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PROTEIN PHYSICS LECTURE 1 Introduction & overview

PROTEIN PHYSICS LECTURE 1 Introduction & overview. Globular proteins. Membrane proteins. Fibrous proteins. H-bonds (NH:::OC) & hydrophobic forces. Protein chain (gene-encoded sequence). PROTEIN HAS DEFINITE 3D STRUCTURE. Homologous (closely related) proteins.

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PROTEIN PHYSICS LECTURE 1 Introduction & overview

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  1. PROTEIN PHYSICS LECTURE 1 Introduction & overview

  2. Globular proteins Membrane proteins Fibrous proteins H-bonds (NH:::OC) & hydrophobic forces

  3. Protein chain (gene-encoded sequence)

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

  5. Globular proteins Sequence & Structure Membrane proteins Fibrous proteins H-bonds (NH:::OC) & hydrophobic forces

  6. C A T H Globular domains

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

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

  9. POST-TRANSLATIONAL MODIFICATIONS Sometimes, CHAIN CUT-INDUCED DEFORMATIONMAKES ENZYME ACTIVE non-active cat. site active cat. site Chymotripsin Chymotripsinogen

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

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

  12. 4-helix bundle COFACTORS: HEME, 2Fe, RNA, … Sometimes: Similar folds with different active sites: different biochemical function

  13. Standard positions of active sites in protein folds

  14. PROTEIN PHYSICS LECTURE 2 Elementary interactions: covalent

  15. Protein chain: regular backbone & gene-encoded sequence of side chains

  16. Protein chain Covalent bond lengths: 0.9 – 1.8 Å Covalent bond angles: 109o – 120o Atom radii: 1 – 2 Å

  17. Side chains

  18. Protein chain Side chains: L-amino acids ___ ______ ______ Main-chain peptide group: flat & rigid

  19. Gly asymmetric backbone- side_chain: Ala _L Thr Two asymmetric side chains: Ile

  20. Peptide group: flat & rigid sp2 + psp2 + p Covalent bonding

  21. Main-chain: f (N-Ca) , y (Ca-C’), w (C’=N) Side-chain: c1, c2, ...

  22. Counting angles: 120o 0o 180o _____________________________________________

  23. sp2 - sp2 (w) w = 180o w = 0o

  24. Potentials: from IR spectra of vibrations _____________________________________________ classical Pro sp2 - sp2 (w) All, but Pro sp3 – sp3 (c) C-CH2-CH2-C CH3-CH3 sp2 – sp3 (f, y)

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