Dissecting amide-I vibration in β-peptide helices

Journal of Physical Chemistry B

Volumn 119, Issue 8, 2015, Pages 3387-3397

  Zhao, Juan ^a   Wang, Jianping ^a  

^a INSTITUTE OF CHEMISTRY   (China)

Author keywords

[No Author keywords available]

Indexed keywords

AMIDES; CALCULATIONS; HYDROGEN; PEPTIDES; POLYPEPTIDES;

AB INITIO CALCULATIONS; AMIDE I MODE; BENCHMARK MEASUREMENTS; HELICAL CONFORMATION; INTRAMOLECULAR HYDROGEN BONDING; PEPTIDE STRUCTURES; TRANSITION ENERGY; VIBRATIONAL PROPERTIES;

HYDROGEN BONDS;

AMIDE; PEPTIDE;

CHEMICAL MODEL; CHEMISTRY; HYDROGEN BOND; PROTEIN SECONDARY STRUCTURE; QUANTUM THEORY; SPECTROSCOPY; VIBRATION;

AMIDES; HYDROGEN BONDING; MODELS, CHEMICAL; PEPTIDES; PROTEIN STRUCTURE, SECONDARY; QUANTUM THEORY; SPECTRUM ANALYSIS; VIBRATION;

EID: 84923884338     PISSN: 15206106     EISSN: 15205207     Source Type: Journal    
DOI: 10.1021/jp5115288     Document Type: Article

References (53)

