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Role of undergraduate biochemistry education in protein function assignment (618.26)
Author(s) -
Craig Paul,
Dodge Greg,
Bernstein Herbert
Publication year - 2014
Publication title -
the faseb journal
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 1.709
H-Index - 277
eISSN - 1530-6860
pISSN - 0892-6638
DOI - 10.1096/fasebj.28.1_supplement.618.26
Subject(s) - protein data bank (rcsb pdb) , function (biology) , computational biology , protein expression , protein data bank , plasmid , gene , biochemistry , microbiology and biotechnology , biology , protein structure , genetics
There are over 3000 unannotated structures in the PDB. Students in our labs have proposed functions for >90 of these structures using template‐based alignments with the ProMOL plugin for PyMOL, BLAST, Dali and Pfam. Subsequently the students confirmed the function of four of these structures in work that they completed with minimal supervision. First they reviewed the putative enzyme function and searched the literature for an assay for that function. If the reagents were available and relatively inexpensive, they obtained the plasmid containing the gene encoding that protein, which they expressed and purified, using metal ion chromatography of the his‐tagged protein. The purified enzyme was then characterized in vitro. The process typically requires 10 ‐ 20 weeks for an individual undergraduate student working full time. We believe that this approach can be easily implemented in undergraduate biochemistry teaching labs, where it would benefit the students and the community. The students will learn about protein expression, purification and characterization using both traditional methods (electrophoresis, UV‐Visible spectroscopy) and modern approaches (plasmid expression, single step chromatographic methods). At the same time, a small army of undergraduates could make a significant dent in the number of unannotated structures in the PDB. Supported by NIGMS 2R15GM078077‐02 and 3R15GM078077‐02S1. Grant Funding Source : Supported by NIGMS 2R15GM078077‐02 and 3R15GM078077‐02S1