Effects of structural differences on the NMR chemical shifts in isostructural dipeptides

Journal of Physical Chemistry A

Volumn 118, Issue 14, 2014, Pages 2618-2628

  Altheimer, Benjamin D ^a   Mehta, Manish A ^a  

^a OBERLIN COLLEGE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

AMIDES; AMINO ACIDS; CALCULATIONS; CRYSTAL STRUCTURE; DIGITAL STORAGE; HYDROGEN BONDS; NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY; PEPTIDES; QUANTUM CHEMISTRY; SOLID STATE PHYSICS; TENSORS;

AB INITIO QUANTUM CHEMICAL CALCULATIONS; GOOD CORRELATIONS; HYDROGEN-BONDING PATTERNS; ISOTROPIC CHEMICAL SHIFTS; NMR CHEMICAL SHIFTS; RESONANCE ASSIGNMENTS; STRUCTURAL DIFFERENCES; STRUCTURAL PARAMETER;

CHEMICAL SHIFT;

CARBON; DIPEPTIDE; NITROGEN;

ARTICLE; CHEMISTRY; NUCLEAR MAGNETIC RESONANCE; PROTEIN CONFORMATION;

CARBON ISOTOPES; DIPEPTIDES; NITROGEN ISOTOPES; NUCLEAR MAGNETIC RESONANCE, BIOMOLECULAR; PROTEIN CONFORMATION;

EID: 84898480067     PISSN: 10895639     EISSN: 15205215     Source Type: Journal    
DOI: 10.1021/jp411220y     Document Type: Article

References (70)

