Recent Advances in X-Ray Hydroxyl Radical Footprinting at the Advanced Light Source Synchrotron

Author(s): Simon A. Morton, Sayan Gupta, Christopher J. Petzold, Corie Y. Ralston*

Journal Name: Protein & Peptide Letters

Volume 26 , Issue 1 , 2019

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Graphical Abstract:


Background: Synchrotron hydroxyl radical footprinting is a relatively new structural method used to investigate structural features and conformational changes of nucleic acids and proteins in the solution state. It was originally developed at the National Synchrotron Light Source at Brookhaven National Laboratory in the late nineties, and more recently, has been established at the Advanced Light Source at Lawrence Berkeley National Laboratory. The instrumentation for this method is an active area of development, and includes methods to increase dose to the samples while implementing high-throughput sample delivery methods.

Conclusion: Improving instrumentation to irradiate biological samples in real time using a sample droplet generator and inline fluorescence monitoring to rapidly determine dose response curves for samples will significantly increase the range of biological problems that can be investigated using synchrotron hydroxyl radical footprinting.

Keywords: Synchrotron, footprinting, hydroxyl radical footprinting, x-ray, beamline, radiolysis, radiolytic labeling, Advanced Light Source.

Xu, G.; Chance, M.R. Hydroxyl radical-mediated modification of proteins as probes for structural proteomics. Chem. Rev., 2007, 107(8), 3514-3543.
Liljenzin, J. Radiation Effects on Matter.Radiochemistry and Nuclear Chemistry, 3rd ed; Choppin, G.R., Ed.; Butterworth-Heinemann: Oxford, United Kingdom, 2002.
Gupta, S.; Sullivan, M.; Toomey, J.; Kiselar, J.; Chance, M.R. The beamline X28C of the center for synchrotron biosciences: A national resource for biomolecular structure and dynamics experiments using synchrotron footprinting. J. Synchrotron Radiat., 2007, 14(Pt 3), 233-243.
Soper, S.F.C.; Dator, R.P.; Limbach, P.A.; Woodson, S.A. In vivo X-ray footprinting of pre-30S ribosomes reveals chaperone-dependent remodeling of late assembly intermediates. Mol. Cell, 2013, 52(4), 506-516.
Hulscher, R.M.; Bohon, J.; Rappe, M.C.; Gupta, S.; D’Mello, R.; Sullivan, M.; Ralston, C.Y.; Chance, M.R.; Woodson, S.A. Probing the structure of ribosome assembly intermediates in vivo using DMS and hydroxyl radical footprinting. Methods, 2016, 103, 49-56.
Orban, T.; Gupta, S.; Palczewski, K.; Chance, M.R. Visualizing water molecules in transmembrane proteins using radiolytic labeling methods. Biochemistry, 2010, 49(5), 827-834.
Bohon, J.; Jennings, L.D.; Phillips, C.M.; Licht, S.; Chance, M.R. Synchrotron protein footprinting supports substrate translocation by ClpA via ATP-induced movements of the D2 loop. Structure, 2008, 16(8), 1157-1165.
Kiselar, J.G.; Mahaffy, R.; Pollard, T.D.; Almo, S.C.; Chance, M.R. Visualizing Arp2/3 complex activation mediated by binding of ATP and WASp using structural mass spectrometry. Proc. Natl. Acad. Sci. USA, 2007, 104(5), 1552-1557.
Gupta, S.; Cheng, H.; Mollah, A.K.; Jamison, E.; Morris, S.; Chance, M.R.; Khrapunov, S.; Brenowitz, M. DNA and protein footprinting analysis of the modulation of DNA binding by the N-terminal domain of the Saccharomyces cerevisiae TATA binding protein. Biochemistry, 2007, 46(35), 9886-9898.
Gupta, S.; Chai, J.; Cheng, J.; D’Mello, R.; Chance, M.R.; Fu, D. Visualizing the kinetic power stroke that drives proton-coupled zinc(II) transport. Nature, 2014, 512(7512), 101-104.
