Comparative protein structure modeling is based on the empirical observation that similar amino acid sequences, in general, have similar three-dimensional structures (Chothia, Lesk, EMBO J (1986) vol. 5 (4) pp. 823-6). Thus, researchers can use a protein structure model determined through x-ray crystallography or nuclear magnetic resonance (NMR) spectroscopy as a template to construct models for all similar protein sequences. The degree of sequence similarity usually determines the quality of the model. The disparity in the number of sequenced proteins versus the number of 3D protein models determined by experiment continues to grow necessitating the use of comparative modeling and other protein structure prediction methods in computational biology and biology in general.
Upon completion of the tutorial, students should in addition to learning the concepts taught in each of the steps also appreciate the value of 3-dimensional structure to our understanding of structure-function relationships in biomolecular systems.
Instructors should read the note about the structure models used in this tutorial.
A worksheet (pdf) is provided for students to complete and turn in to their instructor.
The tutorial relies on relaying information on the enzyme’s structure with the use of JMol. The decision to use JMol means that instructors, students or the department’s IT personnel do not have to worry about installing molecular visualization software nor do they need to figure out how to use these external programs. Nevertheless, JMol has certain limitations and some may desire to use other programs like VMD in conjunction with the tutorial. The data files we use to create various scenes in JMol are all downloadable.
Hyperlinks through this text will trigger JMol scripts, simply clicks these links and watch how the JMol display changes.