1. Cavalli, A.; Salvatella, X.; Dobson, C. M.; Vendruscolo, M. Protein Structure Determination from NMR Chemical Shifts Proc. Natl. Acad. Sci. U.S.A. 2007, 104, 9615-9620 (Pubitemid 47175315)
2. Shen, Y.; Lange, O.; Delaglio, F.; Rossi, P.; Aramini, J. M.; Liu, G.; Eletsky, A.; Wu, Y.; Singarapu, K. K.; Lemak, A. Consistent Blind Protein Structure Generation from NMR Chemical Shift Data Proc. Natl. Acad. Sci. U.S.A. 2008, 105, 4685-4690 (Pubitemid 351753807)
3. Saitô, H.; Ando, I.; Ramamoorthy, A. Chemical Shift Tensor-The Heart of NMR: Insights into Biological Aspects of Proteins Prog. Nucl. Magn. Reson. Spectrosc. 2010, 57, 181-228
4. 13C(Alpha) Chemical Shift Calculations for Protein NMR Structure Determination, Refinement, and Validation Proc. Natl. Acad. Sci. U.S.A. 2008, 105, 14389-14394
5. Havlin, R. H.; Le, H.; Laws, D. D.; de Dios, A. C.; Oldfield, E. An Ab Initio Quantum Chemical Investigation of Carbon-13 NMR Shielding Tensors in Glycine, Alanine, Valine, Isoleucine, Serine, and Threonine: Comparisons between Helical and Sheet Tensors, and the Effects of ?1 on Shielding J. Am. Chem. Soc. 1997, 119, 11951-11958 (Pubitemid 28012761)
6. Heller, J.; Laws, D. D.; Tomaselli, M.; King, D. S.; Wemmer, D. E.; Pines, A.; Havlin, R. H.; Oldfield, E. Determination of Dihedral Angles in Peptides through Experimental and Theoretical Studies of α-Carbon Chemical Shielding Tensors J. Am. Chem. Soc. 1997, 119, 7827-7831 (Pubitemid 27376398)
7. 13Cα Chemical Shift Tensors J. Am. Chem. Soc. 2009, 131, 985-992
8. Zhang, H.; Neal, S.; Wishart, D. S. RefDB: A Database of Uniformly Referenced Protein Chemical Shifts J. Biomol. NMR 2003, 25, 173-195 (Pubitemid 36410583)
9. Wang, Y.; Jardetzky, O. Investigation of the Neighboring Residue Effects on Protein Chemical Shifts J. Am. Chem. Soc. 2002, 124, 14075-14084 (Pubitemid 35386860)
10. 13Cα Chemical Shift Anisotropies for the Identification of Protein Secondary Structure J. Am. Chem. Soc. 2000, 122, 3762-3770 (Pubitemid 30233448)
11. 15N Dipolar Coupling Interactions in a Peptide Bond of Uniaxially Oriented and Polycrystalline Samples by One-Dimensional Dipolar Chemical Shift Solid-State NMR Spectroscopy J. Am. Chem. Soc. 1998, 120, 8868-8874 (Pubitemid 28442926)
12. 13Cα Chemical Shift Anisotropy in Proteins Correlate with Secondary Structure J. Am. Chem. Soc. 1997, 119, 9576-9577 (Pubitemid 27460551)
13. Bhate, M. P.; Woodard, J. C.; Mehta, M. A. Solvation and Hydrogen Bonding in Alanine- and Glycine-Containing Dipeptides Probed Using Solution- and Solid-State NMR Spectroscopy J. Am. Chem. Soc. 2009, 131, 9579-9589
14. Gu, Z.; Zambrano, R.; McDermott, A. Hydrogen Bonding of Carboxyl Groups in Solid-State Amino Acids and Peptides: Comparison of Carbon Chemical Shielding, Infrared Frequencies, and Structures J. Am. Chem. Soc. 1994, 116, 6368-6372
15. Asakawa, N.; Kuroki, S.; Kurosu, H.; Ando, I.; Shoji, A.; Ozaki, T. Hydrogen-Bonding Effect on Carbon-13 NMR Chemical Shifts of l -Alanine Residue Carbonyl Carbons of Peptides in the Solid State J. Am. Chem. Soc. 1992, 114, 3261-3265
16. Ando, S.; Ando, I.; Shoji, A.; Ozaki, T. Intermolecular Hydrogen-Bonding Effect on Carbon-13 NMR Chemical Shifts of Glycine Residue Carbonyl Carbons of Peptides in the Solid State J. Am. Chem. Soc. 1988, 110, 3380-3386
17. Oas, T. G.; Hartzell, C. J.; McMahon, T. J.; Drobny, G. P.; Dahlquist, F. W the Carbonyl Carbon-13 Chemical Shift Tensors of Five Peptides Determined from Nitrogen-15 Dipole-Coupled Chemical Shift Powder Patterns J. Am. Chem. Soc. 1987, 109, 5956-5962
18. 15N Chemical Shift Tensor Vary in Peptides? J. Phys. Chem. B 2004, 108, 16577-16585
19. α Chemical Shift Anisotropy Tensors in Peptides J. Am. Chem. Soc. 2004, 126, 8529-8534 (Pubitemid 38917976)
20. 13Cα Of Alanine, Valine, and Leucine Residues in Solid Peptides and in Proteins in Solution J. Am. Chem. Soc. 2001, 123, 10362-10369 (Pubitemid 32979786)
21. Harris, R. K. NMR Crystallography: The Use of Chemical Shifts Solid State Sci. 2004, 6, 1025-1037
