Chem 425s/578
Protein Engineering Spring
2004
Literature
citations given in class (* indicates assigned reading,
available in reading room CB200). The highlighted references are links to .pdf files.
This list will be
updated periodically, so please check in here weekly.
Reading
for week of 4/5-4/9:
*Chapter
17 from Branden and Tooze
“Introduction to Protein Structure”
*Anthony-Cahill
and Magliery, Current
Pharma. Biotech., 2002, 3, 299-315
*Bilgicer and Kumar, J.
Chem. Ed., 2003, 80,
1275-81
Other
references cited in lecture:
Richardson
and Richardson, Science, 1988, 240, 1648 (aa preferences in helices)
Bryson
et al., Science, 1995, 270,
935 (extensive review of de novo
design)
Smith and
Regan, Acc. Chem. Res., 1997, 30, 153 (review of beta
structure design)
Katz and Kossiakoff, J.
Biol. Chem., 1986, 261,
15480 (engineering disulfides)
Matsumara et al., Nature, 1989, 342,
291 (engineered disulfides in T4L)
Mitchinson and Wells, Biochemistry, 1989, 28,
4807 (engineered disulfides in subtilisin)
Reading
for week of 4/12-4/16:
*Noren et al.,
Science, 1989, 244, 182 (biosynthetic unnatural aa method)
*Beene
et al., Biochemistry, 2002, 41,
10262 (application
of unnatural aa mutagenesis)
*Camarero et al.,
Bioorganic Med. Chem., 2001, 9, 2479 (using inteins
in vivo)
Other
references cited in lecture:
Distefano et al.,
Curr. Op. Struct.
Biol., 1998, 8, 459 (semi-synthesis)
Schnölzer and Kent, Science,
1992, 256, 221 (chemo-selective ligation)
Severinov and Muir, J.
Biol. Chem., 1998, 273, 16205 (expressed
protein ligation = EPL)
Noren, Wang and Perler, Angew. Chem. Int. Ed., 2000, 39, 450 (intein review)
Cotton and
Muir, Chemistry and Biology, 1999, 6, R247 (EPL review)
Camarero and Muir, JACS,
1999, 121, 5597 (cyclic SH3
via EPL)
Iwai and Plückthun, FEBS Lett.,
1999, 459, 166 (cyclic b-lactamase
via EPL)
Cotton
and Muir, JACS, 1999, 121, 1100 (SH3-SH2
biosensor)
Reading
for week of 4/19-4/23:
*Cunningham
and Wells, Science, 1989, 244, 1081 (Ala-scanning mutagenesis)
*Vogel, Cook
and Chmielewski, Chemistry and Biology, 1996,
3, 295 (enzyme
catalyzed peptide ligation)
Other
references cited in lecture:
Jackson
et al., Science, 1994, 266,
243 (subtiligase)
Braisted et al., Meth. Enzymol., 1997, 289, 298 (subtiligase
review)
Wells, Proc. Nat’l. Acad. Sci.
USA, 1996, 93, 1 (review
of hGH hormone/receptor
engineering)
Reading
for week of 4/26-4/30:
*Smith and Petrenko, Chem.
Rev., 1997, 97, 391-410 (review of phage display)
given the
length of this article it is the only assigned reading for this week
Other
references cited in lecture:
Li
et al., Science, 1995, 270,
1657 (minimization of ANP)
Lowman
et al., Biochemistry, 1991, 30,
10832 (affinity maturation of hGH)
Roberts
et al., Proc. Nat'l. Acad. Sci. USA, 1992, 89, 2429 (phage display of
BPTI to make it a good HNE inhibitor)
Atwell
et al., J. Mol. Biol., 1997, 270,
26 (remodeling protein dimmer interface)
Reading
for week of 5/3-5/7:
*Dalal et al.,
Nature Struct.
Biol., 1997, 4, 548
(solution to Paracelsus challenge)
*Cesaro-Tadic et al.,
Nature Biotech., 2003, 21, 679 (directed evolution of antibody catalysts)
Other
references cited in lecture:
Braisted and Wells, Proc.
Nat'l. Acad.
Sci. USA, 1996,
93, 5688 (minimized Z domain)
Starovasnik et al., Proc. Nat'l. Acad. Sci.
USA, 1997, 94, 10080
(optimized Z domain)
Pedersen
et al., Proc. Nat'l. Acad. Sci. USA, 1998, 95, 10523 (evolution of SNase specificity)
Stemmer,
Nature, 1994, 370, 389 (DNA shuffling of b-lactamase)
Crameri et al.,
Nature, 1998, 391, 288 (DNA shuffling with homologous genes)
Crameri et al., Nature Biotechnology,
1997, 15, 436 (pathway
evolution using DNA shuffling)
Reading
for week of 5/10-5/14:
*Yang et al., Nature Struct. Biol., 1997, 4, 548 (solution to
Paracelsus challenge)
Other
references cited in lecture:
Dahiyat and Mayo, Science,
1997, 278, 82 (computer aided
de novo design)
Malakauskas and Mayo, Nature Struct. Biol.,
1998, 5, 470 (design of more
stable B1 domain)
Benson et al., Science, 2001, 293, 1641
(biosensor design)
Looger et al., Nature,
2003, 423, 185 (computational
receptor design)
Reading
for week of 5/17-5/21:
No required reading this week on account of Scholar’s week
activities
Other
references cited in lecture:
Bolon, Voigt and Mayo, Curr. Op. Chem. Biol., 2002,
6, 125 (de novo design of biocatalysts)
Johnsson et al., Nature, 1993, 365,
5301 (oxaldie catalytic peptides)
Tanaka
and Barbas, JACS,
2002, 124, 3510 (modular
catalytic peptides)
Hilvert, D., Ann. Rev. Biochem., 2000,
69, 751 (review of catalytic antibodies)
Wagner,
Lerner and Barbas, Science, 1995, 270, 1797
(Aldolase catalytic antibody)
Rader et al., Proc. Nat'l. Acad. Sci.
USA, 2003, 100, 5396
(extending half-life of small drugs by conjugation to aldolase
antibody)
Quéméneur et al., Nature, 1998, 391,
301 (converting cyclophilin to an endopeptidase)
Lazar et
al., Curr. Op. Struc. Biol.,
2003, 13, 513 (designing
proteins for therapeutic applications)
Luo et al., Protein
Science, 2002, 11, 1218
(design of G-CSF with improved stability)
Kochendoerfer et al., Science, 2003, 299, 884
(synthetic, polymer-modified EPO)
Liu et al., Proc.
Nat'l. Acad. Sci. USA, 2003, 100, 657 (engineered anthrax toxin)
Root, Kay and Kim,
Science, 2001, 291,
884 (HIV-1 entry inhibitor design)
Bewley et al., J.
Biol. Chem., 2002, 277, 14238 (peptide
inhibitor of HIV-1 fusion)
Reading
for the remainder of the course (5/24-6/4):
*The four papers presented by student groups are REQUIRED reading,
you can get the articles at the following URL:
http://atom.chem.wwu.edu/sacahill/425/group_assignments_S04.htm