Mechanical Modeling and Computer Simulation of Protein Folding

Abstract

In this activity, science education and modern technology are bridged to teach students at the high school and undergraduate levels about protein folding and to strengthen their model building skills. Students are guided from a textbook picture of a protein as a rigid crystal structure to a more realistic view: proteins are highly dynamic biological molecules in the heterogeneous environment inside the living cell. Simple mechanical models and computer simulations that evolve in their complexity as the instruction progresses are at the core of this lesson. Methods of statistics and physical chemistry (thermodynamics and kinetics) are employed to investigate a flexible version of a peptide that can sample various conformations within the folded ensemble and ultimately unfold into a random coil.