22. Goward, G. R.; Sebastiani, D.; Schnell, I.; Spiess, H. W.; Kim, H.-D.; Ishida, H. Benzoxazine Oligomers: Evidence for a Helical Structure from Solid-State NMR Spectroscopy and DFT-Based Dynamics and Chemical Shift Calculations J. Am. Chem. Soc. 2003, 125, 5792-5800 (Pubitemid 36592905)
23. Petkova, A. T.; Ishii, Y.; Balbach, J. J.; Antzutkin, O. N.; Leapman, R. D.; Delaglio, F.; Tycko, R. A Structural Model for Alzheimer?s Beta-Amyloid Fibrils Based on Experimental Constraints From Solid State NMR Proc. Natl. Acad. Sci. U.S.A. 2002, 99, 16742-16747 (Pubitemid 36034043)
24. Harris, R. K.; Ghi, P. Y.; Hammond, R. B.; Ma, C.-Y.; Roberts, K. J. Refinement of Hydrogen Atomic Position in a Hydrogen Bond Using a Combination of Solid-State NMR and Computation Chem. Commun. 2003, 2834-2835 (Pubitemid 37467918)
25. 13C High-Resolution Solid-State NMR Study of the Polymorphism of the L-Enantiomer of N-Benzoylphenylalanine J. Phys. Chem. B 2008, 112, 1586-1593 (Pubitemid 351316358)
26. Görbitz, C. H. Microporous Organic Materials from Hydrophobic Dipeptides Chem.-Eur. J. 2007, 13, 1022-1031 (Pubitemid 46180846)
27. Soldatov, D. V.; Moudrakovski, I. L.; Ripmeester, J. A. Dipeptides as Microporous Materials Angew. Chem., Int. Ed. 2004, 43, 6308-6311 (Pubitemid 40029458)
28. Afonso, R.; Mendes, A.; Gales, L. Peptide-Based Solids: Porosity and Zeolitic Behavior J. Mater. Chem. 2012, 22, 1709-1723
29. Görbitz, C. H. Nanotubes from Hydrophobic Dipeptides: Pore Size Regulation through Side Chain Substitution New J. Chem. 2003, 27, 1789-1793 (Pubitemid 38112945)
30. 129Xe NMR Spectroscopy J. Am. Chem. Soc. 2006, 128, 6737-6744
31. Allen, F. H the Cambridge Structural Database: A Quarter of a Million Crystal Structures and Rising Acta Crystallogr., Sect. B 2002, 58, 380-388 (Pubitemid 135702674)
32. Bräuniger, T.; Wormald, P.; Hodgkinson, P. Improved Proton Decoupling in NMR Spectroscopy of Crystalline Solids Using the SPINAL-64 Sequence. In Current Developments in Solid State NMR Spectroscopy; Müller, H.-J.; Madhu, P. K., Eds.; Springer: Vienna, Austria, 2003; pp 69-74.
33. Morcombe, C. R.; Zilm, K. W. Chemical Shift Referencing in MAS Solid State NMR J. Magn. Reson. 2003, 162, 479-486
34. 15N Nuclei Bull. Chem. Soc. Jpn. 1991, 64, 688-690
35. Herzfeld, J.; Berger, A. E. Sideband Intensities in NMR Spectra of Samples Spinning at the Magic Angle J. Chem. Phys. 1980, 73, 6021-6030
36. Eichle, K.; Wasylishen, R. HBA; Universität Tübingen: Tübingen, Germany, 2005.
37. Clark, S. J.; Segall, M. D.; Pickard, C. J.; Hasnip, P. J.; Probert, M. I. J.; Refson, K.; Payne, M. C. First Principles Methods Using CASTEP. Z. Kristallogr. 2005, 220.
38. Yates, J.; Pickard, C.; Mauri, F. Calculation of NMR Chemical Shifts for Extended Systems Using Ultrasoft Pseudopotentials Phys. Rev. B 2007, 76, 024401-1-024401-11
39. Pickard, C.; Mauri, F. All-Electron Magnetic Response with Pseudopotentials: NMR Chemical Shifts Phys. Rev. B 2001, 63, 245101-1-245101-13
40. Vasconcelos, F.; Cristol, S.; Paul, J.-F.; Montagne, L.; Mauri, F.; Delevoye, L. First-Principles Calculations of NMR Parameters for Phosphate Materials Magn. Reson. Chem. 2010, 48, S142-S150
41. Charpentier, T the PAW/GIPAW Approach for Computing NMR Parameters: A New Dimension Added to NMR Study of Solids Solid State Nucl. Magn. Reson. 2011, 40, 1-20
42. 13C SQ Refocused Inept 2D Solid-State NMR Spectra and First Principles GIPAW Calculations Phys. Chem. Chem. Phys. 2010, 12, 6970-6983
43. Harris, R. K.; Hodgkinson, P.; Pickard, C. J.; Yates, J. R.; Zorin, V. Chemical Shift Computations on a Crystallographic Basis: Some Reflections and Comments Magn. Reson. Chem. 2007, 45, S174-S186
44. Gervais, C.; Dupree, R.; Pike, K. J.; Bonhomme, C.; Profeta, M.; Pickard, C. J.; Mauri, F. Combined First-Principles Computational and Experimental Multinuclear Solid-State NMR Investigation of Amino Acids J. Phys. Chem. A 2005, 109, 6960-6969 (Pubitemid 41173765)
45. Gervais, C.; Profeta, M.; Lafond, V.; Bonhomme, C.; Azaïs, T.; Mutin, H.; Pickard, C. J.; Mauri, F.; Babonneau, F. Combined Ab Initio Computational and Experimental Multinuclear Solid-State Magnetic Resonance Study of Phenylphosphonic Acid Magn. Reson. Chem. 2004, 42, 445-452 (Pubitemid 40012918)
