Bioinformatics

Biological Basics

1. Amino acids I 2. Peptide bond I 3. Proteins I 4. DNA I 5. Miscellaneous

3. Proteins

• macromolecules / polymers
• 'workhorses of the cell'
• made up of various L-amino acids connected by peptide bonds
• linear chains (unbranched)
  • protein molecule that consists of a single polypeptide chain is said to be monomeric
  • proteins made up of more than one polypeptide chain are called oligomeric
• interact with other proteins, nucleic acids, small molecules, ions, etc.

Protein Structure

Primary structure

• order of polypeptide sequence
• linear covalently linked amino acid sequence (peptide bonds) and any other covalent linkages between residues in the protein chain (disulfide bridges)

insulin (cow - bos taurus) PDB code: 1CPH Chain A: GIVEQCCASVCSLYQLENYCN Chain B: FVNQHLCGSHLVEALYLVCGERGFFYTPKA

• LIFE - The Science of Biology (7th edition) (by W.K. Purves, D. Sadava, G.H. Orians, H. Craig Heller)
• Protein Structure by Molecular Graphics (University of Cambridge)
• Protein Structure Classification (by O. Lund, Technical University of Denmark)
• Protein Structure: Understanding Protein Conformation (by H. Jakubowski, St. John's University)
• Cozzone, A.J.; Encyclopedia of Life Sciences 2002, 1-10. Proteins: fundamental chemical properties. [PDF]
• Hadley, C.; Jones, D.T.; Structure Fold. Des. 1999, 7(9), 1099-1112. A systematic comparison of protein structure classifications: SCOP, CATH and FSSP. [PubMed]
• Ouzounis, C.A.; Coulson, R.M.; Enright, A.J.; Kunin, V.; Pereira-Leal, J.B.; Nat. Rev. Genet. 2003, 4(7), 508-519. Classification schemes for protein structure and function. [PDF I PubMed]
• Saito, N.; Adv. Biophys. 1989, 25, 95-132. Principles of protein architecture. [PubMed]
• Shakhnovich, B.E.; Max Harvey, J.; J. Mol. Biol. 2004, 337(4), 933-949. Quantifying structure-function uncertainty: a graph theoretical exploration into the origins and limitations of protein annotation. [PubMed]

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