Trifluoroethanol (TFE)-induced conformational changes in dynorphin A (1-13) were investigated using charge-state distribution (CSD) and hydrogen–deuterium exchange (HDX), combined with electrospray ionization (ESI) mass spectrometry (MS). Individual amino acids involved in secondary structural elements were identified by collision-induced dissociation-tandem mass spectrometry (MS/MS). It was observed that dynorphin A (1-13) largely exists in an unfolded conformation and a folded structure in increasing concentrations of TFE. In 50% TFE, it forms an α-helix that encompasses residues 1-9 and remains flexible from residues 10 to 13.
GoldsteinA.FischliW.LowneyL.I.HunkapillerM.HoodL., “Porcine pituitary dynorphin: Complete amino acid sequence of the biologically active heptadecapeptide”, Proc. Natl. Acad. Sci. USA78, 7219 (1981). doi: 10.1073/pnas.78.11.7219
2.
GoldsteinA.TachibanaS.LowneyL.I.HunkapillerM.HoodL., “Dynorphin-(1–13), an extraordinary potent opioid peptide”, Proc. Natl. Acad. Sci. USA76, 6666 (1979). doi: 10.1073/pnas.76.12.6666
3.
ChavkinC.JamesI.F.GoldsteinA., “Dynorphin is a specific endogenous ligand of the kappa opioid receptor”, Science215, 413–415 (1982). doi: 10.1126/science.6120570
4.
SmithD.GriffinJ.F., “Conformation of [Leu5] enkephalin from X-ray diffraction: Features important for recognition at opiate receptor”, Science199, 1214–1216 (1978). doi: 10.1126/science.204006
5.
CamermanA.MastropaoloM.KarleI.KarleJ.CamermanN., “Crystal structure of leucine-enkephalin”, Nature306, 447–450 (1983). doi: 10.1038/306447a0
6.
DoiM.IshidaT.InoueM.FujiwaraT.TomitaK.KimuraT.SakakibaraS., “Three-dimensional structure of monoanionic methionine-enkephalin: X-ray structure of tert-butyloxycarbonyl-Tyr-Gly-Gly-(4-bromo)Phe-Met-OH”, FEBS Lett170, 229–231 (1984). doi: 10.1016/0014-5793(84)81318-6
7.
SchillerP.W.DiMaioJ., “Opiate receptor subclasses differ in their conformational requirements”, Nature297, 74–76 (1982). doi: 10.1038/297074a0
8.
MarounR.MatticeW.L., “Solution conformations of the pituitary opioid peptide dynorphin-(1–13)”, Biochem. Biophys. Res. Commun.103, 442–446 (1981). doi: 10.1016/0006-291X(81)90472-1
9.
RenugopalakrishnanV.RapakaR.S.HuangS.G.MooreS.HutsonT.B., “Dynorphin A (1–13) peptide NH groups are solvent exposed: FT-IR and 500 MHz proton NMR spectroscopic evidence”, Biochem. Biophys. Res. Commun.151, 1220–1225 (1988). doi: 10.1016/S0006-291X(88)80496-0
10.
KallickD.A., “Conformation of dynorphin A(1–17) bound to dodecylphosphocholine micelles”, J. Am. Chem. Soc.115, 9317–9318 (1993). doi: 10.1021/ja00073a069
11.
LancasterC.R.MishraP.K.HughesD.W.St-PierreS.A.Bothner-ByA.A.EpandR.M., “Mimicking the membrane-mediated conformation of dynorphin A-(1–13)-peptide: Circular dichroism and nuclear magnetic resonance studies in methanolic solution”, Biochemistry30, 4715–4726 (1991). doi: 10.1021/bi00233a012
12.
ErneD.SargentD.F.SchwyzerR., “Preferred conformation, orientation, and accumulation of dynorphin A-(1–13)-tridecapeptide on the surface of neutral lipid membranes”, Biochemistry24, 4261–4263 (1985). doi: 10.1021/bi00337a001
13.
UezonoT.TorayaS.ObataM.NishimuraK.TuziS.SaitoH.NaitoA., “Structure and orientation of dynorphin bound to lipidbilayers by 13C solid-state NMR”, J. Mol. Struct.749, 13–19 (2005). doi: 10.1016/j.molstruc.2005.02.037
14.
