Synchrotron X-ray based Investigation of Fe and Zn Atoms in Tissue Samples at Different Growth Stages
The zinc and iron environments in different growth
stages have been studied with EXAFS and XANES with Brookhaven
Synchrotron Light Source. Tissue samples included meat, organ,
vegetable, leaf, and yeast. The project studied the EXAFS and
XANES of tissue samples using Zn and Fe K-edges. Duck embryo
samples show that brain and intestine would contain shorter EXFAS
determined Zn-N/O bond; as with the cases of fresh yeast versus
reconstituted live yeast and green leaf versus yellow leaf. The
XANES Fourier transform characteristic-length would be useful as a
functionality index for selected types of tissue samples in various
physical states. The extension to the development of functional
synchrotron imaging for tissue engineering application based on
spectroscopic technique is discussed.
[1] Shi W, Chance MR. (2011) Metalloproteomics: forward and reverse
approaches in metalloprotein structural and functional characterization
Curr Opin Chem Biol. Feb;15(1):144-8.
[2] Ascone I & Strange R. (2009) Biological X-ray absorption spectroscopy
and metalloproteomics. J Synchrotron Radiat. 2009 May;16(Pt 3):413-
21.
[3] Newcomb M, Halgrimson JA, Horner JH, Wasinger EC, Chen LX,
Sligar SG. (2008) X-ray absorption spectroscopic characterization of a
cytochrome P450 compound II derivative. Proc Natl Acad Sci U S A.
Jun 17;105(24):8179-84.
[4] Liu C, Hong FS, Tao Y, Liu T, Xie YN, Xu JH, Li ZR (2011). The
mechanism of the molecular interaction between cerium (III) and
ribulose-1,5-bisphosphate carboxylase/oxygenase (Rubisco). Biol Trace
Elem Res. Nov;143(2):1110-20. Epub 2010 Oct 30.
[5] Meharenna, Y.T.; Doukov, T.; Li, H.; Soltis, S.M.; Poulos, T.L.
"Crystallographic and single-crystal spectral analysis of the peroxidase
ferryl intermediate," (2010) Biochemistry 49, 2984-2986.
[6] Corbett, M. C., Latimer, M. J., Poulos, T. L., Sevrioukova, I. F.,
Hodgson, K. O., and Hedman, B. (2007) Photoreduction of the active
site of the metalloprotein putidaredoxin by synchrotron radiation. Acta
Crystallogr D Biol Crystallogr 63, 951-960.
[7] Sarret G, Willems G, Isaure MP, Marcus MA, Fakra SC, Frérot H, Pairis
S, Geoffroy N, Manceau A, Saumitou-Laprade P. (2009) Zinc
distribution and speciation in Arabidopsis halleri x Arabidopsis lyrata
progenies presenting various zinc accumulation capacities. New Phytol.
Nov;184(3):581-95.
[8] Giachini L, Veronesi G, Francia F, Venturoli G, Boscherini F. (2010)
Synergic approach to XAFS analysis for the identification of most
probable binding motifs for mononuclear zinc sites in metalloproteins. J
Synchrotron Radiat. Jan;17(1):41-52.
[9] Wang C, Vernon R, Lange O, Tyka M, Baker D. (2010) Prediction of
structures of zinc-binding proteins through explicit modeling of metal
coordination geometry. Protein Sci. Mar;19(3):494-506.
[10] Chen J, Zhang H, Tomov IV, Ding X, Rentzepis PM. (2008)
Photochemistry and electron-transfer mechanism of transition metal
oxalato complexes excited in the charge transfer band. Proc Natl Acad
Sci U S A. Oct 7;105(40):15235-40.
[11] Bugaev L, Farges F, Rusakova E, Sokolenko A, Latokha Y, Avakyan L.
(2005) Fe coordination environment in Fe(II)- and Fe(III)-silicate glasses
via the Fourier-transform analysis of Fe K-XANES. Physica Scripta. Vol.
T115, 215-217.
[12] Colangelo CM, Lewis LM, Cosper NJ, Scott RA. (2000) Structural
evidence for a common zinc binding domain in archaeal and eukaryal
transcription factor IIB proteins J Biol Inorg Chem. Apr; 5(2):276-83.
[13] Wellenreuther G, Parthasarathy V, Meyer-Klaucke W.(2010) Towards a
black-box for biological EXAFS data analysis. II. Automatic BioXAS
Refinement and Analysis (ABRA). J Synchrotron Radiat. Jan; 17(1):25-
35.
[14] Lancaster WA, Praissman JL, Poole FL 2nd, Cvetkovic A, Menon AL,
Scott JW, Jenney FE Jr, Thorgersen MP, Kalisiak E, Apon JV, Trauger
SA, Siuzdak G, Tainer JA, Adams MW. (2011) A computational
framework for proteome-wide pursuit and prediction of metalloproteins
using ICP-MS and MS/MS data. BMC Bioinformatics. Feb 28;12:64.
[15] Shi W, Punta M, Bohon J, Sauder JM, D'Mello R, Sullivan M, Toomey J,
Abel D, Lippi M, Passerini A, Frasconi P, Burley SK, Rost B, Chance
MR. (2011) Characterization of metalloproteins by high-throughput Xray
absorption spectroscopy. Genome Res. Jun;21(6):898-907.
[1] Shi W, Chance MR. (2011) Metalloproteomics: forward and reverse
approaches in metalloprotein structural and functional characterization
Curr Opin Chem Biol. Feb;15(1):144-8.
