On the Hydration State of Amino Acids and Their Derivatives at Different Ionization States: A Comparative Multinuclear NMR and Crystallographic Investigation
2D, 13C, 14N, and 17O NMR and crystallographic data from the literature were critically evaluated in order to provide a coherent hydration model of amino acids and selected derivatives at different ionization states. 17O shielding variations, longitudinal relaxation times (T1) of 2D and 13C and line widths (Δν1/2) of 14N and 17O, may be interpreted with the hypothesis that the cationic form of amino acids is more hydrated by 1 to 3 molecules of water than the zwitterionic form. Similar behaviour was also observed for N-acetylated derivatives of amino acids. An exhaustive search in crystal structure databases demonstrates the importance of six-membered hydrogen-bonded conjugated rings of both oxygens of the α-carboxylate group with a molecule of water in the vicinity. This type of hydrogen bond mode is absent in the case of the carboxylic groups. Moreover, a considerable number of structures was identified with the propensity to form intramolecular hydrogen bond both in the carboxylic acid (NH？O=C) and in the carboxylate ( ？) ionization state. In the presence of bound molecules of water this interaction is significantly reduced in the case of the carboxylate group whereas it is statistically negligible in the carboxylic group. 1. Introduction Water plays a fundamental role in the conformation and activity of every biological macromolecule [1]. Peptide- and protein- hydration is the dominant factor in the stabilization of spatial molecular structure, in the process of protein folding by gating hydrophobic residues, and in the mechanisms of peptide and protein mediated reactions [1–4]. Water molecules, therefore, can be considered as an integral component of biomolecular systems with dynamic, functional, and structural roles [4–7]. Investigation of the structural and functional role of water molecules, bound to proteins and peptides, requires a sufficient understanding of the hydration process of their building blocks [1, 2]. The hydration of amino acids and their derivatives at a molecular level, therefore, is of great importance and has been extensively studied with X-ray crystallography [1, 3] and a variety of spectroscopic techniques including multinuclear magnetic resonance spectroscopy [2, 8–13], IR and Raman spectroscopy [14–16], ICR mass spectrometry [17], and laser ablation in combination with microwave spectroscopy [18]. We present here, for the first time in the international literature, a comparative investigation of literature 2D, 13C, 14N, and 17O NMR and crystallographic data in order to provide a coherent hydration model of amino acids and
References
[1]
G. A. Jeffrey and W. Saenger, Hydrogen Bonding in Biological Structures, Springer, New York, NY, USA, 1991.
[2]
I. P. Gerothanassis, “Multinuclear and multidimensional NMR methodology for studying individual water molecules bound to peptides and proteins in solution: principles and applications,” Progress in Nuclear Magnetic Resonance Spectroscopy, vol. 26, no. 3, pp. 171–237, 1994.
[3]
G. D. Rose and R. Wolfenden, “Hydrogen bonding, hydrophobicity, packing, and protein folding,” Annual Review of Biophysics and Biomolecular Structure, vol. 22, pp. 381–415, 1993.
[4]
Y. Levy and J. N. Onuchic, “Water mediation in protein folding and molecular recognition,” Annual Review of Biophysics and Biomolecular Structure, vol. 35, pp. 389–415, 2006.
[5]
Y. Levy, J. Jortner, and O. M. Becker, “Solvent effects on the energy landscapes and folding kinetics of polyalanine,” Proceedings of the National Academy of Sciences of the United States of America, vol. 98, no. 5, pp. 2188–2193, 2001.
[6]
J. C. Covalt, M. Roy, and P. A. Jennings, “Core and surface mutations affect folding kinetics, stability and cooperativity in IL-1β: does alteration in buried water play a role?” Journal of Molecular Biology, vol. 307, no. 2, pp. 657–669, 2001.
[7]
M. S. Cheung, A. E. García, and J. N. Onuchic, “Protein folding mediated by solvation: water expulsion and formation of the hydrophobic core occur after the structural collapse,” Proceedings of the National Academy of Sciences of the United States of America, vol. 99, no. 2, pp. 685–690, 2002.
[8]
Y. Van Haverbeke, R. N. Muller, and L. Vander Elst, “pH-induced motional and conformational changes of amino acids. A reexamination by deuterium longitudinal nuclear relaxation,” Journal of Physical Chemistry, vol. 88, no. 21, pp. 4978–4980, 1984.
[9]
A. Spisni, E. D. Gotsis, and D. Fiat, “17O？NMR investigation of the hydration of L-Alanine and L-Proline in water/Me2SO mixtures,” Biochemical and Biophysical Research Communications, vol. 135, no. 2, pp. 363–366, 1986.
[10]
J. Lauterwein, I. P. Gerothanassis, R. N. Hunston, and M. Schumacher, “17O？NMR relaxation times of the protein amino acids in aqueous solution. Estimation of the relative hydration numbers in the cationic, anionic, and zwitterionic forms,” Journal of Physical Chemistry, vol. 95, no. 9, pp. 3804–3811, 1991.
