1. PROTEIN STRUCTURE AT ACTION: BIND  TRANSFORM  RELEASE
PROTEIN PHYSICS
LECTURE 24-25
PROTEIN STRUCTURE AT ACTION:
BIND  TRANSFORM  RELEASE

2. BIND: repressors
- turn - 

3. Zn-
fingers
DNA & RNA
BINDING
Leu-zipper

4. BIND   RELEASE: REPRESSOR
-BINDING-INDUCED DEFORMATION
MAKES REPRESSOR ACTIVE, and IT BINDS TO DNA

5. Immunoglobulin

6. Standard positions of active sites in protein folds

7. There are some
with catalytic
(Ser-protease) site

8. Preferential binding of TS: RIGID enzyme
BIND  TRANSFORM  RELEASE
Catalysis: stabilization of the transition state (TS)
Theory: Pauling & Holden
Preferential binding of TS: RIGID enzyme

9. Catalysis: stabilization of the transition state (TS)
Theory: Pauling & Holden
Experimental verification: Fersht
reputed TS
__________
______ P

10. / / / / Catalysis: stabilization of the transition state (TS)
Theory: Pauling & Holden
Experimental verification: Fersht /
This
protein
engineering
reduces
the rate by / /
reputed TS /
__________
______ P
Preferential
binding
of TS:
RIGID
enzyme

11. Catalytic antibodies ABZYM = AntyBody enZYM Transition state (TS)
BIND  TRANSFORM  RELEASE
Catalytic antibodies
ABZYM = AntyBody enZYM
Transition state (TS)
Preferential
binding
of TS:
RIGID
enzyme
Antibodies
are
selected
to TS-like
molecule

12. BIND  TRANSFORM  RELEASE: ENZYME
chymotrypsin
Note:
small
active
site

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

14.  non-active “cat. site” active cat. site
POST-TRANSLATIONAL MODIFICATION
Sometimes, only the CHAIN CUT-INDUCED DEFORMATION
MAKES THE ENZYME ACTIVE READY 
non-active “cat. site”
active
cat. site
CUT
Chymotripsinogen
Chymotripsin

15. Chymotrypsin catalyses hydrolysis of a peptide
Spontaneous hydrolysis: very slow

16. SER-protease:
catalysis

17. CHYMOTRYPSIN ACTIVE SITE with INHIBITOR

18. Preferential binding of TS: RIGID enzyme
F = k1x1 = - k2x 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  sec  (D/nm)2 in water

19. PROTEIN STRUCTURE AT ACTION: BIND  TRANSFORM  RELEASE
RIGID CATALITIC SITE
INDEPENDENT ON OVERALL CHAIN FOLD

20. MOTIONS

21. from one active site to another
Double sieve:
movement of substrate
from one active site to another 
tRNAIle

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

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

24. Movement in quaternary structure: Hemoglobin vs. myoglobin

26. Механохимический цикл
Миозин Актин
АТФ  АДФ + Ф
15 ккал/моль
в клеточных условиях
Механохимический цикл

27. Mechanochemical cycle
Myosin
Actin
Mechanochemical cycle

28. SUMMARY

29. PROTEIN PHYSICS
Interactions
Structures
Selection
States & transitions

30. Intermediates & nuclei
Structure prediction & bioinformatics
Protein engineering & design
Functioning