1. PROTEIN PHYSICS LECTURE 1

2. Globularproteins Fibrous proteins H-bonds (NH:::OC) & hydrophobic forces Membraneproteins

3. Protein chain (gene-encoded sequence)

4. Secondary structures (  -helices,  -strands) are most conserved structural elements. They form a basis of protein classification One protein - various crystallization, NMR Homologous (closely related) proteins PROTEIN HAS DEFINITE 3D STRUCTURE

7. Globular proteins Fibrous proteins H-bonds (NH:::OC) & hydrophobic forces Membraneproteins

8. GlobulardomainsCATH

9. PROTEIN CHAIN CAN FORM ITS UNIQUE 3D STRUCTURE SPONTANEOUSLY IN VITRO

10. PROTEINS AT ACTION BIND  TRANSFORM  BIND : Repressors -BINDING-INDUCED DEFORMATION MAKES REPRESSOR ACTIVE, and IT BINDS TO DNA

11. BIND  TRANSFORM  RELEASE : ENZYMES (chymotrypsin) Note small active site

12. POST-TRANSLATIONAL MODIFICATIONS Sometimes, CHAIN CUT-INDUCED DEFORMATION MAKES ENZYME ACTIVE Chymotripsin Chymotripsino gen active cat. site non- active cat. site

13. POST-TRANSLATIONAL MODIFICATIONS: (especially in eukaryotes): PROTEIN CHAIN CUTS (proteolysis), - SPLICING - CYCLIZATION - INTERNAL CHEM. TRANSFORMATION GLYCOSYLATION, etc. MODIFICATION OF ENDS (acetylation, etc.) MODIFICATION OF SIDE CHAINS (S-S bonding, phosphorilation, etc.) COFACTORS …

14. Usually: Similar folds have similaractive site and similarbiochemical function (homologs) Similar folds have similar active site and similar biochemical function (homologs)

15. Sometimes: Different folds with the same active site: the same biochemical function

16. Sometimes: Similar folds with different active sites: different biochemical function 4-helix bundle COFACTORS: HEME, 2Fe, RNA, …

17. Standard positions of active sites in protein folds