Linking molecular models with ion mobility experiments. Illustration with a rigid nucleic acid structure

Journal of Mass Spectrometry

Volumn 50, Issue 5, 2015, Pages 711-726

  D'Atri, Valentina ^a,b   Porrini, Massimiliano ^a,b   Rosu, Frédéric ^c   Gabelica, Valérie ^a,b  

^a UNIVERSITÉ DE BORDEAUX   (France)

^b INSERM U869   (France)

^c INSTITUT EUROPÉEN DE CHIMIE ET BIOLOGIE   (France)

Author keywords

collision cross section; gas phase ion structure; ion mobility spectrometry; molecular modeling; nucleic acids; simulations; structure

Indexed keywords

BIOINFORMATICS; BIOMOLECULES; GASES; ION MOBILITY SPECTROMETERS; IONIZATION OF GASES; MOLECULAR MODELING; NUCLEIC ACIDS; SPECTROMETRY; STRUCTURE (COMPOSITION);

COLLISION CROSS SECTIONS; EXPERIMENTAL ERRORS; ION MOBILITY SPECTROMETRY; ION STRUCTURES; NUCLEIC ACID STRUCTURE; SIMULATIONS; STRUCTURAL CHARACTERIZATION; THREE-DIMENSIONAL STRUCTURE;

IONS;

GUANINE; GUANINE QUADRUPLEX; ION; NUCLEIC ACID; OLIGONUCLEOTIDE; THYMINE; GAS;

ALGORITHM; ARTICLE; CALCULATION; CALIBRATION; CONFORMATIONAL TRANSITION; CONTROLLED STUDY; CRYSTAL STRUCTURE; DENSITY FUNCTIONAL THEORY; ELECTRIC FIELD; ELECTROSPRAY MASS SPECTROMETRY; GAS; ION MOBILITY SPECTROMETRY; MEASUREMENT; MOLECULAR DYNAMICS; MOLECULAR MODEL; NUCLEIC ACID STRUCTURE; PRIORITY JOURNAL; STATIC ELECTRICITY; CHEMISTRY; COMPUTER SIMULATION; MASS SPECTROMETRY; PROCEDURES;

COMPUTER SIMULATION; GASES; IONS; MASS SPECTROMETRY; MODELS, MOLECULAR; NUCLEIC ACIDS;

EID: 84938858943     PISSN: 10765174     EISSN: 10969888     Source Type: Journal    
DOI: 10.1002/jms.3590     Document Type: Article

References (107)

