Label-free higher order structure and dynamic investigation method of proteins in solution using an enzymatic reactor coupled to electrospray high-resolution mass spectrometry
Grifnee, Elodie ; Université de Liège - ULiège > Département de chimie (sciences) > Laboratoire de spectrométrie de masse (L.S.M.)
Kune, Christopher ; Université de Liège - ULiège > Département de chimie (sciences) > Laboratoire de spectrométrie de masse (L.S.M.)
Delvaux, Cédric ; Université de Liège - ULiège > Molecular Systems (MolSys)
Quinton, Loïc ; Université de Liège - ULiège > Département de chimie (sciences) > Chimie biologique
Far, Johann ; Université de Liège - ULiège > Département de chimie (sciences) > Chimie analytique inorganique
Mazzucchelli, Gabriel ; Université de Liège - ULiège > Département de chimie (sciences) > Laboratoire de spectrométrie de masse (L.S.M.)
De Pauw, Edwin ; Université de Liège - ULiège > Département de chimie (sciences)
Language :
English
Title :
Label-free higher order structure and dynamic investigation method of proteins in solution using an enzymatic reactor coupled to electrospray high-resolution mass spectrometry
Publication date :
2022
Journal title :
Journal of the American Society for Mass Spectrometry
Han, X.; Aslanian, A.; Yates, J. R. Mass Spectrometry for Proteomics. Curr. Opin. Chem. Biol. 2008, 12 (5), 483-490, 10.1016/j.cbpa.2008.07.024
Vitorino, R.; Guedes, S.; Trindade, F.; Correia, I.; Moura, G.; Carvalho, P.; Santos, M. A. S.; Amado, F. De Novo Sequencing of Proteins by Mass Spectrometry. Expert Rev. Proteomics 2020, 17 (7-8), 595-607, 10.1080/14789450.2020.1831387
Pan, S.; Aebersold, R.; Chen, R.; Rush, J.; Goodlett, D. R.; McIntosh, M. W.; Zhang, J.; Brentnall, T. A. Mass Spectrometry Based Targeted Protein Quantification: Methods and Applications. J. Proteome Res. 2009, 8 (2), 787-797, 10.1021/pr800538n
Schaffer, L. V.; Millikin, R. J.; Miller, R. M.; Anderson, L. C.; Fellers, R. T.; Ge, Y.; Kelleher, N. L.; LeDuc, R. D.; Liu, X.; Payne, S. H.; Sun, L.; Thomas, P. M.; Tucholski, T.; Wang, Z.; Wu, S.; Wu, Z.; Yu, D.; Shortreed, M. R.; Smith, L. M. Identification and Quantification of Proteoforms by Mass Spectrometry. Proteomics 2019, 19 (10), 1800361, 10.1002/pmic.201800361
Bantscheff, M.; Schirle, M.; Sweetman, G.; Rick, J.; Kuster, B. Quantitative Mass Spectrometry in Proteomics: A Critical Review. Anal. Bioanal. Chem. 2007, 389 (4), 1017-1031, 10.1007/s00216-007-1486-6
Wales, T. E.; Engen, J. R. Hydrogen Exchange Mass Spectrometry for the Analysis of Protein Dynamics. Mass Spectrom. Rev. 2006, 25 (1), 158-170, 10.1002/mas.20064
Sinz, A. Chemical Cross-Linking and Mass Spectrometry to Map Three-Dimensional Protein Structures and Protein-Protein Interactions. Mass Spectrom. Rev. 2006, 25 (4), 663-682, 10.1002/mas.20082
