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Nick Panasik
JST #221



Assistant Professor in Departments of Biology and Chemistry
B.S.. University of Wisconsin - Madison
Ph.D. Pennsylvania State University
Post Doctoral Johns Hopkins University

Proteins are made of a linear string of amino acids. This string "folds up" in solution into a specific three dimensional shape specified by the order and identity of those amino acids. It is this shape that determines both the function of the enzyme and its specificity to substrates. This three dimensional structure also determines other properties including the enzyme's pH dependence, its stability, and even the ways in which that protein will adapt to future evolutionary selection pressures. The Holy Grail in biochemistry is to predict the three dimensional structure of a protein, its function, and its properties from only the linear amino acid sequence. This would be of great use now that the genomes of many organisms, including humans, have been decoded.

The focus of our research is to contribute to the understanding the rules of protein folding and adaptation through the use of a variety of techniques including Directed Evolution, rational design, and ab initio computational prediction. We concentrate primarily on structural adaptations to temperature and the resulting insights into stability and flexibility. By using methods of directed evolution (introduction of random mutations into an enzyme and then selecting for a desired, new, function) we are able to find enzymes that have dramatically new properties with relatively few changes in amino acid sequence. Through detailed structural analysis and enzymatic characterization, we examine this structure-function relationship and propose new mechanisms of structural adaptation.

When a protein folds up, it adopts a specific three dimensional shape.  Many of these shapes have been classified into protein families called "folds".  Examples of such can be seen in the SCOP database. While many researches have been trying to propose general rules of protein adaptation that cover all proteins (changes in the frequency of certain types of interactions such as ion pairs, hydrogen bonds, and solvent accessible surface area) we are finding that strategies of adaptation to temperature and thermal range of function are often fold-dependent. To wit, we study representatives of the largest of protein folds, the eight stranded alpha/beta barrels (over 10 percent of all known proteins are alpha/beta barrels) for adaptation mechanisms specific to that fold. We are also studying representatives of several other protein folds important to industry and for medicinal purposes.

An advantage to this type of research structure is that we can produce enzymes with novel and useful functions while at the same time discovering basic mechanisms in the structure-function relationship of enzymes.

Current folds of interest to our lab include:
alpha-beta barrels     jelly rolls      all-alpha proteins     all-beta proteins