46. Markley, J. L.; Bax, A.; Arata, Y.; Hilbers, C. W.; Kaptein, R.; Sykes, B. D.; Wright, P. E.; Wüthrich, K. Recommendations for the Presentation of NMR Structures of Proteins and Nucleic Acids J. Mol. Biol. 1998, 280, 933-952 (Pubitemid 28345026)
47. Görbitz, C. H. An Exceptionally Stable Peptide Nanotube System with Flexible Pores Acta Crystallogr., Sect. B 2002, 58, 849-854 (Pubitemid 135701991)
48. Görbitz, C. H.; Gundersen, E. l -Valyl- l -Alanine Acta Crystallogr., Sect. C 1996, 52, 1764-1767
49. Beger, R. D.; Bolton, P. H. Protein Phi and Psi Dihedral Restraints Determined from Multidimensional Hypersurface Correlations of Backbone Chemical Shifts and Their Use in the Determination of Protein Tertiary Structures J. Biomol. NMR 1997, 10, 129-142 (Pubitemid 127504659)
50. de Dios, A. C.; Pearson, J. G.; Oldfield, E. Secondary and Tertiary Structural Effects on Protein NMR Chemical Shifts: An Ab Initio Approach Science 1993, 260, 1491-1496 (Pubitemid 23273262)
51. Chekmenev, E. Y.; Xu, R. Z.; Mashuta, M. S.; Wittebort, R. J. Glycyl Cα Chemical Shielding in Tripeptides: Measurement by Solid-State NMR and Correlation with X-ray Structure and Theory J. Am. Chem. Soc. 2002, 124, 11894-11899
52. de Dios, A. C.; Pearson, J. G.; Oldfield, E. Chemical Shifts in Proteins: An Ab Initio Study of Carbon-13 Nuclear Magnetic Resonance Chemical Shielding in Glycine, Alanine, and Valine Residues J. Am. Chem. Soc. 1993, 115, 9768-9773
53. Gilli, G.; Gilli, P the Nature of the Hydrogen Bond: Outline of a Comprehensive Hydrogen Bond Theory; Oxford University Press: Oxford, 2009; Vol. 23.
54. 13C NMR Chemical Shift Anisotropy Tensors of Polypeptides J. Am. Chem. Soc. 2001, 123, 6118-6126 (Pubitemid 32888481)
55. 13C NMR Chemical Shifts of Amino Acid Residue Carbonyl Carbons of Some Peptides in the Crystalline State J. Mol. Struct. 1995, 350, 233-240
56. de Dios, A. C.; Oldfield, E. Chemical Shifts of Carbonyl Carbons in Peptides and Proteins J. Am. Chem. Soc. 1994, 116, 11485-11488 (Pubitemid 127657955)
57. 13C NMR Chemical Shift Tensor of Amino Acid Residue Carbonyl Carbons of Peptides and Polypeptides in the Crystalline State. Part I J. Mol. Struct. 1996, 384, 17-23 (Pubitemid 27012594)
58. de Dios, A. C.; Laws, D. D.; Oldfield, E. Predicting Carbon-13 Nuclear Magnetic Resonance Chemical Shielding Tensors in Zwitterionic l -Threonine and l -Tyrosine via Quantum Chemistry J. Am. Chem. Soc. 1994, 116, 7784-7786 (Pubitemid 24291820)
59. Gu, Z.; McDermott, A. Chemical Shielding Anisotropy of Protonated and Deprotonated Carboxylates in Amino Acids J. Am. Chem. Soc. 1993, 115, 4282-4285
60. 15N Chemical Shielding in Glycyl Tripeptides: Measurement by Solid-State NMR and Correlation with X-ray Structure J. Am. Chem. Soc. 2004, 126, 379-384 (Pubitemid 38090378)
61. 15N Chemical Shifts in Dipeptides: Applications to Protein NMR Spectroscopy J. Phys. Chem. 1996, 100, 16423-16428 (Pubitemid 126799393)
62. Wylie, B. J.; Sperling, L. J.; Nieuwkoop, A. J.; Franks, W. T.; Oldfield, E.; Rienstra, C. M. Ultrahigh Resolution Protein Structures Using NMR Chemical Shift Tensors Proc. Natl. Acad. Sci. U.S.A. 2011, 108, 16974-16979
63. 15N Shielding Tensors J. Am. Chem. Soc. 2005, 127, 9030-9035 (Pubitemid 40897595)
64. 15N Solid-State NMR Provides a Sensitive Probe of Oxidized Flavin Reactive Sites J. Am. Chem. Soc. 2006, 128, 15200-15208 (Pubitemid 44868075)
65. 15N Chemical Shift Tensors in Nucleic Acid Bases J. Am. Chem. Soc. 1998, 120, 9863-9869 (Pubitemid 28462492)
66. Ramsey, N. F. Magnetic Shielding of Nuclei in Molecules Phys. Rev. 1950, 78, 699-703
67. 13C NMR, Crystallographic, and Quantum Chemical Investigation of Chemical Shifts and Hydrogen Bonding in Histidine Dipeptides J. Am. Chem. Soc. 2005, 127, 12544-12554 (Pubitemid 41292173)
68. 15N Chemical Shift Spectroscopy J. Chem. Phys. 1987, 87, 4324
69. 2O J. Magn. Reson. 1983, 55, 266-273
70. Görbitz, C. H. Nanotube Formation by Hydrophobic Dipeptides Chem.-Eur. J. 2001, 7, 5153-5159 (Pubitemid 34555642)