Lanucara, F.; Holman, S. W.; Gray, C. J.; Eyers, C. E. The Power of Ion Mobility-Mass Spectrometry for Structural Characterization and the Study of Conformational Dynamics. Nat. Chem. 2014, 6 (4), 281-294, 10.1038/nchem.1889
Sinz, A. Cross-Linking/Mass Spectrometry for Studying Protein Structures and Protein-Protein Interactions: Where Are We Now and Where Should We Go from Here?. Angew. Chem., Int. Ed. 2018, 57 (22), 6390-6396, 10.1002/anie.201709559
Österlund, N.; Moons, R.; Ilag, L. L.; Sobott, F.; Gräslund, A. Native Ion Mobility-Mass Spectrometry Reveals the Formation of β-Barrel Shaped Amyloid-β Hexamers in a Membrane-Mimicking Environment. J. Am. Chem. Soc. 2019, 141 (26), 10440-10450, 10.1021/jacs.9b04596
Bleiholder, C.; Dupuis, N. F.; Wyttenbach, T.; Bowers, M. T. Ion Mobility-Mass Spectrometry Reveals a Conformational Conversion from Random Assembly to β-Sheet in Amyloid Fibril Formation. Nat. Chem. 2011, 3 (2), 172-177, 10.1038/nchem.945
Ishima, R.; Torchia, D. A. Protein Dynamics from NMR. Nature structural biology 2000, 7 (9), 740, 10.1038/78963
McPherson, A. In Situ X-Ray Crystallography. J. Appl. Crystallogr. 2000, 33 (2), 397-400, 10.1107/S0021889800001254
Johnson, W. C. Secondary Structure of Proteins Through Circular Dichroism Spectroscopy. Annu. Rev. Biophys. Biophys. Chem. 1988, 17, 145-166, 10.1146/annurev.bb.17.060188.001045
Lerner, E.; Barth, A.; Hendrix, J.; Ambrose, B.; Birkedal, V.; Blanchard, S. C.; Börner, R.; Sung Chung, H.; Cordes, T.; Craggs, T. D.; Deniz, A. A.; Diao, J.; Fei, J.; Gonzalez, R. L.; Gopich, I. V.; Ha, T.; Hanke, C. A.; Haran, G.; Hatzakis, N. S.; Hohng, S.; Hong, S.-C.; Hugel, T.; Ingargiola, A.; Joo, C.; Kapanidis, A. N.; Kim, H. D.; Laurence, T.; Lee, N. K.; Lee, T.-H.; Lemke, E. A.; Margeat, E.; Michaelis, J.; Michalet, X.; Myong, S.; Nettels, D.; Peulen, T.-O.; Ploetz, E.; Razvag, Y.; Robb, N. C.; Schuler, B.; Soleimaninejad, H.; Tang, C.; Vafabakhsh, R.; Lamb, D. C.; Seidel, C. A.; Weiss, S. FRET-Based Dynamic Structural Biology: Challenges, Perspectives and an Appeal for Open-Science Practices. eLife 2021, 10, e60416 10.7554/eLife.60416
Morsa, D.; Baiwir, D.; La Rocca, R.; Zimmerman, T. A.; Hanozin, E.; Grifnée, E.; Longuespée, R.; Meuwis, M.-A.; Smargiasso, N.; Pauw, E. D.; Mazzucchelli, G. Multi-Enzymatic Limited Digestion: The Next-Generation Sequencing for Proteomics?. J. Proteome Res. 2019, 18 (6), 2501-2513, 10.1021/acs.jproteome.9b00044
Pandeswari, P. B.; Sabareesh, V. Middle-down Approach: A Choice to Sequence and Characterize Proteins/Proteomes by Mass Spectrometry. RSC Adv. 2019, 9 (1), 313-344, 10.1039/C8RA07200K
Fontana, A.; Polverino de Laureto, P.; Spolaore, B.; Frare, E.; Zambonin, M. Detecting Disordered Regions in Proteins by Limited Proteolysis. In Instrumental Analysis of Intrinsically Disordered Proteins; Uversky, V. N., Longhi, S., Eds.; John Wiley & Sons, Inc.: Hoboken, 2010; pp 569-626.
