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Volumn 120, Issue 23, 2016, Pages 5114-5124

Collision-Induced Dissociation of Electrosprayed Protein Complexes: An All-Atom Molecular Dynamics Model with Mobile Protons

Author keywords

[No Author keywords available]

Indexed keywords

CHAINS; DISSOCIATION; ELECTRODEPOSITION; ELECTROSPRAY IONIZATION; IONS; MASS SPECTROMETRY; PROTEINS;

EID: 84975231457     PISSN: 15206106     EISSN: 15205207     Source Type: Journal    
DOI: 10.1021/acs.jpcb.6b03035     Document Type: Article
Times cited : (61)

References (86)
  • 2
    • 84866134921 scopus 로고    scopus 로고
    • A high-throughput approach for measuring temporal changes in the interactome
    • Kristensen, A. R.; Gsponer, J.; Foster, L. J. A high-throughput approach for measuring temporal changes in the interactome Nat. Methods 2012, 9, 907-909 10.1038/nmeth.2131
    • (2012) Nat. Methods , vol.9 , pp. 907-909
    • Kristensen, A.R.1    Gsponer, J.2    Foster, L.J.3
  • 3
    • 37249065351 scopus 로고    scopus 로고
    • The molecular sociology of the cell
    • Robinson, C. V.; Sali, A.; Baumeister, W. The molecular sociology of the cell Nature 2007, 450, 973-982 10.1038/nature06523
    • (2007) Nature , vol.450 , pp. 973-982
    • Robinson, C.V.1    Sali, A.2    Baumeister, W.3
  • 4
    • 84923368907 scopus 로고    scopus 로고
    • How cryo-EM is revolutionizing structural biology
    • Bai, X.-C.; McMullan, G.; Scheres, S. H. W. How cryo-EM is revolutionizing structural biology Trends Biochem. Sci. 2015, 40, 49-57 10.1016/j.tibs.2014.10.005
    • (2015) Trends Biochem. Sci. , vol.40 , pp. 49-57
    • Bai, X.-C.1    McMullan, G.2    Scheres, S.H.W.3
  • 5
    • 84876935158 scopus 로고    scopus 로고
    • Allosteric mechanisms can be distinguished using structural mass spectrometry
    • Dyachenko, A.; Gruber, R.; Shimon, L.; Horovitz, A.; Sharon, M. Allosteric mechanisms can be distinguished using structural mass spectrometry Proc. Natl. Acad. Sci. U. S. A. 2013, 110, 7235-7239 10.1073/pnas.1302395110
    • (2013) Proc. Natl. Acad. Sci. U. S. A. , vol.110 , pp. 7235-7239
    • Dyachenko, A.1    Gruber, R.2    Shimon, L.3    Horovitz, A.4    Sharon, M.5
  • 6
    • 80052098908 scopus 로고    scopus 로고
    • Modern Biomolecular Mass Spectrometry and its Role in Studying Virus Structure, Dynamics, and Assembly
    • Uetrecht, C.; Heck, A. J. R. Modern Biomolecular Mass Spectrometry and its Role in Studying Virus Structure, Dynamics, and Assembly Angew. Chem., Int. Ed. 2011, 50, 8248-8262 10.1002/anie.201008120
    • (2011) Angew. Chem., Int. Ed. , vol.50 , pp. 8248-8262
    • Uetrecht, C.1    Heck, A.J.R.2
  • 7
    • 84926488713 scopus 로고    scopus 로고
    • Mass Spectrometry of Protein Complexes: From Origins to Applications
    • Mehmood, S.; Allison, T. M.; Robinson, C. V. Mass Spectrometry of Protein Complexes: From Origins to Applications Annu. Rev. Phys. Chem. 2015, 66, 453-474 10.1146/annurev-physchem-040214-121732
    • (2015) Annu. Rev. Phys. Chem. , vol.66 , pp. 453-474
    • Mehmood, S.1    Allison, T.M.2    Robinson, C.V.3
  • 8
    • 33847614790 scopus 로고    scopus 로고
    • Native Protein MS and Ion Mobility: Large Flying Proteins with ESI
    • Kaddis, C. S.; Loo, J. A. Native Protein MS and Ion Mobility: Large Flying Proteins with ESI Anal. Chem. 2007, 79, 1778-1784 10.1021/ac071878c
    • (2007) Anal. Chem. , vol.79 , pp. 1778-1784
    • Kaddis, C.S.1    Loo, J.A.2
  • 9
    • 80053577815 scopus 로고    scopus 로고
    • Mass spectrometry: Come of age for structural and dynamical biology
    • Benesch, J. L. P.; Ruotolo, B. T. Mass spectrometry: come of age for structural and dynamical biology Curr. Opin. Struct. Biol. 2011, 21, 641-649 10.1016/j.sbi.2011.08.002
    • (2011) Curr. Opin. Struct. Biol. , vol.21 , pp. 641-649
    • Benesch, J.L.P.1    Ruotolo, B.T.2
  • 11
    • 84894501413 scopus 로고    scopus 로고
    • ETD Allows for Native Surface Mapping of a 150 kDa Noncovalent Complex on a Commercial Q-TWIMS-TOF Instrument
    • Lermyte, F.; Konijnenberg, A.; Williams, J. P.; Brown, J. M.; Valkenborg, D.; Sobott, F. ETD Allows for Native Surface Mapping of a 150 kDa Noncovalent Complex on a Commercial Q-TWIMS-TOF Instrument J. Am. Soc. Mass Spectrom. 2014, 25, 343-350 10.1007/s13361-013-0798-3
    • (2014) J. Am. Soc. Mass Spectrom. , vol.25 , pp. 343-350
    • Lermyte, F.1    Konijnenberg, A.2    Williams, J.P.3    Brown, J.M.4    Valkenborg, D.5    Sobott, F.6
  • 12
    • 0035476451 scopus 로고    scopus 로고
    • Thermal Decomposition of a Gaseous Multiprotein Complex Studied by Blackbody Infrared Radiative Dissociation. Investigating the Origin of the Asymmetric Dissociation Behavior
    • Felitsyn, N.; Kitova, E. N.; Klassen, J. S. Thermal Decomposition of a Gaseous Multiprotein Complex Studied by Blackbody Infrared Radiative Dissociation. Investigating the Origin of the Asymmetric Dissociation Behavior Anal. Chem. 2001, 73, 4647-4661 10.1021/ac0103975
    • (2001) Anal. Chem. , vol.73 , pp. 4647-4661
    • Felitsyn, N.1    Kitova, E.N.2    Klassen, J.S.3
  • 13
    • 84948469224 scopus 로고    scopus 로고
    • Surface-Induced Dissociation Mass Spectra as a Tool for Distinguishing Different Structural Forms of Gas-Phase Multimeric Protein Complexes
    • Quintyn, R. S.; Zhou, M.; Yan, J.; Wysocki, V. H. Surface-Induced Dissociation Mass Spectra as a Tool for Distinguishing Different Structural Forms of Gas-Phase Multimeric Protein Complexes Anal. Chem. 2015, 87, 11879-11886 10.1021/acs.analchem.5b03441
    • (2015) Anal. Chem. , vol.87 , pp. 11879-11886
    • Quintyn, R.S.1    Zhou, M.2    Yan, J.3    Wysocki, V.H.4
  • 15
    • 77953912267 scopus 로고    scopus 로고
    • Mass Spectrometry and the Amyloid Problem - How Far Can We Go in the Gas Phase?
