Structural Determination of StAhpC2 and MpGlpO
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Transcript Structural Determination of StAhpC2 and MpGlpO
Structural Studies of StAhpC2
and MpGlpO
By: Callia K. Palioca
Mentor: Dr. P. Andrew Karplus
Department of Biochemistry & Biophysics, OSU
HHMI Summer Program 2010
Proteins are IMPORTANT
Enzymes are vital in all of life’s functions
Most drugs interact with proteins
Myosin
Actin
Protein Structure Matters
Function flows from structure
Structure-based drug design
HIV protease drug
complex
X-Ray Crystallography Methods
Goal: Obtain single, high-quality diffracting crystals and
use the data to solve the structure
Grow
Grow
Crystal
Crystal
Diffraction&
Diffraction
&Data
Data
Processing
Processing
Solve
the
Solve the
Phase
Phase
Problem
Problem
Electron
Electron
Density
Density Map
Map
Refinement
Refinement
of
of Structure
Structure
Food Poisoning
Macrophage attacking bacteria
StAhpC2 and the Peroxiredoxins
Catalytic cycle of this family of proteins
Function: uses cysteine residues to breakdown peroxides
How Motifs Relate to Sensitivity
Correlation
Sensitive
between YF and
a helical
structure
Leads to
sensitive
enzymes
Robust
AhpC2 C50S
YL vs. YF
Seen in significant
human pathogens that
cause African sleeping
sickness, ulcers, malaria,
and Beaver Fever
Hypothesis
StAhpC2 is a representative of the proteins in
deadly human pathogens
Structure gives insights into pathogen survival in
humans and forms basis for drug design
YF motif significance can also be studied
Crystals!
Pure protein from Dr. Leslie Poole’s
lab, WFU
Optimizing conditions
(NH4)2HPO4
pH
Grow Crystal
Diffraction &
Data Processing
Solve the Phase
Problem
Electron
Density Map
Refinement of
Structure
Crystals!
Grow Crystal
Diffraction &
Data Processing
Solve the Phase
Problem
Electron
Density Map
Refinement of
Structure
Crystals!
Predictions do
not line up
Stalled progress
Grow Crystal
Diffraction &
Data Processing
Solve the Phase
Problem
Electron
Density Map
Refinement of
Structure
The Mycoplasma Diseases
Mycoplasma pneumoniae
Walking pneumonia
Mycoplasma mycoides
Contagious bovine pleuropnemonia
GlpO
(Glycerolphosphate oxidase)
What is known
Structure of GlpO
No substrates able to be
bound
DHAP,
tartaric acid,
2-phosphoglycerate,
menadione,
G3P,
phosphoenolpyruvate
Hypothesis
Drug target
Substrates, products and inhibitors in GlpO
Insight into Mycoplasma and other organisms cause
disease
Basis for structure-based drug design
Crystallization
Pure protein from Dr. Al Claiborne’s
lab, WFU
NaCl and neutral-basic pH buffer
Grow Crystal
Diffraction &
Data Processing
Solve the Phase
Problem
Electron
Density Map
Refinement of
Structure
Diffraction and Data Processing
Resolution:
enough to define
atomic structure
(3.0 Å)
Grow Crystal
Diffraction &
Data Processing
Solve the Phase
Problem
Electron
Density Map
Refinement of
Structure
Molecular Replacement
The Phase Problem
Structure of related protein (3DME)
Height
Grow Crystal
Diffraction &
Data Processing
Solving the
Phase Problem
Electron
Density Map
Refinement of
Structure
A Good Solution
Differences between model and map
Grow Crystal
Diffraction &
Data Processing
Solving the
Phase Problem
Electron
Density Map
Refinement of
Structure
Structure Refinement
Process of manually changing sequence
Avoiding model bias
R-free vs. Round of
Refinement
R-free
0.6
0.4
0.2
0
1
Grow Crystal
Diffraction &
Data Processing
Solve the Phase
Problem
2
3
4
5
6
Round of Refinement
Electron
Density Map
7
Refinement of
Structure
Future Work
Continue refinement of
structure
Soaking of substrates
Optimization of
cryo-protectant
R-factor vs. Round of
Refinement
0.6
0.4
0.2
0
1 2 3 4 5 6 7 8 9 10 11 12
15% glycerol
0% glycerol
10% glycerol
15% glycerol
Acknowledgements
Dr. P. Andrew Karplus
The rest of the Karplus lab
Dr. Andrea Hall, Camden Driggers, Ian Winter
HHMI, Cripps
URISC
Our collaborators
at Wake Forest
University
Dr. Leslie Poole
Dr. Al Claiborne
Dr. Kevin Ahern