Secondary Structure Dependence and Hydration Effect of the Infrared Intensity of the Amide II Mode of Peptide Chains

Journal of Physical Chemistry B

Volumn 120, Issue 8, 2016, Pages 1624-1634

  Torii, Hajime ^a   Kawanaka, Megumi ^a  

^a SHIZUOKA UNIVERSITY   (Japan)

Author keywords

[No Author keywords available]

Indexed keywords

AMIDES; CHAINS; CONFORMATIONS; HYDROGEN BONDS; MOLECULES; PEPTIDES; POLARIZATION;

CO-OPERATIVE EFFECTS; GEOMETRICAL RELATIONS; HYDRATING WATER MOLECULES; INFRARED INTENSITY; INTERACTION PROPERTIES; POLARIZATION EFFECT; SECONDARY STRUCTURES; VIBRATIONAL MODES;

HYDRATION;

AMIDE; GLYCYL-GLYCYL-GLYCINE; OLIGOPEPTIDE; PEPTIDE; WATER;

CHEMISTRY; HYDROGEN BOND; INFRARED SPECTROPHOTOMETRY; MOLECULAR MODEL; PROCEDURES; PROTEIN SECONDARY STRUCTURE;

AMIDES; HYDROGEN BONDING; MODELS, MOLECULAR; OLIGOPEPTIDES; PEPTIDES; PROTEIN STRUCTURE, SECONDARY; SPECTROPHOTOMETRY, INFRARED; WATER;

EID: 84960157721     PISSN: 15206106     EISSN: 15205207     Source Type: Journal    
DOI: 10.1021/acs.jpcb.5b08258     Document Type: Article

References (61)

