Teaching 2004/2005
Update: 19.05.2017

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

The SFP course is 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, 2004-2005
Tutorial 1, 27.09.04Amino acids, peptide bonds, spectroscopy
Tutorial 2, 04.10.04Assignment of assessed course work
Downloads: Tutorial notes
Tutorial 3, 18.10.04Protein Folding and Structure Determination
Downloads: Tutorial notes
Tutorial 4, 01.11.04Quaternary structure, Histones, Polyelectrolyte theory
Downloads: Answers, Khorasanizadeh (Cell 2004, 116, 259)
Tutorial 5, 15.11.04Enzyme Mechanisms
Downloads: Tutorial notes
Tutorial 6, 29.11.04Membrane Structure
Downloads: Tutorial notes
Data Interpretation
Molecular Biology Honours: Structural Biology, 2004-2005
Session 03.11.04Structural biology of cyclase-associated protein
Downloads: Paper, Answers
Lectures
Biological Sciences 3rd year module: Structure and Functions of Proteins, 2004-2005
Lecture 3, 30.09.04Protein Architecture
Downloads: Lecture with Notes, Lecture Slides, 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, 04.10.04Protein Crystallography
Downloads: Lecture Slides, Handout
Further reading, original literature and tutorials:
Teaching resources: http://www.iucr.org/cww-top/edu.index.html
Web tutorial: http://ruppweb.dyndns.org/ (X-ray crystallography tutorial)
Web tutorial: http://www.doe-mbi.ucla.edu/~sawaya/tutorials/tutorials.html (Cryst. tutorials)
Biological Sciences Honours: Structural Biology, 2004-2005
Structural Biology 06, 12.10.04The Structural Basis of Transcription: RNA Polymerase II
Downloads: Lecture with Notes, Lecture Slides, Handout
Further reading, original literature and tutorials:
Cramer et al. (2000) Architecture of RNA polymerase II and implications for the transcription mechanism. Science 288, 640.
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. Science92, 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 elongationcomplex. Cell 98, 791.
Zhang & Darst (1998) Structure of the Escherichia coli RNA polymerase alpha subunit amino-terminal domain. Science 281, 262.
Zhang et al. (1999) Crystal structure of Thermus aquaticus core RNA polymerase at 3.3 Å resolution. Cell 98, 811.
Structural Biology 13, 16.11.04The Structural Basis of Translation: The ribosome and protein synthesis
Downloads: Lecture with Notes, Lecture Slides, Handout
Further reading, original literature and tutorials:
Ferbitz et al. (2004) Trigger factor in complex with the ribosome forms a molecular cradle for nascent proteins. Nature 431, 590-596.
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.
Web site: http://www.riboworld.com/
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, 2004-2005
Enzymology 5, 05.10.04Membrane Enzymes
Downloads: Lecture with Notes, Lecture Slides, 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.
Enzymology 6, 05.10.04Enzyme Encapsulation
Downloads: Lecture with Notes, Lecture Slides, 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.
Electives
Structural Biology: Studying Macromolecules in Health and Disease, 2004-2005
Session 1, 05.10.04Lecture: Introduction, General Comments, UV/Vis Spectroscopy
Downloads: Handout
Further reading, original literature and tutorials:
Exam paper 2003/04
Exam paper 2003/04 (Answers)
Session 2, 12.10.04Practical: Peptide Properties; Lecture: Fluorescence Spectroscopy 1
Downloads: Handout
Session 3, 19.10.04Paper Presentations; Lecture: Fluorescence Spectroscopy 2
Downloads: Talks, Lecture, All
Session 4, 26.10.04Paper Presentations; Lecture: Fluorescence Spectroscopy 3
Downloads: Talks, Lecture, All
Further reading, original literature and tutorials:
Skriptum: "Methods in Structural Biochemistry"
Session 5, 02.11.04Lecture: CD Spectroscopy; Practical: Analysis of CD spectra
Downloads: Handout
Session 6, 09.11.04/16.11.04Practical: Fluorescence Spectrosocpy
Downloads: Literature 1, Literature 2
Session 7, 23.11.04Paper Presentations
Downloads: Talks