References
Adams, R., Burnley, R. J., Valenzano, C. R., Qureshi, O., Doyle, C., Lumb, S., Del Carmen Lopez, M., Griffin, R., McMillan, D., Taylor, R. D., Meier, C., Mori, P., Griffin, L. M., Wernery, U., Kinne, J., Rapecki, S., Baker, T. S., Lawson, A. D., Wright, M., Ettorre, A., 2017, Discovery of a junctional epitope antibody that stabilizes IL-6 and gp80 protein:protein interaction and modulates its downstream signaling,Scientific Reports .7:37716.
Adhikari, J., Zhao, H., Fernandez, E., Huang, Y., Diamond, M. S., Fremont, D. H., Gross, M. L., 2021, Hydrogen–deuterium exchange mass spectrometry identifies spatially distinct antibody epitopes on domain III of the Zika virus envelope protein, Journal of Mass Spectrometry .56(1):e4685.
Anderson, K. W., Gallagher, E. S., Hudgens, J. W., 2018, Automated Removal of Phospholipids from Membrane Proteins for H/D Exchange Mass Spectrometry Workflows, Analytical Chemistry .90(11):6409-6412.
Araki, K., Yagi, N., Aoyama, K., Choong, C. J., Hayakawa, H., Fujimura, H., Nagai, Y., Goto, Y., Mochizuki, H., 2019, Parkinson’s disease is a type of amyloidosis featuring accumulation of amyloid fibrils of α-synuclein, Proceedings of the National Academy of Sciences .116(36):17963-17969.
Arkin, M. R., Tang, Y., Wells, J. A., 2014, Small-molecule inhibitors of protein-protein interactions: progressing toward the reality, Cell Chemical Biology .21(9):1102-1114.
Arlt, C., Flegler, V., Ihling, C. H., Schäfer, M., Thondorf, I., Sinz, A., 2017, An Integrated Mass Spectrometry Based Approach to Probe the Structure of the Full-Length Wild-Type Tetrameric p53 Tumor Suppressor,Angewandte Chemie International Edition .56(1):275-279.
Arlt, C., Ihling, C. H., Sinz, A., 2015, Structure of full-length p53 tumor suppressor probed by chemical cross-linking and mass spectrometry,Proteomics .15(16):2746-2755.
Arora, J., Hickey, J. M., Majumdar, R., Esfandiary, R., Bishop, S. M., Samra, H. S., Middaugh, C. R., Weis, D. D., Volkin, D. B., 2015, Hydrogen exchange mass spectrometry reveals protein interfaces and distant dynamic coupling effects during the reversible self-association of an IgG1 monoclonal antibody, MAbs .7(3):525-539.
Beard, H. A., Korovesis, D., Chen, S., Verhelst, S. H. L., 2021, Cleavable linkers and their application in MS-based target identification, Molecular Omics .17(2):197-209.
Borotto, N. B., Zhang, Z., Dong, J., Burant, B., Vachet, R. W., 2017, Increased β-Sheet Dynamics and D-E Loop Repositioning Are Necessary for Cu(II)-Induced Amyloid Formation by β-2-Microglobulin,Biochemistry .56(8):1095-1104.
Bridge, T., Shaikh, S. A., Thomas, P., Botta, J., McCormick, P. J., Sachdeva, A., 2019, Site-Specific Encoding of Photoactivity in Antibodies Enables Light-Mediated Antibody-Antigen Binding on Live Cells, Angewandte Chemie International Edition .58(50):17986-17993.
Brown, M. R., Radford, S. E., Hewitt, E. W., 2020, Modulation of β-Amyloid Fibril Formation in Alzheimer’s Disease by Microglia and Infection, Frontiers in Molecular Neuroscience .13:609073.
Calabrese, A. N., Schiffrin, B., Watson, M., Karamanos, T. K., Walko, M., Humes, J. R., Horne, J. E., White, P., Wilson, A. J., Kalli, A. C., Tuma, R., Ashcroft, A. E., Brockwell, D. J., Radford, S. E., 2020, Inter-domain dynamics in the chaperone SurA and multi-site binding to its outer membrane protein clients, Nature Communications .11(1):2155.
Chavez, J. D., Mohr, J. P., Mathay, M., Zhong, X., Keller, A., Bruce, J. E., 2019, Systems structural biology measurements by in vivo cross-linking with mass spectrometry, Nature Protocols .14(8):2318-2343.
Chen, L., Morrow, J. K., Tran, H. T., Phatak, S. S., Du-Cuny, L., Zhang, S., 2012, From laptop to benchtop to bedside: structure-based drug design on protein targets, Current Pharmaceutical Design .18(9):1217-1239.