    • Ashcroft, A. E. Mass Spectrometry and the Amyloid Problem-How Far Can We Go in the Gas Phase? J. Am. Soc. Mass Spectrom. 2010, 21, 1087-1096 10.1016/j.jasms.2010.02.026
    • (2010) J. Am. Soc. Mass Spectrom. , vol.21 , pp. 1087-1096
    • Ashcroft, A.E.1
  • 16
    • 84951866242 scopus 로고    scopus 로고
    • Water-Mediated Dimerization of Ubiquitin Ions Captured by Cryogenic Ion Mobility-Mass Spectrometry
    • Servage, K. A.; Silveira, J. A.; Fort, K. L.; Clemmer, D. E.; Russell, D. H. Water-Mediated Dimerization of Ubiquitin Ions Captured by Cryogenic Ion Mobility-Mass Spectrometry J. Phys. Chem. Lett. 2015, 6, 4947-4951 10.1021/acs.jpclett.5b02382
    • (2015) J. Phys. Chem. Lett. , vol.6 , pp. 4947-4951
    • Servage, K.A.1    Silveira, J.A.2    Fort, K.L.3    Clemmer, D.E.4    Russell, D.H.5
  • 17
    • 78449267576 scopus 로고    scopus 로고
    • Collision Cross Sections of Proteins and Their Complexes: A Calibration Framework and Database for Gas-Phase Structural Biology
    • Bush, M. F.; Hall, Z.; Giles, K.; Hoyes, J.; Robinson, C. V.; Ruotolo, B. T. Collision Cross Sections of Proteins and Their Complexes: A Calibration Framework and Database for Gas-Phase Structural Biology Anal. Chem. 2010, 82, 9557-9565 10.1021/ac1022953
    • (2010) Anal. Chem. , vol.82 , pp. 9557-9565
    • Bush, M.F.1    Hall, Z.2    Giles, K.3    Hoyes, J.4    Robinson, C.V.5    Ruotolo, B.T.6
  • 18
    • 79953285963 scopus 로고    scopus 로고
    • Tandem Differential Mobility Analysis-Mass Spectrometry Reveals Partial Gas-Phase Collapse of the GroEL Complex
    • Hogan, C. J.; Ruotolo, B. T.; Robinson, C. V.; de la Mora, J. F. Tandem Differential Mobility Analysis-Mass Spectrometry Reveals Partial Gas-Phase Collapse of the GroEL Complex J. Phys. Chem. B 2011, 115, 3614-3621 10.1021/jp109172k
    • (2011) J. Phys. Chem. B , vol.115 , pp. 3614-3621
    • Hogan, C.J.1    Ruotolo, B.T.2    Robinson, C.V.3    De La Mora, J.F.4
  • 19
    • 4444243006 scopus 로고    scopus 로고
    • Investigation of intact protein complexes by mass spectrometry
    • Heck, A. J. R.; Van den Heuvel, R. H. H. Investigation of intact protein complexes by mass spectrometry Mass Spectrom. Rev. 2004, 23, 368-389 10.1002/mas.10081
    • (2004) Mass Spectrom. Rev. , vol.23 , pp. 368-389
    • Heck, A.J.R.1    Van Den Heuvel, R.H.H.2
  • 20
    • 84890500157 scopus 로고    scopus 로고
    • Effects of Polarity on the Structures and Charge States of Native-Like Proteins and Protein Complexes in the Gas Phase
    • Allen, S. J.; Schwartz, A. M.; Bush, M. F. Effects of Polarity on the Structures and Charge States of Native-Like Proteins and Protein Complexes in the Gas Phase Anal. Chem. 2013, 85, 12055-12061 10.1021/ac403139d
    • (2013) Anal. Chem. , vol.85 , pp. 12055-12061
    • Allen, S.J.1    Schwartz, A.M.2    Bush, M.F.3
  • 21
    • 0031010426 scopus 로고    scopus 로고
    • Slow heating methods in tandem mass spectrometry
    • McLuckey, S. A.; Goeringer, D. E. Slow heating methods in tandem mass spectrometry J. Mass Spectrom. 1997, 32, 461-474 10.1002/(SICI)1096-9888(199705)32:5<461::AID-JMS515>3.0.CO;2-H
    • (1997) J. Mass Spectrom. , vol.32 , pp. 461-474
    • McLuckey, S.A.1    Goeringer, D.E.2
  • 22
    • 34548215681 scopus 로고    scopus 로고
    • Protein Complexes in the Gas Phase: Technology for Structural Genomics and Proteomics
    • Benesch, J. L. P.; Ruotolo, B. T.; Simmons, D. A.; Robinson, C. V. Protein Complexes in the Gas Phase: Technology for Structural Genomics and Proteomics Chem. Rev. 2007, 107, 3544-3567 10.1021/cr068289b
    • (2007) Chem. Rev. , vol.107 , pp. 3544-3567
    • Benesch, J.L.P.1    Ruotolo, B.T.2    Simmons, D.A.3    Robinson, C.V.4
  • 23
    • 69849084918 scopus 로고    scopus 로고
    • The Mechanism of Collisional Activation of Ions in Mass Spectrometry
    • Mayer, P. M.; Poon, C. The Mechanism of Collisional Activation of Ions in Mass Spectrometry Mass Spectrom. Rev. 2009, 28, 608-639 10.1002/mas.20225
    • (2009) Mass Spectrom. Rev. , vol.28 , pp. 608-639
    • Mayer, P.M.1    Poon, C.2
  • 24
    • 0028447420 scopus 로고
    • Observation of the Noncovalent Quaternary Association of Proteins by Electrospray Ionization Mass Spectrometry
    • Light-Wahl, K. J.; Schwartz, B. L.; Smith, R. D. Observation of the Noncovalent Quaternary Association of Proteins by Electrospray Ionization Mass Spectrometry J. Am. Chem. Soc. 1994, 116, 5271-5278 10.1021/ja00091a035