1. A. J. R. Heck, R. H. H. van Den Heuvel,. Investigation of intact protein complexes by mass spectrometry. Mass Spectrom. Rev. 2004, 23, 368-389.
2. M. Sharon, C. V. Robinson,. The role of mass spectrometry in structure elucidation of dynamic protein complexes. Annu. Rev. Biochem. 2007, 76, 167-193.
3. D. E. Clemmer, M. F. Jarrold,. Ion mobility measurements and their applications to clusters and biomolecules. J. Mass Spectrom. 1997, 32, 577-592.
4. E. A. Mason, E. W. McDaniel,. Transport Properties of Ions in Gases. Wiley-VCH Verlag GmbH & Co. KGaA: Weinheim, FRG, 1988, 0-471.
5. B. C. Bohrer, S. I. Merenbloom, S. L. Koeniger, A. E. Hilderbrand, D. E. Clemmer,. Biomolecule analysis by ion mobility spectrometry. Annu. Rev. Anal. Chem. (Palo Alto. Calif). 2008, 1, 293-327.
6. A. B. Kanu, P. Dwivedi, M. Tam, L. Matz, H. H. Hill,. Ion mobility-mass spectrometry. J. Mass Spectrom. 2008, 43, 1-22.
7. E. Jurneczko, P. E. Barran,. How useful is ion mobility mass spectrometry for structural biology? The relationship between protein crystal structures and their collision cross sections in the gas phase. Analyst 2011, 136, 20-28.
8. R. Beveridge, S. Covill, K. J. Pacholarz, J. M. D. Kalapothakis, C. E. MacPhee, P. E. Barran,. A mass-spectrometry-based framework to define the extent of disorder in proteins. Anal. Chem. 2014, 86, 10979-10991.
9. M. T. Bowers,. Ion mobility spectrometry: a personal view of its development at UCSB. Int. J. Mass Spectrom. 2014, 370, 75-95.
10. T. Wyttenbach, C. Bleiholder, M. T. Bowers,. Factors contributing to the collision cross section of polyatomic ions in the kilodalton to gigadalton range: application to ion mobility measurements. Anal. Chem. 2013, 85, 2191-2199.
11. K. Phillips, Z. Dauter, A. I. Murchie, D. M. Lilley, B. Luisi,. The crystal structure of a parallel-stranded guanine tetraplex at 0.95 A resolution. J. Mol. Biol. 1997, 273, 171-182.
12. C. Creze, B. Rinaldi, R. Haser, P. Bouvet, P. Gouet,. Structure of a d(TGGGGT) quadruplex crystallized in the presence of Li+ ions. Acta Crystallogr. D Biol. Crystallogr. 2007, 63, 682-688.
13. C. Cáceres, G. Wright, C. Gouyette, G. Parkinson,. J. A subirana. A thymine tetrad in d(TGGGGT) quadruplexes stabilized with Tl+/Na+ ions. Nucleic Acids Res. 2004, 32, 1097-1102.
14. M. P. H. Lee, G. N. Parkinson, P. Hazel, S. Neidle,. Observation of the coexistence of sodium and calcium ions in a DNA G-quadruplex ion channel. J. Am. Chem. Soc. 2007, 129, 10106-10107.
15. S. Cosconati, L. Marinelli, R. Trotta, A. Virno, S. De Tito, R. Romagnoli, B. Pagano, V. Limongelli, C. Giancola, P. G. Baraldi, L. Mayol, E. Novellino, A. Randazzo,. Structural and conformational requisites in DNA quadruplex groove binding: another piece to the puzzle. J. Am. Chem. Soc. 2010, 132, 6425-6433.
16. G. R. Clark, P. D. Pytel, C. J. Squire,. The high-resolution crystal structure of a parallel intermolecular DNA G-4 quadruplex/drug complex employing Syn glycosyl linkages. Nucleic Acids Res. 2012, 40, 5731-5738.
17. L. Martino, A. Virno, B. Pagano, A. Virgilio, S. Di Micco, A. Galeone, C. Giancola, G. Bifulco, L. Mayol, A. Randazzo,. Structural and thermodynamic studies of the interaction of distamycin a with the parallel quadruplex structure [d(TGGGGT)]4. J. Am. Chem. Soc. 2007, 129, 16048-16056.
