The effects of cation adduction upon the conformation of three-helix bundle protein domains

Kanu AB, Dwivedi P, Tam M, Matz L, Hill HH (2008) Ion mobility-mass spectrometry. J Mass Spectrom 43(1):1–22. doi:10.1002/jms.1383 Dwivedi P, Wu C, Matz LM, Clowers BH, Siems WF, Hill HH (2006) Gas-phase chiral separations by ion mobility spectrometry. Anal Chem 78(24):8200–8206. doi:10.1021/ac0608772 Tao L, McLean JR, McLean JA, Russell DH (2007) A collision cross-section database of singly-charged peptide ions. J Am Soc Mass Spectrom 18(7):1232–1238. doi:10.1016/j.jasms.2007.04.003 Barran PE, Polfer NC, Campopiano DJ, Clarke DJ, Langridge-Smith PRR, Langley RJ, Govan JRW, Maxwell A, Dorin JR, Millar RP, Bowers MT (2005) Is it biologically relevant to measure the structures of small peptides in the gas-phase? Int J Mass Spectrom 240(3):273–284. doi:10.1016/j.ijms.2004.09.013 Clemmer DE, Hudgins RR, Jarrold MF (1995) Naked protein conformations–cytochrome-C in the gas-phase. J Am Chem Soc 117(40):10141–10142. doi:10.1021/ja00145a037 Clemmer DE, Jarrold MF (1997) Ion mobility measurements and their applications to clusters and biomolecules. J Mass Spectrom 32(6):577–592. doi:10.1002/(sici)1096-9888(199706)32:6<577::aid-jms530>3.3.co;2-w McLean JA, Ruotolo BT, Gillig KJ, Russell DH (2005) Ion mobility-mass spectrometry: a new paradigm for proteomics. Int J Mass Spectrom 240(3):301–315. doi:10.1016/j.ijms.2004.10.003 Wyttenbach T, Bowers MT (2003) Gas-phase conformations: the ion mobility/ion chromatography method. Mod Mass Spectrom 225:207–232. doi:10.1007/b10470 Wyttenbach T, vonHelden G, Bowers MT (1996) Gas-phase conformation of biological molecules: Bradykinin. J Am Chem Soc 118(35):8355–8364. doi:10.1021/ja9535928 Ruotolo BT, Benesch JLP, Sandercock AM, Hyung SJ, Robinson CV (2008) Ion mobility-mass spectrometry analysis of large protein complexes. Nat Protoc 3(7):1139–1152. doi:10.1038/nprot.2008.78 Uetrecht C, Rose RJ, van Duijn E, Lorenzen K, Heck AJR (2010) Ion mobility mass spectrometry of proteins and protein assemblies. Chem Soc Rev 39(5):1633–1655. doi:10.1039/b914002f Breuker K, McLafferty FW (2008) Stepwise evolution of protein native structure with electrospray into the gas phase, 10(−12) to 10(2) S. Proc Natl Acad Sci U S A 105(47):18145–18152. doi:10.1073/pnas.0807005105 Giles K, Pringle SD, Worthington KR, Little D, Wildgoose JL, Bateman RH (2004) Applications of a travelling wave-based radio-frequency only stacked ring ion guide. Rapid Commun Mass Spectrom 18(20):2401–2414. doi:10.1002/rcm.1641 Pringle SD, Giles K, Wildgoose JL, Williams JP, Slade SE, Thalassinos K, Bateman RH, Bowers MT, Scrivens JH (2007) An investigation of the mobility separation of some peptide and protein ions using a new hybrid quadrupole/travelling wave IMS/oa-ToF instrument. Int J Mass Spectrom 261(1):1–12. doi:10.1016/j.ijms.2006.07.021 Duijn EV, Barendregt A, Synowsky S, Versluis C, Heck AJR (2009) Chaperonin complexes monitored by ion mobility mass spectrometry. J Am Chem Soc 131(4):1452–1459. doi:10.1021/ja8055134 Smith DP, Knapman TW, Campuzano I, Malham RW, Berryman JT, Radford SE, Ashcroft AE (2009) Deciphering drift time measurements from travelling wave ion mobility spectrometry-mass spectrometry studies. Eur J Mass Spectrom 15(2):113–130. doi:10.1255/ejms.947 Hilton GR, Thalassinos K, Grabenauer M, Sanghera N, Slade SE, Wyttenbach T, Robinson PJ, Pinheiro TJT, Bowers MT, Scrivens JH (2010) Structural analysis of prion proteins by means of drift cell and traveling wave ion mobility mass spectrometry. J Am Soc Mass Spectrom 21(5):845–854. doi:10.1016/j.jasms.2010.01.017 Smith DP, Radford SE, Ashcroft AE (2010) Elongated oligomers in beta(2)-microglobulin amyloid assembly revealed by ion mobility spectrometry-mass spectrometry. Proc Natl Acad Sci U S A 107(15):6794–6798. doi:10.1073/pnas.0913046107 Wyttenbach T, Grabenauer M, Thalassinos K, Scrivens JH, Bowers MT (2010) The effect of calcium ions and peptide ligands on the relative stabilities of the calmodulin dumbbell and compact structures. J Phys Chem B 114(1):437–447. doi:10.1021/jp906242m Ruotolo BT, Giles K, Campuzano