    • (1994) J. Am. Chem. Soc. , vol.116 , pp. 5271-5278
    • Light-Wahl, K.J.1    Schwartz, B.L.2    Smith, R.D.3
  • 25
    • 33845222072 scopus 로고    scopus 로고
    • Symmetrical Gas-Phase Dissociation of Noncovalent Protein Complexes via Surface Collisions
    • Jones, C. M.; Beardsley, R. L.; Galhena, A. S.; Dagan, S.; Cheng, G.; Wysocki, V. H. Symmetrical Gas-Phase Dissociation of Noncovalent Protein Complexes via Surface Collisions J. Am. Chem. Soc. 2006, 128, 15044-15045 10.1021/ja064586m
    • (2006) J. Am. Chem. Soc. , vol.128 , pp. 15044-15045
    • Jones, C.M.1    Beardsley, R.L.2    Galhena, A.S.3    Dagan, S.4    Cheng, G.5    Wysocki, V.H.6
  • 26
    • 0037420384 scopus 로고    scopus 로고
    • Origin of Asymmetric Charge Partitioning in the Dissociation of Gas-Phase Protein Homodimers
    • Jurchen, J. C.; Williams, E. R. Origin of Asymmetric Charge Partitioning in the Dissociation of Gas-Phase Protein Homodimers J. Am. Chem. Soc. 2003, 125, 2817-2826 10.1021/ja0211508
    • (2003) J. Am. Chem. Soc. , vol.125 , pp. 2817-2826
    • Jurchen, J.C.1    Williams, E.R.2
  • 27
    • 33745285701 scopus 로고    scopus 로고
    • Gas-phase processes and measurements of macromolecular properties in solution: On the possibility of false positive and false negative signals of protein unfolding
    • Abzalimov, R. R.; Frimpong, A. K.; Kaltashov, I. A. Gas-phase processes and measurements of macromolecular properties in solution: On the possibility of false positive and false negative signals of protein unfolding Int. J. Mass Spectrom. 2006, 253, 207-216 10.1016/j.ijms.2006.03.002
    • (2006) Int. J. Mass Spectrom. , vol.253 , pp. 207-216
    • Abzalimov, R.R.1    Frimpong, A.K.2    Kaltashov, I.A.3
  • 28
    • 84861639125 scopus 로고    scopus 로고
    • Bound Cations Significantly Stabilize the Structure of Multiprotein Complexes in the Gas Phase
    • Han, L.; Hyung, S.-J.; Ruotolo, B. T. Bound Cations Significantly Stabilize the Structure of Multiprotein Complexes in the Gas Phase Angew. Chem., Int. Ed. 2012, 51, 5692-5695 10.1002/anie.201109127
    • (2012) Angew. Chem., Int. Ed. , vol.51 , pp. 5692-5695
    • Han, L.1    Hyung, S.-J.2    Ruotolo, B.T.3
  • 29
    • 80755189415 scopus 로고    scopus 로고
    • An Electrostatic Charge Partitioning Model for the Dissociation of Protein Complexes in the Gas Phase
    • Sciuto, S. V.; Liu, J.; Konermann, L. An Electrostatic Charge Partitioning Model for the Dissociation of Protein Complexes in the Gas Phase J. Am. Soc. Mass Spectrom. 2011, 22, 1679-1689 10.1007/s13361-011-0205-x
    • (2011) J. Am. Soc. Mass Spectrom. , vol.22 , pp. 1679-1689
    • Sciuto, S.V.1    Liu, J.2    Konermann, L.3
  • 30
    • 84879077162 scopus 로고    scopus 로고
    • A Charge Moving Algorithm for Molecular Dynamics Simulations of Gas-Phase Proteins
    • Fegan, S. K.; Thachuk, M. A Charge Moving Algorithm for Molecular Dynamics Simulations of Gas-Phase Proteins J. Chem. Theory Comput. 2013, 9, 2531-2539 10.1021/ct300906a
    • (2013) J. Chem. Theory Comput. , vol.9 , pp. 2531-2539
    • Fegan, S.K.1    Thachuk, M.2
  • 31
    • 14744272834 scopus 로고    scopus 로고
    • Intramolecular Migration of Amide Hydrogens in Protonated Peptides upon Collisional Activation
    • Jørgensen, T. J. D.; Gardsvoll, H.; Ploug, M.; Roepstorff, P. Intramolecular Migration of Amide Hydrogens in Protonated Peptides upon Collisional Activation J. Am. Chem. Soc. 2005, 127, 2785-2793 10.1021/ja043789c
    • (2005) J. Am. Chem. Soc. , vol.127 , pp. 2785-2793
    • Jørgensen, T.J.D.1    Gardsvoll, H.2    Ploug, M.3    Roepstorff, P.4
  • 32
    • 0029810698 scopus 로고    scopus 로고
    • Influence of Peptide Composition, Gas-Phase Basicity, and Chemical Modification on Fragmentation Efficiency: Evidence for the Mobile Proton Model
    • Dongré, A. R.; Jones, J. L.; Somogyi, Á.; Wysocki, V. H. Influence of Peptide Composition, Gas-Phase Basicity, and Chemical Modification on Fragmentation Efficiency: Evidence for the Mobile Proton Model J. Am. Chem. Soc. 1996, 118, 8365-8374 10.1021/ja9542193
    • (1996) J. Am. Chem. Soc. , vol.118 , pp. 8365-8374
    • Dongré, A.R.1    Jones, J.L.2    Somogyi, Á.3    Wysocki, V.H.4
  • 33
    • 78650405796 scopus 로고    scopus 로고
    • The Mobile Proton Hypothesis in Fragmentation of Protonated Peptides: A Perspective
    • Boyd, R. K.; Somogyi, Á. The Mobile Proton Hypothesis in Fragmentation of Protonated Peptides: A Perspective J. Am. Soc. Mass Spectrom. 2010, 21, 1275-1278 10.1016/j.jasms.2010.04.017
