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PROTEIN PHYSICS LECTURE 25

Explore the preferential binding of rigid enzymes, Hooke's law, kinetic energy in catalysis, and movements in protein structures. Learn about active sites, enzyme functions, and protein mechanics in this informative lecture.

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PROTEIN PHYSICS LECTURE 25

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  1. PROTEIN PHYSICS LECTURE 25 PROTEINS AT ACTION

  2. Preferential binding of TS: RIGID enzyme

  3. Preferential binding of TS: RIGID enzyme F = k1x1= - k2x2 Ei = (ki/2)(xi)2 = F2/(2ki) Hooke’s & 2-nd Newton’s Energy is concentrated laws in the softer body. Effective catalysis: when substrate is softer than protein Kinetic energy cannot be stored for catalysis Friction stops a molecule within picoseconds: m(dv/dt) = -(3D)v [Stokes law] D – diameter; m ~ D3 – mass;  – viscosity tkinet 10-13 sec  (D/nm)2in water

  4. Catalysis: stabilization of the transition state Theory: Pauling & Holden Experimental verification: Fersht __________ ______ P

  5. Different folds with the same active site: the same biochemical function

  6. Similar folds with different active sites: different biochemical function

  7. Standard positions of active sites in protein folds

  8. MOTIONS

  9. Double sieve: movement of substrate from one active site to another

  10. Movement in two-domain enzyme: One conformation for binding (and release), another for catalysis

  11. Two-domain dehydrogenases: Universal NAD-binding domain; Individual substrate-binding domain

  12. Movement in quaternary structure: Hemoglobin vs. myoglobin

  13. Myosin Actin Mechanochemical cycle

  14. SUMMARY

  15. PROTEIN PHYSICS • Interactions • Structures • Selection • States & transitions

  16. Intermediates & nuclei • Structure prediction & bioinformatics • Protein engineering & design • Functioning

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