Chen, L., Zhu, C., Guo, H., Li, R., Zhang, L., Xing, Z., Song, Y., Zhang, Z., Wang, F., Liu, X., Zhang, Y., Ma, R. Z., Wang, F., 2020, Epitope-directed antibody selection by site-specific photocrosslinking,Science Advances .6(14):eaaz7825.
Coales, S. J., Tuske, S. J., Tomasso, J. C., Hamuro, Y., 2009, Epitope mapping by amide hydrogen/deuterium exchange coupled with immobilization of antibody, on-line proteolysis, liquid chromatography and mass spectrometry, Rapid Communications in Mass Spectrometry .23(5):639-647.
Comamala, G., Wagner, C., de la Torre, P. S., Jakobsen, R. U., Hilger, M., Brouwer, H.-J., Rand, K. D., 2020, Hydrogen/deuterium exchange mass spectrometry with improved electrochemical reduction enables comprehensive epitope mapping of a therapeutic antibody to the cysteine-knot containing vascular endothelial growth factor,Analytica Chimica Acta .1115:41-51.
Cvicek, V., Goddard, W. A., 3rd, Abrol, R., 2016, Structure-Based Sequence Alignment of the Transmembrane Domains of All Human GPCRs: Phylogenetic, Structural and Functional Implications, PLOS Computational Biology .12(3):e1004805.
Ding, Y. H., Fan, S. B., Li, S., Feng, B. Y., Gao, N., Ye, K., He, S. M., Dong, M. Q., 2016, Increasing the Depth of Mass-Spectrometry-Based Structural Analysis of Protein Complexes through the Use of Multiple Cross-Linkers, Analytical Chemistry .88(8):4461-4469.
Duc, N. M., Du, Y., Zhang, C., Lee, S. Y., Thorsen, T. S., Kobilka, B. K., Chung, K. Y., 2015, Effective application of bicelles for conformational analysis of G protein-coupled receptors by hydrogen/deuterium exchange mass spectrometry, Journal of the American Society for Mass Spectrometry .26(5):808-817.
Dysinger, M., King, L. E., 2012, Practical quantitative and kinetic applications of bio-layer interferometry for toxicokinetic analysis of a monoclonal antibody therapeutic, Journal of Immunological Methods .379(1-2):30-41.
Ferraro, N. A., Cascio, M., 2018, Cross-Linking-Mass Spectrometry Studies of Cholesterol Interactions with Human α1 Glycine Receptor,Analytical Chemistry .90(4):2508-2516.
Freinkman, E., Chng, S. S., Kahne, D., 2011, The complex that inserts lipopolysaccharide into the bacterial outer membrane forms a two-protein plug-and-barrel, Proceedings of the National Academy of Sciences .108(6):2486-2491.
Gabizon, R., Friedler, A., 2014, Allosteric modulation of protein oligomerization: an emerging approach to drug design, Frontiers in Chemistry .2:9.
Gagnon, L., Cao, Y., Cho, A., Sedki, D., Huber, T., Sakmar, T. P., Laporte, S. A., 2019, Genetic code expansion and photocross-linking identify different β-arrestin binding modes to the angiotensin II type 1 receptor, Journal of Biological Chemistry .294(46):17409-17420.
Galzitskaya, O. V., 2019, Oligomers Are Promising Targets for Drug Development in the Treatment of Proteinopathies, Frontiers in Molecular Neuroscience .12:319.
Gershoni, J. M., Roitburd-Berman, A., Siman-Tov, D. D., Tarnovitski Freund, N., Weiss, Y., 2007, Epitope mapping: the first step in developing epitope-based vaccines, BioDrugs .21(3):145-156.
Gong, Z., Ye, S. X., Tang, C., 2020, Tightening the Crosslinking Distance Restraints for Better Resolution of Protein Structure and Dynamics, Structure .28(10):1160-1167.e1163.
Götze, M., Iacobucci, C., Ihling, C. H., Sinz, A., 2019, A Simple Cross-Linking/Mass Spectrometry Workflow for Studying System-wide Protein Interactions, Analytical Chemistry .91(15):10236-10244.
Gramlich, M., Hays, H. C. W., Crichton, S., Kaiser, P. D., Heine, A., Schneiderhan-Marra, N., Rothbauer, U., Stoll, D., Maier, S., Zeck, A., 2021, HDX-MS for Epitope Characterization of a Therapeutic ANTIBODY Candidate on the Calcium-Binding Protein Annexin-A1, Antibodies (Basel) .10(1).