    • (2010) J. Am. Soc. Mass Spectrom. , vol.21 , pp. 1275-1278
    • Boyd, R.K.1    Somogyi, Á.2
  • 34
    • 35648957210 scopus 로고    scopus 로고
    • Ion Mobility-Mass Spectrometry Reveals Long-Lived, Unfolded Intermediates in the Dissociation of Protein Complexes
    • Ruotolo, B. T.; Hyung, S.-J.; Robinson, P. M.; Giles, K.; Bateman, R. H.; Robinson, C. V. Ion Mobility-Mass Spectrometry Reveals Long-Lived, Unfolded Intermediates in the Dissociation of Protein Complexes Angew. Chem., Int. Ed. 2007, 46, 8001-8004 10.1002/anie.200702161
    • (2007) Angew. Chem., Int. Ed. , vol.46 , pp. 8001-8004
    • Ruotolo, B.T.1    Hyung, S.-J.2    Robinson, P.M.3    Giles, K.4    Bateman, R.H.5    Robinson, C.V.6
  • 35
    • 60649094510 scopus 로고    scopus 로고
    • Collisional Activation of Protein Complexes: Picking Up the Pieces
    • Benesch, J. L. P. Collisional Activation of Protein Complexes: Picking Up the Pieces J. Am. Soc. Mass Spectrom. 2009, 20, 341-348 10.1016/j.jasms.2008.11.014
    • (2009) J. Am. Soc. Mass Spectrom. , vol.20 , pp. 341-348
    • Benesch, J.L.P.1
  • 36
    • 84971283914 scopus 로고    scopus 로고
    • Salt Bridge Rearrangement (SaBRe) Explains the Dissociation Behavior of Noncovalent Complexes
    • Ogorzalek Loo, R. R.; Loo, J. A. Salt Bridge Rearrangement (SaBRe) Explains the Dissociation Behavior of Noncovalent Complexes J. Am. Soc. Mass Spectrom. 2016, 27, 975-990 10.1007/s13361-016-1375-3
    • (2016) J. Am. Soc. Mass Spectrom. , vol.27 , pp. 975-990
    • Ogorzalek Loo, R.R.1    Loo, J.A.2
  • 38
    • 84919827786 scopus 로고    scopus 로고
    • Development of Multiscale Models for Complex Chemical Systems: From H+H-2 to Biomolecules (Nobel Lecture)
    • Karplus, M. Development of Multiscale Models for Complex Chemical Systems: From H+H-2 to Biomolecules (Nobel Lecture) Angew. Chem., Int. Ed. 2014, 53, 9992-10005 10.1002/anie.201403924
    • (2014) Angew. Chem., Int. Ed. , vol.53 , pp. 9992-10005
    • Karplus, M.1
  • 39
    • 0033620367 scopus 로고    scopus 로고
    • Thermal unfolding of unsolvated cytochrome c: Experiment and molecular dynamics simulations
    • Mao, Y.; Woenckhaus, J.; Kolafa, J.; Ratner, M. A.; Jarrold, M. F. Thermal unfolding of unsolvated cytochrome c: Experiment and molecular dynamics simulations J. Am. Chem. Soc. 1999, 121, 2712-2721 10.1021/ja980324b
    • (1999) J. Am. Chem. Soc. , vol.121 , pp. 2712-2721
    • Mao, Y.1    Woenckhaus, J.2    Kolafa, J.3    Ratner, M.A.4    Jarrold, M.F.5
  • 40
    • 84903718401 scopus 로고    scopus 로고
    • Metal-Induced Conformational Changes of Human Metallothionein-2A: A Combined Theoretical and Experimental Study of Metal-Free and Partially Metalated Intermediates
    • Chen, S. H.; Chen, L. X.; Russell, D. H. Metal-Induced Conformational Changes of Human Metallothionein-2A: A Combined Theoretical and Experimental Study of Metal-Free and Partially Metalated Intermediates J. Am. Chem. Soc. 2014, 136, 9499-9508 10.1021/ja5047878
    • (2014) J. Am. Chem. Soc. , vol.136 , pp. 9499-9508
    • Chen, S.H.1    Chen, L.X.2    Russell, D.H.3
  • 41
    • 84919949421 scopus 로고    scopus 로고
    • Combining Ion Mobility Spectrometry with Hydrogen-Deuterium Exchange and Top-Down MS for Peptide Ion Structure Analysis
    • Khakinejad, M.; Kondalaji, S. G.; Maleki, H.; Arndt, J. R.; Donohoe, G. C.; Valentine, S. J. Combining Ion Mobility Spectrometry with Hydrogen-Deuterium Exchange and Top-Down MS for Peptide Ion Structure Analysis J. Am. Soc. Mass Spectrom. 2014, 25, 2103-2115 10.1007/s13361-014-0990-0
    • (2014) J. Am. Soc. Mass Spectrom. , vol.25 , pp. 2103-2115
    • Khakinejad, M.1    Kondalaji, S.G.2    Maleki, H.3    Arndt, J.R.4    Donohoe, G.C.5    Valentine, S.J.6
  • 42
    • 84863416219 scopus 로고    scopus 로고
    • Charge-State Dependent Compaction and Dissociation of Protein Complexes: Insights from Ion Mobility and Molecular Dynamics
    • Hall, Z.; Politis, A.; Bush, M. F.; Smith, L. J.; Robinson, C. V. Charge-State Dependent Compaction and Dissociation of Protein Complexes: Insights from Ion Mobility and Molecular Dynamics J. Am. Chem. Soc. 2012, 134, 3429-3438 10.1021/ja2096859
    • (2012) J. Am. Chem. Soc. , vol.134 , pp. 3429-3438
    • Hall, Z.1    Politis, A.2    Bush, M.F.3    Smith, L.J.4    Robinson, C.V.5
  • 44
    • 37149028376 scopus 로고    scopus 로고
    • A direct comparison of protein structure in the gas and solution phase: The TRP-cage