I, Sandercock AM, Bateman RH, Robinson CV (2005) Evidence for macromolecular protein rings in the absence of bulk water. Science 310(5754):1658–1661. doi:10.1126/science.1120177 Jenner M, Ellis J, Huang WC, Raven EL, Roberts GCK, Oldham NJ (2011) Detection of a protein conformational equilibrium by electrospray ionisation-ion mobility-mass spectrometry. Angew Chem Int Ed 50(36):8291–8294. doi:10.1002/anie.201101077 Bleiholder C, Dupuis NF, Wyttenbach T, Bowers MT (2011) Ion mobility-mass spectrometry reveals a conformational conversion from random assembly to beta-sheet in amyloid fibril formation. Nat Chem 3(2):172–177. doi:10.1038/nchem.945 De Cecco M, Seo ES, Clarke DJ, McCullough BJ, Taylor K, Macmillan D, Dorin JR, Campopiano DJ, Barran PE (2010) Conformational preferences of linear beta-defensins are revealed by ion mobility-mass spectrometry. J Phys Chem B 114(6):2312–2318. doi:10.1021/jp9111662 Loo JA, Berhane B, Kaddis CS, Wooding KM, Xie YM, Kaufman SL, Chernushevich IV (2005) Electrospray ionization mass spectrometry and ion mobility analysis of the 20S proteasome complex. J Am Soc Mass Spectrom 16(7):998–1008. doi:10.1016/j.jasms.2005.02.017 Halgand F, Laprevote O (2001) Mean charge state and charge state distribution of proteins as structural probes. An electrospray ionisation mass spectrometry study of lysozyme and ribonuclease A. Eur J Mass Spectrom 7(6):433–439. doi:10.1255/ejms.458 Lemaire D, Marie G, Serani L, Laprevote O (2001) Stabilization of gas-phase noncovalent macromolecular complexes in electrospray mass spectrometry using aqueous triethylammonium bicarbonate buffer. Anal Chem 73(8):1699–1706. doi:10.1021/ac001276s Pagel K, Hyung SJ, Ruotolo BT, Robinson CV (2010) Alternate dissociation pathways identified in charge-reduced protein complex ions. Anal Chem 82(12):5363–5372. doi:10.1021/ac101121r Touboul D, Jecklin MC, Zenobi R (2008) Investigation of deprotonation reactions on globular and denatured proteins at atmospheric pressure by ESSI-MS. J Am Soc Mass Spectrom 19(4):455–466. doi:10.1016/j.jasms.2007.12.011 Winger BE, Lightwahl KJ, Smith RD (1992) Gas-phase proton-transfer reactions involving multiply charged cytochrome-C ions and water under thermal conditions. J Am Soc Mass Spectrom 3(6):624–630 Loo RRO, Udseth HR, Smith RD (1991) Evidence of charge inversion in the reaction of singly charged anions with multiply charged macroions. J Phys Chem 95(17):6412–6415. doi:10.1021/j100170a006 Zhao Q, Schieffer GM, Soyk MW, Anderson TJ, Houk RS, Badman ER (2010) Effects of ion/ion proton transfer reactions on conformation of gas-phase cytochrome C ions. J Am Soc Mass Spectrom 21(7):1208–1217. doi:10.1016/j.jasms.2010.03.032 Zhao Q, Soyk MW, Schieffer GM, Fuhrer K, Gonin MM, Houk RS, Badman ER (2009) An ion trap-ion mobility-time of flight mass spectrometer with three ion sources for ion/ion reactions. J Am Soc Mass Spectrom 20(8):1549–1561. doi:10.1016/j.jasms.2009.04.014 Hopper JTS, Sokratous K, Oldham NJ (2012) Charge state and adduct reduction in electrospray ionization-mass spectrometry using solvent vapor exposure. Anal Biochem 421(2):788–790. doi:10.1016/j.ab.2011.10.034 Sokratous K, Roach LV, Channing D, Strachan J, Long J, Searle MS, Layfield R, Oldham NJ (2012) Probing affinity and ubiquitin linkage selectivity of ubiquitin-binding domains using mass spectrometry. J Am Chem Soc 134(14):6416–6424. doi:10.1021/ja300749d Kaltashov IA, Abzalimov RR (2008) Do ionic charges in ESI MS provide useful information on macromolecular structure? J Am Soc Mass Spectrom 19(9):1239–1246. doi:10.1016/j.jasms.2008.05.018 Benesch JLP (2009) Collisional activation of protein complexes: picking up the pieces. J Am Soc Mass Spectrom 20(3):341–348. doi:10.1016/j.jasms.2008.11.014 Hopper JTS, Oldham NJ (2011) Alkali metal cation-induced destabilization of gas-phase protein-ligand complexes: consequences and prevention. Anal Chem 83(19):7472–7479. doi:10.1021/ac201686f Rozman M, Gaskell SJ (2010) Non-covalent interactions of alkali metal cations with singly charged tryptic peptides. J Mass Spectrom 45(12):1409–1415. doi:10.1002/jms.1856 Wu C, Klasmeier J, Hill