Understanding the Amide-II Vibrations in β-Peptides

Journal of Physical Chemistry B

Volumn 119, Issue 47, 2015, Pages 14831-14839

  Zhao, Juan ^a   Wang, Jianping ^a  

^a INSTITUTE OF CHEMISTRY   (China)

Author keywords

[No Author keywords available]

Indexed keywords

AMIDES; BENCHMARKING; HYDROGEN BONDS; PEPTIDES;

AB INITIO COMPUTATIONS; BACKBONE STRUCTURES; COUPLING STRENGTHS; HELICAL CONFORMATION; HYDROGEN BONDING INTERACTIONS; INFRARED SPECTRUM; INTRAMOLECULAR HYDROGEN BONDING; VIBRATIONAL COUPLINGS;

VIBRATION ANALYSIS;

AMIDE; PEPTIDE;

CHEMISTRY; HYDROGEN BOND; PROTEIN CONFORMATION;

AMIDES; HYDROGEN BONDING; PEPTIDES; PROTEIN CONFORMATION;

EID: 84948419755     PISSN: 15206106     EISSN: 15205207     Source Type: Journal    
DOI: 10.1021/acs.jpcb.5b08070     Document Type: Article

References (53)

1. Montalvo, G. L.; Gai, F.; Roder, H.; DeGrado, W. F. Slow Folding-Unfolding Kinetics of an Octameric β-Peptide Bundle ACS Chem. Biol. 2014, 9, 276-281 10.1021/cb400621y
2. 3-Peptides J. Biomol. Struct. Dyn. 2015, 33, 597-605 10.1080/07391102.2014.897260
3. 2O Helv. Chim. Acta 2014, 97, 1591-1605 10.1002/hlca.201400219
4. 10-Helical Secondary Structure in Aib Oligopeptides Probed by Coherent 2D IR Spectroscopy J. Am. Chem. Soc. 2008, 130, 6556-6566 10.1021/ja8007165
5. Backus, E. H. G.; Bloem, R.; Donaldson, P. M.; Ihalainen, J. A.; Pfister, R.; Paoli, B.; Caflisch, A.; Hamm, P. 2D-IR Study of a Photoswitchable Isotope-Labeled α-Helix J. Phys. Chem. B 2010, 114, 3735-3740 10.1021/jp911849n
6. 6-OtBu J. Phys. Chem. B 2014, 118, 58-68 10.1021/jp408818g
7. 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
8. Panman, M. R.; van Dijk, C. N.; Meuzelaar, H.; Woutersen, S. Communication: Nanosecond Folding Dynamics of an Alpha Helix: Time-Dependent 2D-IR Cross Peaks Observed using Polarization-Sensitive Dispersed Pump-Probe Spectroscopy J. Chem. Phys. 2015, 142, 041103 10.1063/1.4906456
9. 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
10. Falvo, C.; Zhuang, W.; Kim, Y. S.; Axelsen, P. H.; Hochstrasser, R. M.; Mukamel, S. Frequency Distribution of the Amide-I Vibration Sorted by Residues in Amyloid Fibrils Revealed by 2D-IR Measurements and Simulations J. Phys. Chem. B 2012, 116, 3322-3330 10.1021/jp2096423
11. Arkin, I. T. Isotope-Edited IR Spectroscopy for the Study of Membrane Proteins Curr. Opin. Chem. Biol. 2006, 10, 394-401 10.1016/j.cbpa.2006.08.013
12. Kim, Y. S.; Hochstrasser, R. M. Applications of 2D IR Spectroscopy to Peptides, Proteins, and Hydrogen-Bond Dynamics J. Phys. Chem. B 2009, 113, 8231-8251 10.1021/jp8113978
13. Kim, Y. S.; Liu, L.; Axelsen, P. H.; Hochstrasser, R. M. 2D IR Provides Evidence for Mobile Water Molecules in β-Amyloid Fibrils Proc. Natl. Acad. Sci. U. S. A. 2009, 106, 17751-17756 10.1073/pnas.0909888106
14. 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
15. 18O Isotopomers of Alanine Residues in an α-Helix J. Phys. Chem. B 2005, 109, 18652-18663 10.1021/jp052525p
16. Hamm, P.; Helbing, J.; Bredenbeck, J. Two-Dimensional Infrared Spectroscopy of Photoswitchable Peptides Annu. Rev. Phys. Chem. 2008, 59, 291-317 10.1146/annurev.physchem.59.032607.093757
17. Han, C.; Zhao, J.; Yang, F.; Wang, J. P. Structural Dynamics of N-Propionyl-D-glucosamine Probed by Infrared Spectroscopies and Ab Initio Computations J. Phys. Chem. A 2013, 117, 6105-6115 10.1021/jp400096a
