Teaching 2005/2006
Update: 15.08.2017

Links of interest
The BTO web site of the University of Edinburgh.

Some courses (SFP, Biochemistry Honours) are managed online via WebCT.

Tools:
The web site of the European Bioinformatics Institute (EBI) provides a variety of services: http://www.ebi.ac.uk/.

Rasmol is a free molecular viewer available for PC, Mac and UNIX platforms.

Protein Explorer has been developed based on RasMol and is more powerful.
The software is free and runs on PC, Mac and Linux platforms.
Download of Chime may be required.

Peptides is a stand-alone Java application for calculation of protein and peptide parameters.

Databases:
The PubMed database of scientific literature: http://www.ncbi.nlm.nih.gov/PubMed/.
The GenBank database holds nucleotide and amino acid sequences: http://www.ncbi.nlm.nih.gov/GenBank/.
The Protein Data Bank (PDB) is a repository for protein structures: http://www.rcsb.org/.

Contents
Tutorials
Biological Sciences 3rd year module: Structure and Functions of Proteins, 2005-2006
Tutorial 1, 26.09.05Amino acid structures, primary/secondary structure, spectroscopy, peptide synthesis
Downloads: Handout
Tutorial 2, 03.10.05Assignment of, introduction to and guidance on assessed course work
Tutorial 3, 17.10.05Protein Folding
Downloads: Notes
Tutorial 4, 31.10.05Protein Interactions
Downloads: Notes, ppt notes
Tutorial 5, 14.11.05Enzyme Mechanisms
Downloads: Notes
Tutorial 6, 28.11.05Membrane Structure
Downloads: Notes
Data Interpretation
Molecular Biology Honours: Structural Biology, 2005-2006
Data Interpretation, 02.11.05Structure of the N-terminal domain of Adenylyl Cyclase -Associated Protein
Downloads: Paper, Notes
Lectures
Biological Sciences 3rd year module: Structure and Functions of Proteins, 2005-2006
Lecture 3, 29.09.05Macromolecules 2: Protein Architecture
Downloads: Lecture slides (large), Lecture slides (small), Lecture slides with notes, Handout
Further reading, original literature and tutorials:
Further reading: Conformational energy calculations (from Introduction to Protein Science, A Lesk, 2004, p. 208ff)
Web tutorial: http://www.cryst.bbk.ac.uk/PPS2/course/
Lecture 4, 03.10.05Macromolecules 3: X-ray crystallography
Downloads: Lecture slides (large), Lecture slides (small), Lecture slides with notes, Handout
Further reading, original literature and tutorials:
Web tutorial: http://ruppweb.dyndns.org/ (X-ray crystallography tutorial)
Web tutorial: http://www.doe-mbi.ucla.edu/~sawaya/tutorials/tutorials.html (Cryst. tutorials)
Web tutorial: Metal surfaces (Explanation of crystal packing, Miller indices)
Biological Sciences Honours: Structural Biology, 2005-2006
Structural Biology 06, 11.10.05The structural basis of transcription: RNA polymerase II
Downloads: Lecture slides (large), Lecture slides (small), Lecture slides with notes, Handout
Further reading, original literature and tutorials:
Cramer et al. (2001) Structural basis of transcription: RNA polymerase II at 2.8 Å resolution. Science 292, 1863.
Gnatt et al. (2001) Structural basis of transcription: An RNA polymerase II elongation complex at 3.3Å resolution. Science 92, 1876.
Meinhart & Cramer (2004) Recognition of RNA polymerase II carboxy-terminal domain by 3''-RNA-processing factors. Nature 430, 223.
Poglitsch et al. (1999) Electron crystal structure of an RNA polymerase II transcription elongation complex. Cell 98, 791.
Westover et al. (2004) Structural basis of transcription: separation of RNA from DNA by RNA polymerase II. Science 303,1014-1016.
Structural Biology 13, 15.11.05The structural basis of translation: The ribosome
Downloads: Lecture slides (large), Lecture slides (small), Lecture slides with notes, Handout
Further reading, original literature and tutorials:
Beckmann et al. (2001) Architecture of the protein-conducting channel associated with the translating 80S ribosome. Cell 107, 361-372.
Cochella & Green (2005) An active role for tRNA in decoding beyond codon:anticodon pairing. Science 308, 1178-1180.
Daviter et al. (2005) A renewed focus on transfer RNA. Science 308, 1123-1124.
Gabashvili et al. (2000) Solution structure of the E. coli 70S ribosome at 11.5 Å resolution. Cell 100, 537-549.
Moore & Steitz (2002) The involvement of RNA in ribosome function. Nature 418, 229-235.
Ogle et al. (2001) Recognition of cognate transfer RNA by the 30S ribosomal subunit. Science 292, 897-902.
Web site: Ribosome translation and protein targetting (Nine animations of the translation process)
Web site: The ribosome (http://www.riboworld.com/)
Web site: Translation (tutorial and quiz)
Wimberly et al. (2000) Structure of the 30S ribosomal subunit. Nature 407, 327-339.
Yusupov et al. (2001) Crystal structure of the ribosome at 5.5 Å resolution. Science 292, 883-896.
Biotechnology Honours: Enzymology, 2005-2006
Enzymology 4, 04.10.05Enzyme Encapsulation
Downloads: Lecture slides (large), Lecture slides (small), Lecture slides with notes, Handout
Further reading, original literature and tutorials:
Lasic (1998) Novel applications of liposomes. Trends Biotechnol. 16, 307.
Sawada & Ueda (2001) Enzyme processing of textiles in reverse micellar solution. J. Biotechnol. 89, 263.
Walde & Ichikawa (2001) Enzymes inside lipid vesicles: preparation, reactivity and applications. Biomol. Eng. 18, 143.
Enzymology 5, 04.10.05Membrane Enzymes
Downloads: Lecture slides (large), Lecture slides (small), Lecture slides with notes, Handout
Further reading, original literature and tutorials:
Giorno & Drioli (2000) Biocatalytic membrane reactors: applications and perspectives. TIBTECH 18, 339-349.
Sastry (2002) Entrapment of proteins and DNA in thermally evaporated lipid films. TIBTECH 20, 185-188.
Stahl & Uhlen (1997) Bacterial surface display: trends and progress. TIBTECH 15, 185-192.
Electives
Structural Biology: Studying Macromolecules in Health and Disease, 2005-2006
Session 01, 20.09.05Lecture: Introduction, General Comments, UV/Vis Spectroscopy
Downloads: Introduction (slides only), Introduction (notes), Lecture (slides only), Lecture (notes)
Further reading, original literature and tutorials:
Exam paper 2003/2004
Exam paper 2004/2005
Session 02, 27.09.05Lecture: Fluorescence Spectroscopy 1
Downloads: Lecture slides (large), Lecture slides (small), Lecture (notes)
Session 03, 04.10.05Practical: Peptide properties
Session 04, 11.10.05Lecture: Fluorescence spectroscopy 2
Downloads: Lecture slides (large), Lecture slides (small), Lecture (notes)
Session 05, 18.10.05Paper presentations
Downloads:  Slides (large), Slides (small)
Session 06, 25.10.05Lecture: CD Spectroscopy
Downloads: Lecture slides (large), Lecture slides (small), Lecture (notes)
Session 07, 01.11.05Practical: CD Spectroscopy
Downloads: Notes
Session 08, 08.11.05Paper presentations
Downloads: Slides
Session 09, 15.11.05Practical: Fluorescence spectrosocpy
Session 10, 22.11.05Practical: Fluorescence spectrosocpy
Session 11, 29.11.05Problem session