HH (1999) Atmospheric pressure ion mobility spectrometry of protonated and sodiated peptides. Rapid Commun Mass Spectrom 13(12):1138–1142. doi:10.1002/(sici)1097-0231(19990630)13:12<1138::aid-rcm625>3.0.co;2-8 Counterman AE, Valentine SJ, Srebalus CA, Henderson SC, Hoaglund CS, Clemmer DE (1998) High-order structure and dissociation of gaseous peptide aggregates that are hidden in mass spectra. J Am Soc Mass Spectrom 9(8):743–759. doi:10.1016/s1044-0305(98)00052-x Salbo R, Bush MF, Naver H, Campuzano I, Robinson CV, Pettersson I, Jorgensen TJD, Haselmann KF (2012) Traveling-wave ion mobility mass spectrometry of protein complexes: accurate calibrated collision cross-sections of human insulin oligomers. Rapid Commun Mass Spectrom 26(10):1181–1193. doi:10.1002/rcm.6211 Mesleh MF, Hunter JM, Shvartsburg AA, Schatz GC, Jarrold MF (1996) Structural information from ion mobility measurements: effects of the long-range potential. J Phys Chem 100(40):16082–16086. doi:10.1021/jp961623v Shvartsburg AA, Jarrold MF (1996) An exact hard-spheres scattering model for the mobilities of polyatomic ions. Chem Phys Lett 261(1–2):86–91. doi:10.1016/0009-2614(96)00941-4 Williams JP, Lough JA, Campuzano I, Richardson K, Sadler PJ (2009) Use of ion mobility mass spectrometry and a collision cross-section algorithm to study an organometallic ruthenium anticancer complex and its adducts with a DNA oligonucleotide. Rapid Commun Mass Spectrom 23(22):3563–3569. doi:10.1002/rcm.4285 Chen VB, Arendall WB, Headd JJ, Keedy DA, Immormino RM, Kapral GJ, Murray LW, Richardson JS, Richardson DC (2010) MolProbity: all-atom structure validation for macromolecular crystallography. Acta Crystallogr D: Biol Crystallogr 66:12–21. doi:10.1107/s0907444909042073 Davis IW, Leaver-Fay A, Chen VB, Block JN, Kapral GJ, Wang X, Murray LW, Arendall WB, Snoeyink J, Richardson JS, Richardson DC (2007) MolProbity: all-atom contacts and structure validation for proteins and nucleic acids. Nucleic Acids Res 35:W375–W383. doi:10.1093/nar/gkm216 Bertini I, Case DA, Ferella L, Giachetti A, Rosato A (2011) A grid-enabled web portal for NMR structure refinement with AMBER. Bioinformatics 27(17):2384–2390. doi:10.1093/bioinformatics/btr415 Case DA, Cheatham TE, Darden T, Gohlke H, Luo R, Merz KM, Onufriev A, Simmerling C, Wang B, Woods RJ (2005) The Amber biomolecular simulation programs. J Comput Chem 26(16):1668–1688. doi:10.1002/jcc.20290 Zhang D, Raasi S, Fushman D (2008) Affinity makes the difference: nonselective interaction of the UBA domain of ubiquilin-1 with monomeric ubiquitin and polyubiquitin chains. J Mol Biol 377(1):162–180. doi:10.1016/j.jmb.2007.12.029 Benesch JLP, Ruotolo BT (2011) Mass spectrometry: come of age for structural and dynamical biology. Curr Opin Struct Biol 21(5):641–649. doi:10.1016/j.sbi.2011.08.002 Julian RR, Beauchamp JL (2002) The unusually high proton affinity of aza-18-crown-6 ether: implications for the molecular recognition of lysine in peptides by lariat crown ethers. J Am Soc Mass Spectrom 13(5):493–498. doi:10.1016/s1044-0305(02)00368-9 Lomeli SH, Peng IX, Yin S, Loo RRO, Loo JA (2010) New reagents for increasing ESI multiple charging of proteins and protein complexes. J Am Soc Mass Spectrom 21(1):127–131. doi:10.1016/j.jasms.2009.09.014 Verkerk UH, Kebarle P (2005) Ion-ion and ion-molecule reactions at the surface of proteins produced by nanospray. Information on the number of acidic residues and control of the number of ionized acidic and basic residues. J Am Soc Mass Spectrom 16(8):1325–1341. doi:10.1016/j.jasms.2005.03.018 Steinberg MZ, Elber R, McLafferty FW, Gerber RB, Breuker K (2008) Early structural evolution of native cytochrome C after solvent removal. ChemBioChem 9(15):2417–2423. doi:10.1002/cbic.200800167 Wyttenbach T, Bushnell JE, Bowers MT (1998) Salt bridge structures in the absence of solvent? the case for the oligoglycines. J Am Chem Soc 120(20). doi:10.1021/ja9801238 Felitsyn N, Peschke M, Kebarle P (2002) Origin and number of charges observed on multiply-protonated native proteins produced by ESI. Int J Mass Spectrom 219(1):39–62. doi:10.1016/s1387-3806(02)00588-2