[11]
A. N. Troganis, C. Tsanaktsidis, and I. P. Gerothanassis, “14N？NMR relaxation times of several protein amino acids in aqueous solution—comparison with 17O？NMR data and estimation of the relative hydration numbers in the cationic and zwitterionic forms,” Journal of Magnetic Resonance, vol. 164, no. 2, pp. 294–303, 2003.
[12]
I. P. Gerothanassis, “Oxygen-17？NMR spectroscopy: basic principles and applications (part II),” Progress in Nuclear Magnetic Resonance Spectroscopy, vol. 57, no. 1, pp. 1–110, 2010.
[13]
I. P. Gerothanassis, “Oxygen-17？NMR spectroscopy: basic principles and applications (Part I),” Progress in Nuclear Magnetic Resonance Spectroscopy, vol. 56, no. 2, pp. 95–197, 2010.
[14]
J. L. Hollenberg and J. B. Ifft, “Hydration numbers by near-infrared spectrophotometry. 1. Amino acids,” Journal of Physical Chemistry, vol. 86, no. 11, pp. 1938–1941, 1982.
[15]
B. Hernández, F. Pflüger, M. Nsangou, and M. Ghomi, “Vibrational analysis of amino acids and short peptides in hydrated media. IV. amino acids with hydrophobic side chains: L-Alanine, L-Valine, and L-Isoleucine,” Journal of Physical Chemistry B, vol. 113, no. 10, pp. 3169–3178, 2009.
[16]
R. M. Balabin, “The first step in glycine solvation: the glycine-water complex,” Journal of Physical Chemistry B, vol. 114, no. 46, pp. 15075–15078, 2010.
[17]
M. J. Locke and R. T. McIver, “Effect of solvation on the acid/base properties of glycine,” Journal of the American Chemical Society, vol. 105, no. 13, pp. 4226–4232, 1983.
[18]
J. L. Alonso, E. J. Cocinero, A. Lesarri, M. E. Sanz, and J. C. López, “The glycine-water complex,” Angewandte Chemie—International Edition, vol. 45, no. 21, pp. 3471–3474, 2006.
[19]
D. Fiat, T. E. St Amour, M. I. Burgar, A. Steinschneider, B. Valentine, and D. Dhawan, “17O nuclear magnetic resonance and its biological applications,” The Bulletin of Magnetic Resonance, vol. 1, p. 18, 1980.
[20]
J. G. Pearson and E. Oldfield, “17O？NMR: applications in biochemistr,” in Encyclopedia of Nuclear Magnetic Resonance, D. M. Grant and R. K. Harris, Eds., pp. 3440–3443, John Wiley & Sons, 1995.
[21]
D. W. Boykin, 17O？NMR Spectroscopy in Organic Chemistry, CRC Press, Boston, Mass, USA, 1991.
[22]
S. Berger, S. Braun, and H. O. Kalinowski, NMR Spectroscopy of Non-Metallic Elements, John Wiley & Sons, Chichester, UK, 1997.
[23]
J. Lauterwein, I. P. Gerothanassis, and R. N. Hunston, “17O？NMR of enriched acetic-acid, glycine, glutamic-acid and aspartic-acid in aqueous-solution.1. Chemical-shift studies,” Helvetica Chimica Acta, vol. 65, no. 6, pp. 1764–1773, 1982.
[24]
J. Lauterwein, I. P. Gerothanassis, and R. N. Hunston, “17O？NMR of enriched acetic-acid, glycine, glutamic-acid and aspartic-acid in aqueous-solution.2. Relaxation studies,” Helvetica Chimica Acta, vol. 65, no. 6, pp. 1774–1784, 1982.
[25]
A. Steinschneider, M. I. Burgar, A. Buku, and D. Fiat, “Labeling of amino acids and peptides with isotopic oxygen as followed by 17O？NMR,” International Journal of Peptide and Protein Research, vol. 18, no. 3, pp. 324–333, 1981.
[26]
B. Valentine, T. S. Amour, R. Walter, and D. Fiat, “pH dependence of oxygen-17 chemical shifts and linewidths of l-alanine and glycine,” Journal of Magnetic Resonance, vol. 38, no. 3, pp. 413–418, 1980.
[27]
G. W. Kabalka and N. M. Goudgaon, “17O enrichment methods,” in 17O？NMR Spectroscopy in Organic Chemistry, D. W. Boykin, Ed., chapter 2, pp. 21–37, CRC Press, Boston, Mass, USA, 1991.
[28]
T. Karayannis, I. P. Gerothanassis, M. Sakarellos-Daitsiotis, C. Sakarellos, and M. Marraud, “17O- and 14N-nmr studies of leu-enkephalin and enkephalin-related fragments in aqueous solution,” Biopolymers, vol. 29, no. 2, pp. 423–439, 1990.
[29]
J. Reuben, “Hydrogen-bonding effects on oxygen-17 chemical shifts,” Journal of the American Chemical Society, vol. 91, no. 21, pp. 5725–5729, 1969.
[30]
J. Tritt Goc and D. Fiat, “Determination of dynamic parameters in amino-acids from 17O？NMR line-width measurements,” Magnetic Resonance in Chemistry, vol. 29, no. 2, pp. 156–163, 1991.