18. F. Rosu, V. Gabelica, E. De Pauw, R. Antoine, M. Broyer, P. Dugourd,. UV spectroscopy of DNA duplex and quadruplex structures in the gas phase. J. Phys. Chem. A 2012, 116, 5383-5391.
19. V. Gabelica, F. Rosu, E. De Pauw, J. Lemaire, J. Gillet, J.-C. Poully, F. Lecomte, G. Grégoire, J. Schermann, C. Desfrançois,. Infrared signature of DNA G-quadruplexes in the gas phase. J. Am. Chem. Soc. 2008, 130, 1810-1811.
20. J. Gidden, E. S. Baker, A. Ferzoco, M. T. Bowers,. Structural motifs of DNA complexes in the gas phase. Int. J. Mass Spectrom. 2005, 240, 183-193.
21. R. Ferreira, A. Marchand, V. Gabelica,. Mass spectrometry and ion mobility spectrometry of G-quadruplexes. A study of solvent effects on dimer formation and structural transitions in the telomeric DNA sequence d(TAGGGTTAGGGT). Methods 2012, 57, 56-63.
22. H. E. Revercomb, E. A. Mason,. Theory of plasma chromatography/gaseous electrophoresis. Review. Anal. Chem. 1975, 47, 970-983.
23. T. Meyer, V. Gabelica, H. Grubmüller, M. Orozco,. Proteins in the gas phase. Wiley Interdiscip. Rev. Comput. Mol. Sci. 2013, 3, 408-425.
24. M. S. Wilm, M. Mann,. Electrospray and Taylor-Cone theory, Dole's beam of macromolecules at last? Int. J. Mass Spectrom. Ion Process. 1994, 136, 167-180.
25. J. F. de la Mora,. Electrospray ionization of large multiply charged species proceeds via Dole's charged residue mechanism. Anal. Chim. Acta 2000, 406, 93-104.
26. D. Morsa, V. Gabelica, E. De Pauw,. Effective temperature of ions in traveling wave ion mobility spectrometry. Anal. Chem. 2011, 83, 5775-5782.
27. F. Balthasart, J. Plavec, V. Gabelica,. Ammonium ion binding to DNA G-quadruplexes: do electrospray mass spectra faithfully reflect the solution-phase species? J. Am. Soc. Mass Spectrom. 2013, 24, 1-8.
28. A. A. Shvartsburg, R. D. Smith,. Fundamentals of traveling wave ion mobility spectrometry. Anal. Chem. 2008, 80, 9689-9699.
29. J. Rus, D. Moro, J. A. Sillero, J. Royuela, A. Casado, F. Estevez-Molinero, J. Fernández de la Mora,. IMS-MS studies based on coupling a differential mobility analyzer (DMA) to commercial API-MS systems. Int. J. Mass Spectrom. 2010, 298, 30-40.
30. J. F. de la Mora, L. de Juan, T. Eichler, J. Rosell,. Differential mobility analysis of molecular ions and nanometer particles. TrAC Trends Anal. Chem. 1998, 17, 328-339.
31. A. Shvartsburg,. Differential Ion Mobility Spectrometry: Nonlinear Ion Transport and Fundamentals of FAIMS. CRC Press: Boca Raton, 2009.
32. J. A. Silveira, M. E. Ridgeway, M. A. Park,. High resolution trapped ion mobility spectrometery of peptides. Anal. Chem. 2014, 86, 5624-5627.
33. J. L. Mergny, J. Gros, A. De Cian, A. Bourdoncle, F. Rosu, B. Sacca, L. Guittat, S. Amrane, M. Mills, P. Alberti, M. Takasugi, L. Lacroix,. Energetics, kinetics and dynamics of quadruplex folding. In Quadruplex Nucleic Acids, S. Neidle, S. Balasubramanian, (Eds). The Royal Society of Chemistry: Cambridge, 2006, pp. 31-80.
34. T. Wyttenbach, P. R. Kemper, M. T. Bowers,. Design of a new electrospray ion mobility mass spectrometer. Int. J. Mass Spectrom. 2001, 212, 13-23.