Fontana, A.; de Laureto, P. P.; Spolaore, B.; Frare, E.; Picotti, P.; Zambonin, M. Probing Protein Structure by Limited Proteolysis 2019, 51, 299, 10.18388/abp.2004_3573
Kuwata, K.; Era, S.; Hoshino, M.; Forge, V.; Goto, Y.; Batt, C. A. Solution Structure and Dynamics of Bovine β-Lactoglobulin A. Protein Sci. 1999, 8 (11), 2541-2545, 10.1110/ps.8.11.2541
Banci, L.; Bertini, I.; Gray, H. B.; Luchinat, C.; Reddig, T.; Rosato, A.; Turano, P. Solution Structure of Oxidized Horse Heart Cytochrome c. Biochemistry 1997, 36 (32), 9867-9877, 10.1021/bi970724w
Andrews, A. L.; Atkinson, D.; Evans, M. T. A.; Finer, E. G.; Green, J. P.; Phillips, M. C.; Robertson, R. N. The Conformation and Aggregation of Bovine?-Casein A. I. Molecular Aspects of Thermal Aggregation. Biopolymers 1979, 18 (5), 1105-1121, 10.1002/bip.1979.360180507
Sipos, T.; Merkel, J. R. An Effect of Calcium Ions on the Activity, Heat Stability, and Structure of Trypsin. Biochemistry 1970, 9, 2766, 10.1021/bi00816a003
Vandermarliere, E.; Mueller, M.; Martens, L. Getting Intimate with Trypsin, the Leading Protease in Proteomics: TRYPSIN IN PROTEOMICS. Mass Spectrom. Rev. 2013, 32 (6), 453-465, 10.1002/mas.21376
Gardner, Q.-A. A.; Younas, H.; Akhtar, M. Studies on the Regioselectivity and Kinetics of the Action of Trypsin on Proinsulin and Its Derivatives Using Mass Spectrometry. Biochim. Biophys. Acta, Proteins Proteomics 2013, 1834 (1), 182-190, 10.1016/j.bbapap.2012.09.004
Liigand, P.; Kaupmees, K.; Kruve, A. Influence of the Amino Acid Composition on the Ionization Efficiencies of Small Peptides. J. Mass Spectrom. 2019, 54 (6), 481-487, 10.1002/jms.4348
Tolkach, A.; Kulozik, U. Reaction Kinetic Pathway of Reversible and Irreversible Thermal Denaturation of β-Lactoglobulin. Lait 2007, 87 (4-5), 301-315, 10.1051/lait:2007012
Lee, B.; Richards, F. M. The Interpretation of Protein Structures: Estimation of Static Accessibility. J. Mol. Biol. 1971, 55 (3), 379-IN4, 10.1016/0022-2836(71)90324-X
Shrake, A.; Rupley, J. A. Environment and Exposure to Solvent of Protein Atoms. Lysozyme and Insulin. J. Mol. Biol. 1973, 79 (2), 351-371, 10.1016/0022-2836(73)90011-9
Papaleo, E.; Saladino, G.; Lambrughi, M.; Lindorff-Larsen, K.; Gervasio, F. L.; Nussinov, R. The Role of Protein Loops and Linkers in Conformational Dynamics and Allostery. Chem. Rev. 2016, 116 (11), 6391-6423, 10.1021/acs.chemrev.5b00623
Nick Pace, C.; Martin Scholtz, J. A Helix Propensity Scale Based on Experimental Studies of Peptides and Proteins. Biophys. J. 1998, 75 (1), 422-427, 10.1016/S0006-3495(98)77529-0
Fisher, W. R.; Taniuchi, H.; Anfinsen, C. B. On the Role of Heme in the Formation of the Structure of Cytochrome c. J. Biol. Chem. 1973, 248 (9), 3188-3195, 10.1016/S0021-9258(19)44026-X
Farrell, H. M., Jr.; Wickham, E. D.; Unruh, J. J.; Qi, P. X.; Hoagland, P. D. Secondary Structural Studies of Bovine Caseins: Temperature Dependence of b-Casein Structure as Analyzed by Circular Dichroism and FTIR Spectroscopy and Correlation with Micellizationq. Food Hydrocolloids 2001, 15, 341, 10.1016/S0268-005X(01)00080-7
Livney, Y. D.; Schwan, A. L.; Dalgleish, D. G. A Study of β-Casein Tertiary Structure by Intramolecular Crosslinking and Mass Spectrometry. J. Dairy Sci. 2004, 87 (11), 3638-3647, 10.3168/jds.S0022-0302(04)73502-X
Kumosinski, T. F.; Brown, E. M.; Farrell, H. M., Jr. Three-Dimensional Molecular Modeling of Bovine Caseins: An Energy-Minimized-Casein Structure1 1993, 76 (4), 931, 10.3168/jds.S0022-0302(93)77420-2
