Distance Learning: Techniques in Structural Molecular Biology (TSMB)

Postgraduate Certificate

TSMB Syllabus

Section 1	Section 2	Section 3	Section 4	Section 5	Section 6
Section 7	Section 8	Section 9	Section 10	Section 11	Section 12

Section 12: Example - Three Dimensional Structures

This section gives the students a chance to apply the techniques they have studied to a selection of protein structures of importance in modern structural biology. Each of the 12 structures illustrates a different aspect or aspects of structural biology covered earlier in the course. The students are expected to read and extract information from the original papers as well as examining the structures themselves in detail.

Structure (PDB)	Techniques	Reference	Skills in Exercise	Biology
Methylmalonyl-CoA Mutase 1REQ	Mixed MAD/MIR Multi crystal averaging	Structure 4:339-350. (1997)	Basic rasmol	Enzymology Genetic Disease
Hep B 1QGT	EM, Icosahedral Symm	Nature 386, 88-91. (1997)	EBI MSD	Virus
Acetylcholine receptor	Helical Reconstruction	J. Mol. Biol. 288 765-786. (1999)
F actin 1ATN	Fibre diffraction	Nature 347, 44-49. (1990)		Cytoskeleton
Tubulin 1TUB	Electron diffraction	Nature 391, 199-203. (1998)	Superposition of structure websites	Cytoskeleton
GroEL	Single Particle EM, Atomic Structure fitting	Cell 97 325-338. (1999)		Protein Folding Chaperonin
FepA 1FEP	Membrane protein Crystallisation, See MAD	Nature Struct. Biol 6, 56-63. (1999)		Membrane Transport
F1 Fo ATPase 1QO1	Molecular Replacement	Science 286, 1700-1705. (1999)		Energy Transduction
Prion 1QLX	NMR	PNAS 97 (1): 145-150. (2000)		Prion diseases
Dbl Domain Bpix (1BY1)	Deuterated NMR	Nature Struct. Biol. 5 1098 -1107 (1998)		Signal transduction
Nucleosome (1AOI)	DNA and protein Clusters for derivatives Expression and reconstitution	Nature 389: 251. (1997)	Handling DNA and protein in graphics	DNA Structure
Ribosome and IF1 (1HR0)	RNA and Protein Ligand binding to crystals	Science 291:498-501. (2001)	Handling large structures.	Ribosome

Objectives

To give the students practice in reading research papers in Structural Biology and extracting detail from them. To give students illustrations of the use of some of the techniques studied in the course. To place the rest of the course in the context of areas of biology where Structural Biology has in important input. At the end of this section, students should:

Have demonstrated the ability to extract answers to technical questions from a research paper
Have an appreciation of what questions Structural Biology is addressing in areas of current biological study
Have practised retrieving structures from the database and handling structures in simple graphics packages