We welcome collaborations and new users. Most of our publications are from collaborations or from methods development at the beamline.
"Residue-Specific Epitope Mapping of the PD-1/Nivolumab Interaction Using X-ry Footprinting Mass Spectrometry," L.G. Kristensen, S. Gupta, Y. Chen, C.J. Petzold, C.Y. Ralston, Antibodies, 13, 77, 2024, doi.org/10.3390/antib1303077
We validated the interaction of the monoclonal antibody nivolumab with its antigen target PD-1 using X-ray footprinting.
"Comparative Pore Structure and Dynamics for Bacterial Microcompartment Shell Protein Assemblies in Sheets or Shells," S. Raza, D. Sarkar, L.G. Chan, J. Mae, M. Sutter, C.J. Petzold, C.A. Kerfeld, C.Y. Ralston, S. Gupta, J.V. Vermaas, ACS Omega, July 18, 2024, doi.org/10.1021/acsomega.4c02406
X-ray footprinting experimental data was used to corroborate molecular simulations of permeability in bacterial microsome shell proteins.
"Structure and interactions of HIV-1 gp41 CHR-NHR hairpin constructs reveal molecular determinants of antiviral activity," L. He, R. McAndrew, R. Barbu, G. Gifford, C. Halacoglu, C. Drouin-Allaire, L. Weber, L.G. Kristiensen, S. Gupta, Y. Chen, C.J. Petzold, M. Allaire, K.H. Li, C.Y. Ralston, M. Gochin, J. Molecular Biology, 436, 168650, 2024, doi.org/10.1016/j.jmb.2024.168650
Our collaborator M. Gochin used several biochemical and structural methods, including X-ray footprinting and crystallography, to investigate the structures and possible mechanisms of potency of gp41 fusion proteins toward HIV inactivation.
"A novel platform for evaluating dose rate effects on oxidative damage to peptides: toward a high-throughput method to characterize the mechanisms underlying the FLASH effect," S. Gupta, J.L. Inman, J. De Chant, L. Obst-Huebl, K. Nakamura, S.M. Costello, S. Marqusee, J.-H. Mao, L. Kunz, R. Paisley, M.-C. Vozenin, A.M. Snijders, C.Y. Ralston, Radiation Research, 200(6):523-530, 2023, doi.org/10.1667/RADE-23-00131.1
Using high-dose rate radiation "FLASH radiation" to treat cancer is emerging as a promising new avenue in oncology. In this paper we present a new platform for comparing high dose rate and low dose rate radiation effects on peptides in solution at a fundamental level.
"Sneaking in SpyCatcher using cell penetrating peptides for in vivo imaging," J. Tyler, C.Y. Ralston, B. Rad, Nanotechnology, online June 19, 2023, doi.org/10.1088/1361/6528/acdf65
Investigating the use of cell penetrating peptides to introduce SpyCatcher into cells for labeling or imaging studies.
"Structural Investigation of therapeutic antibodies using hydroxyl radical protein footprinting methods," C.Y. Ralston, J.S. Sharp, Antibodies, 11(4), 2022, www.mdpi.com/2073-4468/11/4/71/htm
A mini-review of how hydroxyl radical footprinting can be applied for investigation of antibody structure.
"An automated liquid jet for fluorescence dosimetry and microsecond radiolytic labeling of proteins," M. Rosi, B. Russell, L.G. Kristensen, E.R. Farquhar, R. Jain, D. Abel, M. Sullivan, S.M. Costello, M.A. Dominguez-Martin, Y. Chen, S. Marqusee, C.J. Petzold, C.A. Kerfeld, D.P. DePonte, F. Farahmand, S. Gupta, C.Y. Ralston, Comms. Biol., 5, 2022, Article number: 866, doi.org/10.1038/s42003-022-03775-1
Description of our sample jet delivery system implemented at the 3.3.1 endstation.
