structural characterization of non- crystalline systems biophysics and synchrotron radiation james...
DESCRIPTION
Zn Penner-Hahn group’s view of protein structure The good stuff The chicken fatTRANSCRIPT
![Page 1: Structural characterization of non- crystalline systems Biophysics and Synchrotron Radiation James E. Penner-Hahn Department of Chemistry & Biophysics](https://reader035.vdocuments.site/reader035/viewer/2022062317/5a4d1b117f8b9ab05998fbe2/html5/thumbnails/1.jpg)
Structural characterization of non-crystalline systems
Biophysics and Synchrotron Radiation
James E. Penner-HahnDepartment of Chemistry &
Biophysics Research DivisionThe University of Michigan
![Page 2: Structural characterization of non- crystalline systems Biophysics and Synchrotron Radiation James E. Penner-Hahn Department of Chemistry & Biophysics](https://reader035.vdocuments.site/reader035/viewer/2022062317/5a4d1b117f8b9ab05998fbe2/html5/thumbnails/2.jpg)
Outline
• Motivation – why do we want to do this• Experimental – spectrometer details• Theory – physical background• System – biological background• Results
![Page 3: Structural characterization of non- crystalline systems Biophysics and Synchrotron Radiation James E. Penner-Hahn Department of Chemistry & Biophysics](https://reader035.vdocuments.site/reader035/viewer/2022062317/5a4d1b117f8b9ab05998fbe2/html5/thumbnails/3.jpg)
Zn
Penner-Hahn group’s view of protein structure
The good stuff
The chicken fat
![Page 4: Structural characterization of non- crystalline systems Biophysics and Synchrotron Radiation James E. Penner-Hahn Department of Chemistry & Biophysics](https://reader035.vdocuments.site/reader035/viewer/2022062317/5a4d1b117f8b9ab05998fbe2/html5/thumbnails/4.jpg)
Techniques for studying metal sites in proteins
• UV-visible spectroscopy• EPR spectroscopy• Magnetic susceptibility• MCD
Require open d shell
Requires I=1/2 nucleus
Requires crystals• X-ray crystallography
• NMR spectroscopy
![Page 5: Structural characterization of non- crystalline systems Biophysics and Synchrotron Radiation James E. Penner-Hahn Department of Chemistry & Biophysics](https://reader035.vdocuments.site/reader035/viewer/2022062317/5a4d1b117f8b9ab05998fbe2/html5/thumbnails/5.jpg)
Outline
• Motivation – why do we want to do this• Experimental – spectrometer details• Theory – physical background• System – biological background• Results
![Page 6: Structural characterization of non- crystalline systems Biophysics and Synchrotron Radiation James E. Penner-Hahn Department of Chemistry & Biophysics](https://reader035.vdocuments.site/reader035/viewer/2022062317/5a4d1b117f8b9ab05998fbe2/html5/thumbnails/6.jpg)
![Page 7: Structural characterization of non- crystalline systems Biophysics and Synchrotron Radiation James E. Penner-Hahn Department of Chemistry & Biophysics](https://reader035.vdocuments.site/reader035/viewer/2022062317/5a4d1b117f8b9ab05998fbe2/html5/thumbnails/7.jpg)
![Page 8: Structural characterization of non- crystalline systems Biophysics and Synchrotron Radiation James E. Penner-Hahn Department of Chemistry & Biophysics](https://reader035.vdocuments.site/reader035/viewer/2022062317/5a4d1b117f8b9ab05998fbe2/html5/thumbnails/8.jpg)
![Page 9: Structural characterization of non- crystalline systems Biophysics and Synchrotron Radiation James E. Penner-Hahn Department of Chemistry & Biophysics](https://reader035.vdocuments.site/reader035/viewer/2022062317/5a4d1b117f8b9ab05998fbe2/html5/thumbnails/9.jpg)
![Page 10: Structural characterization of non- crystalline systems Biophysics and Synchrotron Radiation James E. Penner-Hahn Department of Chemistry & Biophysics](https://reader035.vdocuments.site/reader035/viewer/2022062317/5a4d1b117f8b9ab05998fbe2/html5/thumbnails/10.jpg)