1. Miyazawa, T.; Shimanouchi, T.; Mizushima, S. Normal Vibrations of N-Methylacetamide J. Chem. Phys. 1958, 29, 611-616 10.1063/1.1744547
2. Miyazawa, T.; Blout, E. R. The Infrared Spectra of Polypeptides in Various Conformations: Amide I and II Bands J. Am. Chem. Soc. 1961, 83, 712-719 10.1021/ja01464a042
3. Krimm, S.; Bandekar, J. Vibrational Spectroscopy and Conformation of Peptides, Polypeptides, and Proteins Adv. Protein Chem. 1986, 38, 181-364 10.1016/S0065-3233(08)60528-8
4. Barth, A. Infrared Spectroscopy of Proteins Biochim. Biophys. Acta, Bioenerg. 2007, 1767, 1073-1101 10.1016/j.bbabio.2007.06.004
5. Kato, K.; Matsui, T.; Tanaka, S. Quantitative Estimation of α-Helix Coil Content in Bovine Serum Albumin by Fourier Transform-Infrared Spectroscopy Appl. Spectrosc. 1987, 41, 861-865 10.1366/0003702874448049
6. Byler, D. M.; Susi, H. Examination of the Secondary Structure of Proteins by Deconvolved FTIR Spectra Biopolymers 1986, 25, 469-487 10.1002/bip.360250307
7. Surewicz, W. K.; Mantsch, H. H.; Chapman, D. Determination of Protein Secondary Structure by Fourier Transform Infrared Spectroscopy: A Critical Assessment Biochemistry 1993, 32, 389-394 10.1021/bi00053a001
8. Schweitzer-Stenner, R. Visible and UV-Resonance Raman Spectroscopy of Model Peptides J. Raman Spectrosc. 2001, 32, 711-732 10.1002/jrs.757
9. Brauner, J. W.; Flach, C. R.; Mendelsohn, R. A Quantitative Reconstruction of the Amide I Contour in the IR Spectra of Globular Proteins: From Structure to Spectrum J. Am. Chem. Soc. 2005, 127, 100-109 10.1021/ja0400685
10. Krimm, S.; Abe, Y. Intermolecular Interaction Effects in the Amide I Vibrations of β Polypeptides Proc. Natl. Acad. Sci. U. S. A. 1972, 69, 2788-2792 10.1073/pnas.69.10.2788
11. Torii, H.; Tasumi, M. Model Calculations on the Amide-I Infrared Bands of Globular Proteins J. Chem. Phys. 1992, 96, 3379-3387 10.1063/1.461939
12. Torii, H.; Tasumi, M. Ab Initio Molecular Orbital Study of the Amide I Vibrational Interactions between the Peptide Groups in Di- and Tripeptides and Considerations on the Conformation of the Extended Helix J. Raman Spectrosc. 1998, 29, 81-86 10.1002/(SICI)1097-4555(199801)29:1<81::AID-JRS214>3.0.CO;2-H
13. Hamm, P.; Woutersen, S. Coupling of the Amide I Modes of the Glycine Dipeptide Bull. Chem. Soc. Jpn. 2002, 75, 985-988 10.1246/bcsj.75.985
14. Gorbunov, R. D.; Kosov, D. S.; Stock, G. Ab Initio-Based Exciton Model of Amide I Vibrations in Peptides: Definition, Conformational Dependence, and Transferability J. Chem. Phys. 2005, 122, 224904 10.1063/1.1898215
15. Ham, S.; Cho, M. Amide I Modes in the N-Methylacetamide Dimer and Glycine Dipeptide Analog: Diagonal Force Constants J. Chem. Phys. 2003, 118, 6915-6922 10.1063/1.1559681
16. Bouř, P.; Keiderling, T. A. Empirical Modeling of the Peptide Amide I Band IR Intensity in Water Solution J. Chem. Phys. 2003, 119, 11253-11262 10.1063/1.1622384
17. Watson, T. M.; Hirst, J. D. Influence of Electrostatic Environment on the Vibrational Frequencies of Proteins J. Phys. Chem. A 2003, 107, 6843-6849 10.1021/jp0344500
18. Hayashi, T.; Zhuang, W.; Mukamel, S. Electrostatic DFT Map for the Complete Vibrational Amide Band of NMA J. Phys. Chem. A 2005, 109, 9747-9759 10.1021/jp052324l
19. Jansen, T. l. C.; Knoester, J. A Transferable Electrostatic Map for Solvation Effects on Amide I Vibrations and its Application to Linear and Two-Dimensional Spectroscopy J. Chem. Phys. 2006, 124, 044502 10.1063/1.2148409
20. Wang, L.; Middleton, C. T.; Zanni, M. T.; Skinner, J. L. Development and Validation of Transferable Amide I Vibrational Frequency Maps for Peptides J. Phys. Chem. B 2011, 115, 3713-3724 10.1021/jp200745r
21. Torii, H. Amide I Vibrational Properties Affected by Hydrogen Bonding Out-of-Plane of the Peptide Group J. Phys. Chem. Lett. 2015, 6, 727-733 10.1021/acs.jpclett.5b00004
22. Asher, S. A.; Ianoul, A.; Mix, G.; Boyden, M. N.; Karnoup, A.; Diem, M.; Schweitzer-Stenner, R. Dihedral ψ Angle Dependence of the Amide III Vibration: A Uniquely Sensitive UV Resonance Raman Secondary Structural Probe J. Am. Chem. Soc. 2001, 123, 11775-11781 10.1021/ja0039738
