Early Protein Footprinting Publications

Ground breaking paper reviewing the chemistry of hydroxyl radical modifications of amino acids for footprinting research

1. Xu, G., Chance, M.R., Hydroxyl radical-mediated modification of proteins as probes for structural proteomics, Chem Rev. (2007) Aug;107(8):3514-43. PMID: 17683160 DOI: 10.1021/cr0682047

 

Early review paper highlighting the method of hydroxyl radical protein footprinting

2. Takamoto, K., Chance, M.R., Radiolytic protein footprinting with mass spectrometry to probe the structure of macromolecular complexes, Annu Rev Biophys Biomol Struct. (2006);35:251- 76. DOI: 10.1146/annurev.biophys.35.040405.102050

Review of Protein Footprinting Methods

3. Wang L, Chance MR Protein Footprinting Comes of Age: Mass Spectrometry for Biophysical Structure Assessment Mol Cell Proteomics. 2017 May;16(5):706-716. doi: 10.1074/mcp.O116.064386. Epub 2017 Mar 8

4. Kiselar J, Chance MR High-Resolution Hydroxyl Radical Protein Footprinting: Biophysics Tool for Drug Discovery Annu Rev Biophys. 2018 Mar 14. doi: 10.1146/annurev-biophys-070317-033123. [Epub ahead of print]

Epitope Mapping Publications

Benchmarking footprinting studies for monoclonal antibodies to assess epitopes and paratopes

5. Kaur, P., Kiselar, J.G., Shi, W., Yang, S., Chance, M.R. “Covalent Labeling Techniques for Characterizing Higher Order Structure of Monoclonal Antibodies”, in State of the Art and Emerging Technologies for Therapeutic Monoclonal Antibody Characterization. Volume 3. Defining the Next Generation of Analytical and Biophysical Techniques. Editors: Darryl Lee Davis, Oleg Borisov, and John Schiel, ACS Symposium Series # 1202, Chapter 3, pp 45- 73, (2015).


Assessment of monoclonal antibody structure and epitopes using GEE labeling

6. Kaur P, Tomechko SE, Kiselar J, Shi W, Deperalta G, Wecksler AT, Gokulrangan G, Ling V, Chance MR. Characterizing monoclonal antibody structure by carboxyl group footprinting. MAbs (2015) 7(3):540-52. doi: 10.1080/19420862.2015.1023683. PMID: 25933350 PMCID: PMC4622658

Protein-Drug Interaction Publications

Binding and allostery in drug binding to membrane proteins.

7. Gustavsson M, Wang L, van Gils N, Stephens BS, Zhang P, Schall TJ, Yang S, Abagyan R, Chance MR, Kufareva I, Handel TM; Structural basis of ligand interaction with atypical chemokine receptor 3 Nat Commun. 2017 Jan 18;8:14135. doi: 1038/ncomms14135


Protein Phosphatase 2A binding to a small molecule mapped at high resolution.

8. Sangodkar J, Perl A, Tohme R, Kiselar J, Kastrinsky DB, Zaware N, Izadmehr S, Mazhar S, Wiredja DD, O’Connor CM, Hoon D, Dhawan NS, Schlatzer D, Yao S, Leonard D, Borczuk AC, Gokulrangan G, Wang L, Svenson E, Farrington CC, Yuan E, Avelar RA, Stachnik A, Smith B, Gidwani V, Giannini HM, McQuaid D, McClinch K, Wang Z, Levine AC, Sears RC, Chen EY, Duan Q, Datt M, Haider S, Ma’ayan A, DiFeo A, Sharma N, Galsky MD, Brautigan DL, Ioannou YA, Xu W, Chance MR, Ohlmeyer M, Narla G Activation of tumor suppressor protein PP2A inhibits KRAS- driven tumor growth J Clin Invest. 2017 Jun 1;127(6):2081-2090. doi: 10.1172/JCI89548. Epub 2017 May 15

 

Low molecular weight protein phosphatase binding to a small molecule mapped at high resolution