    • Patriksson, A.; Adams, C. M.; Kjeldsen, F.; Zubarev, R. A.; van der Spoel, D. A direct comparison of protein structure in the gas and solution phase: The TRP-cage J. Phys. Chem. B 2007, 111, 13147-13150 10.1021/jp709901t
    • (2007) J. Phys. Chem. B , vol.111 , pp. 13147-13150
    • Patriksson, A.1    Adams, C.M.2    Kjeldsen, F.3    Zubarev, R.A.4    Van Der Spoel, D.5
  • 45
    • 54349118212 scopus 로고    scopus 로고
    • Early Structural Evolution of Native Cytochrome c after Solvent Removal
    • Steinberg, M. Z.; Elber, R.; McLafferty, F. W.; Gerber, R. B.; Breuker, K. Early Structural Evolution of Native Cytochrome c After Solvent Removal ChemBioChem 2008, 9, 2417-2423 10.1002/cbic.200800167
    • (2008) ChemBioChem , vol.9 , pp. 2417-2423
    • Steinberg, M.Z.1    Elber, R.2    McLafferty, F.W.3    Gerber, R.B.4    Breuker, K.5
  • 46
    • 84907467876 scopus 로고    scopus 로고
    • Molecular Simulation of Water and Hydration Effects in Different Environments: Challenges and Developments for DFTB Based Models
    • Goyal, P.; Qian, H. J.; Irle, S.; Lu, X. Y.; Roston, D.; Mori, T.; Elstner, M.; Cui, Q. Molecular Simulation of Water and Hydration Effects in Different Environments: Challenges and Developments for DFTB Based Models J. Phys. Chem. B 2014, 118, 11007-11027 10.1021/jp503372v
    • (2014) J. Phys. Chem. B , vol.118 , pp. 11007-11027
    • Goyal, P.1    Qian, H.J.2    Irle, S.3    Lu, X.Y.4    Roston, D.5    Mori, T.6    Elstner, M.7    Cui, Q.8
  • 47
    • 72249090402 scopus 로고    scopus 로고
    • Energy Transfer, Unfolding, and Fragmentation Dynamics in Collisions of N-Protonated Octaglycine with an H-SAM Surface
    • Barnes, G. L.; Hase, W. L. Energy Transfer, Unfolding, and Fragmentation Dynamics in Collisions of N-Protonated Octaglycine with an H-SAM Surface J. Am. Chem. Soc. 2009, 131, 17185-17193 10.1021/ja904925p
    • (2009) J. Am. Chem. Soc. , vol.131 , pp. 17185-17193
    • Barnes, G.L.1    Hase, W.L.2
  • 48
    • 77951245193 scopus 로고    scopus 로고
    • Aqueous Basic Solutions: Hydroxide Solvation, Structural Diffusion, and Comparison to the Hydrated Proton
    • Marx, D.; Chandra, A.; Tuckerman, M. E. Aqueous Basic Solutions: Hydroxide Solvation, Structural Diffusion, and Comparison to the Hydrated Proton Chem. Rev. 2010, 110, 2174-2216 10.1021/cr900233f
    • (2010) Chem. Rev. , vol.110 , pp. 2174-2216
    • Marx, D.1    Chandra, A.2    Tuckerman, M.E.3
  • 49
    • 15944385626 scopus 로고    scopus 로고
    • On the amphiphilic behavior of the hydrated proton: An ab initio molecular dynamics study
    • Iyengar, S. S.; Day, T. J. F.; Voth, G. A. On the amphiphilic behavior of the hydrated proton: an ab initio molecular dynamics study Int. J. Mass Spectrom. 2005, 241, 197-204 10.1016/j.ijms.2004.12.003
    • (2005) Int. J. Mass Spectrom. , vol.241 , pp. 197-204
    • Iyengar, S.S.1    Day, T.J.F.2    Voth, G.A.3
  • 51
    • 84955297312 scopus 로고    scopus 로고
    • Divide-and-Conquer-Type Density-Functional Tight-Binding Molecular Dynamics Simulations of Proton Diffusion in a Bulk Water System
    • Nakai, H.; Sakti, A. W.; Nishimura, Y. Divide-and-Conquer-Type Density-Functional Tight-Binding Molecular Dynamics Simulations of Proton Diffusion in a Bulk Water System J. Phys. Chem. B 2016, 120, 217-221 10.1021/acs.jpcb.5b12439
    • (2016) J. Phys. Chem. B , vol.120 , pp. 217-221
    • Nakai, H.1    Sakti, A.W.2    Nishimura, Y.3
  • 52
    • 0035504327 scopus 로고    scopus 로고
    • Molecular dynamics simulation of proton transport with quantum mechanically derived proton hopping rates (Q-HOP MD)
    • Lill, M. A.; Helms, V. Molecular dynamics simulation of proton transport with quantum mechanically derived proton hopping rates (Q-HOP MD) J. Chem. Phys. 2001, 115, 7993-8005 10.1063/1.1407293
    • (2001) J. Chem. Phys. , vol.115 , pp. 7993-8005
    • Lill, M.A.1    Helms, V.2
  • 53
    • 79959283736 scopus 로고    scopus 로고
    • Constant pH Molecular Dynamics in Explicit Solvent with lambda-Dynamics
    • Donnini, S.; Tegeler, F.; Groenhof, G.; Grubmuller, H. Constant pH Molecular Dynamics in Explicit Solvent with lambda-Dynamics J. Chem. Theory Comput. 2011, 7, 1962-1978 10.1021/ct200061r
    • (2011) J. Chem. Theory Comput. , vol.7 , pp. 1962-1978
    • Donnini, S.1    Tegeler, F.2    Groenhof, G.3    Grubmuller, H.4
  • 54
    • 84937917680 scopus 로고    scopus 로고
    • Hydrated Excess Protons Can Create Their Own Water Wires
