Homework for section 2
Web
site with a good overview of forces
8-Mon Feb 28 > hand in March 7
Thermodynamics
I will have a review of homework after class March 4 if needed.
web ref Look
especially at Explaining Chemical Equilibria and Le Chatelier's Principle
reading & homework
(hand in homework 5,6,7 today)
9-Wed Mar 2 Thermodynamics
see
reading & homework
for lecture 8.
10-Mon Mar 7: Hydrogen bonds; Lennard Jones Interactions
& Molecular Volume & Packing
Please read this
for background.
Thermodynamic
homework (lecture 8,9) due today.
There will be a review after class today if needed.
Ion association and packing homework. (PDF
here) Due Monday March 14
Good web definition here
;
a movie of He coming together
A powerpoint view of torsion
here
Amino acid hydrophobicity, volume,
surface area
TIBS (2003) 28 593-597"
Atom depth in protein structure and function Pintar et al.
Biochemistry (2001) 40 15280-15289
Packing is a key selection factor in the evolution of protein hydrophobic cores.
Chen and Sites
Packing m&ms here
Angew. Chem. Int. Ed. 2002, 41,
48-76. The hydrogen bond in the solid state.
TIBS (2001) 26 521. More hydrogen
bonds for the (structural) biologist.
11-Wed Mar 9: Solvation energy
Solvation homework Due Monday
March 14 (PDF
here) You
will need the class handout to do this homework.
Bockris & Reddy: Modern Electrochemistsry
Vol 1 pg 45-58
Science
1999 July 2; 285: 100-102 The Cavity
and Pore Helices in the KcsA K+ Channel: Electrostatic Stabilization of Monovalent
Cations Benoît Roux and Roderick MacKinnon
12-Mon Mar 14: .
Hydrophobicity Homework 10, 11 (Solvation energy and Hbd)
due..
Hydrophobicity homework Due Monday March 14
(PDF here)
Creighton. Page 153-162
Science (1983) 222 p 1087-1093 Wolfenden Waterlogged Molecules
Science (1994) 265 p 936-937 On the probability of finding a water moldcule
in a nonpolar cavity. PDF
Radzicka, A., and Wolfenden, R. (1988) Comparing the polarities of the amino
acids: Side chain distribution coeffients between the vapor phase, cyclohexane,
1-octonal, and neutral aqueous solution, Biochemistry 27, 1664-1670. PDF
Biophysical Chemistry (2003)
105 179-182 Hydrophobicity-getting into hot water Lesk
13-Wed Mar 16: Sums of small forces Creighton Page
163-167
Sum of small forces homework Due
Monday March 21 (PDF here)
You will need the class handout to do this homework.
14-Mon Mar 21: Protein structure determination.Homework 12, 13 (Hydrophobicity and sum of small forces due)
15-Wed Mar 23: pKs and stat. mech
Homework Due Monday March 30
(PDF here)
web ref
here
.
Mon Mar. 28 - No class
16-Wed Mar 30: Reactions and catalysis (hand in Homework lecture 14,15)
Acc.Chem.Res 2001, 34, 939-946 The depth of chemical time and the power
of enzymes as catalysts Wolfenden and Snider
17-Mon Apr 4 Summary forces; Connection to motor proteins (hand in Homework lecture 15,16)
Protein folding reading
Daggett and Fersht: The present view of
the mechanism of protein folding
Dobson Protein folding and misfolding
Nauli, Kuhlman, Baker Computer-based redesign
of a protein folding pathway
Ferguson and Fersht Early events in protein
folding
Last revised