Advertisement

Tailoring peptide conformational space with organic gas modifiers in TIMS-MS

  • Alyssa Garabedian
  • Fenfei Leng
  • Mark E. Ridgeway
  • Melvin A. Park
  • Francisco Fernandez-Lima
Original Research

Abstract

Recently, we showed the advantages of Trapped Ion Mobility Spectrometry for the study of kinetic intermediates of biomolecules as a function of the starting solvent composition (e.g., organic content and pH) and collisional induced activation. In the present work, we further characterize the influence of the bath composition (e.g., organic content) on the conformational space of an intrinsically disordered, DNA binding peptide: AT-hook 3 (Lys-Arg-Pro-Arg-Gly-Arg-Pro-Arg-Lys-Trp). Results show the dependence of the charge state distribution and mobility profiles by doping the solution and the bath gas with organic modifiers (e.g., methanol and acetone). The high resolving power of the TIMS analyzer allowed the separation of multiple IMS band per charge state, and their relative abundances are described as a function of the experimental conditions. The use of gas modifiers resulted in larger inverse  mobilities, with a direct correlation between the size of the modifier and the 1/K0 differences. Conformational isomer inter-conversion rates were observed as a function of the trapping time. Different from solution experiments, a larger variety of organic gas modifiers can be used to tailor the peptide conformational space, since peptide precipitation is not a problem.

Keywords

Trapped ion mobility mass spectrometry Intrinsically disordered protein HMGA2 ATHP 

Notes

Acknowledgments

This work was supported by the National Science Foundation Division of Chemistry, under CAREER award CHE-1654274, with co-funding from the Division of Molecular and Cellular Biosciences to F.F.-L. The authors will also like to acknowledge the helpful discussions and technical support from Dr. Mark E. Ridgeway and Dr. Melvin A. Park from Bruker Daltonics Inc. during the development and installation of the custom-built TIMS-TOF MS instrument.