"A hybrid structural method for investigating low molecular weight oligomeric structures of amyloid beta," S. Gupta, J. A. Raskatov, C.Y. Ralston, ChemBioChem, 2022, 18 August, doi.org/10.1002/cbic.202200333
A concept for hybrid measurement of global fluorescence and residue-specific footprinting, as applied specifically to study amyloid beta aggregation.
"Hydroxyl radical mediated damage of proteins in low oxygen solution investigated using X-ray footprinting mass spectrometry," L.G. Kristensen, J.M. Holton, B. Rad, Y. Chen, C.J. Petzold, C.Y. Ralston, J. Sync. Rad., 2021 , 28, 1333-1342. doi:10:1107/S1600577521004744
Low dissolved oxygen in solution leads to less overall modification of proteins, and some interesting differences in the modification profiles.
"Structure of an affinity-matured inhibitory recombinant fab against urokinase plasminogen activator reveals basis of potency and specificity," N. Sevillano, M.F. Bohn, M Zimanyi, Y. Chen, C. Petzold, S. Gupta, C.Y. Ralston, C.S. Craik. BBA Proteins and Proteomics, V1869, Issue 2, February 2021, doi.org/10.1016/j.bbapap.2020.140562
Our collaborators in the Craik group used footprinting to investigate antibodies against uPA, a biomarker of aggressive cancers.
"Integrated Structural Studies for Elucidating Carotenoid-Protein Interactions," C.Y. Ralston, C.A. Kerfeld, Adv Exp Med Biol, 2021 May 8. doi:10.1007/5584_2020_615
A brief overview of combining multiple structural methods to understand carotenoid-protein interactions.
“An ultra-high affinity synthetic nanobody blocks SARS-CoV-2 infection by locking Spike into an inactive conformation,” M. Schoof, B. Faust, Reuben A. Saunders, S. Sangwan, V. Rezelj, N.Hoppe, M. Boone, C.B. Billesbølle, M. Zimanyi, I. Deshpande, J. Liang, A.A. Anand, N. Dobzinski, B.S. Zha, B. Barsi-Rhyne, V. Belyy, Andrew W. Barile-Hill, S. Gupta, C.R. Simoneau, K. Leon, K.M. White, S. Nock, Y. Liu, N.J. Krogan, C.Y. Ralston, D. L. Swaney, A. García-Sastre, M. Ott, M. Vignuzzi, P. Walter, A. Manglik. Science, 2020 Dec 18;370(6523):1473-1479. doi: 10.1126/science.abe3255
Our collaborators used footprinting along with crystallography and cryoEM to investigate a new nanobody against the famous virus.
"Structural analysis of a new carotenoid-binding protein: the C-terminal domain homolog of the OCP," M.A. Dominguez-Martin, M. Hammel, S. Gupta, S. Lechno-Yossef, M. Sutter, D.J. Rosenberg, Y. Chen, C.J. Petzold, C.Y. Ralston, T. Polika, C. A. Kerfeld, Scientific Reports 2020, v10, Article number: 15564. doi:10.1038/s41598-020-72383-y
A nice combination of SAXS and XFMS to investigate how a carotenoid is bound within a protein, and the effect on oligomeric structure.
"Allosteric Priming of E. coli CheY by the Flagellar Motor Protein FliM," P. Wheatley, S. Gupta, A. Pandini, Y. Chen, C.J. Petzold, C.Y. Ralston, D.F. Blair, and S. Khan, Biophysical Journal 2020, 119(6), 1108-1122 doi:10.1016/j.bpj.2020.08.009. Biosciences highlight and accompanying movie can be found here.
XFMS and molecular dynamics combined to investigate how a bacterial motor protein functions.
"Fast protein footprinting by X-ray mediated radical trifluoromethylation," M Cheng, A. Asuri, J. Kiselar, G. Mathai, M.R. Chance, M.L. Gross, J. Am. Soc. Mass Spectrometry 2020, 31(5), 1019-1024. doi:10.1021/jasms.0c00085
Our collaborators from the NSLS-II footprinting beamline used our beamline to help figure out a new footprinting method using CF3.
