Biochemistry 565

Proteins and Enzymes - Cordes section

useful website links

Dates in bold black, e.g. Monday Aug 20, are completely updated for 2007. Dates in bold red are not updated at all from 2006, while dates in bold brown are "beta" versions that are partly updated but still in progress! The section will follow the same general structure as in 2006, but specific powerpoint notes, readings and assignments will change.

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Date

Title

Reading

Homework, Links, Info, Notes

Monday
Aug. 20

Review of amino acid backbone and side chain properties (ppt file)

none

 

IUPAC amino acid nomenclature rules:

http://www.chem.qmw.ac.uk/iupac/AminoAcid/index.html

 

Wednesday

Aug. 22

Chemistry of side chains/Anatomy of Protein Structure I (ppt file)

 

Muralidharan

paper, p.429-434 plus box 2

Muralidharan & Muir, Nat Methods 3, 429 (2006);

related, possibly helpful readings:

Tam et al. Biopolymers 60, 194 (2001);

Perler & Adam, Curr Opin Biotech, 11, 377 (2000).

Reading guide

Friday

Aug 24

Anatomy of Protein Structure II (ppt file)

 

Richardson online paper, Anatomy section up to turns

"The Anatomy and Taxonomy of Protein Structure,"

J.S. Richardson, Adv. Protein Chem, 34, 167 (1981)

updated, annotated online version:

http://kinemage.biochem.duke.edu/~jsr/index.html

Reading guide

Monday
Aug. 27

Anatomy of Protein Structure III (ppt file)

Richardson online paper, rest of Anatomy section

Also work on Deep View tutorial (tips handout),

and try to finish by Wednesday.

Deep View tutorial link:

http://www.usm.maine.edu/~rhodes/SPVTut/index.html

see updated reading guide for Friday above

 

Wednesday

Aug. 29

 

catch up on previous lectures

No new reading, work on problem set

Problem set 1, due September 5

Lovell article for problem set

Optional review session, BSW 219, 5-6 pm

 

Friday

Aug. 31

 

Thermodynamic stability of proteins (ppt file)

Razvi review on thermophiles

Razvi & Scholtz, Protein Science, 15, 1569-78 (2006) .

optional additional reading on osmolytes:

Street, Bolen & Rose, PNAS 103, 13997-14002.

In-class handout on water properties, vdW radii, H-bonds

(see Matt if you didn't get a copy).

Reading guide for Razvi, Street

 

Monday

Sept. 3

NO CLASS

 

 

Wednesday

Sept. 5

 

Determinants of protein stability and structure

ppt file

Matthews review

Problem Set 1 due; see Wed Aug 29

(answer key for Problem set 1)

Matthews, Annu Rev Biochem 62, 139-60 (1990)

Reading guide for Matthews

 

Friday

Sept. 7


continuation from Wednesday, with discussion of Matthews review

 

no new reading

Problem set 2, due Wed Sep 12.

In-class handout on double mutant cycles.

 

Monday

Sept. 10

 

Evolution and comparison of
protein sequences ppt file

Suel paper

Suel et al Nat Struct Biol 10, 59-68 (2003)

Reading guide for Suel

Also work on problem set 2.

In-class handout on substitution matrices.

 

Wednesday

Sept. 12

 

Evolution, classification and comparison of protein structures ppt file

 

Orengo paper

Problem set 2 due; answer key

Review session, 5-6 pm in BSW 208

Orengo et al Structure 5, 1093-1108 (1997)

Reading guide

(optional) Holm & Sander J Mol Biol 233, 123-38 (1993).

(optional)Ppt appendix on automated structure comparison

 

Friday

Sept. 14


In class exam covering first four weeks

 

 

2006 exam with answers

2007 exam key

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Department of Biochemistry
The University of Arizona

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