SankararamakrishnanR.WeinsteinH., “Molecular dynamics simulations predict a tilted orientation for the helical region of dynorphin A(1–17) in dimyristoylphosphatidylcholine bilayers”, Biophys. J.79, 2331–2344 (2000).
15.
BehnamB.A.DeberC.M., “Evidence for a folded conformation of methionine- and leucine-enkephalin in a membrane environment”, J. Biol. Chem.259, 14935–14940 (1984).
16.
RajanR.BalaramP., “A model for the interaction of trifluoroethanol with peptides and proteins”, Int. J. Pept. Protein Res.48, 328–336 (1996).
17.
AwasthiS.K.ShankarammaS.C.RaghothamaS.BalaramP., “Solvent-induced beta-hairpin to helix conformational transition in a designed peptide”, Biopolymers58, 465–76 (2001). doi: 10.1002/1097-0282(20010415)58:5<465::AID-BIP1022>3.0.CO;2-T
18.
DongS.L.CadamuroS.A.FiorinoF.BertschU.MoroderL.RennerC., “Copper binding and conformation of the N-terminal octarepeats of the prion protein in the presence of DPC micelles as membrane mimetic”, Biopolymers88, 840–847 (2007). doi: 10.1002/bip.20860
19.
SonnichsenF.D.Van EykJ.E.HodgesR.S.SykesB.D., “Effect of trifluoroethanol on protein secondary structure: An NMR and CD study using a synthetic actin peptide”, Biochemistry31, 8790–8798 (1992). doi: 10.1021/bi00152a015
20.
NelsonJ.W.KallenbachN.R., “Stabilization of the ribonuclease S-peptide alpha-helix by trifluoroethanol”, Proteins1, 211–217 (1986). doi: 10.1002/prot.340010303
21.
LehrmanS.R.TulsJ.L.LundM., “Peptide alpha-helicity in aqueous trifluoroethanol: Correlations with predicted alpha-helicity and the secondary structure of the corresponding regions of bovine growth hormone”, Biochemistry29, 5590–5596 (1990). doi: 10.1021/bi00475a025
22.
DysonH.J.MerutkaG.WalthoJ.P.LernerR.A.WrightP.E., “Folding of peptide fragments comprising the complete sequence of proteins. Models for initiation of protein folding”, J. Mol. Biol.226, 795–817 (1992). doi: 10.1016/0022-2836(92)90633-U
23.
KrausM.JanekK.BienertM.KrauseE., “Characterization of intermolecular β-sheet peptides by mass spectrometry and hydrogen isotope exchange”, Rapid Commun. Mass Spectrom.14, 1094–1104 (2000). doi: 10.1002/1097-0231(20000715)14:13<1094::AID-RCM994>3.0.CO;2-5
24.
MirankerA.RobinsonC.V.RadfordS.E.AplinR.T.DobsonC.M., “Detection of transient protein folding populations by mass spectrometry”, Science262, 896–900 (1993). doi: 10.1126/science.8235611
25.
LinH.DassC., “A mass spectrometry investigation of the conformational changes in adrenocorticotropic hormones”, Eur. J. Mass Spectrom.8, 381–387 (2002). doi: 10.1255/ejms.513
26.
KonermannL.SimmonsD.A., “Protein-folding kinetics and mechanisms studied by pulse-labeling and mass spectrometry”, Mass Spectrom. Rev.22, 1–26 (2003). doi: 10.1002/mas.10044
27.
DassC., Principle and Practice of Biological Mass Spectrometry.Wiley-Interscience, New York, pp. 416 (2001).
28.
DassC., Fundamentals of Contemporary Mass Spectrometry.Wiley-Interscience, New York, pp. 585 (2007).
29.
CaiX.DassC., “Conformational analysis of proteins and peptides”, Curr. Org. Chem.7, 1841–1854 (2003). doi: 10.2174/1385272033486161
30.
MandellJ.G.FalickA.M.KomivesE.A., “Measurement of amide hydrogen exchange by MALDI-TOF mass spectrometry”, Anal. Chem.70, 3987–3995 (1998). doi: 10.1021/ac980553g
31.
EngenJ.R.SmithD.L., “Investigating protein structure and dynamics by hydrogen exchange MS”, Anal. Chem.73, 256A-265A (2001).
32.
RaschkeT.M.MarquseeS., “Hydrogen exchange studies of protein structure”, Curr. Opin. Biotech.9, 80–86 (1998). doi: 10.1016/S0958-1669(98)80088-8
33.