"Development of container free sample exposure for synchrotron X-ray footprinting," S. Gupta, Y. Chen, C.J. Petzold, D.P. DePonte, C.Y. Ralston, Analytical Chemistry 2020, 92, 1, 1565–1573. doi:10.1021/acs.analchem.9b04849
Description of our new jet sample delivery system, and how it compares to standard sample delivery systems for XFMS.
"Comparative ultrafast spectroscopy and structural analysis of OCP1 and OCP2 from Tolypothrix," V. Kuznetsova, M.A. Dominguez-Martin, H. Bao, S. Gupta, M. Sutter, M. Kloz, M. Rebarz, M. Precek, Y. Chen, C.J. Petzold, C.Y. Ralston, C.A Kerfeld, T. Polivka, Biochimica et Biophysica Acta Bioenergetics, 2020 V1861(2), 148120 . doi:10.1016/j.bbabio.2019.148120
Here we combined crystallography, spectroscopy, and XFMS to delineate the differences between homologous forms of the Orange Carotenoid protein.
"POT1-TPP1 differentially regulates telomerase via POT1 His266 and as a function of single-stranded telomere DNA length," M. Xu, J. Kiselar, T.L.Whited , W. Hernandez-Sanchez, D.J. Taylor, Proceedings National Academy of Sciences 2019, Nov 19, 116(47):23527-23533. Epub 2019 Nov 4. doi: 10.1073/pnas.1905381116
Our collaborators used our beamline to investigate a protein-DNA binding interaction, and how that regulates telomere length.
"X-ray radiolytic labeling reveals the molecular basis of orange carotenoid protein photoprotection and its interactions with fluorescence recovery protein," S. Gupta, M. Sutter, S.G. Ramesh, M.-A. Dominguez-Martin, H. Bao, X.A. Feng, L.J.G. Chan, C.J. Petzold, C.A. Kerfeld, C.Y. Ralston, J. Biol. Chem. 2019, 294(22), 8848. doi: 10.1074/JBC.RA119.007592
We used XFMS to determine the sequence of events in photoactivation of the Orange Carotenoid Protein and its de-activation by the Fluorescence Recovery Protein.
"Heterohexamers Formed by CcmK3 and CcmK4 Increase the Complexity of Beta Carboxysome Shells," M. Sommer, M. Sutter, S. Gupta, H. Kirst, A. Turmo, S. Lechno-Yossef, R.L. Burton, C. Saechao, N.B. Sloan, X. Cheng, L.-J. Chan, C.J. Petzold, M. Fuentes-Cabrera, C.Y. Ralston, and C.A. Kerfeld, Plant Physiology 2019 179(1), 156-167. doi.org/10.1104/pp.18.01190
XFMS was used to determine interaction regions between proteins that make up bacterial microcompartment shells.
"Recent Advances in X-Ray Hydroxyl Radical Footprinting at the Advanced Light Source Synchrotron," S.A. Morton, S. Gupta, C.J. Petzold, C.Y. Ralston, Protein and Peptide Letters, 2019 Volume 26, Number 1, pp. 70-75(6), doi:10.2174/0929866526666181128125725
Latest updates in XFMS instrumentation at the ALS, as of 2019. (More recent updates are in articles listed above.)
"Water molecules mediate zinc mobility in the bacterial zinc diffusion channel ZIPB," S. Gupta, C. Merriman, C.J. Petzold, C.Y. Ralston, D. Fu, " J. Biol. Chem. 2019 Sep 6;294(36):13327-13335. doi: 10.1074/jbc.RA119.009239
XFMS was used to help work out the water-mediated transport of Zn through a bacterial ion channel.