35. K. Giles, S. D. Pringle, K. R. Worthington, D. Little, J. L. Wildgoose, R. H. Bateman,. Applications of a travelling wave-based radio-frequency-only stacked ring ion guide. Rapid Commun. Mass Spectrom. 2004, 18, 2401-2414.
36. K. Thalassinos, S. E. Slade, K. R. Jennings, J. H. Scrivens, K. Giles, J. Wildgoose, J. Hoyes, R. H. Bateman, M. T. Bowers,. Ion mobility mass spectrometry of proteins in a modified commercial mass spectrometer. Int. J. Mass Spectrom. 2004, 236, 55-63.
37. B. T. Ruotolo, J. L. P. Benesch, A. M. Sandercock, S.-J. Hyung,. C. V Robinson. Ion mobility-mass spectrometry analysis of large protein complexes. Nat. Protoc. 2008, 3, 1139-1152.
38. M. F. Bush, Z. Hall, K. Giles, J. Hoyes, C. V. Robinson, B. T. Ruotolo,. Collision cross sections of proteins and their complexes: a calibration framework and database for gas-phase structural biology. Anal. Chem. 2010, 82, 9557-9565.
39. J. C. May, C. R. Goodwin, N. M. Lareau, K. L. Leaptrot, C. B. Morris, R. T. Kurulugama, A. Mordehai, C. Klein, W. Barry, E. Darland, G. Overney, K. Imatani, G. C. Stafford, J. C. Fjeldsted, J. A. McLean,. Conformational ordering of biomolecules in the gas phase: nitrogen collision cross sections measured on a prototype high resolution drift tube ion mobility-mass spectrometer. Anal. Chem. 2014, 86, 2107-2116.
40. K. S. Bose, R. H. Sarma,. Delineation of the intimate details of the backbone conformation of pyridine nucleotide coenzymes in aqueous solution. Biochem. Biophys. Res. Commun. 1975, 66, 1173-1179.
41. E. S. Baker, S. L. Bernstein, V. Gabelica, E. De Pauw, M. T. Bowers,. G-quadruplexes in telomeric repeats are conserved in a solvent-free environment. Int. J. Mass Spectrom. 2006, 253, 225-237.
42. V. Gabelica, E. S. Baker, M.-P. Teulade-Fichou, E. De Pauw, M. T. Bowers,. Stabilization and structure of telomeric and c-Myc region intramolecular G-quadruplexes: the role of central cations and small planar ligands. J. Am. Chem. Soc. 2007, 129, 895-904.
43. N. Smargiasso, F. Rosu, W. Hsia, P. Colson, E. S. Baker, M. T. Bowers, E. De Pauw, V. Gabelica,. G-quadruplex DNA assemblies: loop length, cation identity, and multimer formation. J. Am. Chem. Soc. 2008, 130, 10208-10216.
44. A. Arcella, G. Portella, M. L. Ruiz, R. Eritja, M. Vilaseca, V. Gabelica, M. Orozco,. Structure of triplex DNA in the gas phase. J. Am. Chem. Soc. 2012, 134, 6596-6606.
45. I. Campuzano, M. F. Bush, C. V. Robinson, C. Beaumont, K. Richardson, H. Kim, H. I. Kim,. Structural characterization of drug-like compounds by ion mobility mass spectrometry: comparison of theoretical and experimentally derived nitrogen collision cross sections. Anal. Chem. 2012, 84, 1026-1033.
46. R. Salbo, M. F. Bush, H. Naver, I. Campuzano, C. V. Robinson, I. Pettersson, T. J. D. Jørgensen, K. F. Haselmann,. Traveling-wave ion mobility mass spectrometry of protein complexes: accurate calibrated collision cross-sections of human insulin oligomers. Rapid Commun. Mass Spectrom. 2012, 26, 1181-1193.
47. The Bush Research Group http://depts.washington.edu/bushlab/ (accessed Dec 17, 2014).