![Page 11: Structural characterization of non- crystalline systems Biophysics and Synchrotron Radiation James E. Penner-Hahn Department of Chemistry & Biophysics](https://reader035.vdocuments.site/reader035/viewer/2022062317/5a4d1b117f8b9ab05998fbe2/html5/thumbnails/11.jpg)
![Page 12: Structural characterization of non- crystalline systems Biophysics and Synchrotron Radiation James E. Penner-Hahn Department of Chemistry & Biophysics](https://reader035.vdocuments.site/reader035/viewer/2022062317/5a4d1b117f8b9ab05998fbe2/html5/thumbnails/12.jpg)
![Page 13: Structural characterization of non- crystalline systems Biophysics and Synchrotron Radiation James E. Penner-Hahn Department of Chemistry & Biophysics](https://reader035.vdocuments.site/reader035/viewer/2022062317/5a4d1b117f8b9ab05998fbe2/html5/thumbnails/13.jpg)
![Page 14: Structural characterization of non- crystalline systems Biophysics and Synchrotron Radiation James E. Penner-Hahn Department of Chemistry & Biophysics](https://reader035.vdocuments.site/reader035/viewer/2022062317/5a4d1b117f8b9ab05998fbe2/html5/thumbnails/14.jpg)
![Page 15: Structural characterization of non- crystalline systems Biophysics and Synchrotron Radiation James E. Penner-Hahn Department of Chemistry & Biophysics](https://reader035.vdocuments.site/reader035/viewer/2022062317/5a4d1b117f8b9ab05998fbe2/html5/thumbnails/15.jpg)
Outline
• Motivation – why do we want to do this• Experimental – spectrometer details• Theory – physical background• System – biological background• Results
![Page 16: Structural characterization of non- crystalline systems Biophysics and Synchrotron Radiation James E. Penner-Hahn Department of Chemistry & Biophysics](https://reader035.vdocuments.site/reader035/viewer/2022062317/5a4d1b117f8b9ab05998fbe2/html5/thumbnails/16.jpg)
X-ray absorption spectroscopy
SA
A S
E 2E 1
![Page 17: Structural characterization of non- crystalline systems Biophysics and Synchrotron Radiation James E. Penner-Hahn Department of Chemistry & Biophysics](https://reader035.vdocuments.site/reader035/viewer/2022062317/5a4d1b117f8b9ab05998fbe2/html5/thumbnails/17.jpg)
coordinationnumber
bondlength
scatterer
scatterer
-10
-5
0
5
10
0 2 4 6 8 10 12
EXA
FS•k
3
k (Å -1)
Amplitude
Frequency
Phase
Shape
![Page 18: Structural characterization of non- crystalline systems Biophysics and Synchrotron Radiation James E. Penner-Hahn Department of Chemistry & Biophysics](https://reader035.vdocuments.site/reader035/viewer/2022062317/5a4d1b117f8b9ab05998fbe2/html5/thumbnails/18.jpg)
where
and
-10
-5
0
5
10
0 2 4 6 8 10 12
EXA
FS•k
3
k (Å -1 )
Amplitude
coordinationnumber
Frequency
bondlength
Phase
scatterer
Shape
scatterer
k N sAs k S02
kRas2 exp 2k 2as
2 exp 2Ras sin 2kRas as k
k 2me E Eo 2
k E o E o E
E s E
b E
![Page 19: Structural characterization of non- crystalline systems Biophysics and Synchrotron Radiation James E. Penner-Hahn Department of Chemistry & Biophysics](https://reader035.vdocuments.site/reader035/viewer/2022062317/5a4d1b117f8b9ab05998fbe2/html5/thumbnails/19.jpg)
X-ray fluorescence spectra give element sensitivity
![Page 20: Structural characterization of non- crystalline systems Biophysics and Synchrotron Radiation James E. Penner-Hahn Department of Chemistry & Biophysics](https://reader035.vdocuments.site/reader035/viewer/2022062317/5a4d1b117f8b9ab05998fbe2/html5/thumbnails/20.jpg)
0
10000
20000
30000
40000
50000
0 200 400 600 800 1000
Cou
nts
[Zn(II)] (M)
Sensitivity of XRFWide dynamic range
![Page 21: Structural characterization of non- crystalline systems Biophysics and Synchrotron Radiation James E. Penner-Hahn Department of Chemistry & Biophysics](https://reader035.vdocuments.site/reader035/viewer/2022062317/5a4d1b117f8b9ab05998fbe2/html5/thumbnails/21.jpg)
0
1000
2000
3000
4000
5000
0 20 40 60 80 100
Cou
nts
[Zn(II)] (M)
Detection limit (S/N=3)ca. 8 M
Sensitivity of XRF
femtomole detection limits< 1 nL irradiated volume
