Structure of Sodiated Octa-Glycine: IRMPD Spectroscopy and Molecular Modeling

Journal of the American Society for Mass Spectrometry

Volumn 21, Issue 5, 2010, Pages 728-738

  Semrouni, David ^a   Balaj, O Petru ^a,c   Calvo, Florent ^b   Correia, Catarina F ^a,d   Clavagura, Carine ^a   Ohanessian, Gilles ^a  

^a LABORATOIRE HÉTÉROÉLÉMENTS ET COORDINATION   (France)

^b UNIVERSITÉ LYON 1   (France)

^c UNIVERSITY OF KIEL   (Germany)

^d UNIVERSITÉ D EVRY VAL D ESSONNE   (France)

Author keywords

[No Author keywords available]

Indexed keywords

C-TERMINUS; CHARGE SOLVATION; CLOSE-IN; HYDROGEN BONDINGS; INFRARED MULTIPLE PHOTON DISSOCIATIONS; IRMPD SPECTROSCOPY; LOW ENERGY STRUCTURES; POLARIZABLE FORCE FIELD; QUANTUM CHEMICAL; ROOM TEMPERATURE; SALT BRIDGES; SPECTRAL RANGE; STABLE STRUCTURES; STRETCHING REGION;

HYDROGEN BONDS; MOLECULAR DYNAMICS; PEPTIDES; QUANTUM CHEMISTRY;

INFRARED SPECTROSCOPY;

GLYCINE DERIVATIVE; HYDROGEN; NITROGEN; SODIUM ION;

ACIDITY; ARTICLE; CARBOXY TERMINAL SEQUENCE; CHEMICAL STRUCTURE; CONTROLLED STUDY; ENERGY TRANSFER; HYDROGEN BOND; INFRARED SPECTROSCOPY; MOLECULAR DYNAMICS; MOLECULAR MODEL; PROTON TRANSPORT; QUANTUM CHEMISTRY; ROOM TEMPERATURE; SOLVATION;

GLYCINE; MOLECULAR DYNAMICS SIMULATION; OLIGOPEPTIDES; PEPTIDES; SODIUM COMPOUNDS; SPECTROPHOTOMETRY, INFRARED;

EID: 77951207219     PISSN: 10440305     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.jasms.2010.01.029     Document Type: Article

References (44)