48. M. Froimowitz,. HyperChem: a software package for computational chemistry and molecular modeling. Biotechniques 1993, 14, 1010-1013.
49. Accelrys Software Inc. Discovery Studio Modeling Environment, Release 4.0. Accelrys Software Inc.: San Diego, 2013.
50. Maestro, Version 10.0, Schrödinger. LLC: New York, NY, 2014.
51. T. J. Macke, D. A. Case,. Molecular Modeling of Nucleic Acids, Leontis N. B., SantaLucia J., (Eds). ACS Symposium Series; American Chemical Society: Washington, DC, 1997; Vol. 682, pp. 379-393.
52. M. D. Hanwell, D. E. Curtis, D. C. Lonie, T. Vandermeersch, E. Zurek, G. R. Hutchison,. Avogadro: an advanced semantic chemical editor, visualization, and analysis platform. J. Cheminform. 2012, 4, 17.
53. J. E. Šponer, A. Mládek, P. Banáš, P. Jurec,. How to understand quantum chemical computations on DNA and RNA systems ? a practical guide for non-specialists. Methods 2013, 64, 3-11.
54. M. Orozco,. A theoretical view of protein dynamics. Chem. Soc. Rev. 2014, 43, 5051-5066.
55. S. R. Harvey, M. Porrini, A. Konijnenberg, D. J. Clarke, R. C. Tyler, P. R. R. Langridge-Smith, C. E. MacPhee, B. F. Volkman, P. E. Barran,. Dissecting the dynamic conformations of the metamorphic protein lymphotactin. J. Phys. Chem. B 2014, 118, 12348-12359.
56. K. J. Pacholarz, M. Porrini, R. A. Garlish, R. J. Burnley, R. J. Taylor, A. J. Henry, P. E. Barran,. Dynamics of intact immunoglobulin G explored by drift-tube ion-mobility mass spectrometry and molecular modeling. Angew. Chem. Int. Ed. Engl. 2014, 53, 7765-7769.
57. S. Kirkpatrick, C. D. Gelatt, M. P. Vecchi,. Optimization by simulated annealing. Science 1983, 220, 671-680.
58. F. A Fernandez-Lima, H. Wei, Y. Q. Gao, D. H. Russell,. On the structure elucidation using ion mobility spectrometry and molecular dynamics. J. Geophys. Res. Chem. A 2009, 113, 8221-8234.
59. H. A. Sawyer, J. T. Marini, E. G. Stone, B. T. Ruotolo, K. J. Gillig, D. H. Russell,. The structure of gas-phase bradykinin fragment 1-5 (RPPGF) ions: an ion mobility spectrometry and H/D exchange ion-molecule reaction chemistry study. J. Am. Soc. Mass Spectrom. 2005, 16, 893-905.
60. T. Wyttenbach, G. von Helden, M. T. Bowers,. Gas-phase conformation of biological molecules: bradykinin. J. Am. Chem. Soc. 1996, 118, 8355-8364.
61. Y. Sugita, Y. Okamoto,. Replica-exchange molecular dynamics method for protein folding. Chem. Phys. Lett. 1999, 314, 141-151.
62. F. Albrieux, F. Calvo, F. Chirot, A. Vorobyev, Y. O. Tsybin, V. Lepère, R. Antoine, J. Lemoine, P. Dugourd,. Conformation of polyalanine and polyglycine dications in the gas phase: insight from ion mobility spectrometry and replica-exchange molecular dynamics. J. Phys. Chem. A 2010, 114, 6888-6896.
63. A. Baumketner, S. L. Bernstein, T. Wyttenbach, G. Bitan, D. B. Teplow, M. T. Bowers, J. Shea,. Amyloid beta-protein monomer structure: a computational and experimental study. Protein Sci. 2006, 15, 420-428.
64. F. Chirot, F. Calvo, F. Albrieux, J. Lemoine, Y. O. Tsybin, P. Dugourd,. Statistical analysis of ion mobility spectrometry. I. Unbiased and guided replica-exchange molecular dynamics. J. Am. Chem. Soc. 2012, 23, 386-396.
