A number of links to PDB files are included, and also to several resources
external to PPS. Do not be concerned with digesting all this external material
at this stage, but try and browse through some of them if you have time.
This is meant to provide a quick and dirty overview, and is not exhaustive, although it is hoped that it helps in appreciating the wide variety of roles that various different forms of protein fulfill. You will appreciate the links on this resource best if you have RasMol installed, and configured for Chemical MIME.
eg photosynthetic reaction centre, bacteriorhodopsin, 7-trans-membrane helix G-protein-coupled receptors, nicotinic acetylcholine receptor, various proton and ion pumps, voltage-gated ion channels, gap junction proteins, etc.
- we will be studying these in Section 11 (Quaternary Structure)
muscle proteins, actin, myosin, dystrophin, troponins
cellular cytoskeleton, F- and G-actin, dynein, microtubules, ankyrin, vilin,
etc
Extra-cellular Matrix, collagen, fibronectin, laminin, vitronectin, fibrinogen,
fibrin
titin, twitchin, adhesion proteins, glycoproteins
keratin, silks
- we will be studying these in Section 11 (Quaternary Structure)
Coat proteins, integrases, proteases 1mvp (164Kb) [Bbk|BNL|ExP|Waw|Hal], RNaseH/Reverse Transcriptase
Hundreds or thousands of them - catalysing all the biochemical pathways,
mostly in the cytosol - transferases, hydrolases, lyases, isomerases, etc.
Many are variations on the basic Rossman-fold (as in lactate dehydrogenase
2ldb (225Kb)
[Bbk|BNL|ExP|Waw|Hal])
Many use ATP and/or other co-factors, such as metal ions, mono- or dinucleotides,
flavins, etc.
Often multimers, with allosteric cooperativity
Polymerases, nucleases, ligases, gyrases, topo-isomerases, DNA-binding proteins1ahd (3.0Mb) [Bbk|BNL|ExP|Waw|Hal], transcription factors, zinc-fingers 1znf (1.3Mb) [Bbk|BNL|ExP|Waw|Hal], repressors, histones, steroid receptors
Elements of 2nd.messenger pathways - kinases, phosphatases, G-proteins,
calmodulin 3cln (110Kb)
[Bbk|BNL|ExP|Waw|Hal],
lipases, adaptors ( SH2
1shb (80Kb)
[Bbk|BNL|ExP|Waw|Hal],
SH3 1shg (41Kb)
[Bbk|BNL|ExP|Waw|Hal],
PH domains), etc.
Calcium ions and phosphate groups play a large role here.
Some of these are membrane associated.
e.g. glutathione reductase
3grs (354Kb)
[Bbk|BNL|ExP|Waw|Hal],
s-transferase 1gsr (285Kb)
[Bbk|BNL|ExP|Waw|Hal],
dismutases 2sod (410Kb)
[Bbk|BNL|ExP|Waw|Hal],
cytochromes 2cpp (298Kb)
[Bbk|BNL|ExP|Waw|Hal],
thioredoxin 2trx (171Kb)
[Bbk|BNL|ExP|Waw|Hal],
ferredoxin 1fdn (45Kb)
[Bbk|BNL|ExP|Waw|Hal],
etc.
Haem groups and metal ions often employed as co-factors
Nucleases cut nucleic acids (eg pancreatic RNase
3rn3 (98Kb)
[Bbk|BNL|ExP|Waw|Hal])
and
Lipases cut and process lipid chains, and
Glycosidases cut sugar moieties, (eg lysozyme 1lyz
(117Kb)
[Bbk|BNL|ExP|Waw|Hal],
and
Proteinases `cut' other peptide chains - there are FOUR main classes
Storage and Carrier Proteins, eg albumin, retinol-binding protein, ferritin
Hormones (eg insulin 4ins (117Kb)
[Bbk|BNL|ExP|Waw|Hal]),
Cytokines, Growth Factors (TGF-B2 1tfg
(87Kb)
[Bbk|BNL|ExP|Waw|Hal]),
Receptor domains, Adhesion domains
Recognition/Immune Response proteins, eg immunoglobulins, lectins
Epidermal growth factor (EGF)-type domains, Fibronectin type I and II, complement, kringle, etc.
The space between the bacterial membrane and its outer cell wall is somewhat special, as is the mitochondrial matrix. Here we find a number of specialised binding and transport proteins, such as arabinose-binding protein, sulphate-binding protein, phosphate-binding protein 1abh (34Kb) [Bbk|BNL|ExP|Waw|Hal] , Leu-Ile-Val-binding protein.
There are groups of proteins that in various ways assist in the correct folding of polypeptides. Chaperonins prevent mis-aggregation, peptidyl-prolyl isomerase assists in converting cis-proline to trans, and disulphide isomerase helps to shuffle cysteines paired in disulphide bridges until the `correct' linking is acheived.
Last updated 7th April '97