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human proteins

Wednesday 4 June 2003

Proteins are made of amino acids arranged in a linear chain and joined together by peptide bonds.

Many proteins are the enzymes that catalyze the chemical reactions in metabolism. Other proteins have structural or mechanical functions, such as the proteins that form the cytoskeleton, a system of scaffolding that maintains the cell shape.

Proteins are also important in cell signaling, immune responses, cell adhesion, active transport across membranes, and the cell cycle.

Structure

The particular series of amino acids that form a protein is known as that protein’s primary structure. This sequence is determined by the genetic makeup of the individual.

Proteins have several, well-classified, elements of local structure formed by intermolecular attraction, this forms the secondary structure of protein.

They are broadly divided in two, alpha helix and beta sheet, also called beta pleated sheets. Alpha helices are formed of coiling of protein due to attraction between amine group of one amino acid with carboxylic acid group of other. The coil contains about 3.6 amino acids per turn and the alkyl group of amino acid lie outside the plane of coil.

Beta pleated sheets are formed by strong continuous hydrogen bond over the length of protein chain. Bonding may be parallel or antiparallel in nature. Structurally, natural silk is formed of beta pleated sheets. Usually, a protein is formed by action of both these structures in variable ratios. Coiling may also be random.

The overall 3D structure of a protein is termed its tertiary structure. It is formed as result of various forces like hydrogen bonding, disulphide bridges, hydrophobic interactions, hydrophilic interactions, van der Waals force etc.

When two or more different polypeptide chains cluster to form a protein, quaternary structure of protein is formed. Quarternary structure is a unique attribute of polymeric and heteromeric proteins like haemoglobin, which consists of two alpha and two beta peptide chains.

Biosynthesis

Translation of messenger RNA (mRNA) occurs on the ribosome. Folding of the nascent polypeptide begins, assisted by chaperones.

The polypeptide proceeds to post-translational folding. The new protein is correctly folded into its tertiary structure.

Some proteins are translocated into organelles, such as mitochondria. Unfolded and misfolded polypeptides aggrgate and precipitate in an inclusion body.

Unfolded or partially folded polypeptides are freed from the aggregates by chaperones and refolded or degraded in the proteasome.

Functional classification (According to Vallee et al., 11237009)

- 1. enzymes
- 2. modulator proteins
- 3. receptor proteins
- 4. transcription factors
- 5. intracellular matrix component
- 6. extracellular matrix component
- 7. transmembrane transporter
- 8. channel
- 9. proteic hormon
- 10. immunoglobulin
- 11. cell signaling

Also

- ligand binding protein or carrier proteins
- nucleic-acid binding proteins
- 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 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

- 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

Links

- Human Protein Atlas
- PROW, Protein Reviews on the Web
- InterPro at EMBL-EBI
- tigr protein families
- SwissProt
- PFAM, Protein families database of alignments and HMMs
- Preotein Explorer
- Rasmol
- SCOP, Structural Classification of Proteins at the WEHI, Melbourne, Australia
- The Human Protein Reference Database at Johns Hopkins Laboratory

See also

- biomolecules
- immunochemistry

Videos

- Protein synthesis

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- Protein structure

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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

Portfolio

  • Proportion of proteins in bacterias
  • Protein structures
  • Main metabolic pathways of metabolism