[2] Ascone I & Strange R. (2009) Biological X-ray absorption spectroscopy
and metalloproteomics. J Synchrotron Radiat. 2009 May;16(Pt 3):413-
21.
[3] Newcomb M, Halgrimson JA, Horner JH, Wasinger EC, Chen LX,
Sligar SG. (2008) X-ray absorption spectroscopic characterization of a
cytochrome P450 compound II derivative. Proc Natl Acad Sci U S A.
Jun 17;105(24):8179-84.
[4] Liu C, Hong FS, Tao Y, Liu T, Xie YN, Xu JH, Li ZR (2011). The
mechanism of the molecular interaction between cerium (III) and
ribulose-1,5-bisphosphate carboxylase/oxygenase (Rubisco). Biol Trace
Elem Res. Nov;143(2):1110-20. Epub 2010 Oct 30.
[5] Meharenna, Y.T.; Doukov, T.; Li, H.; Soltis, S.M.; Poulos, T.L.
"Crystallographic and single-crystal spectral analysis of the peroxidase
ferryl intermediate," (2010) Biochemistry 49, 2984-2986.
[6] Corbett, M. C., Latimer, M. J., Poulos, T. L., Sevrioukova, I. F.,
Hodgson, K. O., and Hedman, B. (2007) Photoreduction of the active
site of the metalloprotein putidaredoxin by synchrotron radiation. Acta
Crystallogr D Biol Crystallogr 63, 951-960.
[7] Sarret G, Willems G, Isaure MP, Marcus MA, Fakra SC, Frérot H, Pairis
S, Geoffroy N, Manceau A, Saumitou-Laprade P. (2009) Zinc
distribution and speciation in Arabidopsis halleri x Arabidopsis lyrata
progenies presenting various zinc accumulation capacities. New Phytol.
Nov;184(3):581-95.
[8] Giachini L, Veronesi G, Francia F, Venturoli G, Boscherini F. (2010)
Synergic approach to XAFS analysis for the identification of most
probable binding motifs for mononuclear zinc sites in metalloproteins. J
Synchrotron Radiat. Jan;17(1):41-52.
[9] Wang C, Vernon R, Lange O, Tyka M, Baker D. (2010) Prediction of
structures of zinc-binding proteins through explicit modeling of metal
coordination geometry. Protein Sci. Mar;19(3):494-506.
[10] Chen J, Zhang H, Tomov IV, Ding X, Rentzepis PM. (2008)
Photochemistry and electron-transfer mechanism of transition metal
oxalato complexes excited in the charge transfer band. Proc Natl Acad
Sci U S A. Oct 7;105(40):15235-40.
[11] Bugaev L, Farges F, Rusakova E, Sokolenko A, Latokha Y, Avakyan L.
(2005) Fe coordination environment in Fe(II)- and Fe(III)-silicate glasses
via the Fourier-transform analysis of Fe K-XANES. Physica Scripta. Vol.
T115, 215-217.
[12] Colangelo CM, Lewis LM, Cosper NJ, Scott RA. (2000) Structural
evidence for a common zinc binding domain in archaeal and eukaryal
transcription factor IIB proteins J Biol Inorg Chem. Apr; 5(2):276-83.
[13] Wellenreuther G, Parthasarathy V, Meyer-Klaucke W.(2010) Towards a
black-box for biological EXAFS data analysis. II. Automatic BioXAS
Refinement and Analysis (ABRA). J Synchrotron Radiat. Jan; 17(1):25-
35.
[14] Lancaster WA, Praissman JL, Poole FL 2nd, Cvetkovic A, Menon AL,
Scott JW, Jenney FE Jr, Thorgersen MP, Kalisiak E, Apon JV, Trauger
SA, Siuzdak G, Tainer JA, Adams MW. (2011) A computational
framework for proteome-wide pursuit and prediction of metalloproteins
using ICP-MS and MS/MS data. BMC Bioinformatics. Feb 28;12:64.
[15] Shi W, Punta M, Bohon J, Sauder JM, D'Mello R, Sullivan M, Toomey J,
Abel D, Lippi M, Passerini A, Frasconi P, Burley SK, Rost B, Chance
MR. (2011) Characterization of metalloproteins by high-throughput Xray
absorption spectroscopy. Genome Res. Jun;21(6):898-907.
@article{"International Journal of Biological, Life and Agricultural Sciences:56643", author = "Sunil Dehipawala and Todd Holden and E. Cheung and Robert Regan and P. Schneider and G. Tremberger Jr and D.
Lieberman and T. Cheung", title = "Synchrotron X-ray based Investigation of Fe and Zn Atoms in Tissue Samples at Different Growth Stages", abstract = "The zinc and iron environments in different growth
stages have been studied with EXAFS and XANES with Brookhaven
Synchrotron Light Source. Tissue samples included meat, organ,
vegetable, leaf, and yeast. The project studied the EXAFS and
XANES of tissue samples using Zn and Fe K-edges. Duck embryo
samples show that brain and intestine would contain shorter EXFAS
determined Zn-N/O bond; as with the cases of fresh yeast versus
reconstituted live yeast and green leaf versus yellow leaf. The
XANES Fourier transform characteristic-length would be useful as a
functionality index for selected types of tissue samples in various
physical states. The extension to the development of functional
synchrotron imaging for tissue engineering application based on
spectroscopic technique is discussed.", keywords = "EXAFS, Fourier Transform, metalloproteins,
XANES", volume = "6", number = "7", pages = "477-5", }
