A Rough Guide to Protein Types
Index to Course Material
Index 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 :-
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)
Intracellular
muscle proteins, actin, myosin, dystrophin, troponins
cellular cytoskeleton, F- and G-actin, dynein, microtubules,
ankyrin, vilin, etc
Extracellular
Extra-cellular Matrix, collagen,
fibronectin, laminin, vitronectin, fibrinogen, fibrin
titin, twitchin, adhesion proteins, glycoproteins
keratin, silks
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
INTRACELLULAR
- Includes cytosolic and nuclear
- Mostly all-alpha or alpha-beta (alternating)
- This is a mildly reducing environment
- Most cysteines are free thiols -SH
- Many are globular and soluble
- Often oligomeric
Enzymes
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
EXTRACELLULAR
- Includes interior of lysosomes and endoplasmic reticulum
- Mostly all-beta or mixed alpha + beta (BUT 4-helix bundles in cytokines)
- Many are globular and soluble
- The environment is oxidizing
- Most cysteines are in disulphide bridges
Hydrolases
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