Grunbeck, A., Huber, T., Abrol, R., Trzaskowski, B., Goddard, W. A., 3rd, Sakmar, T. P., 2012, Genetically encoded photo-cross-linkers map the binding site of an allosteric drug on a G protein-coupled receptor,ACS Chemical Biology .7(6):967-972.
Grunbeck, A., Huber, T., Sachdev, P., Sakmar, T. P., 2011, Mapping the ligand-binding site on a G protein-coupled receptor (GPCR) using genetically encoded photocrosslinkers,Biochemistry .50(17):3411-3413.
Guan, X., Noble, K. A., Tao, Y., Roux, K. H., Sathe, S. K., Young, N. L., Marshall, A. G., 2015, Epitope mapping of 7S cashew antigen in complex with antibody by solution-phase H/D exchange monitored by FT-ICR mass spectrometry, Journal of Mass Spectrometry .50(6):812-819.
Hamuro, Y., Zhang, T., 2019, High-Resolution HDX-MS of Cytochrome c Using Pepsin/Fungal Protease Type XIII Mixed Bed Column, Journal of the American Society for Mass Spectrometry .30(2):227-234.
Hauseman, Z. J., Harvey, E. P., Newman, C. E., Wales, T. E., Bucci, J. C., Mintseris, J., Schweppe, D. K., David, L., Fan, L., Cohen, D. T., Herce, H. D., Mourtada, R., Ben-Nun, Y., Bloch, N. B., Hansen, S. B., Wu, H., Gygi, S. P., Engen, J. R., Walensky, L. D., 2020, Homogeneous Oligomers of Pro-apoptotic BAX Reveal Structural Determinants of Mitochondrial Membrane Permeabilization, Molecular Cell .79(1):68-83.e67.
He, D., Xie, X., Yang, F., Zhang, H., Su, H., Ge, Y., Song, H., Chen, P. R., 2017, Quantitative and Comparative Profiling of Protease Substrates through a Genetically Encoded Multifunctional Photocrosslinker,Angewandte Chemie International Edition .56(46):14521-14525.
Holding, A. N., 2015, XL-MS: Protein cross-linking coupled with mass spectrometry, Methods .89:54-63.
Hollingsworth, L. R., Sharif, H., Griswold, A. R., Fontana, P., Mintseris, J., Dagbay, K. B., Paulo, J. A., Gygi, S. P., Bachovchin, D. A., Wu, H., 2021, DPP9 sequesters the C terminus of NLRP1 to repress inflammasome activation, Nature .592(7856):778-783.
Horne, J. E., Walko, M., Calabrese, A. N., Levenstein, M. A., Brockwell, D. J., Kapur, N., Wilson, A. J., Radford, S. E., 2018, Rapid Mapping of Protein Interactions Using Tag-Transfer Photocrosslinkers,Angewandte Chemie International Edition .57(51):16688-16692.
Huang, R. Y., Garai, K., Frieden, C., Gross, M. L., 2011, Hydrogen/deuterium exchange and electron-transfer dissociation mass spectrometry determine the interface and dynamics of apolipoprotein E oligomerization, Biochemistry .50(43):9273-9282.
Huang, R. Y., Krystek, S. R., Jr., Felix, N., Graziano, R. F., Srinivasan, M., Pashine, A., Chen, G., 2018, Hydrogen/deuterium exchange mass spectrometry and computational modeling reveal a discontinuous epitope of an antibody/TL1A Interaction, MAbs .10(1):95-103.
Iacobucci, C., Götze, M., Ihling, C. H., Piotrowski, C., Arlt, C., Schäfer, M., Hage, C., Schmidt, R., Sinz, A., 2018, A cross-linking/mass spectrometry workflow based on MS-cleavable cross-linkers and the MeroX software for studying protein structures and protein–protein interactions, Nature Protocols .13(12):2864-2889.
Ihling, C. H., Springorum, P., Iacobucci, C., Hage, C., Götze, M., Schäfer, M., Sinz, A., 2020, The Isotope-Labeled, MS-Cleavable Cross-Linker Disuccinimidyl Dibutyric Urea for Improved Cross-Linking/Mass Spectrometry Studies, Journal of the American Society for Mass Spectrometry .31(2):183-189.
Iversen, R., Mysling, S., Hnida, K., Jørgensen Thomas, J. D., Sollid Ludvig, M., 2014, Activity-regulating structural changes and autoantibody epitopes in transglutaminase 2 assessed by hydrogen/deuterium exchange, Proceedings of the National Academy of Sciences .111(48):17146-17151.
Jang, H., Smith, I. N., Eng, C., Nussinov, R., 2021, The mechanism of full activation of tumor suppressor PTEN at the phosphoinositide-enriched membrane, iScience .24(5):102438.