9. Stanford SM, Aleshin AE, Zhang V, Ardecky RJ, Hedrick MP, Zou J, Ganji SR, Bliss MR, Yamamoto F, Bobkov AA, Kiselar J, Liu Y, Cadwell GW, Khare S, Yu J, Barquilla A, Chung TDY, Mustelin T, Schenk S, Bankston LA, Liddington RC, Pinkerton AB, Bottini N; Diabetes reversal by inhibition of the low-molecular-weight tyrosine phosphatase. Nat Chem Biol. 2017 Jun;13(6):624-632. doi: 10.1038/nchembio.2344. Epub 2017 Mar 27

Integrated Structural Biology Services Publications

Using footprinting data to measure quantitative solvent accessibility of proteins at the side chain level

10. Kaur P, Kiselar J, Yang S, Chance MR. Quantitative protein topography analysis and high- resolution structure prediction using hydroxyl radical labeling and tandem-ion mass spectrometry (MS). Molecular & cellular proteomics : MCP. (2015);14(4):1159-68. doi:10.1074/mcp.O114.044362. PubMed PMID: 25687570; PubMed Central PMCID:PMC4390260.

 

Using footprinting data to measure quantitative solvent accessibility of proteins at the peptide level

11. Huang W, Ravikumar KM, Chance MR, Yang S. “Quantitative mapping of protein structure by hydroxyl radical footprinting-mediated structural mass spectrometry: a protection factor analysis”. Biophys J (2015); 108(1):107-15. doi: 10.1016/j.bpj.2014.11.013. PMCID: PMC4286602

 

Using footprinting to explore kinetics of protein complex formation leading to G-protein signaling

12. Du Y, Duc NM, Rasmussen SGF, Hilger D, Kubiak X, Wang L, Bohon J, Kim HR, Wegrecki M, Asuru A, Jeong KM, Lee J, Chance MR, Lodowski DT, Kobilka BK, Chung KY Assembly of a GPCR-G Protein Complex Cell. 2019 May 16;177(5):1232-1242.e11. doi: 10.1016/j.cell.2019.04.022. Epub 2019 May9

 

Using footprinting and small-angle x-ray scattering to solve the structure of protein  complexes

13. Huang W, Peng Y, Kiselar J, Zhao X, Albaqami A, Mendez D, Chen Y, Chakravarthy S, Gupta S, Ralston C, Kao HY, Chance MR, Yang S; Multidomain architecture of estrogen receptor reveals interfacial cross-talk between its DNA-binding and ligand-binding domains. Nat Commun. 2018 Aug 30;9(1):3520. doi: 1038/s41467-018-06034-2.

 

Review of Integrated Methods with Protein Footprinting.

14. Protein Footprinting: Auxiliary Engine to Power the Structural Biology Revolution.

Chance MR, Farquhar ER, Yang S, Lodowski DT, Kiselar J.J Mol Biol. 2020 Apr 17;432(9):2973-2984. doi: 10.1016/j.jmb.2020.02.011. Epub 2020 Feb 21.PMID: 32088185 Free PMC article. Review.

 

Assessment of Dynamics of Disordered Protein Structure

15. A metastable contact and structural disorder in the estrogen receptor transactivation domain

Y Peng, S Cao, J Kiselar, X Xiao, Z Du, A Hsieh, S Ko, Y Chen, P Agrawal, …

Structure 27 (2), 229-240. e4

New and Novel Publications

Footprinting of brain prion samples

Structurally distinct external solvent-exposed domains drive replication of major human prions.

Siddiqi MK, Kim C, Haldiman T, Kacirova M, Wang B, Bohon J, Chance MR, Kiselar J, Safar JG.PLoS Pathog. 2021 Jun 17;17(6):e1009642. doi: 10.1371/journal.ppat.1009642. eCollection 2021 Jun.PMID: 34138981 Free PMC article

Novel Chemistry of Footprinting

Fast Protein Footprinting by X-ray Mediated Radical Trifluoromethylation.

Cheng M, Asuru A, Kiselar J, Mathai G, Chance MR, Gross ML.J Am Soc Mass Spectrom. 2020 May 6;31(5):1019-1024. doi: 10.1021/jasms.0c00085. Epub 2020 Apr 21.PMID: 32255631 Free PMC article.