RoderH.WüthrickK., “Protein folding kinetics by combined use of rapid mixing techniques and NMR observation of individual amide protons”, Proteins1, 34–42 (1986). doi: 10.1002/prot.340010107
34.
UdgaonkarJ.B.BaldwinR.L., “NMR evidence for an early framework intermediate on the folding pathway of ribonuclease A”, Nature335, 694–699 (1988). doi: 10.1038/335694a0
35.
RoderH.EloveG.A.EnglanderS.W., “Structural characterization of folding intermediates in cytochrome c by H-exchange labelling and proton NMR”, Nature335, 700–704 (1988). doi: 10.1038/335700a0
36.
KattaV.ChaitB.T., “Conformational changes in proteins probed by hydrogen-exchange electrospray-ionization mass spectrometry”, Rapid Commun. Mass Spectrom.5, 214–217 (1991). doi: 10.1002/rcm.1290050415
37.
DengY.PanH.SmithD.L., “Selective isotope labeling demonstrates that hydrogen exchange at individual peptide amide linkages can be determined by collision-induced dissociation mass spectrometry”, J. Am. Chem. Soc.121, 1966–1967 (1999). doi: 10.1021/ja982814+
38.
AndereggR. J.WagnerD. S.StevensonC.L.BorchardtR.T., “The mass spectrometry of helical unfolding in peptides”, J. Am. Soc. Mass Spectrom.5, 425–433 (1994). doi: 10.1016/1044-0305(94)85058-5
39.
AkashiS.NaitoY.TakioK., “Observation of hydrogen-deuterium exchange of ubiquitin by direct analysis of electrospray capillary-skimmer dissociation with Fourier transform ion cyclotron resonance mass spectrometry”, Anal. Chem.71, 4974–4980 (1999). doi: 10.1021/ac990444h
40.
BuijsJ.HakanssonK.HagmanC.HakanssonP.OscarssonS., “A new method for the accurate determination of the isotopic state of single amide hydrogens within peptides using Fourier transform ion cyclotron resonance mass spectrometry”, Rapid Commun. Mass Spectrom.14, 1751–1756 (2000). doi: 10.1002/1097-0231(20001015)14:19<1751::AID-RCM89>3.0.CO;2-T
41.
CaiX.DassC., “Structural characterization of methionine and leucine enkephalins by hydrogen/deuterium exchange and electrospray ionization tandem mass spectrometry”, Rapid Commun. Mass Spectrom.19, 1–8 (2005). doi: 10.1002/rcm.1739
42.
ChowdhuryS.K.KattaV.ChaitB.T., “Probing conformational changes in proteins by mass spectrometry”, J. Am. Chem. Soc.112, 9012–9013 (1990). doi: 10.1021/ja00180a074
43.
KonermannL., “A minimalist model for exploring conformational effects on the electrospray charge state distribution of proteins”, J. Phys. Chem. B111, 6534–6543 (2007). doi: 10.1021/jp070720t
44.
RoccatanoD.ColomboG.FioroniM.MarkA.E., “Mechanism by which 2,2,2-trifluoroethanol/water mixtures stabilize secondary-structure formation in peptides: A molecular dynamics study”, Proc. Natl. Acad. Sci. USA99, 12179–12184 (2002). doi: 10.1073/pnas.182199699
45.
SmithD.L.DengY.ZhangZ., “Probing the non-covalent structure of proteins by amide hydrogen exchange and mass spectrometry”, J. Mass Spectrom.32, 135–146 (1997). doi: 10.1002/(SICI)1096-9888(199702)32:2<135::AID-JMS486>3.0.CO;2-M
LinH.DassC., “Conformational changes in β-endorphin as studied by electrospray ionization mass spectrometry”, Rapid Commun. Mass Spectrom.15, 2341–2346 (2001). doi: 10.1002/rcm.513
48.
KimM.-Y.MaierC.S.ReedD.J.DeinzerM.L., “Site-specific amide hydrogen/deuterium exchange in E. coli thioredoxins measured by electrospray ionization mass spectrometry”, J. Am. Chem. Soc.123, 9860–9866 (2001). doi: 10.1021/ja010901n
49.
JaravineV.A.AlexandrescuA.T.GrzesiekS., “Observation of the closing of individual hydrogen bonds during TFE-induced helix formation in a peptide”Protein Sci.10, 943–950 (2001). doi: 10.1110/ps.48501