Jebarupa, B., Mathew, B., Srinivasu, B. Y., Sasikumaran, A., Joseph, S., Mandal, A. K., Thomas, T., Mitra, G., 2019, Understanding molecular features of aggregation-resistant tau conformer using oxidized monomer,Biochimica et Biophysica Acta .1863(6):993-1005.
Jensen, P. F., Larraillet, V., Schlothauer, T., Kettenberger, H., Hilger, M., Rand, K. D., 2015, Investigating the interaction between the neonatal Fc receptor and monoclonal antibody variants by hydrogen/deuterium exchange mass spectrometry, Molecular & Cellular Proteomics .14(1):148-161.
Kaiser, A., Coin, I., 2020, Capturing Peptide-GPCR Interactions and Their Dynamics, Molecules .25(20).
Karagöz, G. E., Acosta-Alvear, D., Nguyen, H. T., Lee, C. P., Chu, F., Walter, P., 2017, An unfolded protein-induced conformational switch activates mammalian IRE1, Elife .6.
Kim, M., Sun, Z.-Y. J., Rand, K. D., Shi, X., Song, L., Cheng, Y., Fahmy, A. F., Majumdar, S., Ofek, G., Yang, Y., Kwong, P. D., Wang, J.-H., Engen, J. R., Wagner, G., Reinherz, E. L., 2011, Antibody mechanics on a membrane-bound HIV segment essential for GP41-targeted viral neutralization, Nature Structural & Molecular Biology .18(11):1235-1243.
Krist, D. T., Statsyuk, A. V., 2015, Catalytically Important Residues of E6AP Ubiquitin Ligase Identified Using Acid-Cleavable Photo-Cross-Linkers, Biochemistry .54(29):4411-4414.
Kumari, N., Yadav, S., 2019, Modulation of protein oligomerization: An overview, Progress in Biophysics and Molecular Biology .149:99-113.
Lau, A. M. C., Ahdash, Z., Martens, C., Politis, A., 2019, Deuteros: software for rapid analysis and visualization of data from differential hydrogen deuterium exchange-mass spectrometry,Bioinformatics .35(17):3171-3173.
Lee, S. J., Nam, E., Lee, H. J., Savelieff, M. G., Lim, M. H., 2017, Towards an understanding of amyloid-β oligomers: characterization, toxicity mechanisms, and inhibitors, Chemical Society Reviews .46(2):310-323.
Leitner, A., Joachimiak, L. A., Unverdorben, P., Walzthoeni, T., Frydman, J., Förster, F., Aebersold, R., 2014, Chemical cross-linking/mass spectrometry targeting acidic residues in proteins and protein complexes, Proceedings of the National Academy of Sciences .111(26):9455-9460.
Li, J., Wei, H., Krystek, S. R., Bond, D., Brender, T. M., Cohen, D., Feiner, J., Hamacher, N., Harshman, J., Huang, R. Y. C., Julien, S. H., Lin, Z., Moore, K., Mueller, L., Noriega, C., Sejwal, P., Sheppard, P., Stevens, B., Chen, G., Tymiak, A. A., Gross, M. L., Schneeweis, L. A., 2017, Mapping the Energetic Epitope of an Antibody/Interleukin-23 Interaction with Hydrogen/Deuterium Exchange, Fast Photochemical Oxidation of Proteins Mass Spectrometry, and Alanine Shave Mutagenesis,Analytical Chemistry .89(4):2250-2258.
Liang, Y. L., Belousoff, M. J., Zhao, P., Koole, C., Fletcher, M. M., Truong, T. T., Julita, V., Christopoulos, G., Xu, H. E., Zhang, Y., Khoshouei, M., Christopoulos, A., Danev, R., Sexton, P. M., Wootten, D., 2020, Toward a Structural Understanding of Class B GPCR Peptide Binding and Activation, Molecular Cell .77(3):656-668.e655.
Liu, L., 2018, Pharmacokinetics of monoclonal antibodies and Fc-fusion proteins, Protein Cell .9(1):15-32.
Liu, Q., Remmelzwaal, S., Heck, A. J. R., Akhmanova, A., Liu, F., 2017, Facilitating identification of minimal protein binding domains by cross-linking mass spectrometry, Scientific Reports .7(1):13453.
Lössl, P., Kölbel, K., Tänzler, D., Nannemann, D., Ihling, C. H., Keller, M. V., Schneider, M., Zaucke, F., Meiler, J., Sinz, A., 2014, Analysis of nidogen-1/laminin γ1 interaction by cross-linking, mass spectrometry, and computational modeling reveals multiple binding modes,PLOS ONE .9(11):e112886.
