Birkbeck College
University of London
Crystallography Department
Advanced Certificate in
Principles of Protein Structure
Monday 16th  September 1996 3 hours (afternoon)
Answer 5 questions
  1. Discuss the important characteristics which distinguish the naturally occurring amino acids. Why do glycine and proline residues often occur in irregular regions of globular protein structure?

2. Outline the applications of NMR spectroscopy to the study of three of the following topics.

(a) primary structure of proteins

(b) secondary structure of proteins

(c) tertiary structure of proteins

(d) protein-ligand interactions

(e) protein mobility and dynamics

3. (a) Describe the essential features of the Pauling-Corey a -helix and b -sheet, indicating how these models were originally arrived at.

    (b) Sketch a Ramachandran plot indicating the a R, b and a L regions. Why might the main chain torsion angles observed in the protein structures differ slightly from those predicted by Ramachandran?

    (c) What factors lead to the distortion of a-helices in proteins? Why are all-parallel b -sheets thought to be less stable than antiparallel sheets?

4. Write an essay on icosahedral virus structures, including a discussion of the role of quasi-equivalence.

5. What are the non-covalent interactions involved in stabilising proteins? Use the example of myoglobin to illustrate how the same forces allow proteins to bind ligands. Include in your answer an indication of why globular proteins are only marginally stable in terms of D Gfolding.

6. Describe the commonly-occurring DNA-binding motifs in proteins, indicating which parts, if any, are involved in direct recognition of the base sequence.

7. (a) A two-stranded b -sheet is an unlikely motif for the transmembrane part of a membrane protein. Explain the reason for this and discuss what is a more likely type of motif for strands of b -structure to adopt in this environment and why.

    (b) One structural motif that appears to be common to a number of membrane proteins is the seven-helical bundle. Discuss examples of membrane proteins that have this type of motif and for one of these briefly describe its function.

  8. What are the structures of the major components of cytoskeleton in cells? Explain their functional roles.

 9. Describe the 3-dimensional structure and function of an enzyme of your choice. Include a brief indication of how the mechanism of the catalytic activity was elucidated.

10. (a) What is meant by protein supersecondary structure? Draw and discuss the folding pattern of two elements of supersecondary structure (or 'motifs'), giving examples of where they are found.

      (b) Explain the principles of packing of elements of secondary structure, mentioning the three main types of packing.

     (c ) Explain the use of the terms domain and domain fold in relation to protein tertiary structure.

11. Discuss protein quaternary structure and its functional role, particularly as contrasted with tertiary structure. Use examples to illustrate your answer where possible.

12. What is bioinformatics and what is its importance in the study of protein structure?