![Page 22: Structural characterization of non- crystalline systems Biophysics and Synchrotron Radiation James E. Penner-Hahn Department of Chemistry & Biophysics](https://reader035.vdocuments.site/reader035/viewer/2022062317/5a4d1b117f8b9ab05998fbe2/html5/thumbnails/22.jpg)
Kirkpatrick-Baez focusing optics ~ 1 m spot size
Zone plate ~ 30 nm spot size
![Page 23: Structural characterization of non- crystalline systems Biophysics and Synchrotron Radiation James E. Penner-Hahn Department of Chemistry & Biophysics](https://reader035.vdocuments.site/reader035/viewer/2022062317/5a4d1b117f8b9ab05998fbe2/html5/thumbnails/23.jpg)
Outline
• Motivation – why do we want to do this• Experimental – spectrometer details• Theory – physical background• System – biological background• Results
![Page 24: Structural characterization of non- crystalline systems Biophysics and Synchrotron Radiation James E. Penner-Hahn Department of Chemistry & Biophysics](https://reader035.vdocuments.site/reader035/viewer/2022062317/5a4d1b117f8b9ab05998fbe2/html5/thumbnails/24.jpg)
Hippocampus
• Located within the temporal lobe • Important for converting short term
memory into permanent memory• Early target of Alzheimer’s disease
Hippocampus
![Page 25: Structural characterization of non- crystalline systems Biophysics and Synchrotron Radiation James E. Penner-Hahn Department of Chemistry & Biophysics](https://reader035.vdocuments.site/reader035/viewer/2022062317/5a4d1b117f8b9ab05998fbe2/html5/thumbnails/25.jpg)
CA3Dentategyrus
Hippocampus is rich in “chelatable” Zn, as determined using TIMM’s staining (sulfide/silver)
![Page 26: Structural characterization of non- crystalline systems Biophysics and Synchrotron Radiation James E. Penner-Hahn Department of Chemistry & Biophysics](https://reader035.vdocuments.site/reader035/viewer/2022062317/5a4d1b117f8b9ab05998fbe2/html5/thumbnails/26.jpg)
Outline
• Motivation – why do we want to do this• Experimental – spectrometer details• Theory – physical background• System – biological background• Results
![Page 27: Structural characterization of non- crystalline systems Biophysics and Synchrotron Radiation James E. Penner-Hahn Department of Chemistry & Biophysics](https://reader035.vdocuments.site/reader035/viewer/2022062317/5a4d1b117f8b9ab05998fbe2/html5/thumbnails/27.jpg)
X-ray microprobe allows determination of total Zn (and other metals) on the m scale
![Page 28: Structural characterization of non- crystalline systems Biophysics and Synchrotron Radiation James E. Penner-Hahn Department of Chemistry & Biophysics](https://reader035.vdocuments.site/reader035/viewer/2022062317/5a4d1b117f8b9ab05998fbe2/html5/thumbnails/28.jpg)
![Page 29: Structural characterization of non- crystalline systems Biophysics and Synchrotron Radiation James E. Penner-Hahn Department of Chemistry & Biophysics](https://reader035.vdocuments.site/reader035/viewer/2022062317/5a4d1b117f8b9ab05998fbe2/html5/thumbnails/29.jpg)
Cu may be localized in myelin in older rats
Fe: 0.18 mM average conc.
Cu: 0.24 mM average conc.
Zn: 0.23 mM average conc.
![Page 30: Structural characterization of non- crystalline systems Biophysics and Synchrotron Radiation James E. Penner-Hahn Department of Chemistry & Biophysics](https://reader035.vdocuments.site/reader035/viewer/2022062317/5a4d1b117f8b9ab05998fbe2/html5/thumbnails/30.jpg)
Zn EXAFS for Hilus of Dentate Gyrus
k0 2 4 6 8 10 12
Frac
tiona
l Mod
ulat
ion
-10-8-6-4-202468
Zn EXAFSFit
![Page 31: Structural characterization of non- crystalline systems Biophysics and Synchrotron Radiation James E. Penner-Hahn Department of Chemistry & Biophysics](https://reader035.vdocuments.site/reader035/viewer/2022062317/5a4d1b117f8b9ab05998fbe2/html5/thumbnails/31.jpg)
Fourier Transform and Fit
R+0 1 2 3 4 5
FT m
agni
tude
0
2
4
6
8
10
FTFit Fits as 3.8 O/N at
1.945 Angstroms
Debye-Waller=0.006