[31]
D. E. Woessner, “Nuclear magnetic dipole-dipole relaxation in molecules with internal motion,” The Journal of Chemical Physics, vol. 42, no. 6, pp. 1855–1859, 1965.
[32]
P. G. Takis, V. S. Melissas, and A. N. Troganis, private communication, 2011.
[33]
C. H. Gorbitz, “Hydrogen-bond distances and angles in the structures of amino-acids and peptides,” Acta Crystallogrica B, vol. 45, pp. 390–395, 1989.
[34]
E. Arunan, G. R. Desiraju, R. A. Klein et al., “Defining the hydrogen bond: an account (IUPAC Technical Report),” Pure and Applied Chemistry, vol. 83, no. 8, pp. 1619–1636, 2011.
[35]
C. B. Aaker？y and K. R. Seddon, “The hydrogen bond and crystal engineering,” Chemical Society Reviews, vol. 22, no. 6, pp. 397–407, 1993.
[36]
T. Steiner, “The hydrogen bond in the solid state,” Angewandte Chemie—International Edition, vol. 41, no. 1, pp. 49–76, 2002.
[37]
R. Taylor, O. Kennard, and W. Versichel, “Geometry of the hydrogen bond. 2. Three-center (“bifurcated”) and four-center ((“trifurcated”) bonds,” Journal of the American Chemical Society, vol. 106, no. 1, pp. 244–248, 1984.
[38]
L. Infantes and W. D. S. Motherwell, “Hydrogen bond competition between chemical groups: new methodology and the Cambridge Structural Database,” Zeitschrift fur Kristallographie, vol. 220, no. 4, pp. 333–339, 2005.
[39]
R. Taylor, O. Kennard, and W. Versichel, “The geometry of the hydrogen-bond .3. Hydrogen-bond distances and angles,” Acta Crystallographica B, vol. 40, pp. 280–288, 1984.
[40]
G. N. J. Port and A. Pullman, “Quantum-mechanical studies of environmental effects on biomolecules. III. Ab-initio model studies of hydration of peptides and proteins,” International Journal of Quantum Chemistry, vol. 8, supplement 1, pp. 21–32, 1974.
[41]
G. A. Jeffrey and H. Maluszynska, “The stereochemistry of the water molecules in the hydrates of small biological molecules,” Acta Crystallographica. Section B, vol. 46, part 4, pp. 546–549, 1990.
[42]
C. H. G？rbitz and M. C. Etter, “Hydrogen bonds to carboxylate groups. Syn/anti distributions and steric effects,” Journal of the American Chemical Society, vol. 114, no. 2, pp. 627–631, 1992.
[43]
T. F. Koetzle and M. S. Lehmann, “The hydrogen bond—recent developments,” in Theory and Experiments, P. Schuster, G. Zundel, and C. Sandorfy, Eds., chapter 2, pp. 457–469, North Holland, Amsterdam, The Netherlands, 1976.
[44]
S. Xu, J. M. Nilles, and K. H. Bowen, “Zwitterion formation in hydrated amino acid, dipole bound anions: how many water molecules are required?” The Journal of Chemical Physics, vol. 119, no. 20, pp. 10696–10701, 2003.
[45]
S. Tiwari, P. C. Mishra, and S. Suhai, “Solvent effect of aqueous media on properties of glycine: significance of specific and bulk solvent effects, and geometry optimization in aqueous media,” International Journal of Quantum Chemistry, vol. 108, no. 5, pp. 1004–1016, 2008.
[46]
S. M. Bachrach, “Microsolvation of glycine: a DFT study,” Journal of Physical Chemistry A, vol. 112, no. 16, pp. 3722–3730, 2008.
[47]
A. E. García and J. N. Onuchic, “Folding a protein in a computer: an atomic description of the folding/unfolding of protein A,” Proceedings of the National Academy of Sciences of the United States of America, vol. 100, no. 2, pp. 13898–13903, 2003.
[48]
A. C. De Dios, “Ab initio calculations of the NMR chemical shift,” Progress in Nuclear Magnetic Resonance Spectroscopy, vol. 29, no. 3-4, pp. 229–278, 1996.
[49]
R. A. Klein, B. Mennucci, and J. Tomasi, “Ab initio calculations of 17O？NMR-chemical shifts for water. The limits of PCM theory and the role of hydrogen-bond geometry and cooperativity,” Journal of Physical Chemistry A, vol. 108, no. 27, pp. 5851–5863, 2004.
[50]
A. Klamt, B. Mennucci, J. Tomasi et al., “On the performance of continuum solvation methods. A comment on “Universal Approaches to Solvation Modeling”,” Accounts of Chemical Research, vol. 42, no. 4, pp. 489–492, 2009.
[51]
V. G. Malkin, O. L. Malkina, G. Steinebrunner, and H. Huber, “Solvent effect on the NMR chemical shieldings in water calculated by a combination of molecular dynamics and density functional theory,” Chemistry, vol. 2, pp. 452–457, 1996.
[52]
G. Wu, “Solid-state 17O？NMR studies of organic and biological molecules,” Progress in Nuclear Magnetic Resonance Spectroscopy, vol. 52, no. 2-3, pp. 118–169, 2008.