1. The Clinical Biology of Sodium: The Physiology and Pathophysiology of Sodium in Mammals 1995, 16. Pergamon, Oxford, UK. A.R. Michell (Ed.).
2. Skou J.C., Norby J.G., Maunsbach A.B., Esmann M. Progress in Clinical and Biological Research 1987, Vol. CCLXVIIIA:401-632. Alan R. Liss, Inc, New York.
3. Aidley D.J., Stanfield P.R. Ion Channels: Molecules in Action 1994, 1-58. Cambridge University Press, Cambridge.
4. Teesch L.M., Orlando R.C., Adams J. Location of the Alkali Metal Ion in Gas-Phase Peptide Complexes. J. Am. Chem. Soc. 1991, 113. 36682675.
5. Lin T., Payne A.H., Glish G.L. Dissociation Pathways of Alkali-Cationized Peptides: Opportunities for C-Terminal Peptide Sequencing. J. Am. Soc. Mass Spectrom. 2001, 12:497-504.
6. Feng W.Y., Gronert S., Fletcher K.A., Warres A., Lebrilla C.B. The Mechanism of C-Terminal Fragmentations in Alkali Metal Ion Complexes of Peptides. Int. J. Mass Spectrom. 2003, 222:117-134.
7. Bulleigh K., Howard A., Do T., Wu Q., Anbalagan V., van Stipdonk M. Investigation of Intramolecular Proton Migration in a Series of Model, Metal-Cationized Tripeptides Using In Situ Generation of an Isotope Label. Rapid Commun. Mass Spectrom. 2006, 20:227-232.
8. Lee S.W., Kim H.S., Beauchamp J.L. Salt Bridge Chemistry Applied to Gas-Phase Peptide Sequencing: Selective Fragmentation of Sodiated Peptide Ions Adjacent to Aspartic Acid Residues. J. Am. Chem. Soc. 1998, 120:3188-3195.
9. Wyttenbach T., Bushnell J.E., Bowers M.T. Salt Bridge Structures in the Absence of Solvent?. The Case for the Oligoglycines. J. Am. Chem. Soc. 1998, 120:5098-5103.
10. Kohtani M., Jarrold M.F., Wee S., O'Hair R.A.J. Metal-Ion Interactions with Polyalanine Peptides. J. Phys. Chem. B 2004, 108:6093-6097.
11. 3: Exchange Kinetics Do Not Reflect Parent Ion Structures. J. Am. Chem. Soc. 2004, 126:6485-6490.
12. Kish M.M., Wesdemiotis C., Ohanessian G. The Sodium Ion Affinity of Glycylglycine. J. Phys. Chem. B 2004, 108:3086-3091.
13. Wang P., Kapota C., Ohanessian G., Wesdemiotis C. The Sodium Ion Affinities of Simple Di-, Tri-, and Tetrapeptides. J. Am. Soc. Mass Spectrom. 2007, 18:541-552.
14. Ye S.J., Armentrout P.B. Absolute Thermodynamic Measurements of Alkali Metal Cation Interactions with a Simple Dipeptide and Tripeptide. J. Phys. Chem. A 2008, 112:3587-3596.
15. +) in the Gas Phase. Int. J. Mass Spectrom. 2008, 269:196-209.
16. Semrouni D., Ohanessian G., Clavagura C. Structural, Energetic, and Dynamical Properties of Sodiated Oligoglycines: Relevance of a Polarizable Force Field. Phys. Chem. Chem. Phys. 2010, DOI: 10.1039/b924317h.
17. Ren P.Y., Ponder J.W. Consistent Treatment of Inter- and Intramolecular Polarization in Molecular Mechanic Calculations. J. Comput. Chem. 2002, 23:1497-1506.
18. Grossfield A., Ren P.Y., Ponder J.W. Ion Solvation Thermodynamics from Simulation with a Polarizable Force Field. J. Am. Chem. Soc. 2003, 125:15671-15682.
19. Voelz V.A., Shell M.S., Dill K.A. Predicting Peptide Structures in Native Proteins from Physical Simulations of Fragments. PloS Comp. Biol. 2009, 5(2):e1000281.
20. Buchete N.V., Hummer G. Protein Folding Kinetics from Replica Exchange Molecular Dynamics. Phys. Rev. E 2008, 77(3):030902.
21. Weinstock D.S., Narayanan C., Felts A.K., Andrec M., Levy R.M., Wu K.P., Baum J. Distinguishing Between Structural Ensembles of the GB1 Peptides : REMD Simulations and NMR Experiments. J. Am. Chem. Soc. 2007, 129:4858-4859.
22. Sugita Y., Okamoto Y. Replica-Exchange Molecular Dynamics Method for Protein Folding. Chem. Phys. Lett. 1999, 314:141-151.
23. Ponder J.W. TINKER, Software Tools for Molecular Design, Version 4.2 2004.
24. Penev E.S., Lampoudi S., Shea J.-E. TiReX: Replica-Exchange Molecular Dynamics Using TINKER. Comp. Phys. Commun. 2009, 180:2013-2019.
25. Grimme S. Accurate Description of van der Waals Complexes by Density Functional Theory Including Empirical Corrections. J. Comput. Chem. 2004, 25:1463-1473.
