Some Like It Cold: A Computer-Based Laboratory Introduction to Sequence and Tertiary Structure Comparison of Cold-Adapted Lactate Dehydrogenases Using Bioinformatics Tools

• Published in: Journal of chemical education Vol. 80; no. 11; p. 1300
• Main Authors: Lowery, M. Sue, Plesniak, Leigh A
• Format: Journal Article
• Language: English
• Published: Easton Division of Chemical Education 01.11.2003; American Chemical Society
• Subjects: Adaptation; Biochemistry; Bioinformatics; Biology; Chemistry; Computers; Downloading; Internet; Internet resources; Laboratories; Modelling; Molecular biology; Proteins; Stability; Students; Concepts in Biochemistry; Enzymes; Biochemistry; Computer-Based Learning; First-Year Undergraduate / General
• ISSN: 0021-9584; 1938-1328
• DOI: 10.1021/ed080p1300

The dramatic increase in publicly available genomic and protein sequence information creates new opportunities for comparative investigations of the structure and function of proteins and enzymes. Biochemists of all levels will need the skills to efficiently make use of these growing databases. The goals of this computer-based exercise are to reinforce principles of protein stability, function, and temperature adaptation, and to train students to use Internet resources for bioinformatics and molecular modeling. We have found the bioinformatics tools developed by the San Diego Supercomputer Center (SDSC) at the Biology Workbench to be especially user-friendly. Students download sequences and structures from appropriate databases, create sequence alignments, and carry out molecular modeling exercises, and then form hypotheses about the mechanism of biochemical adaptation for function and stability. This laboratory is appropriate for biochemistry and molecular biology laboratory courses, special topics, and advanced biochemistry lecture courses, and can be adapted for honors high school programs. Students found the exercise to be challenging but instrumental in enhancing their understanding of protein structure and function.