The Search for Noncovalent Interactions

Molecular Visualization of Proteins and Protein Complexes

Dr. J. Ricky Cox
 Department of Chemistry
Murray State University

 

"Biology is dominated by the chemistry of the noncovalent bond"

     -Alan R. Fersht, Andreas Matouschek and Luis Serrano

(J. Mol. Biol. (1992) 224, 771-782.)

 

PURPOSE OF THESE PAGES.   These pages are designed to highlight and emphasize noncovalent interactions in proteins and protein-ligand complexes.  One of the major goals of the biochemistry curriculum is to understand the type and nature of noncovalent interactions that occur within and between biomolecules.  These pages are designed to show SPECIFIC noncovalent interactions that exist in the structure of proteins and protein-ligand complexes.  The importance of p-type interactions in protein systems are also emphasized in these pages.  The search for noncovalent interactions is possible through the use of molecular visualization software such as RasMol, RasTop and Protein Explorer.  Links to these programs are provided below. 

 

 ARRANGEMENT OF PAGES.  The search for noncovalent interactions have been undertaken by biochemistry students at all levels.  The interactions visualized by students have been cataloged and organized below by the level of biochemistry course.  Many of the pages are chime-based (get chime), while some only contain images of proteins and potential noncovalent interactions.

Advanced Biochemistry Courses...Click HERE.

Basic Biochemistry Course...Click HERE.

Introductory Chemistry Course...Click HERE.

Miscellaneous Examples...Click HERE.
VISUALIZATION LINKS.  There are several molecular visualization programs that can be used to study molecular systems.  A variety of excellent tutorials are also available that allow the user to interactively investigate the structure and function of a diverse collection of biological molecules.  A rich source of coordinate files is necessary to unleash the power of molecular visualization software.

Visualization Programs 

•RasMol
•RasTop
•Protein Explorer
•Swiss PDB-Viewer
•Kinemage

Visualization Tutorials/Information

•World Index of Molecular Visualization Resources
•Molecular Visualization Freeware Page
•Molecular Models for Biochemistry
•The Online Macromolecular Museum
•Molecules in Motion
•MolVisions

Coordinate Files

•Protein Data Bank at the RCSB
•Molecules R Us
•Swiss-Prot
•Molecules at Okanagan University College

 

 

 

 PUBLICATIONS/PRESENTATIONS.  JRC has been fortunate to have several papers/presentations dealing with the use of molecular visualization in the biochemistry curriculum.

Papers

Cox, J. R. "Teaching Noncovalent Interactions in the Biochemistry Curriculum Through Molecular Visualization: The Search for p Interactions" J. Chem. Educ. 2000, 77, 1424-1428. MORE

Canning, D. R. and Cox, J. R. “Teaching the Structural Nature of Biological Molecules: Molecular Visualization in the Classroom and in the Hands of Students” Chem. Educ. Res. Prac. Eur. 2001, 2, 109-122. (Invited Paper). MORE

Peterson, R. R. and Cox, J. R. “Integrating Computational Chemistry into a Project-Oriented Biochemistry Laboratory Experience: A New Twist on the Lysozyme Experiment” J. Chem. Educ. 2001, 78, 1551-1555. MORE

Presentations

Cox, J. R.   The Kentucky Conference on Building a Scholarly Structure for Teaching and Learning, Bowling Green, KY, May 20-22, 2001.  Talk entitled “Molecular Visualization in the Biochemistry Curriculum”

Cox, J. R. Abstracts of Papers, 53rd Southeast Regional Meeting of the American Chemical Society, Savannah, GA; American Chemical Society: Washington, DC, 2001; CHED 176.  Talk entitled “Integrating Molecular Visualization Throughout the Biochemistry Curriculum” [Organized symposium at SERMACS-01 entitled “Teaching Biochemistry”].

 

 

    

 

This site was created by Ricky Cox in the Department of Chemistry
Last Modified:  June 25, 2001