65. F. Calvo, F. Chirot, F. Albrieux, J. Lemoine, Y. O. Tsybin, P. Pernot, P. Dugourd,. Statistical analysis of ion mobility spectrometry. II. Adaptively biased methods and shape correlations. J. Am. Soc. Mass Spectrom. 2012, 23, 1279-1288.
66. F. Canon, R. Ballivian, F. Chirot, R. Antoine, P. Sarni-Manchado, J. Lemoine, P. Dugourd,. Folding of a salivary intrinsically disordered protein upon binding to tannins. J. Am. Chem. Soc. 2011, 133, 7847-7852.
67. S. L. Bernstein, N. F. Dupuis, N. D. Lazo, T. Wyttenbach, M. M. Condron, G. Bitan, D. B. Teplow, J.-E. Shea, B. T. Ruotolo, C. V. Robinson, M. T. Bowers,. Amyloid-Β protein oligomerization and the importance of tetramers and dodecamers in the aetiology of Alzheimer's disease. Nat. Chem. 2009, 1, 326-331.
68. A. Politis, A. Y. Park, S.-J. Hyung, D. Barsky, B. T. Ruotolo, C. V. Robinson,. Integrating ion mobility mass spectrometry with molecular modelling to determine the architecture of multiprotein complexes. PLoS One 2010, 5, e12080.
69. B. T. Ruotolo, K. Giles, I. Campuzano, A. M. Sandercock, R. H. Bateman, C. V. Robinson,. Evidence for macromolecular protein rings in the absence of bulk water. Science 2005, 310, 1658-1661.
70. J. Wang, P. Cieplak, P. A. Kollman,. How well does a restrained electrostatic potential (RESP) model perform in calculating conformational energies of organic and biological molecules? J. Comput. Chem. 2000, 21, 1049-1074.
71. A. D. MacKerell, D. Bashford, M. Bellott, R. L. Dunbrack, J. D. Evanseck, M. J. Field, S. Fischer, J. Gao, H. Guo, S. Ha, D. Joseph-McCarthy, L. Kuchnir, K. Kuczera, F. T. Lau, C. Mattos, S. Michnick, T. Ngo, D. T. Nguyen, B. Prodhom, W. E. Reiher, B. Roux, M. Schlenkrich, J. C. Smith, R. Stote, J. Straub, M. Watanabe, J. Wiõrkiewicz-Kuczera, D. Yin, M. Karplus,. All-atom empirical potential for molecular modeling and dynamics studies of proteins. J. Phys. Chem. B 1998, 102, 3586-3616.
72. Z. Hall, A. Politis, M. F. Bush, L. J. Smith,. C. V Robinson. Charge-state dependent compaction and dissociation of protein complexes: insights from ion mobility and molecular dynamics. J. Am. Chem. Soc. 2012, 134, 3429-3438.
73. M. Miteva, P. A. Demirev, A. D. Karshikoff,. Multiply-protonated protein ions in the gas phase: calculation of the electrostatic interactions between charged sites. J. Phys. Chem. B 1997, 101, 9645-9650.
74. A. Patriksson, E. Marklund, D. van der Spoel,. Protein structures under electrospray conditions. Biochemistry 2007, 46, 933-945.
75. M. Rueda, S. G. Kalko, F. J. Luque, M. Orozco,. The structure and dynamics of DNA in the gas phase. J. Am. Chem. Soc. 2003, 125, 8007-8014.
76. M. Rueda, F. J. Luque, M. Orozco,. G-quadruplexes can maintain their structure in the gas phase. J. Am. Chem. Soc. 2006, 128, 3608-3619.
77. A. Arcella, J. Dreyer, E. Ippoliti, I. Ivani, G. Portella, V. Gabelica, P. Carloni, M. Orozco,. Structure and dynamics of oligonucleotides in the gas phase. Angew. Chemie 2015, 127, 477-481.