18. Ghosh, A.; Tucker, M. J.; Gai, F. 2D IR Spectroscopy of Histidine: Probing Side-Chain Structure and Dynamics via Backbone Amide Vibrations J. Phys. Chem. B 2014, 118, 7799-7805 10.1021/jp411901m
19. Baiz, C. R.; Lin, Y. S.; Peng, C. S.; Beauchamp, K. A.; Voelz, V. A.; Pande, V. S.; Tokmakoff, A. A Molecular Interpretation of 2D IR Protein Folding Experiments with Markov State Models Biophys. J. 2014, 106, 1359-1370 10.1016/j.bpj.2014.02.008
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. Adamczyk, K.; Candelaresi, M.; Robb, K.; Gumiero, A.; Walsh, M. A.; Parker, A. W.; Hoskisson, P. A.; Tucker, N. P.; Hunt, N. T. Measuring Protein Dynamics with Ultrafast Two-Dimensional Infrared Spectroscopy Meas. Sci. Technol. 2012, 23, 062001 10.1088/0957-0233/23/6/062001
22. Bondarenko, A. S.; Jansen, T. L. C. Application of Two-Dimensional Infrared Spectroscopy to Benchmark Models for the Amide I Band of Proteins J. Chem. Phys. 2015, 142, 212437 10.1063/1.4919716
23. Lessing, J.; Roy, S.; Reppert, M.; Baer, M.; Marx, D.; Jansen, T. L. C.; Knoester, J.; Tokmakoff, A. Identifying Residual Structure in Intrinsically Disordered Systems: A 2D IR Spectroscopic Study of the GVGXPGVG Peptide J. Am. Chem. Soc. 2012, 134, 5032-5035 10.1021/ja2114135
24. Woys, A. M.; Almeida, A. M.; Wang, L.; Chiu, C.-C.; McGovern, M.; de Pablo, J. J.; Skinner, J. L.; Gellman, S. H.; Zanni, M. T. Parallel β-Sheet Vibrational Couplings Revealed by 2D IR Spectroscopy of an Isotopically Labeled Macrocycle: Quantitative Benchmark for the Interpretation of Amyloid and Protein Infrared Spectra J. Am. Chem. Soc. 2012, 134, 19118-19128 10.1021/ja3074962
25. Roeters, S. J.; van Dijk, C. N.; Torres-Knoop, A.; Backus, E. H. G.; Campen, R. K.; Bonn, M.; Woutersen, S. Determining In Situ Protein Conformation and Orientation from the Amide-I Sum-Frequency Generation Spectrum: Theory and Experiment J. Phys. Chem. A 2013, 117, 6311-6322 10.1021/jp401159r
26. 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
27. Hayashi, T.; Mukamel, S. Vibrational-Exciton Couplings for the Amide I, II, III, and A Modes of Peptides J. Phys. Chem. B 2007, 111, 11032-11046 10.1021/jp070369b
28. Choi, J.-H.; Cho, M. Calculations of Intermode Coupling Constants and Simulations of Amide I, II, and III Vibrational spectra of Dipeptides Chem. Phys. 2009, 361, 168-175 10.1016/j.chemphys.2009.05.016
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. DeFlores, L. P.; Ganim, Z.; Ackley, S. F.; Chung, H. S.; Tokmakoff, A. The Anharmonic Vibrational Potential and Relaxation Pathways of the Amide I and II Modes of N-Methylacetamide J. Phys. Chem. B 2006, 110, 18973-18980 10.1021/jp0603334
31. 10-Helical Hydrogen Bond Revealed by Two-Dimensional Infrared Spectroscopy J. Am. Chem. Soc. 2009, 131, 2042-2043 10.1021/ja807572f
32. Maekawa, H.; Ge, N.-H. Comparative Study of Electrostatic Models for the Amide-I and -II Modes: Linear and Two-Dimensional Infrared Spectra J. Phys. Chem. B 2010, 114, 1434-1446 10.1021/jp908695g
33. Dunkelberger, E. B.; Woys, A. M.; Zanni, M. T. 2D IR Cross Peaks Reveal Hydrogen Deuterium Exchange with Single Residue Specificity J. Phys. Chem. B 2013, 117, 15297-15305 10.1021/jp402942s
34. Zhao, J.; Wang, J. Dissecting Amide-I Vibration in β-Peptide Helices J. Phys. Chem. B 2015, 119, 3387-3397 10.1021/jp5115288
