Your tools for this session.

1. Access to SRS6, a centralised facility to do Sequence Related Searches. Once in the front page of this database, please press the ‘Start’ button and take time to explore what is at your fingertips. You can use this point to search SWISSPROT or other databases. For instance, you will select the PATHWAY database from the ‘Metabolic Pathways’ option for exercise 5. Or you could explore the 'Allelic variants' for certain human genes.

2. Access to the Protein Data Base (PDB) at Gaithersburg, MD. Please save these datafiles to your zip disk. Here you will search for the following entries;

1F88.pdb, the X-ray diffraction data of bovine rhodopsin, by Palczewski et al (Science 289; 739-746, 2000).
1BOJ.pdb and 1BOK.pdb, an earlier 3D theoretical model of the bundle of seven transmembrane helices reported by Pogozheva et al (Biophys. J. 70; 1963-1985, 1997).

3. Two 3D viewers to render atomic coordinates derived from X-ray diffraction (or data from theoretical models) into three-dimensional structures. You can use RASMOL or SPDBV 3.7b2, kindly made available by the authors. SPDBV has a facility for introducing aminoacid substitutions in 3D structures.

4. SWISSPROT accession Nos. P08100 (human) and P02699 (bovine) linear protein sequences of rhodopsins. Just enter the accession Nos. in the access box on the top left corner of the Swissprot database.

5. My ‘Aminoacid Information Resource’ (AIR) summarizing physico-chemical and biological properties of aminoacids. This requires ‘Chime’, another molecular 3-d viewer.

6. A link to a simplified sequence alignment program adapted for two sequences. But notice that the SWISSPROT home page contains a facility to do multiple alignments on the sequences selected using the ‘Quick BlastP’ algorithm accessible from its front page.

7. The University of Iowa’s Database of Human Rhodopsin Mutations. Find both the 2D and table formats.

8. TMPRED, an algorithm to predict transmembrane domains and their orientation across the membrane. These algorithms check for runs of 17-33 hydrophobic aminoacids in alpha-helix structure using some of the hydrophobicity parameters that you find in AIR.

9. The 'Helical Wheel' demo from the University of Virginia. Helical wheels provide a polar view of alpha helices showing the chemical characteristics and relative distribution of aminoacid residues around the helix. You will use this tool in the prion exercise.