    • Peng, Y. X.; Swanson, J. M. J.; Kang, S. G.; Zhou, R. H.; Voth, G. A. Hydrated Excess Protons Can Create Their Own Water Wires J. Phys. Chem. B 2015, 119, 9212-9218 10.1021/jp5095118
    • (2015) J. Phys. Chem. B , vol.119 , pp. 9212-9218
    • Peng, Y.X.1    Swanson, J.M.J.2    Kang, S.G.3    Zhou, R.H.4    Voth, G.A.5
  • 55
    • 84882398607 scopus 로고    scopus 로고
    • Perspective on the Martini model
    • Marrink, S. J.; Tieleman, D. P. Perspective on the Martini model Chem. Soc. Rev. 2013, 42, 6801-6822 10.1039/c3cs60093a
    • (2013) Chem. Soc. Rev. , vol.42 , pp. 6801-6822
    • Marrink, S.J.1    Tieleman, D.P.2
  • 56
    • 17044393884 scopus 로고    scopus 로고
    • Coarse-grained models for proteins
    • Tozzini, V. Coarse-grained models for proteins Curr. Opin. Struct. Biol. 2005, 15, 144-150 10.1016/j.sbi.2005.02.005
    • (2005) Curr. Opin. Struct. Biol. , vol.15 , pp. 144-150
    • Tozzini, V.1
  • 57
    • 0000849231 scopus 로고
    • Electrostatic Forces and Dielectric Polarizability of Multiply Protonated Gas-Phase Cytochrome c Ions Probed by Ion/Molecule Chemistry
    • Schnier, P. D.; Gross, D. S.; Williams, E. R. Electrostatic Forces and Dielectric Polarizability of Multiply Protonated Gas-Phase Cytochrome c Ions Probed by Ion/Molecule Chemistry J. Am. Chem. Soc. 1995, 117, 6747-6757 10.1021/ja00130a015
    • (1995) J. Am. Chem. Soc. , vol.117 , pp. 6747-6757
    • Schnier, P.D.1    Gross, D.S.2    Williams, E.R.3
  • 58
    • 0037075426 scopus 로고    scopus 로고
    • Nanocrystalline aggregation of serine detected by electrospray ionization mass spectrometry: Origin of the stable homochiral gas-phase serine octamer
    • Julian, R. R.; Hodyss, R.; Kinnear, B.; Jarrold, M. F.; Beauchamp, J. L. Nanocrystalline aggregation of serine detected by electrospray ionization mass spectrometry: Origin of the stable homochiral gas-phase serine octamer J. Phys. Chem. B 2002, 106, 1219-1228 10.1021/jp012265l
    • (2002) J. Phys. Chem. B , vol.106 , pp. 1219-1228
    • Julian, R.R.1    Hodyss, R.2    Kinnear, B.3    Jarrold, M.F.4    Beauchamp, J.L.5
  • 59
    • 80054978929 scopus 로고    scopus 로고
    • Negative-Ion Electron Capture Dissociation: Radical-Driven Fragmentation of Charge-Increased Gaseous Peptide Anions
    • Yoo, H. J.; Wang, N.; Zhuang, S. Y.; Song, H. T.; Hakansson, K. Negative-Ion Electron Capture Dissociation: Radical-Driven Fragmentation of Charge-Increased Gaseous Peptide Anions J. Am. Chem. Soc. 2011, 133, 16790-16793 10.1021/ja207736y
    • (2011) J. Am. Chem. Soc. , vol.133 , pp. 16790-16793
    • Yoo, H.J.1    Wang, N.2    Zhuang, S.Y.3    Song, H.T.4    Hakansson, K.5
  • 61
    • 37049036339 scopus 로고    scopus 로고
    • Infrared spectroscopy of arginine cation complexes: Direct observation of gas-phase zwitterions
    • Forbes, M. W.; Bush, M. F.; Polfer, N. C.; Oomens, J.; Dunbar, R. C.; Williams, E. R.; Jockusch, R. A. Infrared spectroscopy of arginine cation complexes: Direct observation of gas-phase zwitterions J. Phys. Chem. A 2007, 111, 11759-11770 10.1021/jp074859f
    • (2007) J. Phys. Chem. A , vol.111 , pp. 11759-11770
    • Forbes, M.W.1    Bush, M.F.2    Polfer, N.C.3    Oomens, J.4    Dunbar, R.C.5    Williams, E.R.6    Jockusch, R.A.7
  • 62
    • 84897015968 scopus 로고    scopus 로고
    • Exploring Salt Bridge Structures of Gas-Phase Protein Ions using Multiple Stages of Electron Transfer and Collision Induced Dissociation
    • Zhang, Z.; Browne, S. J.; Vachet, R. W. Exploring Salt Bridge Structures of Gas-Phase Protein Ions using Multiple Stages of Electron Transfer and Collision Induced Dissociation J. Am. Soc. Mass Spectrom. 2014, 25, 604-613 10.1007/s13361-013-0821-8
    • (2014) J. Am. Soc. Mass Spectrom. , vol.25 , pp. 604-613
    • Zhang, Z.1    Browne, S.J.2    Vachet, R.W.3
  • 63
    • 0001041828 scopus 로고    scopus 로고
    • Structure of cationized arginine (Arg center dot M+, M = H, Li, Na, K, Rb, and Cs) in the gas phase: Further evidence for zwitterionic arginine
    • Jockusch, R. A.; Price, W. D.; Williams, E. R. Structure of cationized arginine (Arg center dot M+, M = H, Li, Na, K, Rb, and Cs) in the gas phase: Further evidence for zwitterionic arginine J. Phys. Chem. A 1999, 103, 9266-9274 10.1021/jp9931307
    • (1999) J. Phys. Chem. A , vol.103 , pp. 9266-9274
    • Jockusch, R.A.1    Price, W.D.2    Williams, E.R.3
  • 64
    • 84935034804 scopus 로고    scopus 로고