35. Hamm, P.; Woutersen, S.; Rueping, M. On the Thermal Stability of β-Peptides: A Two-Dimensional Vibrational Spectroscopy Study Helv. Chim. Acta 2002, 85, 3883-3894 10.1002/1522-2675(200211)85:11<3883::AID-HLCA3883>3.0.CO;2-G
36. Scheurer, C.; Piryatinski, A.; Mukamel, S. Signatures of β-Peptide Unfolding in Two-Dimensional Vibrational Echo Spectroscopy: A Simulation Study J. Am. Chem. Soc. 2001, 123, 3114-3124 10.1021/ja003412g
37. Montalvo, G.; Waegele, M. M.; Shandler, S.; Gai, F.; DeGrado, W. F. Infrared Signature and Folding Dynamics of a Helical β-Peptide J. Am. Chem. Soc. 2010, 132, 5616-5618 10.1021/ja100459a
38. Shi, J.; Zhao, J.; Yang, F.; Wang, J. Femtosecond Two-Dimensional Infrared Spectroscopy of N-Ethypropionamide Acta. Phys. Chim. Sin. 2013, 29, 695-700 10.3866/PKU.WHXB201302213
39. Zhao, J.; Shi, J.; Wang, J. Amide-I Characteristics of Helical β-Peptides by Linear Infrared Measurement and Computations J. Phys. Chem. B 2014, 118, 94-106 10.1021/jp4095936
40. 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
41. Frisch, M. J.; Trucks, G. W.; Schlegel, H. B.; Scuseria, G. E.; Robb, M. A.; Cheeseman, J. R.; Scalmani, G.; Barone, V.; Mennucci, B.; Petersson, G. A., et al., Gaussian 09, revision A.02; Gaussian, Inc.: Wallingford, CT, 2009.
42. Wu, Y.-D.; Lin, J.-Q.; Zhao, Y.-L. Theoretical Study of β-Peptide Models: Intrinsic Preferences of Helical Structures Helv. Chim. Acta 2002, 85, 3144-3160 10.1002/1522-2675(200210)85:10<3144::AID-HLCA3144>3.0.CO;2-P
43. Wu, Y.-D.; Han, W.; Wang, D.-P.; Gao, Y.; Zhao, Y.-L. Theoretical Analysis of Secondary Structures of β-Peptides Acc. Chem. Res. 2008, 41, 1418-1427 10.1021/ar800070b
44. Wang, J. Ab Initio-Based All-Mode Two-Dimensional Infrared Spectroscopy of a Sugar Molecule J. Phys. Chem. B 2007, 111, 9193-9196 10.1021/jp074757p
45. Wang, J. Conformational Dependence of Anharmonic Vibrations in Peptides: Amide-I Modes in Model Dipeptide J. Phys. Chem. B 2008, 112, 4790-4800 10.1021/jp710641x
46. 1-5 Clusters: A Simulation Study J. Phys. Chem. A 2014, 118, 9157-9162 10.1021/jp5028299
47. Moran, A.; Mukamel, S. The Origin of Vibrational Mode Couplings in Various Secondary Structural Motifs of Polypeptides Proc. Natl. Acad. Sci. U. S. A. 2004, 101, 506-510 10.1073/pnas.2533089100
48. Lu, T.; Chen, F. Multiwfn: A Multifunctional Wavefunction Analyzer J. Comput. Chem. 2012, 33, 580-592 10.1002/jcc.22885
49. Jamróz, M. H.; Dobrowolski, J. C. Potential Energy Distribution (PED) Analysis of DFT Calculated IR Spectra of the Most Stable Li, Na, and Cu(I) Diformate Molecules J. Mol. Struct. 2001, 565-566, 475-480 10.1016/S0022-2860(00)00908-X
50. 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
51. Chirgadze, Y. N.; Brazhnikov, E. V. Intensities and Other Spectral Parameters of Infrared Bands of Polypeptides in the Alpha-Helical Form Biopolymers 1974, 13, 1701-1712 10.1002/bip.1974.360130902
52. Chirgadze, Y. N.; Shestopalov, B. V.; Venyaminov, S. Y. Intensities and Other Spectral Parameters of Infrared Amide Bands of Polypeptides in the Beta- and Random Forms Biopolymers 1973, 12, 1337-1351 10.1002/bip.1973.360120610
53. Mennucci, B.; Tomasi, J. Continuum Solvation Models: A New Approach to the Problem of Solute's Charge Distribution and Cavity Boundaries J. Chem. Phys. 1997, 106, 5151-5158 10.1063/1.473558