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Using Interactive Computer Technology to Teach Protein Purification

Introduction:

Jeanette Mowery, Biotechnology Laboratory Technician Program, Madison Area Technical College, Madison, Wisconsin, USA, jmowery@madison.tec.wi.us, (608) 243-4307

Software:

"Protein Lab", by A.G. Booth, School of Biochemistry and Biotechnology, University of Leeds, Leeds, United Kingdom.

 

Introduction:

About the software:

"Protein Lab", by A.G. Booth, is a computer simulation of protein purification. This program is extremely helpful for beginners in the art of protein purification. It gives them a chance to get beyond the details of individual techniques and get a sense of the overall process of a protein purification strategy. Users try their hand at purifying a particular protein while balancing purity, yield and cost. "Protein Lab" demonstrates that there are some general guidelines in the selection of techniques for protein purification but that each protein has unique characteristics and the methods for isolation of a particular enzyme are determined largely through trial and error.

This software can be downloaded free of charge from the following website: http://www.booth1.demon.co.uk/archive. Windows and Mac versions are available, or the software may be used on-line. (Special thanks to the author of this program, Andrew Booth, for updating this excellent program and making it available to all free of charge.)

Classroom applications for this software:

We use this program at the beginning of our course in protein purification to give students an idea of what a complete protein purification strategy will be like. We work with the computer simulation again at the end of the course, after the students' protein purification project is complete. This second exercise reinforces concepts that they have learned and illustrates that there are separation methods other than those used in class. Even if a course in protein purification is not part of your curriculum, this software would be an excellent choice for a teacher who is trying to broaden the concepts introduced in a relatively simple protein purification demonstration (such as purification of green fluorescent protein), or only introduced in lecture.

Summary of program features:

(Note: The description below applies to the versions of "Protein Lab" available for download. The on-line Java version is slightly different.)

The program follows an imagined scenario: purification of a protein in a research setting. For background information, as well as an explanation of the concepts needed to effectively use this program, we recommend that students start with the following HELP menu topics: SCENARIO, GETTING STARTED and STRATEGY.

Once students understand the general layout of the program, they may begin the actual purification. "Protein Lab" offers the student a chance to purify one of twenty different proteins from a mixture. There is also an option to save an ongoing purification and then later return to the stored material. All of the target proteins are enzymes whose activity may be assayed. The student chooses BEGIN: START FROM THE BEGINNING to select a protein to purify. The program will then provide basic information about the chosen protein, including its pH and temperature stability range.

Next, the student chooses the first purification procedure using the SEPARATION menu. There are numerous purification procedures available; the optimal procedure depends on the structural and functional properties of the desired protein. Use the HELP menu to get specific information about each of these procedures, which include Ammonium Sulfate Precipitation, Gel Filtration Chromatography, Ion Exchange Chromatography and others. If a chromatography technique is chosen for separation, the computer generates a chromatogram of A280 vs. fraction number. Following the purification, using a pull-down menu titled FRACTIONS, the fractions can then be assayed for enzyme activity and selected fractions pooled.

At any step in the purification, the student may assess his or her progress in one of three ways: by asking for a PROGRESS REPORT (using the HELP menu), by using the ELECTROPHORESIS menu to run a virtual 1-dimensional or 2-dimensional PAGE gel, or by running a PAGE gel and then requesting an IMMUNOBLOT (Western Blot). PROGRESS REPORT includes information on yield, enrichment and efficiency (expressed in person hours). There is no fixed end-point for a given purification, except in the case where the student spends too much virtual money and is "fired". However, the instructor could set some standards for the class in terms of either purity or yield.

Sources of Background Information:

Students benefit most from this software when it is preceded by at least one lecture of background material on protein purification. Some useful sources include:

    • Lisa A. Seidman and Cynthia J. Moore, Basic Laboratory Methods for Biotechnology: Textbook and Laboratory Reference, Prentice Hall, 2000 (especially Chapters 23 and 27).
    • Jeanette Mowery and Lisa Seidman, Protein Purification Manual: Purification of ß-galactosidase from E.coli, Madison Area Technical College. (Manuscript in preparation, please contact Jeanette Mowery for an advance copy.)
    • Material from the HELP screens of "Protein Lab" itself.

Software:

"Protein Lab" by A.J. Booth may be downloaded or used on-line by visiting http://www.booth1.demon.co.uk/archive.

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