References

  1. 1.
    Adams KJ, Montero D, Aga D, Fernandez-Lima F (2016) Isomer separation of polybrominated diphenyl ether metabolites using nanoESI-TIMS-MS. Int J Ion Mobil Spectrom 19(2-3):69–76.  https://doi.org/10.1007/s12127-016-0198-z CrossRefPubMedPubMedCentralGoogle Scholar
  2. 2.
    Benigni P, Fernandez-Lima F (2016) Oversampling Selective Accumulation Trapped Ion Mobility Spectrometry Coupled to FT-ICR MS: Fundamentals and Applications. Anal Chem 88(14):7404–7412.  https://doi.org/10.1021/acs.analchem.6b01946 CrossRefPubMedGoogle Scholar
  3. 3.
    Benigni P, Marin R, Fernandez-Lima F (2015) Towards unsupervised polyaromatic hydrocarbons structural assignment from SA-TIMS –FTMS data. Int J Ion Mobil Spectrom:1–7.  https://doi.org/10.1007/s12127-015-0175-y
  4. 4.
    Benigni P et al (2016) Towards the analysis of high molecular weight proteins and protein complexes using TIMS-MS. Int J Ion Mobil Spec 19:95–104.  https://doi.org/10.1007/s12127-016-0201-8 CrossRefGoogle Scholar
  5. 5.
    Chen S-H, Russell DH (2015) How closely related are conformations of protein ions sampled by IM-MS to native solution structures? J Am Soc Mass Spectrom 26(9):1433–1443CrossRefPubMedGoogle Scholar
  6. 6.
    Feng X, Liu X, Luo Q, Liu B-F (2008) Mass spectrometry in systems biology: an overview. Mass Spectrom Rev 27(6):635–660.  https://doi.org/10.1002/mas.20182 CrossRefPubMedGoogle Scholar
  7. 7.
    Fernandez-Lima FA, Kaplan DA, Park MA (2011a) Note: Integration of trapped ion mobility spectrometry with mass spectrometry. Rev Sci Instrum 82:126106CrossRefPubMedPubMedCentralGoogle Scholar
  8. 8.
    Fernandez-Lima FA, Kaplan DA, Suetering J, Park MA (2011b) Gas-phase separation using a Trapped Ion Mobility Spectrometer. Int J Ion Mobil Spec 14:93–98CrossRefGoogle Scholar
  9. 9.
    Fernández-Maestre R, Wu C, Hill HH (2012) Buffer gas modifiers effect resolution in ion mobility spectrometry through selective ion-molecule clustering reactions. Rapid Commun Mass Spectrom 26(19):2211–2223.  https://doi.org/10.1002/rcm.6335 CrossRefPubMedPubMedCentralGoogle Scholar
  10. 10.
    Frost L, Baez MAM, Harrilal C, Garabedian A, Fernandez-Lima F, Leng F (2015) The dimerization state of the mammalian high mobility group protein AT-hook 2 (HMGA2). PLoS One 10(6):e0130478.  https://doi.org/10.1371/journal.pone.0130478 CrossRefPubMedPubMedCentralGoogle Scholar
  11. 11.
    Gonzalez WG, Ramos V, Diaz M, Garabedian A, Molano-Arevalo JC, Fernandez-Lima F, Miksovska J (2016) Characterization of the Photophysical, thermodynamic, and structural properties of the terbium (III)–DREAM complex. Biochemistry 55(12):1873–1886CrossRefPubMedPubMedCentralGoogle Scholar
  12. 12.
    Hernandez DR, DeBord JD, Ridgeway ME, Kaplan DA, Park MA, Fernandez-Lima FA (2014) Ion dynamics in a trapped ion mobility spectrometer. Analyst 139(8):1913–1921.  https://doi.org/10.1039/C3AN02174B CrossRefPubMedPubMedCentralGoogle Scholar
  13. 13.
    Kafle A, Coy SL, Wong BM, Fornace AJ Jr, Glick JJ, Vouros P (2014) Understanding gas phase modifier interactions in rapid analysis by differential mobility-tandem mass spectrometry. J Am Soc Mass Spectrom 25(7):1098–1113.  https://doi.org/10.1007/s13361-013-0808-5 CrossRefPubMedPubMedCentralGoogle Scholar
  14. 14.
    Levin DS, Vouros P, Miller RA, Nazarov EG, Morris JC (2006) Characterization of gas-phase molecular interactions on differential mobility ion behavior utilizing an electrospray ionization-differential mobility-mass spectrometer system. Anal Chem 78(1):96–106.  https://doi.org/10.1021/ac051217k CrossRefPubMedGoogle Scholar
  15. 15.
    Liu FC, Kirk SR, Bleiholder C (2016) On the structural denaturation of biological analytes in trapped ion mobility spectrometry - mass spectrometry. Analyst 141(12):3722–3730.  https://doi.org/10.1039/C5AN02399H CrossRefPubMedGoogle Scholar
  16. 16.
    Loo JA (1997) Studying noncovalent protein complexes by electrospray ionization mass spectrometry. Mass Spectrom Rev 16(1):1–23.  https://doi.org/10.1002/(sici)1098-2787(1997)16:1<1::aid-mas1>3.0.co;2-l CrossRefPubMedGoogle Scholar
  17. 17.
    McDaniel EW, Mason EA (1973) Mobility and diffusion of ions in gases. Wiley series in plasma physics. John Wiley and Sons, Inc., New YorkGoogle Scholar
  18. 18.
    Meyer T, Gabelica V, Grubmüller H, Orozco M (2013) Proteins in the gas phase. Wiley Interdiscip Rev: Comput Mol Sci 3:408–425Google Scholar
  19. 19.
    Miranker A, Robinson CV, Radford SE, Aplin RT, Dobson CM (1993) Detection of transient protein folding populations by mass spectrometry. Science 262(5135):896–900.  https://doi.org/10.1126/science.8235611 CrossRefPubMedGoogle Scholar
  20. 20.
    Molano-Arevalo JC, Hernandez DR, Gonzalez WG, Miksovska J, Ridgeway ME, Park MA, Fernandez-Lima F (2014) Flavin adenine dinucleotide structural motifs: from solution to gas phase. Anal Chem 86(20):10223–10230.  https://doi.org/10.1021/ac5023666 CrossRefPubMedPubMedCentralGoogle Scholar
  21. 21.
    Pi J, Sael L (2013) Mass spectrometry coupled experiments and protein structure modeling methods. Int J Mol Sci 14:20635–20657.  https://doi.org/10.3390/ijms141020635 CrossRefPubMedPubMedCentralGoogle Scholar
  22. 22.