78. D. A. Case, T. A. Darden, T. E. C. Iii, C. L. Simmerling, J. Wang, R. E. Duke, R. Luo, R. C. Walker, W. Zhang, K. M. Merz, B. Roberts, S. Hayik, A. Roitberg, G. Seabra, J. Swails, A. W. Götz, I. Kolossváry, K.F.Wong, F. Paesani, J. Vanicek, R.M.Wolf, J. Liu, X. Wu, S. R. Brozell, T. Steinbrecher, H. Gohlke, Q. Cai, X. Ye, M.-J. Hsieh, G. Cui, D. R. Roe, D. H. Mathews, M. G. Seetin, R. Salomon-Ferrer, C. Sagui, V. Babin, T. Luchko, S. Gusarov, A. Kovalenko, P. A. Kollman,. Amber 12, University of California: San Francisco, 2012.
79. A. Pérez, I. Marchán, D. Svozil, J. Sponer, T. E. Cheatham, C. A. Laughton, M. Orozco,. Refinement of the AMBER force field for nucleic acids: improving the description of alpha/gamma conformers. Biophys. J. 2007, 92, 3817-3829.
80. W. D. Cornell, P. Cieplak, C. I. Bayly, I. R. Gould, K. M. Merz, D. M. Ferguson, D. C. Spellmeyer, T. Fox, J. W. Caldwell, P. A. Kollman,. A second generation force field for the simulation of proteins, nucleic acids, and organic molecules. J. Am. Chem. Soc. 1995, 117, 5179-5197.
81. B. R. Brooks, R. E. Bruccoleri, B. D. Olafson, D. J. States, S. Swaminathan, M. Karplus,. CHARMM: a program for macromolecular energy, minimization, and dynamics calculations. J. Comput. Chem. 1983, 4, 187-217.
82. A. Pérez, F. J. Luque, M. Orozco,. Dynamics of B-DNA on the microsecond time scale. J. Am. Chem. Soc. 2007, 22, 14739-14745.
83. T. Darden, D. York, L. Pedersen,. Particle mesh Ewald: an N·log(N) method for Ewald sums in large systems. J. Chem. Phys. 1993, 98, 10089.
84. H. J. C. Berendsen, J. P. M. Postma, W. F. van Gunsteren, A. DiNola, J. R. Haak,. Molecular dynamics with coupling to an external bath. J. Chem. Phys. 1984, 81, 3684.
85. D. R. Roe, T. E. Cheatham,. PTRAJ and CPPTRAJ: software for processing and analysis of molecular dynamics trajectory data. J. Chem. Theory Comput. 2013, 9, 3084-3095.
86. D. A. Case, T. A. Darden, T. E. Cheatham III, C. L. Simmerling, J. Wang, R. E. Duke, R. Luo, R. C. Walker, W. Zhang, K. M. Merz, B. Roberts, S. Hayik, A. Roitberg, G. Seabra, J. Swails, A. W. Götz, I. Kolossváry, K. F. Wong, F. Paesani, J. Vanicek, R. M. Wolf, J. Liu, X. Wu, S. R. Brozell, T. Steinbrecher, H. Gohlke, Q. Cai, X. Ye, M.-J. Hsieh, G. Cui, D. R. Roe, D. H. Mathews, M. G. Seetin, R. Salomon-Ferrer, C. Sagui, V. Babin, T. Luchko, S. Gusarov, A. Kovalenko, P. A. Kollman,. Amber13, University of California: San Francisco, 2012.
87. W. Humphrey, A. Dalke, K. Schulten,. VMD: visual molecular dynamics. J. Mol. Graph. 1996, 14, 33-38.
88. M. F. Mesleh, J. M. Hunter, A. A. Shvartsburg, G. C. Schatz, M. F. Jarrold,. Structural information from ion mobility measurements: effects of the long-range potential. J. Phys. Chem. 1996, 100, 16082-16086.
89. A. A. Shvartsburg, G. C. Schatz, M. F. Jarrold,. Mobilities of carbon cluster ions: critical importance of the molecular attractive potential. J. Chem. Phys. 1998, 108, 2416.
90. A. A. Shvartsburg, M. F. Jarrold,. An exact hard-spheres scattering model for the mobilities of polyatomic ions. Chem. Phys. Lett. 1996, 261, 86-91.
91. C.-K. Siu, Y. Guo, I. S. Saminathan, A. C. Hopkinson, K. W. M. Siu,. Optimization of parameters used in algorithms of ion-mobility calculation for conformational analyses. J. Phys. Chem. B 2010, 114, 1204-1212.