    • Distinguishing Loss of Structure from Subunit Dissociation for Protein Complexes with Variable Temperature Ion Mobility Mass Spectrometry
    • Pacholarz, K. J.; Barran, P. E. Distinguishing Loss of Structure from Subunit Dissociation for Protein Complexes with Variable Temperature Ion Mobility Mass Spectrometry Anal. Chem. 2015, 87, 6271-6279 10.1021/acs.analchem.5b01063
    • (2015) Anal. Chem. , vol.87 , pp. 6271-6279
    • Pacholarz, K.J.1    Barran, P.E.2
  • 66
    • 46249092554 scopus 로고    scopus 로고
    • GROMACS 4: Algorithms for Highly Efficient, Load-Balanced, and Scalable Molecular Simulation
    • Hess, B.; Kutzner, C.; van der Spoel, D.; Lindahl, E. GROMACS 4: Algorithms for Highly Efficient, Load-Balanced, and Scalable Molecular Simulation J. Chem. Theory Comput. 2008, 4, 435-447 10.1021/ct700301q
    • (2008) J. Chem. Theory Comput. , vol.4 , pp. 435-447
    • Hess, B.1    Kutzner, C.2    Van Der Spoel, D.3    Lindahl, E.4
  • 68
    • 0000388705 scopus 로고    scopus 로고
    • LINCS: A linear constraint solver for molecular simulations
    • Hess, B.; Bekker, H.; Berendsen, H. J. C.; Fraaije, J. G. E. M. LINCS: A linear constraint solver for molecular simulations J. Comput. Chem. 1997, 18, 1463-1472 10.1002/(SICI)1096-987X(199709)18:12<1463::AID-JCC4>3.0.CO;2-H
    • (1997) J. Comput. Chem. , vol.18 , pp. 1463-1472
    • Hess, B.1    Bekker, H.2    Berendsen, H.J.C.3    Fraaije, J.G.E.M.4
  • 69
    • 84943611630 scopus 로고    scopus 로고
    • Release of Native-Like Gaseous Proteins from Electrospray Droplets via the Charged Residue Mechanism: Insights from Molecular Dynamics Simulations
    • McAllister, R. G.; Metwally, H.; Sun, Y.; Konermann, L. Release of Native-Like Gaseous Proteins from Electrospray Droplets via The Charged Residue Mechanism: Insights from Molecular Dynamics Simulations J. Am. Chem. Soc. 2015, 137, 12667-12676 10.1021/jacs.5b07913
    • (2015) J. Am. Chem. Soc. , vol.137 , pp. 12667-12676
    • McAllister, R.G.1    Metwally, H.2    Sun, Y.3    Konermann, L.4
  • 70
    • 0001538909 scopus 로고
    • Canonical dynamics: Equilibrium phase-space distributions
    • Hoover, W. G. Canonical dynamics: Equilibrium phase-space distributions Phys. Rev. A: At., Mol., Opt. Phys. 1985, 31, 1695-1697 10.1103/PhysRevA.31.1695
    • (1985) Phys. Rev. A: At., Mol., Opt. Phys. , vol.31 , pp. 1695-1697
    • Hoover, W.G.1
  • 71
    • 33846086933 scopus 로고    scopus 로고
    • Canonical sampling through velocity rescaling
    • Bussi, G.; Donadio, D.; Parrinello, M. Canonical sampling through velocity rescaling J. Chem. Phys. 2007, 126, 0141011 10.1063/1.2408420
    • (2007) J. Chem. Phys. , vol.126 , pp. 0141011
    • Bussi, G.1    Donadio, D.2    Parrinello, M.3
  • 72
    • 0000795938 scopus 로고
    • Free Energies of Hydration and Pure Liquid Properties of Hydrocarbons from the OPLS All-Atom Model
    • Kaminski, G.; Duffy, E. M.; Matsui, T.; Jorgensen, W. L. Free Energies of Hydration and Pure Liquid Properties of Hydrocarbons from the OPLS All-Atom Model J. Phys. Chem. 1994, 98, 13077-13082 10.1021/j100100a043
    • (1994) J. Phys. Chem. , vol.98 , pp. 13077-13082
    • Kaminski, G.1    Duffy, E.M.2    Matsui, T.3    Jorgensen, W.L.4
  • 73
    • 84882643757 scopus 로고    scopus 로고
    • CHARMM36 all-atom additive protein force field: Validation based on comparison to NMR data
    • Huang, J.; MacKerell, A. D. CHARMM36 all-atom additive protein force field: Validation based on comparison to NMR data J. Comput. Chem. 2013, 34, 2135-2145 10.1002/jcc.23354
    • (2013) J. Comput. Chem. , vol.34 , pp. 2135-2145
    • Huang, J.1    MacKerell, A.D.2
  • 74
    • 77957766617 scopus 로고    scopus 로고
    • Novel Zn2+-binding Sites in Human Transthyretin: Implications for Amyloidogenesis and Retinol-Binding Protein Recognition
    • Palmieri, L. D.; Lima, L.; Freire, J. B. B.; Bleicher, L.; Polikarpov, I.; Almeida, F. C. L.; Foguel, D. Novel Zn2+-binding Sites in Human Transthyretin: Implications for Amyloidogenesis and Retinol-Binding Protein Recognition J. Biol. Chem. 2010, 285, 31731-31741 10.1074/jbc.M110.157206
    • (2010) J. Biol. Chem. , vol.285 , pp. 31731-31741
    • Palmieri, L.D.1    Lima, L.2    Freire, J.B.B.3    Bleicher, L.4    Polikarpov, I.5    Almeida, F.C.L.6    Foguel, D.7
  • 76
    • 33947308284 scopus 로고    scopus 로고
    • Influence of Coulombic Repulsion on the Dissociation Pathways and Energetics of Multiprotein Complexes in the Gas Phase