Ma, S., Shen, Q., Zhao, L. H., Mao, C., Zhou, X. E., Shen, D. D., de Waal, P. W., Bi, P., Li, C., Jiang, Y., Wang, M. W., Sexton, P. M., Wootten, D., Melcher, K., Zhang, Y., Xu, H. E., 2020, Molecular Basis for Hormone Recognition and Activation of Corticotropin-Releasing Factor Receptors, Molecular Cell .77(3):669-680.e664.
Martens, C., Politis, A., 2020, A glimpse into the molecular mechanism of integral membrane proteins through hydrogen-deuterium exchange mass spectrometry, Protein Science .29(6):1285-1301.
Martens, C., Shekhar, M., Borysik, A. J., Lau, A. M., Reading, E., Tajkhorshid, E., Booth, P. J., Politis, A., 2018, Direct protein-lipid interactions shape the conformational landscape of secondary transporters, Nature Communications .9(1):4151.
Martens, C., Shekhar, M., Lau, A. M., Tajkhorshid, E., Politis, A., 2019, Integrating hydrogen-deuterium exchange mass spectrometry with molecular dynamics simulations to probe lipid-modulated conformational changes in membrane proteins, Nature Protocols .14(11):3183-3204.
Masson, G. R., Burke, J. E., Ahn, N. G., Anand, G. S., Borchers, C., Brier, S., Bou-Assaf, G. M., Engen, J. R., Englander, S. W., Faber, J., Garlish, R., Griffin, P. R., Gross, M. L., Guttman, M., Hamuro, Y., Heck, A. J. R., Houde, D., Iacob, R. E., Jørgensen, T. J. D., Kaltashov, I. A., Klinman, J. P., Konermann, L., Man, P., Mayne, L., Pascal, B. D., Reichmann, D., Skehel, M., Snijder, J., Strutzenberg, T. S., Underbakke, E. S., Wagner, C., Wales, T. E., Walters, B. T., Weis, D. D., Wilson, D. J., Wintrode, P. L., Zhang, Z., Zheng, J., Schriemer, D. C., Rand, K. D., 2019, Recommendations for performing, interpreting and reporting hydrogen deuterium exchange mass spectrometry (HDX-MS) experiments,Nature Methods .16(7):595-602.
Masson, G. R., Jenkins, M. L., Burke, J. E., 2017, An overview of hydrogen deuterium exchange mass spectrometry (HDX-MS) in drug discovery, Expert Opinion on Drug Discovery .12(10):981-994.
Masson, G. R., Perisic, O., Burke, J. E., Williams, R. L., 2016, The intrinsically disordered tails of PTEN and PTEN-L have distinct roles in regulating substrate specificity and membrane activity, Biochem J .473(2):135-144.
Mintseris, J., Gygi, S. P., 2020, High-density chemical cross-linking for modeling protein interactions, Proceedings of the National Academy of Sciences .117(1):93-102.
Mishra, P. K., Yoo, C. M., Hong, E., Rhee, H. W., 2020, Photo-crosslinking: An Emerging Chemical Tool for Investigating Molecular Networks in Live Cells, Chembiochem .21(7):924-932.
Oganesyan, I., Lento, C., Wilson, D. J., 2018, Contemporary hydrogen deuterium exchange mass spectrometry, Methods .144:27-42.
Oganesyan, V., Damschroder, M. M., Cook, K. E., Li, Q., Gao, C., Wu, H., Dall’Acqua, W. F., 2014, Structural insights into neonatal Fc receptor-based recycling mechanisms, Journal of Biological Chemistry .289(11):7812-7824.
Owens, T. W., Taylor, R. J., Pahil, K. S., Bertani, B. R., Ruiz, N., Kruse, A. C., Kahne, D., 2019, Structural basis of unidirectional export of lipopolysaccharide to the cell surface,Nature .567(7749):550-553.
Ozohanics, O., Ambrus, A., 2020, Hydrogen-Deuterium Exchange Mass Spectrometry: A Novel Structural Biology Approach to Structure, Dynamics and Interactions of Proteins and Their Complexes, Life (Basel) .10(11).
Parker, B., Goncz, E., Krist, D. T., Statsyuk, A., Nesvizhskii, A. I., Weiss, E., 2018, LiF-MS: Mapping unstructured peptide-protein interactions using Ligand-Footprinting Mass Spectrometry,bioRxiv .361857.
Payandeh, J., Volgraf, M., 2021, Ligand binding at the protein-lipid interface: strategic considerations for drug design, Nature Reviews Drug Discovery .20(9):710-722.