26. Grimme S. Semiempirical GGA-Type Density Functional Constructed with a Long-Range Dispersion Correction. J. Comput. Chem. 2006, 27:1787-1799.
27. Bouteiller Y., Poully J.-C., Desfranois C., Grgoire G. Evaluation of MP2, DFT, and DFT-D Methods for the Prediction of Infrared Spectra of Peptides. J. Phys. Chem. A 2009, 113:6301-6307.
28. Ahlrichs R., Br M., Hser M., Horn H., Klmel C. Electronic Structure Calculations on Workstation Computers: The Program System Turbomole. Chem. Phys. Lett. 1989, 162:165-169. For the current version, see http://www.turbomole.com.
29. MacAleese L., Simon A., McMahon T.B., Ortega J.M., Scuderi D., Lemaire J., Maitre P. Mid-IR Spectroscopy of Protonated Leucine Methyl Ester Performed with an FTICR or a Paul Type Ion-Trap. Int. J. Mass Spectrom. 2006, 249:14-20.
30. MacAleese L., Matre P. Infrared Spectroscopy of Organometallic Ions in the Gas Phase: From Model to Real World Complexes. Mass Spectrom. Rev. 2007, 26:583-605.
31. Bakker J.M., Besson T., Lemaire J., Scuderi D., Matre P. Gas-Phase Structure of a π-Allyl-Palladium Complex: Efficient Infrared Spectroscopy in a 7 T Fourier Transform Mass Spectrometer. J. Phys. Chem. A 2007, 111:13415-13424.
32. Bakker J.M., Sinha R.K., Besson T., Brugnara M., Tosi P., Salpin J.Y., Maitre P. Tautomerism of Uracil Probed Via Infrared Spectroscopy of Singly Hydrated Protonated Uracil. J. Phys. Chem. A 2008, 112:12393-12400.
33. Stearns J.A., Mercier S., Seaiby C., Guidi M., Boyarkin O., Rizzo T.R. Conformation-Specific Spectroscopy and Photodissociation of Cold, Protonated Tyrosine and Phenylalanine. J. Am. Chem. Soc. 2007, 129:11814-11820.
34. Bush M.F., O'Brien J.T., Prell J.S., Saykally R.J., Williams E.R. Infrared Spectroscopy of Cationized Arginine in the Gas Phase: Direct Evidence for the Transition from Nonzwitterionic to Zwitterionic Structure. J. Am. Chem. Soc. 2007, 129:1612-1622.
35. Vaden T.D., de Boer T.S.J.A., Simons J.P., Snoek L.C., Suhai S., Paizs B. Vibrational Spectroscopy and Conformational Structure of Protonated Polyalanine Peptides Isolated in the Gas Phase. J. Phys. Chem. A 2008, 112:4608-4616.
36. Stearns J.A., Seaiby C., Boyarkin O., Rizzo T.R. Spectroscopy and Conformational Preferences of Gas-Phase Helices. Phys. Chem., Chem. Phys. 2009, 11:125-132.
37. Oomens J., Steill J.D., Redlich B. Gas-Phase IR Spectroscopy of Deprotonated Amino Acids. J. Am. Chem. Soc. 2009, 131:4310-4319.
38. Prell J.S., O'Brien J.T., Steill J.D., Oomens J., Williams E.R. Structures of Protonated Dipeptides: The Role of Arginine in Stabilizing Salt Bridges. J. Am. Chem. Soc. 2009, 131:11442-11449.
39. Prell J.S., Demireva M., Oomens J., Williams E.R. Role of Sequence in Salt-Bridge Formation for Alkali Metal Cationized GlyArg and ArgGly Investigated with IRMPD Spectroscopy and Theory. J. Am. Chem. Soc. 2009, 131:1232-1242.
40. Polfer N.C., Oomens J. Vibrational Spectroscopy of Bare and Solvated Ionic Complexes of Biological Relevance. Mass Spectrom. Rev. 2009, 28:468-494.
41. Polfer N.C., Paizs B., Snoek L.C., Compagnon I., Suhai S., Meijer G., von Helden G., Oomens J. Infrared Fingerprint Spectroscopy and Theoretical Studies of Potassium Ion Tagged Amino Acids and Peptides in the Gas Phase. J. Am. Chem. Soc. 2005, 127:8571-8579.
42. Polfer N.C., Oomens J., Dunbar R.C. Alkali Metal Complexes of the Dipeptides PheAla and AlaPhe: IRMPD Spectroscopy. Chem. Phys. Chem. 2008, 9:579-589.
43. Dunbar R.C., Steill J.D., Polfer N.C., Oomens J. Peptide Length, Steric Effects, and Ion Solvation Govern Zwitterion Stabilization in Barium-Chelated Di- and Tripeptides Dunbar. J. Phys. Chem. B 2009, 113:10552-10554.
44. Cimas A., Vaden T.D., de Boer T.S.J.A., Snoek L.C., Gaigeot M.P. Vibrational Spectra of Small Protonated Peptides from Finite Temperature MD Simulations and IRMPD Spectroscopy. J. Chem. Theor. Comput. 2009, 5:1068-1078.