    Pierson NA, Chen L, Valentine SJ, Russell DH, Clemmer DE (2011) Number of solution states of bradykinin from ion mobility and mass spectrometry measurements. J Am Chem Soc 133(35):13810–13813.  https://doi.org/10.1021/ja203895j CrossRefPubMedPubMedCentralGoogle Scholar
  23. 23.
    Porta T, Varesio E, Hopfgartner G (2013) Gas-phase separation of drugs and metabolites using modifier-assisted differential ion mobility spectrometry hyphenated to liquid extraction surface analysis and mass spectrometry. Anal Chem 85(24):11771–11779.  https://doi.org/10.1021/ac4020353 CrossRefPubMedGoogle Scholar
  24. 24.
    Ridgeway ME, Silveira JA, Meier JE, Park MA (2015) Microheterogeneity within conformational states of ubiquitin revealed by high resolution trapped ion mobility spectrometry. Analyst 140(20):6964–6972CrossRefPubMedGoogle Scholar
  25. 25.
    Rosu F, Gabelica V, Joly L, Gregoire G, De Pauw E (2010) Zwitterionic i-motif structures are preserved in DNA negatively charged ions produced by electrospray mass spectrometry. Phys Chem Chem Phys 12(41):13448–13454CrossRefPubMedGoogle Scholar
  26. 26.
    Schenk ER, Ridgeway ME, Park MA, Leng F, Fernandez-Lima F (2013) Isomerization kinetics of AT hook Decapeptide solution structures. Anal Chem 86(2):1210–1214.  https://doi.org/10.1021/ac403386q CrossRefGoogle Scholar
  27. 27.
    Schenk ER, Mendez V, Landrum JT, Ridgeway ME, Park MA, Fernandez-Lima F (2014a) Direct observation of differences of carotenoid polyene chain cis/trans isomers resulting from structural topology. Anal Chem 86(4):2019–2024.  https://doi.org/10.1021/ac403153m CrossRefPubMedPubMedCentralGoogle Scholar
  28. 28.
    Schenk ER, Mendez V, Landrum JT, Ridgeway ME, Park MA, Fernandez-Lima FA (2014b) Direct observation of differences of carotenoid polyene chain cis/trans isomers resulting from structural topology. Anal Chem 86(4):2019–2024.  https://doi.org/10.1021/ac403153m CrossRefPubMedPubMedCentralGoogle Scholar
  29. 29.
    Schenk ER, Ridgeway ME, Park MA, Leng F, Fernandez-Lima F (2014c) Isomerization kinetics of AT hook decapeptide solution structures. Anal Chem 86(2):1210–1214.  https://doi.org/10.1021/ac403386q CrossRefPubMedPubMedCentralGoogle Scholar
  30. 30.
    Schenk ER, Ridgeway ME, Park MA, Leng F, Fernandez-Lima FA (2014d) Isomerization kinetics of AT hook Decapeptide solution structures. Anal Chem 86(2):1210–1214.  https://doi.org/10.1021/ac403386q CrossRefPubMedPubMedCentralGoogle Scholar
  31. 31.
    Schenk ER, Almeida R, Miksovska J, Ridgeway ME, Park MA, Fernandez-Lima F (2015) Kinetic intermediates of holo- and apo-myoglobin studied using HDX-TIMS-MS and molecular dynamic simulations. J Am Soc Mass Spectrom 26(4):555–563.  https://doi.org/10.1007/s13361-014-1067-9 CrossRefPubMedPubMedCentralGoogle Scholar
  32. 32.
    Schneider B, Covey T, Nazarov E (2013) DMS-MS separations with different transport gas modifiers vol 16.  https://doi.org/10.1007/s12127-013-0130-8
  33. 33.
    Seo J, Hoffmann W, Warnke S, Bowers MT, Pagel K, von Helden G (2016) Retention of native protein structures in the absence of solvent: a coupled ion mobility and spectroscopic study. Angew Chem Int Ed 55(45):14173–14176.  https://doi.org/10.1002/anie.201606029 CrossRefGoogle Scholar
  34. 34.
    Shelimov KB, Jarrold MF (1997) Conformations, unfolding, and refolding of Apomyoglobin in vacuum: an activation barrier for gas-phase protein folding. J Am Chem Soc 119(13):2987–2994.  https://doi.org/10.1021/ja962914k CrossRefGoogle Scholar
  35. 35.
    Shi L, Holliday AE, Glover MS, Ewing MA, Russell DH, Clemmer DE (2016) Ion mobility-mass spectrometry reveals the energetics of intermediates that guide Polyproline folding. J Am Soc Mass Spectrom 27(1):22–30CrossRefPubMedGoogle Scholar
  36. 36.
    Silveira JA, Fort KL, Kim D, Servage KA, Pierson NA, Clemmer DE, Russell DH (2013) From solution to the gas phase: stepwise dehydration and kinetic trapping of substance P reveals the origin of peptide conformations. J Am Chem Soc 135(51):19147–19153.  https://doi.org/10.1021/ja4114193 CrossRefPubMedGoogle Scholar
  37. 37.
    Simoneit BRT (2005) A review of current applications of mass spectrometry for biomarker/molecular tracer elucidations. Mass Spectrom Rev 24(5):719–765.  https://doi.org/10.1002/mas.20036 CrossRefPubMedGoogle Scholar
  38. 38.
    Voronina L, Masson A, Kamrath M, Schubert F, Clemmer D, Baldauf C, Rizzo T (2016) Conformations of prolyl–peptide bonds in the bradykinin 1–5 fragment in solution and in the gas phase. J Am Chem Soc 138(29):9224–9233.  https://doi.org/10.1021/jacs.6b04550 CrossRefPubMedGoogle Scholar
  39. 39.
    Waraksa E, Gaik U, Namieśnik J, Sillanpää M, Dymerski T, Wójtowicz M, Puton J (2016) Dopants and gas modifiers in ion mobility spectrometry vol 82.  https://doi.org/10.1016/j.trac.2016.06.009
  40. 40.
    Winston RL, Fitzgerald MC (1997) Mass spectrometry as a readout of protein structure and function. Mass Spectrom Rev 16(4):165–179.  https://doi.org/10.1002/(sici)1098-2787(1997)16:4<165::aid-mas1>3.0.co;2-f CrossRefPubMedGoogle Scholar

Copyright information

© Springer-Verlag GmbH Germany, part of Springer Nature 2018

Authors and Affiliations

  1. 1.Department of Chemistry and BiochemistryFlorida International UniversityMiamiUSA
  2. 2.Biomolecular Sciences InstituteFlorida International UniversityMiamiUSA
  3. 3.Bruker Daltonics Inc.BillericaUSA

Personalised recommendations