My research is concerned with the three-dimensional structures
of proteins and their biochemical functions. Most of my
work is done in collaboration with Prof.
Dagmar Ringe; we share facilities, students, and a number
of projects. The tools used by our group are X-ray crystallography,
molecular biology (especially site-directed mutagenesis),
yeast genetics, organic synthesis, enzyme kinetics and molecular
dynamics calculations. These methods are being applied to
several general problems; the ones I am most involved with
include: the structural basis for efficient enzymic catalysis
of proton and hydride transfer; the role of the metal ions
in bridged bimetalloenzyme active sites; direct visualization
of proteins in action by time-resolved protein crystallography;
the evolution of new enzyme activities from old ones; and
the biology of the quiescent state in eukaryotic cells.
In
some of these projects, we are trying to understand the
structural basis for the catalytic power of the enzymes
triose phosphate isomerase, xylose isomerase, mandelate
racemase, aminopeptidase, mutarotase and ketosteroid isomerase.
For all of them, structural information is being used to
guide site-directed mutagenesis of the active site residues
and combined quantum mechanics/molecular mechanics simulations
of the catalytic reaction.
Protein crystallography is normally a static tool and cannot
be used to follow biological reactions in real time. We
have been involved in the development of new diffraction
techniques, including Laue diffraction, that are capable
of recording entire protein crystal data sets in a millisecond.
When combined with low-temperature techniques, such methods
can be used to determine the structures of catalytic intermediates.
A new area of research in the laboratory is the use of
yeast genetics and biochemical techniques to study the quiscent
state of eukaryotic cells. We have recently shown that cells
arrest their cell cycle in G1 and then exit to the G0 state
when unfolded proteins accumulate in the cytoplasm. Accompanying
these cell cycle changes is a global shutdown in ribosomal
protein expression. This process is partly under control
of the heat shock transcription factor HSF. Another project
that uses yeast genetics and molecular biology is our attempt
to design a new metabolic pathway that will allow yeast
to grow on lactonitrile or lactamide as sole carbon sources.
The enzymes in this new pathway are being engineered from
enzymes of the mandelonitrile pathway in bacteria by a combination
of structure-directed and random mutagenesis.
Selected Publications:
Lieberman RL, Wustman BA, Huertas P, Powe AC Jr, Pine CW,
Khanna R, Schlossmacher MG, Ringe D, Petsko GA. (2007) Structure
of acid beta-glucosidase with pharmacological chaperone
provides insight into Gaucher disease. Nat Chem Biol.
2007 Feb;3(2):101-107. [abstract]
Ding X, Rasmussen BF, Petsko GA, Ringe D. (2006) Direct
crystallographic observation of an acyl-enzyme intermediate
in the elastase-catalyzed hydrolysis of a peptidyl ester
substrate: Exploiting the "glass transition" in protein
dynamics. Bioorg Chem. 2006 Dec;34(6):410-23. [abstract]
Kraut DA, Sigala PA, Pybus B, Liu CW, Ringe D, Petsko GA,
Herschlag D. (2006) Testing electrostatic complementarity
in enzyme catalysis: hydrogen bonding in the ketosteroid
isomerase oxyanion hole. PLoS Biol. 2006 Apr;4(4):e99.
Desmarais W, Bienvenue DL, Bzymek KP, Petsko GA, Ringe
D, Holz RC. (2006) The high-resolution structures of the
neutral and the low pH crystals of aminopeptidase from Aeromonas
proteolytica. J Biol Inorg Chem. 2006 Jun;11(4):398-408.
[abstract]
Das C, Hoang QQ, Kreinbring CA, Luchansky SJ, Meray RK,
Ray SS, Lansbury PT, Ringe D, Petsko GA. (2006) Structural
basis for conformational plasticity of the Parkinson's disease-associated
ubiquitin hydrolase UCH-L1. Proc Natl Acad Sci U S A.
2006 Mar 21;103(12):4675-80. [abstract]
Mattos C, Bellamacina CR, Peisach E, Pereira A, Vitkup
D, Petsko GA, Ringe D. (2006) Multiple solvent crystal structures:
probing binding sites, plasticity and hydration. J Mol
Biol. 2006 Apr 14;357(5):1471-82. [abstract]
Zhou W, Zhu M, Wilson MA, Petsko GA, Fink AL. (2006) The
oxidation state of DJ-1 regulates its chaperone activity
toward alpha-synuclein. J Mol Biol. 2006 Mar 3;356(4):1036-48.
[abstract]
Wilson MA, Ringe D, Petsko GA. (2005) The atomic resolution
crystal structure of the YajL (ThiJ) protein from Escherichia
coli: a close prokaryotic homologue of the Parkinsonism-associated
protein DJ-1. J Mol Biol. 2005 Oct 28;353(3):678-91.
[abstract]
Bzymek KP, Moulin A, Swierczek SI, Ringe D, Petsko GA,
Bennett B, Holz RC. (2005) Kinetic, spectroscopic, and X-ray
crystallographic characterization of the functional E151H
aminopeptidase from Aeromonas proteolytica. Biochemistry.
2005 Sep 13;44(36):12030-40. [abstract]
Liu D, Lepore BW, Petsko GA, Thomas PW, Stone EM, Fast
W, Ringe D. (2005) Three-dimensional structure of the quorum-quenching
N-acyl homoserine lactone hydrolase from Bacillus thuringiensis.
Proc Natl Acad Sci U S A. 2005 Aug 16;102(33):11882-7.
[abstract]
View Complete Publication List on PubMed:
Gregory Petsko
Last update: February 6, 2007. E-mail comments
or questions to the webmaster.