23. Mikhonin, A. V.; Bykov, S. V.; Myshakina, N. S.; Asher, S. A. Peptide Secondary Structure Folding Reaction Coordinate: Correlation between UV Raman Amide III Frequency, Ψ Ramachandran Angle, and Hydrogen Bonding J. Phys. Chem. B 2006, 110, 1928-1943 10.1021/jp054593h
24. Anderle, G.; Mendelsohn, R. Thermal Denaturation of Globular Proteins. Fourier Transform-Infrared Studies of the Amide III Spectral Region Biophys. J. 1987, 52, 69-74 10.1016/S0006-3495(87)83189-2
25. Kaiden, K.; Matsui, T.; Tanaka, S. A Study of the Amide III Band by FT-IR Spectrometry of the Secondary Structure of Albumin, Myoglobin, and γ-Globulin Appl. Spectrosc. 1987, 41, 180-184 10.1366/000370287774986714
26. Cai, S.; Singh, B. R. A Distinct Utility of the Amide III Infrared Band for Secondary Structure Estimation of Aqueous Protein Solutions Using Partial Least Squares Methods Biochemistry 2004, 43, 2541-2549 10.1021/bi030149y
27. Hamm, P.; Lim, M.; DeGrado, W. F.; Hochstrasser, R. M. The Two-Dimensional IR Nonlinear Spectroscopy of a Cyclic Penta-Peptide in Relation to Its Three-Dimensional Structure Proc. Natl. Acad. Sci. U. S. A. 1999, 96, 2036-2041 10.1073/pnas.96.5.2036
28. 2 J. Phys. Chem. B 2001, 105, 6520-6535 10.1021/jp0100093
29. Rubtsov, I. V.; Wang, J.; Hochstrasser, R. M. Dual-Frequency 2D-IR Spectroscopy Heterodyned Photon Echo of the Peptide Bond Proc. Natl. Acad. Sci. U. S. A. 2003, 100, 5601-5606 10.1073/pnas.0931292100
30. Bloem, R.; Dijkstra, A. G.; Jansen, T. l. C.; Knoester, J. Simulation of Vibrational Energy Transfer in Two-Dimensional Infrared Spectroscopy of Amide I and Amide II Modes in Solution J. Chem. Phys. 2008, 129, 055101 10.1063/1.2961020
31. DeFlores, L. P.; Ganim, Z.; Nicodemus, R. A.; Tokmakoff, A. Amide I′-II′ 2D IR Spectroscopy Provides Enhanced Protein Secondary Structural Sensitivity J. Am. Chem. Soc. 2009, 131, 3385-3391 10.1021/ja8094922
32. 10-Helical Hydrogen Bond Revealed by Two-Dimensional Infrared Spectroscopy J. Am. Chem. Soc. 2009, 131, 2042-2043 10.1021/ja807572f
33. Maekawa, H.; Ballano, G.; Toniolo, C.; Ge, N.-H. Linear and Two-Dimensional Infrared Spectroscopic Study of the Amide I and II Modes in Fully Extended Peptide Chains J. Phys. Chem. B 2011, 115, 5168-5182 10.1021/jp105527n
34. 15N Isotope Dependence of the Amide-I/II 2D IR Cross Peaks for the Fully Extended Peptides J. Phys. Chem. C 2014, 118, 29448-29457 10.1021/jp5091679
35. Moran, A. M.; Park, S.-M.; Mukamel, S. Infrared Photon Echo Signatures of Hydrogen Bond Connectivity in the Cyclic Decapeptide Antamanide J. Chem. Phys. 2003, 118, 9971-9980 10.1063/1.1571527
36. Chung, H. S.; Khalil, M.; Tokmakoff, A. Nonlinear Infrared Spectroscopy of Protein Conformational Change during Thermal Unfolding J. Phys. Chem. B 2004, 108, 15332-15342 10.1021/jp0479926
37. Torii, H. Effects of Intermolecular Vibrational Coupling and Liquid Dynamics on the Polarized Raman and Two-Dimensional Infrared Spectral Profiles of Liquid N,N-Dimethylformamide Analyzed with a Time-Domain Computational Method J. Phys. Chem. A 2006, 110, 4822-4832 10.1021/jp060014c
38. Jansen, T. l. C.; Knoester, J. Nonadiabatic Effects in the Two-Dimensional Infrared Spectra of Peptides: Application to Alanine Dipeptide J. Phys. Chem. B 2006, 110, 22910-22916 10.1021/jp064795t
39. Ganim, Z.; Tokmakoff, A. Spectral Signatures of Heterogeneous Protein Ensembles Revealed by MD Simulations of 2DIR Spectra Biophys. J. 2006, 91, 2636-2646 10.1529/biophysj.106.088070
40. Torii, H. Mechanism of the Secondary Structure Dependence of the Infrared Intensity of the Amide II Mode of Peptide Chains J. Phys. Chem. Lett. 2012, 3, 112-116 10.1021/jz201540r
41. Torii, H. Intermolecular Charge Flux as the Origin of Infrared Intensity Enhancement upon Halogen-Bond Formation of the Peptide Group J. Chem. Phys. 2010, 133, 034504 10.1063/1.3456183
