Protein Structure and Function

• Credit value: 15 credits at Level 5
• Convenor: Dr Amandine Marechal
• Assessment: homework arising from practicals, a computer-based test and short in-class tests (40%) and a 2.5-hour examination (60%)

In this module you will learn about laboratory techniques and approaches with application in the investigation of protein structure and function. The module follows logically from Molecular Biology, where the emphasis was on recombinant DNA technology, by moving to the next stage in a typical workflow: the translation of proteins from recombinant DNA molecules (i.e. protein expression and purification).

You will learn about numerous laboratory techniques for studying biophysical properties of proteins, and will perform some of these in laboratory practicals. The knowledge and experience you will gain in this module will serve as essential preparation for work at Level 6, especially in the final-year laboratory research projects.

Indicative syllabus

• Protein structure: the basic building blocks of proteins and the ways in which their sequences fold to form higher order structure and assemblies
• Recombinant protein expression: examination of prokaryotic vs. eukaryotic expression systems
• Protein purification: general considerations and survey of chromatography methods
• Theory and practice of selected biochemical and biophysical techniques to assess protein purity, concentration, structure and ligand-binding properties
• Site-directed mutagenesis: strategies and applications in the study of structure-function relationships based on the computational analysis of protein structures and their associated DNA sequences
• Computational analysis of protein and DNA sequences using basic bioinformatics tools

By the end of this module, you will be able to:

• explain how the amino acids comprising a primary sequence determine the fold as well as the surface properties of a protein
• select an appropriate system (e.g. prokaryotic vs. eukaryotic) for production of a specified recombinant protein, evaluate the major factors that could limit protein yield in this expression system, and suggest how these limitations can be minimised or overcome
• given appropriate information, design and justify a protein purification scheme involving a logical sequence of multiple chromatographic steps
• select and justify the application of named biophysical techniques to examine the concentration, purity, identity, and/or structural integrity of a specified protein(s)
• design the introduction of a specific mutation into a given protein, describing the workflow necessary to introduce this mutation and outlining the approaches you would take to select and verify mutants
• given the appropriate information, design and justify a mutagenesis strategy with the goal of investigating either protein-ligand or protein-protein interactions.