Gupta, S.; Guttman, M.; Leverenz, R.L.; Zhumadilova, K.; Pawlowski, E.G.; Petzold, C.J.; Lee, K.K.; Ralston, C.Y.; Kerfeld, C.A. Local and global structural drivers for the photoactivation of the orange carotenoid protein. Proc. Natl. Acad. Sci. USA, 2015, 112(41), E5567-E5574.
Deperalta, G.; Alvarez, M.; Bechtel, C.; Dong, K.; McDonald, R.; Ling, V. Structural analysis of a therapeutic monoclonal antibody dimer by hydroxyl radical footprinting. MAbs, 2013, 5(1), 86-101.
Gupta, S.; Celestre, R.; Petzold, C.J.; Chance, M.R.; Ralston, C. Development of a microsecond X-ray protein footprinting facility at the advanced light source. J. Synchrotron Radiat., 2014, 21(Pt 4), 690-699.
Bohon, J.; D’Mello, R.; Ralston, C.; Gupta, S.; Chance, M.R. Synchrotron X-ray footprinting on tour. J. Synchrotron Radiat., 2014, 21, 8.
Baud, A.; Ayme, L.; Gonnet, F.; Salard, I.; Gohon, Y.; Jolivet, P.; Brodolin, K.; Da Silva, P.; Giuliani, A.; Sclavi, B.; Chardot, T.; Mercere, P.; Roblin, P.; Daniel, R. SOLEIL shining on the solution-state structure of biomacromolecules by synchrotron X-ray footprinting at the Metrology beamline. J. Synchrotron Radiat., 2017, 24(Pt 3), 576-585.
Earnest, T.; Padmore, H.; Cork, C.; Behrsing, R.; Kim, S.H. The macromolecular crystallography facility at the advanced light source. J. Cryst. Growth, 1996, 168(1-4), 5.
MacDowell, A.A.; Celestre, R.S.; Howells, M.; McKinney, W.; Krupnick, J.; Cambie, D.; Domning, E.E.; Duarte, R.M.; Kelez, N.; Plate, D.W.; Cork, C.W.; Earnest, T.N.; Dickert, J.; Meigs, G.; Ralston, C.; Holton, J.M.; Alber, T.; Berger, J.M.; Agard, D.A.; Padmore, H.A. Suite of three protein crystallography beamlines with single superconducting bend magnet as the source. J. Synchrotron Radiat., 2004, 11(Pt 6), 447-455.
Gupta, S.; Feng, J.; Chan, L.J.; Petzold, C.J.; Ralston, C.Y. Synchrotron X-ray footprinting as a method to visualize water in proteins. J. Synchrotron Radiat., 2016, 23(Pt 5), 1056-1069.
Gupta, S.; Bavro, V.N.; D’Mello, R.; Tucker, S.J.; Venien-Bryan, C.; Chance, M.R. Conformational changes during the gating of a potassium channel revealed by structural mass spectrometry. Structure, 2010, 18(7), 839-846.
Schneider, C.A.; Rasband, W.S.; Eliceiri, K.W. NIH Image to Image J: 25 years of image analysis. Nat. Methods, 2012, 9(7), 671-675.
Ehrlich, S.N.; Hanson, J.C.; Camara, A.L.; Barrio, L.; Estrella, M.; Zhou, G.; Si, R.; Khalid, S.; Wang, Q. Combined XRD and XAS. Nucl. Instrum. Methods Phys. Res. A, 2011, 646(1), 3.
del Rio, M.S.; Canestrari, N.; Jiang, F.; Cerrina, F. SHADOW3: A new version of the synchrotron X-ray optics modelling package. J. Synchrotron Radiat., 2011, 18(Pt 5), 708-716.
Gonzalez Fernandez-Nino, S.M.; Smith-Moritz, A.M.; Chan, L.J.; Adams, P.D.; Heazlewood, J.L.; Petzold, C.J. Standard flow liquid chromatography for shotgun proteomics in bioenergy research. Front. Bioeng. Biotechnol., 2015, 3, 44.
MacLean, B.; Tomazela, D.M.; Shulman, N.; Chambers, M.; Finney, G.L.; Frewen, B.; Kern, R.; Tabb, D.L.; Liebler, D.C.; MacCoss, M.J. Skyline: An open source document editor for creating and analyzing targeted proteomics experiments. Bioinformatics, 2010, 26(7), 966-968.
Kaur, P.; Kiselar, J.G.; Chance, M.R. Integrated algorithms for high-throughput examination of covalently labeled biomolecules by structural mass spectrometry. Anal. Chem., 2009, 81(19), 8141-8149.

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Article Details

Year: 2019
Page: [70 - 75]
Pages: 6
DOI: 10.2174/0929866526666181128125725
Price: $65

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