Biochem 652

Macromolecular Structure & Dynamics

Dokholyan; 843-2513;; 1/8/14-2/10/14; MWF 11; 3007 GM. Registration limited to 12 except with permission Course Director. .  (Recitation will meet on Tuesdays and Thursdays, Time and location will be determined)

A. Conformational thermodynamics of macromolecules: Understanding polymers (1)

B. Thermodynamics of protein folding (2)

a.   Protein folding

i. Two-state protein folding

ii. Differential Scanning Calorimetry

iii. Effect of mutations on folding

iv. Cold denaturation

v. Solvent-induced denaturation

vi. Protein surface area

vii. Protein stability

b.   Helix-coil transition (1)

C. Kinetics of chemical reactions (4)

a.   Chemical reactions: Terminology; Treatment; Equilibrium

b.   First-order chemical reactions

c.   Second-order chemical reactions

d.   Transition state theory

e.   Enzyme kinetics

f.    Diffusion-limited reactions

g.   Relaxation to equilibrium

h.   Consecutive reactions

i.    Diffusion in the external field

D. Protein folding kinetics (4)

a.   Two-state folding kinetics

i. Stopped-Flow Fluorescence

ii. Chevron plot

iii. Tanford β-value

b.   Three-state folding kinetics, nucleation

c.   Timescales of protein motion

d.   H/D exchange

e.   Nucleation mechanism of protein folding

E. Stochastic processes (2)

a.   Markov Process

b.   Random walk: Poisson Process

c.   Brownian Motion: Langevin Equation

d.   Fluctuation-Dissipation Theorem

e.   Fokker-Plack Equation