42. Torii, H. Intra- and Intermolecular Charge Fluxes Induced by the OH Stretching Mode of Water and Their Effects on the Infrared Intensities and Intermolecular Vibrational Coupling J. Phys. Chem. B 2010, 114, 13403-13409 10.1021/jp106952q
43. Torii, H. Intermolecular Electron Density Modulations in Water and Their Effects on the Far-Infrared Spectral Profiles at 6 THz J. Phys. Chem. B 2011, 115, 6636-6643 10.1021/jp201695b
44. Torii, H. Extended Nature of the Molecular Dipole of Hydrogen-Bonded Water J. Phys. Chem. A 2013, 117, 2044-2051 10.1021/jp4013015
45. Torii, H. Delocalized Electrons in Infrared Intensities J. Mol. Struct. 2014, 1056-1057, 84-96 10.1016/j.molstruc.2013.09.050
46. Chirgadze, Yu. N.; Shestopalov, B. V.; Venyaminov, S. Yu. Intensities and Other Spectral Parameters of Infrared Amide Bands of Polypeptides in the β- and Random Forms Biopolymers 1973, 12, 1337-1351 10.1002/bip.1973.360120610
47. Chirgadze, Yu. N.; Brazhnikov, E. V. Intensities and Other Spectral Parameters of Infrared Amide Bands of Polypeptides in the α-Helical Form Biopolymers 1974, 13, 1701-1712 10.1002/bip.1974.360130902
48. Wasacz, F. M.; Olinger, J. M.; Jakobsen, R. J. Fourier Transform Infrared Studies of Proteins Using Nonaqueous Solvents. Effects of Methanol and Ethylene Glycol on Albumin and Immunoglobulin G Biochemistry 1987, 26, 1464-1470 10.1021/bi00379a038
49. Ishida, K. P.; Griffiths, P. R. Comparison of the Amide I/II Intensity Ratio of Solution and Solid-State Proteins Sampled by Transmission, Attenuated Total Reflectance, and Diffuse Reflectance Spectrometry Appl. Spectrosc. 1993, 47, 584-589 10.1366/0003702934067306
50. Litvinov, R. I.; Faizullin, D. A.; Zuev, Y. F.; Weisel, J. W. The α-Helix to β-Sheet Transition in Stretched and Compressed Hydrated Fibrin Clots Biophys. J. 2012, 103, 1020-1027 10.1016/j.bpj.2012.07.046
51. Buchanan, E. G.; James, W. H.; Choi, S. H.; Guo, L.; Gellman, S. H.; Müller, C. W.; Zwier, T. S. Single-Conformation Infrared Spectra of Model Peptides in the Amide I and Amide II Regions: Experiment-Based Determination of Local Mode Frequencies and Inter-Mode Coupling J. Chem. Phys. 2012, 137, 094301 10.1063/1.4747507
52. Torii, H. Vibrational Interactions in the Amide I Subspace of the Oligomers and Hydration Clusters of N-Methylacetamide J. Phys. Chem. A 2004, 108, 7272-7280 10.1021/jp048320i
53. Frisch, M. J.; Trucks, G. W.; Schlegel, H. B.; Scuseria, G. E.; Robb, M. A.; Cheeseman, J. R.; Montgomery, J. A., Jr.; Vreven, T.; Kudin, K. N.; Burant, J. C.; et al., Gaussian 03, revision D.01; Gaussian, Inc.: Wallingford, CT, 2004.
54. Decius, J. C. An Effective Atomic Charge Model for Infrared Intensities J. Mol. Spectrosc. 1975, 57, 348-362 10.1016/0022-2852(75)90296-9
55. van Straten, A. J.; Smit, W. M. A. Bond Charge Parameters from Integrated Infrared Intensities J. Mol. Spectrosc. 1976, 62, 297-312 10.1016/0022-2852(76)90271-X
56. Gussoni, M.; Castiglioni, C.; Zerbi, G. Physical Meaning of Electrooptical Parameters Derived from Infrared Intensities J. Phys. Chem. 1984, 88, 600-604 10.1021/j150647a053
57. Torii, H.; Tasumi, M. Infrared Intensities of Vibrational Modes of an α-Helical Polypeptide: Calculations Based on the Equilibrium Charge/Charge Flux (ECCF) Model J. Mol. Struct. 1993, 300, 171-179 10.1016/0022-2860(93)87015-2
58. Galimberti, D.; Milani, A.; Castiglioni, C. Charge Mobility in Molecules: Charge Fluxes from Second Derivatives of the Molecular Dipole J. Chem. Phys. 2013, 138, 164115 10.1063/1.4802009
59. Breneman, C. M.; Wiberg, K. B. Determining Atom-Centered Monopoles from Molecular Electrostatic Potentials. The Need for High Sampling Density in Formamide Conformational Analysis J. Comput. Chem. 1990, 11, 361-373 10.1002/jcc.540110311
60. Torii, H. Vibrational Polarizabilities of Hydrogen-Bonded Water Chem. Phys. 2013, 419, 90-96 10.1016/j.chemphys.2012.12.042
61. Torii, H. Cooperative Contributions of the Intermolecular Charge Fluxes and Intramolecular Polarizations in the Far-Infrared Spectral Intensities of Liquid Water J. Chem. Theory Comput. 2014, 10, 1219-1227 10.1021/ct4011147