    • Sinelnikov, I.; Kitova, E. N.; Klassen, J. S. Influence of Coulombic Repulsion on the Dissociation Pathways and Energetics of Multiprotein Complexes in the Gas Phase J. Am. Soc. Mass Spectrom. 2007, 18, 617-631 10.1016/j.jasms.2006.11.006
    • (2007) J. Am. Soc. Mass Spectrom. , vol.18 , pp. 617-631
    • Sinelnikov, I.1    Kitova, E.N.2    Klassen, J.S.3
  • 77
    • 84888151791 scopus 로고    scopus 로고
    • Proton affinities of the anions of aromatic carboxylic acids measured by kinetic method
    • Bienkowski, T.; Swider, P.; Blaziak, K.; Danikiewicz, W. Proton affinities of the anions of aromatic carboxylic acids measured by kinetic method Int. J. Mass Spectrom. 2014, 357, 29-33 10.1016/j.ijms.2013.10.006
    • (2014) Int. J. Mass Spectrom. , vol.357 , pp. 29-33
    • Bienkowski, T.1    Swider, P.2    Blaziak, K.3    Danikiewicz, W.4
  • 79
    • 0347193736 scopus 로고
    • Reaction-rate theory: Fifty years after Kramers
    • Hanggi, P.; Talkner, P.; Borkovec, M. Reaction-rate theory: fifty years after Kramers Rev. Mod. Phys. 1990, 62, 251-342 10.1103/RevModPhys.62.251
    • (1990) Rev. Mod. Phys. , vol.62 , pp. 251-342
    • Hanggi, P.1    Talkner, P.2    Borkovec, M.3
  • 80
    • 33749043747 scopus 로고    scopus 로고
    • Et tu, Grotthuss! and other unfinished stories
    • Cukierman, S. Et tu, Grotthuss! and other unfinished stories Biochim. Biophys. Acta, Bioenerg. 2006, 1757, 876-885 10.1016/j.bbabio.2005.12.001
    • (2006) Biochim. Biophys. Acta, Bioenerg. , vol.1757 , pp. 876-885
    • Cukierman, S.1
  • 81
    • 84865088597 scopus 로고    scopus 로고
    • Comparison of Secondary Structure Formation Using 10 Different Force Fields in Microsecond Molecular Dynamics Simulations
    • Cino, E. A.; Choy, W. Y.; Karttunen, M. Comparison of Secondary Structure Formation Using 10 Different Force Fields in Microsecond Molecular Dynamics Simulations J. Chem. Theory Comput. 2012, 8, 2725-2740 10.1021/ct300323g
    • (2012) J. Chem. Theory Comput. , vol.8 , pp. 2725-2740
    • Cino, E.A.1    Choy, W.Y.2    Karttunen, M.3
  • 82
    • 0029110821 scopus 로고
    • Experimental Measurement of Coulomb Energy and Intrinsic Dielectric Polarizibility of a Multiply Protonated Peptide Ion Using Electrospray Ionization Fourier-Transform Mas Spectrometry
    • Gross, D. S.; Williams, E. R. Experimental Measurement of Coulomb Energy and Intrinsic Dielectric Polarizibility of a Multiply Protonated Peptide Ion Using Electrospray Ionization Fourier-Transform Mas Spectrometry J. Am. Chem. Soc. 1995, 117, 883-890 10.1021/ja00108a004
    • (1995) J. Am. Chem. Soc. , vol.117 , pp. 883-890
    • Gross, D.S.1    Williams, E.R.2
  • 83
    • 0030939178 scopus 로고    scopus 로고
    • Protein Structure in Vacuo: The Gas-Phase Conformation of BPTI and Cytochrome c
    • Shelimov, K. B.; Clemmer, D. E.; Hudgins, R. R.; Jarrold, M. F. Protein Structure in Vacuo: The Gas-Phase Conformation of BPTI and Cytochrome c J. Am. Chem. Soc. 1997, 119, 2240-2248 10.1021/ja9619059
    • (1997) J. Am. Chem. Soc. , vol.119 , pp. 2240-2248
    • Shelimov, K.B.1    Clemmer, D.E.2    Hudgins, R.R.3    Jarrold, M.F.4
  • 84
    • 34547860941 scopus 로고    scopus 로고
    • Influence of thermostats and carrier gas on simulations of nucleation
    • Wedekind, J.; Reguera, D.; Strey, R. Influence of thermostats and carrier gas on simulations of nucleation J. Chem. Phys. 2007, 127, 0645011 10.1063/1.2752154
    • (2007) J. Chem. Phys. , vol.127 , pp. 0645011
    • Wedekind, J.1    Reguera, D.2    Strey, R.3
  • 85
    • 84904342151 scopus 로고    scopus 로고
    • Analytical Approaches for Size and Mass Analysis of Large Protein Assemblies
    • Snijder, J.; Heck, A. J. R. Analytical Approaches for Size and Mass Analysis of Large Protein Assemblies Annu. Rev. Anal. Chem. 2014, 7, 43-64 10.1146/annurev-anchem-071213-020015
    • (2014) Annu. Rev. Anal. Chem. , vol.7 , pp. 43-64
    • Snijder, J.1    Heck, A.J.R.2
  • 86
    • 84865788284 scopus 로고    scopus 로고
    • Structural Modeling of Heteromeric Protein Complexes from Disassembly Pathways and Ion Mobility-Mass Spectrometry
    • Hall, Z.; Politis, A.; Robinson, C. V. Structural Modeling of Heteromeric Protein Complexes from Disassembly Pathways and Ion Mobility-Mass Spectrometry Structure 2012, 20, 1596-1609 10.1016/j.str.2012.07.001
    • (2012) Structure , vol.20 , pp. 1596-1609
    • Hall, Z.1    Politis, A.2    Robinson, C.V.3


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