What role can physical modeling of proteins play in our project? Eric Sawyer
Contents
Advantages of Protein Modeling in General
- An amino acid sequence alone does not describe the secondary, tertiary, and quaternary structures of a protein that provide functionality.
- "Seeing" a protein increases understanding.
Advantages of Physical Modeling over 2D Computer Modeling
- Comprehensive view and feel of protein secondary/tertiary/quaternary structure.
- Demonstrate the interactions between enzyme and substrate
- Universal--does not require knowledge of computer commands specific to a program
- 2D imaging is dependent on learners' spacial visualization ability
- Appeals to tactile learners
Feasibility
Rapid prototyping--the computer guided construction of 3 dimensional objects--allows autonomous assembly of complex structures. XYZ coordinate data from the popular molecular viewer, Rasmol, can be used to guide the production of these models. Our connection with the SMART Program through the Milwaukee School of Engineering gives us access to these technologies. The number of proteins we can reasonably expect Milwaukee to produce models of on budget may be limited to very few. The cost of model production varies greatly, including about $600 for a simple, 5-inch, backbone model to quite possibly in excess of $1000 for larger, more complex models. The balance between cost and usefulness to the project is important to consider.
How can we use physical modeling in our research?
Harris, et al (2009) (below) found that physical modeling in conjunction with computer-based imaging improved student understanding of complex protein concepts better than computer modeling alone. Students used physical models to assist them in answering application-, analysis-, and synthesis-type questions. Understanding and utilizing physical modeling could help us choose proper sites for adding or removing amino acids from a protein, and compare the wild type and modified protein. It would also allow us to understand substrate-enzyme interactions, and how changes to either would affect functionality. Additionally, one or more physical models would be a good addition to our display at iGEM in the fall.
