catalogued, one of the next major challenges is to identify proteins and their interactions. The current issue of CSH Protocols, published online (www.cshprotocols.org), features two freely available, cutting-edge methods that address this challenge.

Elucidation of protein-DNA interactions has been a tedious process, limited to one protein-interaction partner at a time. But the advent of high-throughput, genomics-based technologies has enabled scientists to build large-scale maps of protein-DNA and protein-protein interactions. These methods-released in CSH Protocols-will be useful to researchers seeking to map these interactions and better understand fundamental biological processes.

One of the freely accessible protocols, developed by Dr. Marian Walhout and her colleagues at the University of Massachusetts Medical School, describes a means for identifying protein-DNA interactions in complex organisms. Her team has used this method to generate a protein-DNA interaction network by characterizing the DNA sequences to which proteins bind in the model organism C. elegans (the "worm" used in many developmental studies). Because it relies on basic molecular biology techniques, this method will also be useful for analyzing the intricately coordinated patterns of gene regulation in other species.

Another technical challenge facing researchers is that in a typical cell, proteins are present in relatively small quantities. The second free method in this release of CSH Protocols is "MuDPIT" (for Multidimensional Protein Identification Technology), a means of identifying rare proteins in complex mixtures. This method combines advanced protein identification technologies with computational analysis, and has already been successfully employed in characterizing interacting proteins in yeast.

These methods are among more than 40 new peer-reviewed protocols added to the CSH Protocols database this month. Launched in May of 2006, CSH Protocols now includes more than 700 protocols spanning many fields in cell and molecular biology.

Source : Cold Spring Harbor Laboratory