PROTEINS BETWEEN ORDER AND DISORDER

Primary, secondary, tertiary and quaternary protein structures

Cellular Crowding, Chaperones, Co-translational folding/assembly

Standard form of the 20 naturally occurring amino acids: chirality of amino acids, formation of the peptide bond

Special amino acids: glycine, histydine, proline, cysteine (disulphide bridges)

Dihedral angles and Ramachandran plots: regions of standard secondary structures

Stabilizing forces in protein structure (electrostatic, van der Waals, hydrogen bonds, hydrophobic,…)

Water and protein conformations: role of hydrogen bonds

Principles of evolutionary protein design: positive/negative design

What is bioinformatics

Protein Data Bank (PDB): to visualize protein structures use Pymol, Chimera, Litemol on the .pdb files (see The language of the protein universe by M. Levitt)

free energy and the folding processstructural and functional protein domains (what is a protein domain? see also as a suggested reading: Pawson’s interaction domains, Pawson2002).

sequences determine protein structures (suggested reading: Anfinsen’s dogma, Anfinsen1973) and structures are more conserved than sequences

proteins: between order and disorder. CH plot (Uversky2002)

intrinsically disordered proteins (see databases: DISPROT, MobiDB)

Dihedral angles and Ramachandran plots: regions of standard secondary structures

Stabilizing forces in protein structure (electrostatic, van der Waals, hydrogen bonds, hydrophobic,…)

Water and protein conformations: role of hydrogen bonds

Principles of evolutionary protein design: positive/negative design

SUPERPOSING PROTEIN STRUCTURES