92. Optimization of Algorithms for Ion Mobility Calculations, A. A. Shvartsburg, S. V. Mashkevich, E. S. Baker, R. D. Smith,. J. Phys. Chem. A 2007, 111, 2002-2010.
93. H. I. Kim, H. Kim, E. S. Pang, E. K. Ryu, L. W. Beegle, J. A. Loo, W. A. Goddard, I. Kanik,. Structural characterization of unsaturated phosphatidylcholines using traveling wave ion mobility spectrometry. Anal. Chem. 2009, 81, 8289-8297.
94. H. Kim, H. I. Kim, P. V. Johnson, L. W. Beegle, J. L. Beauchamp, W. A. Goddard, I. Kanik,. Experimental and theoretical investigation into the correlation between mass and ion mobility for choline and other ammonium cations in N2. Anal. Chem. 2008, 80, 1928-1936.
95. S. E. Anderson, C. Bleiholder, E. R. Brocker, P. J. Stang, M. T. Bowers,. A novel projection approximation algorithm for the fast and accurate computation of molecular collision cross sections (III): Application to supramolecular coordination-driven assemblies with complex shapes. Int. J. Mass Spectrom. 2012, 330-332, 78-84.
96. C. Bleiholder, S. Contreras, M. T. Bowers,. A novel projection approximation algorithm for the fast and accurate computation of molecular collision cross sections (IV). Application to polypeptides. Int. J. Mass Spectrom 2013, 354-355, 275-280.
97. C. Bleiholder, S. Contreras, T. D. Do, M. T. Bowers,. A novel projection approximation algorithm for the fast and accurate computation of molecular collision cross sections (II). Model parameterization and definition of empirical shape factors for proteins. Int. J. Mass Spectrom 2013, 345-347, 89-96.
98. C. Bleiholder, T. Wyttenbach, M. T. Bowers,. A novel projection approximation algorithm for the fast and accurate computation of molecular collision cross sections (I). Method. Int. J. Mass Spectrom. 2011, 308, 1-10.
99. C. Larriba, C. J. Hogan,. Free molecular collision cross section calculation methods for nanoparticles and complex ions with energy accommodation. J. Comput. Phys. 2013, 251, 344-363.
100. Y. Alexeev, D. G. Fedorov, A. A. Shvartsburg,. Effective ion mobility calculations for macromolecules by scattering on electron clouds. J. Phys. Chem. A 2014, 118, 6763-6772.
101. The Martin Jarrold Research Group http://www.indiana.edu/~nano/software.html (accessed Dec 10, 2014).
102. A. K. Rappe, C. J. Casewit, K. S. Colwell, W. A. Goddard, W. M. Skiff,. UFF, a full periodic table force field for molecular mechanics and molecular dynamics simulations. J. Am. Chem. Soc. 1992, 114, 10024-10035.
103. The Bowers Research Group http://bowers.chem.ucsb.edu/theory-analysis/cross-sections/sigma.shtml (accessed Dec 10, 2014).
104. WebPSA http://luschka.bic.ucsb.edu:8080/WebPSA/index.jsp (accessed Dec 10, 2014).
105. S. C. Gibson, C. S. Feigerle, K. D. Cook,. Fluorometric measurement and modeling of droplet temperature changes in an electrospray plume. Anal. Chem. 2014, 86, 464-472.
106. M. Z. Steinberg, K. Breuker, R. Elber, R. B. Gerber,. The dynamics of water evaporation from partially solvated cytochrome c in the gas phase. Phys. Chem. Chem. Phys. 2007, 9, 4690-4697.
107. M. Z. Steinberg, R. Elber, F. W. McLafferty, R. B. Gerber, K. Breuker,. Early structural evolution of native cytochrome c after solvent removal. Chembiochem 2008, 9, 2417-2423.