Pham, N. D., Parker, R. B., Kohler, J. J., 2013, Photocrosslinking approaches to interactome mapping, Current Opinion in Structural Biology .17(1):90-101.
Pierce, M. M., Raman, C. S., Nall, B. T., 1999, Isothermal titration calorimetry of protein-protein interactions,Methods .19(2):213-221.
Piersimoni, L., Sinz, A., 2020, Cross-linking/mass spectrometry at the crossroads, Analytical and Bioanalytical Chemistry .412(24):5981-5987.
Przygońska, K., Poznański, J., Mistarz, U. H., Rand, K. D., Dadlez, M., 2018, Side-chain moieties from the N-terminal region of Aβ are Involved in an oligomer-stabilizing network of interactions, PLOS ONE .13(8):e0201761.
Puchades, C., Kűkrer, B., Diefenbach, O., Sneekes-Vriese, E., Juraszek, J., Koudstaal, W., Apetri, A., 2019, Epitope mapping of diverse influenza Hemagglutinin drug candidates using HDX-MS, Scientific Reports .9(1):4735.
Pulkoski-Gross, M. J., Jenkins, M. L., Truman, J. P., Salama, M. F., Clarke, C. J., Burke, J. E., Hannun, Y. A., Obeid, L. M., 2018, An intrinsic lipid-binding interface controls sphingosine kinase 1 function, Journal of Lipid Research .59(3):462-474.
Qi, H., Ma, M., Hu, C., Xu, Z. W., Wu, F. L., Wang, N., Lai, D. Y., Li, Y., Zhang, H., Jiang, H. W., Meng, Q. F., Guo, S., Kang, Y., Zhao, X., Li, H., Tao, S. C., 2021, Antibody Binding Epitope Mapping (AbMap) of Hundred Antibodies in a Single Run, Molecular & Cellular Proteomics .20:100059.
Rao, V. S., Srinivas, K., Sujini, G. N., Kumar, G. N., 2014, Protein-protein interaction detection: methods and analysis,International Journal of Proteomics .2014:147648.
Rappsilber, J., 2011, The beginning of a beautiful friendship: cross-linking/mass spectrometry and modelling of proteins and multi-protein complexes, Journal of Structural Biology .173(3):530-540.
Rich, R. L., Myszka, D. G., 2011, Survey of the 2009 commercial optical biosensor literature, Journal of Molecular Recognition .24(6):892-914.
Rual, J. F., Venkatesan, K., Hao, T., Hirozane-Kishikawa, T., Dricot, A., Li, N., Berriz, G. F., Gibbons, F. D., Dreze, M., Ayivi-Guedehoussou, N., Klitgord, N., Simon, C., Boxem, M., Milstein, S., Rosenberg, J., Goldberg, D. S., Zhang, L. V., Wong, S. L., Franklin, G., Li, S., Albala, J. S., Lim, J., Fraughton, C., Llamosas, E., Cevik, S., Bex, C., Lamesch, P., Sikorski, R. S., Vandenhaute, J., Zoghbi, H. Y., Smolyar, A., Bosak, S., Sequerra, R., Doucette-Stamm, L., Cusick, M. E., Hill, D. E., Roth, F. P., Vidal, M., 2005, Towards a proteome-scale map of the human protein-protein interaction network,Nature .437(7062):1173-1178.
Rubino, F. A., Mollo, A., Kumar, S., Butler, E. K., Ruiz, N., Walker, S., Kahne, D. E., 2020, Detection of Transport Intermediates in the Peptidoglycan Flippase MurJ Identifies Residues Essential for Conformational Cycling, Journal of the American Chemical Society .142(12):5482-5486.
Ryan, D. P., Matthews, J. M., 2005, Protein-protein interactions in human disease, Current Opinion in Structural Biology .15(4):441-446.
Salahuddin, P., Fatima, M. T., Uversky, V. N., Khan, R. H., Islam, Z., Furkan, M., 2021, The role of amyloids in Alzheimer’s and Parkinson’s diseases, International Journal of Biological Macromolecules .190:44-55.
Schneider, M., Belsom, A., Rappsilber, J., 2018, Protein Tertiary Structure by Crosslinking/Mass Spectrometry, Trends in Biochemical Sciences .43(3):157-169.
Schreiber, G., Protein–protein interaction interfaces and their functional implications, Protein–Protein Interaction Regulators2020.
Scott, D. E., Bayly, A. R., Abell, C., Skidmore, J., 2016, Small molecules, big targets: drug discovery faces the protein-protein interaction challenge, Nature Reviews Drug Discovery .15(8):533-550.
Seidel, L., Zarzycka, B., Zaidi, S. A., Katritch, V., Coin, I., 2017, Structural insight into the activation of a class B G-protein-coupled receptor by peptide hormones in live human cells, Elife .6.