"Using X-ray Footprinting and Mass Spectrometry to Study the Structure and Function of Membrane Proteins," S. Gupta, Protein and Peptide Letters, Volume 26, Number 1, 2019, pp. 44-54(11) DOI:10.2174/0929866526666181128142401
A brief review of how XFMS can be helpful in characterizing structure and function of membrane proteins.
"A Metastable Contact and Structural Disorder in the Estrogen Receptor Transactivation Domain," Yi Peng, Shufe Cao, Janna Kiselar, Xiangzhu Xiao, Zhanwen Du, An Hsieh, Soobin Ko, Yinghua Chen, Prashansa Agrawal, Wenwei Zheng, Wuxian Shi, Wei Jiang, Lin Yang, Mark R. Chance, Witold K. Surewicz, Matthias Buck, Sichun Yang, Structure 2019 Volume 27, Issue 2, 5 , Pages 229-240.e4, doi:10.1016/j.str.2018.10.026
Our collaborators used XFMS, SAXS, and computational modeling to determine the ensemble structure of the transactivation domain of a human estrogen receptor.
Selected publications prior to 2019
"Multidomain architecture of estrogen receptor reveals interfacial cross-talk between its DNA-binding and ligand-binding domains," Huang, W., Peng, Y., Kiselar, J., Zhao, X., Albaqami, A., Mendez, D., Chen, Y.-H., Chakravarthy, S., Gupta, S., Ralston, C.Y., Kao, H.-Y., Chance, M., and Yang, S. Nature Communications, 2018, 9, Article number: 3520. doi:10.1038/s41467-018-06034-2
XFMS, SAXS, and computational modeling were used together to determine the architecture of a human estrogen receptor.
"The Molecular Basis for Binding of an Electron Transfer Protein to a Metal Oxide Surface," T. Fukushima, S. Gupta, B. Rad, J.A. Cornejo, C.J. Petzold, L.G. Chan, R.A. Mizrahi, C.Y. Ralston, and C.M. Ajo-Franklin, J. Am. Chem. Soc. 2017, 139 (36), pp 12647–12654. doi: 10.1021/jacs.7b06560
We used XFMS to determine the sites of interaction between metal nanoparticles and an iron-binding protein. A Berkeley news release about the work can be found here.
"Carotenoid translocation in the Orange Carotenoid Protein activates a photoprotective mechanism in cyanobacteria," R.L. Leverenz, M. Sutter, A. Wilson, S. Gupta, A. Thurotte, C. Boucier de Carbon, C. Petzold, C. Ralston, D. Kirilovsky, C.A. Kerfeld, Science 2015 V348, 6242, p1463. doi: 10.1126/science.aaa7234
We used XFMS and crystallography to show that the carotenoid molecule within the Orange Carotenoid Protein makes a very large shift within protein domains upon photoactivation. A Berkeley news release about the work can be found here.
"Local and global structural drivers for the photoactivation of the orange carotenoid protein," S. Gupta, M. Guttman, R.L. Leverenz, K. Zhumadilova, E.G. Pawlowski, C.J. Petzold, K.K. Lee, C. Ralston, C.A. Kerfeld, Proceedings National Academy of Sciences 2015 V112 No41, E5567. doi: 10.1073/pnas.1512240112
We used XFMS, crystallography, SAXS, and HDX-MS to investigate conformational changes in the Orange Carotenoid Protein during photoactivation.
"Development of a microsecond x-ray protein footprinting facility at the Advanced Light Source," S. Gupta, R. Celestre, C. Petzold, M.R. Chance, C. Ralston, J. Sync. Rad., 2014 21, 690. doi: 10.1107/S1600577514007000
Our very first paper from the newly developed footprinting beamline at the ALS.
"Synchrotron footprinting on tour," J. Bohon, R. D'Mello, C. Ralston, S. Gupta, M. R Chance, J. Sync. Rad., 2014 21, 24-31. doi: 10.1107/S1600577513024715
This is the first paper demonstrating that X-ray footprinting could be done at a synchrotron other than the NSLS.