Structural classification

Functional classification

 ligand binding protein or carrier proteins
 nucleic-acid binding proteins

• transcription factors

 enzymes
 transporter proteins (tranport proteins)
 storage proteins
 structural proteins
 signal transducer proteins
 motor proteins
 unknown or not assigned

According to the localization

 membrane proteins
 coat proteins
 cytosolic proteins

• cytoskeletal proteins

 organelles proteins
 nuclear proteins

Features

 protein synthesis
 vesicle-mediated sorting of proteins
 intracellular transport of proteins
 protein mutations
 protein folding and protein misfolding
 protein transport (protein trafficking)
 protein sorting
 protein function
 protein localization
 protein carbonylation
 protein farnsesylation
 protein phosphorylations
 protein domains

Protein pathology (Proteins citated in www.humpath.com)

 by genic mutation (proteins mutated in human diseases) (In july 2004, 1,484 human genes implicated in human diseases have been listed in Online Mendelian Inheritance in Man - OMIM)
 by fixation of an antibody
 by fixation of a microbial toxin
 by interaction with viral proteins
 by chemical inactivation

 protein surexpression

• gene amplification in tumors
• translocation downstream an activated promoter
  • immunoglobulin promoter (IGH, UGK, IGL)

• retroviral insertion near the promoter
  • HTLV1
  • genic therapy by retroviral vector

 fusion proteins in tumors

• Fusion proteins
• proteins involved in Fusion proteins)

 inactivation by mutations

• haploinsufficiency
• recessive loss of function mutations

 activation by mutations

• resistance to degradation
• creation of new functions

For one protein

 splice variant products
 post-translational modifications,
 subcellular localizations
 assembly into vomplexes
 protein-protein interactions

References

 Chung JJ, Shikano S, Hanyu Y, Li M. Functional diversity of protein C-termini: more than zipcoding? Trends Cell Biol. 2002 Mar;12(3):146-50. PMID: #11859027#

 Yewdell JW. Not such a dismal science: the economics of protein synthesis, folding, degradation and antigen processing. Trends Cell Biol. 2001 Jul;11(7):294-7. PMID: #11413040#

 Frand AR, Cuozzo JW, Kaiser CA. Pathways for protein disulphide bond formation. Trends Cell Biol. 2000 May;10(5):203-10. PMID: #10754564#

Elementary courses

 BMB 211: ELEMENTARY BIOCHEMISTRY > Peptides and Proteins at Penn Sate