Seidel, S. A., Dijkman, P. M., Lea, W. A., van den Bogaart, G., Jerabek-Willemsen, M., Lazic, A., Joseph, J. S., Srinivasan, P., Baaske, P., Simeonov, A., Katritch, I., Melo, F. A., Ladbury, J. E., Schreiber, G., Watts, A., Braun, D., Duhr, S., 2013, Microscale thermophoresis quantifies biomolecular interactions under previously challenging conditions, Methods .59(3):301-315.
Shin, G., Lim, S. I., 2020, Site-specific proximity ligation provides molecular insights into biologically relevant interfaces of protein-protein interaction, Biochem Biophys Res Commun .533(4):932-937.
Shukla, A. K., Westfield, G. H., Xiao, K., Reis, R. I., Huang, L.-Y., Tripathi-Shukla, P., Qian, J., Li, S., Blanc, A., Oleskie, A. N., Dosey, A. M., Su, M., Liang, C.-R., Gu, L.-L., Shan, J.-M., Chen, X., Hanna, R., Choi, M., Yao, X. J., Klink, B. U., Kahsai, A. W., Sidhu, S. S., Koide, S., Penczek, P. A., Kossiakoff, A. A., Woods Jr, V. L., Kobilka, B. K., Skiniotis, G., Lefkowitz, R. J., 2014, Visualization of arrestin recruitment by a G-protein-coupled receptor,Nature .512(7513):218-222.
Simms, J., Uddin, R., Sakmar, T. P., Gingell, J. J., Garelja, M. L., Hay, D. L., Brimble, M. A., Harris, P. W., Reynolds, C. A., Poyner, D. R., 2018, Photoaffinity Cross-Linking and Unnatural Amino Acid Mutagenesis Reveal Insights into Calcitonin Gene-Related Peptide Binding to the Calcitonin Receptor-like Receptor/Receptor Activity-Modifying Protein 1 (CLR/RAMP1) Complex, Biochemistry .57(32):4915-4922.
Ständer, S., L, R. G., Scarselli, M., Norais, N., Rand, K., 2021, Epitope Mapping of Polyclonal Antibodies by Hydrogen-Deuterium Exchange Mass Spectrometry (HDX-MS), Analytical Chemistry .93(34):11669-11678.
Stephens, A. D., Nespovitaya, N., Zacharopoulou, M., Kaminski, C. F., Phillips, J. J., Kaminski Schierle, G. S., 2018, Different Structural Conformers of Monomeric α-Synuclein Identified after Lyophilizing and Freezing, Analytical Chemistry .90(11):6975-6983.
Suchanek, M., Radzikowska, A., Thiele, C., 2005, Photo-leucine and photo-methionine allow identification of protein-protein interactions in living cells, Nature Methods .2(4):261-268.
Sun, H., Ma, L., Wang, L., Xiao, P., Li, H., Zhou, M., Song, D., 2021, Research advances in hydrogen-deuterium exchange mass spectrometry for protein epitope mapping, Analytical and Bioanalytical Chemistry .413(9):2345-2359.
Uhrik, L., Hernychova, L., Muller, P., Kalathiya, U., Lisowska, M. M., Kocikowski, M., Parys, M., Faktor, J., Nekulova, M., Nortcliffe, C., Zatloukalova, P., Ruetgen, B., Fahraeus, R., Ball, K. L., Argyle, D. J., Vojtesek, B., Hupp, T. R., 2021, Hydrogen deuterium exchange mass spectrometry identifies the dominant paratope in CD20 antigen binding to the NCD1.2 monoclonal antibody, Biochemical Journal .478(1):99-120.
von Bergen, M., Friedhoff, P., Biernat, J., Heberle, J., Mandelkow, E. M., Mandelkow, E., 2000, Assembly of tau protein into Alzheimer paired helical filaments depends on a local sequence motif ((306)VQIVYK(311)) forming beta structure, Proceedings of the National Academy of Sciences .97(10):5129-5134.
Wang, X., Ni, D., Liu, Y., Lu, S., 2021, Rational Design of Peptide-Based Inhibitors Disrupting Protein-Protein Interactions,Frontiers in Chemistry .9:682675.
Whittaker, J., Whittaker, L. J., Roberts, C. T., Jr., Phillips, N. B., Ismail-Beigi, F., Lawrence, M. C., Weiss, M. A., 2012, α-Helical element at the hormone-binding surface of the insulin receptor functions as a signaling element to activate its tyrosine kinase, Proceedings of the National Academy of Sciences .109(28):11166-11171.
