(Logo) A Rough Guide to Protein Types

IndexIndex to Course Material IndexIndex to Section 10

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.

Firstly three classes that are a little separate from the bulk of proteins :-

1.Integral Membrane Proteins

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.

2.Fibrous and Structural Proteins

- we will be studying these in Section 11 (Quaternary Structure)

3.Viral Proteins

- 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

Nucleic Acid Manipulation and Regulation Proteins

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

Response Elements

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.

Redox and Electron Transport Proteins

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