Wu, B., Peisley, A., Richards, C., Yao, H., Zeng, X., Lin, C., Chu, F., Walz, T., Hur, S., 2013, Structural Basis for dsRNA Recognition, Filament Formation, and Antiviral Signal Activation by MDA5,Cell .152(1):276-289.
Xie, Y., Chen, S., Li, Q., Sheng, Y., Alvarez, M. R., Reyes, J., Xu, G., Solakyildirim, K., Lebrilla, C. B., 2021, Glycan-protein cross-linking mass spectrometry reveals sialic acid-mediated protein networks on cell surfaces, Chemical Science .12(25):8767-8777.
Yadav, S., Sreedhara, A., Kanai, S., Liu, J., Lien, S., Lowman, H., Kalonia, D. S., Shire, S. J., 2011, Establishing a link between amino acid sequences and self-associating and viscoelastic behavior of two closely related monoclonal antibodies, Pharmaceutical Research .28(7):1750-1764.
Yang, T., Li, X., Li, X. D., 2020, A bifunctional amino acid to study protein–protein interactions, RSC Advances .10(69):42076-42083.
Yang, Y., Song, H., Chen, P. R., 2016, Genetically encoded photocrosslinkers for identifying and mapping protein-protein interactions in living cells, IUBMB Life .68(11):879-886.
Yang, Y., Song, H., He, D., Zhang, S., Dai, S., Lin, S., Meng, R., Wang, C., Chen, P. R., 2016, Genetically encoded protein photocrosslinker with a transferable mass spectrometry-identifiable label, Nature Communications .7:12299.
Yang, Y., Song, H., He, D., Zhang, S., Dai, S., Xie, X., Lin, S., Hao, Z., Zheng, H., Chen, P. R., 2017, Genetically encoded releasable photo-cross-linking strategies for studying protein-protein interactions in living cells, Nature Protocols .12(10):2147-2168.
Zehl, M., Rand, K. D., Jensen, O. N., Jørgensen, T. J., 2008, Electron transfer dissociation facilitates the measurement of deuterium incorporation into selectively labeled peptides with single residue resolution, Journal of the American Chemical Society .130(51):17453-17459.
Zhang, M. M., Beno, B. R., Huang, R. Y., Adhikari, J., Deyanova, E. G., Li, J., Chen, G., Gross, M. L., 2019, An Integrated Approach for Determining a Protein-Protein Binding Interface in Solution and an Evaluation of Hydrogen-Deuterium Exchange Kinetics for Adjudicating Candidate Docking Models, Analytical Chemistry .91(24):15709-15717.
Zhang, M. M., Huang, R. Y., Beno, B. R., Deyanova, E. G., Li, J., Chen, G., Gross, M. L., 2020, Epitope and Paratope Mapping of PD-1/Nivolumab by Mass Spectrometry-Based Hydrogen-Deuterium Exchange, Cross-linking, and Molecular Docking, Analytical Chemistry .92(13):9086-9094.
Zhang, Q., Noble, K. A., Mao, Y., Young, N. L., Sathe, S. K., Roux, K. H., Marshall, A. G., 2013, Rapid Screening for Potential Epitopes Reactive with a Polycolonal Antibody by Solution-Phase H/D Exchange Monitored by FT-ICR Mass Spectrometry, Journal of The American Society for Mass Spectrometry .24(7):1016-1025.
Zhang, Q., Willison, L. N., Tripathi, P., Sathe, S. K., Roux, K. H., Emmett, M. R., Blakney, G. T., Zhang, H. M., Marshall, A. G., 2011, Epitope mapping of a 95 kDa antigen in complex with antibody by solution-phase amide backbone hydrogen/deuterium exchange monitored by Fourier transform ion cyclotron resonance mass spectrometry,Analytical Chemistry .83(18):7129-7136.
Zhang, Z., Zhang, A., Xiao, G., 2012, Improved protein hydrogen/deuterium exchange mass spectrometry platform with fully automated data processing, Analytical Chemistry .84(11):4942-4949.
Zhu, S., Liuni, P., Ettorre, L., Chen, T., Szeto, J., Carpick, B., James, D. A., Wilson, D. J., 2019, Hydrogen-Deuterium Exchange Epitope Mapping Reveals Distinct Neutralizing Mechanisms for Two Monoclonal Antibodies against Diphtheria Toxin, Biochemistry .58(6):646-656.
Zhu, S., Shala, A., Bezginov, A., Sljoka, A., Audette, G., Wilson, D. J., 2015, Hyperphosphorylation of intrinsically disordered tau protein induces an amyloidogenic shift in its conformational ensemble,PLOS ONE .10(3):e0120416.