1. Gademann, K.; Ernst, M.; Hoyer, D.; Seebach, D. Synthesis and Biological Evaluation of a Cyclo-β-Tetrapeptide as a Somatostatin Analogue Angew. Chem., Int. Ed. 1999, 38, 1223-1226
2. Porter, E. A.; Wang, X.; Lee, H.; Weisblum, B.; Gellman, S. H. Antibiotics: Non-Haemolytic β-Amino-Acid Oligomers Nature 2000, 404, 565-565
3. 3-Amino Acids Org. Lett. 2011, 13, 3474-3477
4. Abele, S.; Seiler, P.; Seebach, D. Synthesis, Crystal Structures, and Modelling of β-Oligopeptides Consisting of 1-(Aminomethyl)cyclopropanecarboxylic Acid: Ribbon-Type Arrangement of Eight-Membered H-Bonded Rings Helv. Chim. Acta 1999, 82, 1559-1571
5. 8-Helix of a β-Hexapeptide Consisting of (2R,3S)-3-amino-2-hydroxy Acid Residues Angew. Chem., Int. Ed. 2003, 42, 1534-1537
6. Claridge, T. D. W.; Goodman, J. M.; Moreno, A.; Angus, D.; Barker, S. F.; Taillefumier, C.; Watterson, M. P.; Fleet, G. W. J. 10-Helical Conformations in Oxetane β-Amino Acid Hexamers Tetrahedron Lett. 2001, 42, 4251-4255
7. Appella, D. H.; Christianson, L. A.; Klein, D. A.; Powell, D. R.; Huang, X.; Barchi, J. J.; Gellman, S. H. Residue-Based Control of Helix Shape in β-Peptide Oligomers Nature 1997, 387, 381-384
8. Appella, D. H.; Christianson, L. A.; Klein, D. A.; Richards, M. R.; Powell, D. R.; Gellman, S. H. Synthesis and Structural Characterization of Helix-Forming β-Peptides: trans -2-Aminocyclopentanecarboxylic Acid Oligomers J. Am. Chem. Soc. 1999, 121, 7574-7581
9. Lee, H.; Syud, F.; Wang, X.; Gellman, S. H. Diversity in Short β-Peptide 12-Helices: High-Resolution Structural Analysis in Aqueous Solution of a Hexamer Containing Sulfonylated Pyrrolidine Residues J. Am. Chem. Soc. 2001, 123, 7721-7722
10. Appella, D. H.; Christianson, L. A.; Karle, I. L.; Powell, D. R.; Gellman, S. H. β-Peptide Foldamers: Robust Helix Formation in a New Family of β-Amino Acid Oligomers J. Am. Chem. Soc. 1996, 118, 13071-13072
11. Seebach, D.; Overhand, M.; Kühnle, F. N. M.; Martinoni, B.; Oberer, L.; Hommel, U.; Widmer, H. β-Peptides: Synthesis by Arndt-Eistert Homologation with Concomitant Peptide Coupling. Structure Determination by NMR and CD Spectroscopy and by X-ray Crystallography. Helical Secondary Structure of a β-Hexapeptide in Solution and its Stability towards Pepsin Helv. Chim. Acta 1996, 79, 913-941
12. Raguse, T. L.; Lai, J. R.; Gellman, S. H. Environment-Independent 14-Helix Formation in Short β-Peptides: Striking a Balance between Shape Control and Functional Diversity J. Am. Chem. Soc. 2003, 125, 5592-5593
13. 3-Peptides in Aqueous Buffer Org. Lett. 2006, 8, 807-810
14. 3-Peptides in Water via Covalent Bridging of Side Chains Org. Lett. 2006, 8, 4199-4202
15. Vaz, E.; Pomerantz, W. C.; Geyer, M.; Gellman, S. H.; Brunsveld, L. Comparison of Design Strategies for Promotion of β-Peptide 14-Helix Stability in Water Chembiochem 2008, 9, 2254-2259
16. 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
17. 3-Nonapeptides Folding to (P)-Helices with Alternating Twelve- and Ten-Membered Hydrogen-Bonded Rings Helv. Chim. Acta 2002, 85, 2577-2593
18. 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
19. Zhuang, W.; Abramavicius, D.; Hayashi, T.; Mukamel, S. Simulation Protocols for Coherent Femtosecond Vibrational Spectra of Peptides J. Phys. Chem. B 2006, 110, 3362-3374
20. Wang, J. Conformational Dependence of Anharmonic Vibrations in Peptides: Amide-I Modes in Model Dipeptide J. Phys. Chem. B 2008, 112, 4790-4800
21. Wang, J.; Zhuang, W.; Mukamel, S.; Hochstrasser, R. Two-Dimensional Infrared Spectroscopy as a Probe of the Solvent Electrostatic Field for a Twelve Residue Peptide J. Phys. Chem. B 2008, 112, 5930-5937
22. Maekawa, H.; De Poli, M.; Toniolo, C.; Ge, N.-H. Couplings between Peptide Linkages across a 3(10)-Helical Hydrogen Bond Revealed by Two-Dimensional Infrared Spectroscopy J. Am. Chem. Soc. 2009, 131, 2042-2043
23. 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
24. Jackson, M.; Haris, P. I.; Chapman, D. Conformational Transitions in Poly(-lysine): Studies using Fourier Transform Infrared Spectroscopy Biochim. Biophys. Acta 1989, 998, 75-79
25. 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
26. Beke, T.; Somlai, C.; Magyarfalvi, G.; Perczel, A.; Tarczay, G. Chiral and Achiral Fundamental Conformational Building Units of β-Peptides: A Matrix Isolation Conformational Study on Ac-β-HGly-NHMe and Ac-β-HAla-NHMe J. Phys. Chem. B 2009, 113, 7918-7926
27. Gobi, S.; Knapp, K.; Vass, E.; Majer, Z.; Magyarfalvi, G.; Hollosi, M.; Tarczay, G. Is β-Homo-Proline a Pseudo-γ-Turn forming Element of β-Peptides? An IR and VCD Spectroscopic Study on Ac-β-HPro-NHMe in Cryogenic Matrices and Solutions Phys. Chem. Chem. Phys. 2010, 12, 13603-13615
28. 3-hPhe-NHMe J. Am. Chem. Soc. 2008, 130, 4795-4807
29. 3-hTyr-NHMe J. Am. Chem. Soc. 2008, 130, 4784-4794
30. Zhao, J.; Wang, J. Amide Vibrations and Their Conformational Dependences in β-Peptide J. Phys. Chem. B 2010, 114, 16011-16019
31. Wang, J.; Hochstrasser, R. M. Anharmonicity of Amide Modes J. Phys. Chem. B 2006, 110, 3798-3807
32. Choi, J.-H.; Ham, S.; Cho, M. Local Amide I Mode Frequencies and Coupling Constants in Polypeptides J. Phys. Chem. B 2003, 107, 9132-9138
33. Ham, S.; Cha, S.; Choi, J.-H.; Cho, M. Amide I Modes of Tripeptides: Hessian Matrix Reconstruction and Isotope Effects J. Chem. Phys. 2003, 119, 1451-1461
34. 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
35. 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
36. 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
37. 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., Gaussian 09, revision A.02; Gaussian, Inc.; Pittsburgh, PA, 2009.
38. Krimm, S.; Bandekar, J. Vibrational Spectroscopy and Conformation of Peptides, Polypeptides, and Proteins Adv. Protein Chem. 1986, 38, 181-364
39. Jamróz, M. H. Vibrational Energy Distribution Analysis VEDA 4; Warsaw, 2004.
40. Meier, T.; Zhao, Y.; Chernyak, V.; Mukamel, S. Polarons, Localization, and Excitonic Coherence in Superradiance of Biological Antenna Complexes J. Chem. Phys. 1997, 107, 3876-3893
41. Edler, J.; Hamm, P. Self-Trapping of the Amide I Band in a Peptide Model Crystal J. Chem. Phys. 2002, 117, 2415-2424
42. Zhao, J.; Wang, J. Chain-Length and Mode-Delocalization Dependent Amide-I Anharmonicity in Peptide Oligomers J. Chem. Phys. 2012, 136, 214112-11
43. Wang, J.; Hochstrasser, R. M. Characteristics of the Two-Dimensional Infrared Spectroscopy of Helices from Approximate Simulations and Analytic Models Chem. Phys. 2004, 297, 195-219
44. Mukherjee, S.; Chowdhury, P.; Gai, F. Infrared Study of the Effect of Hydration on the Amide I Band and Aggregation Properties of Helical Peptides J. Phys. Chem. B 2007, 111, 4596-4602
45. Hamm, P.; Lim, M.; Hochstrasser, R. M. Structure of the Amide I Band of Peptides Measured by Femtosecond Nonlinear-Infrared Spectroscopy J. Phys. Chem. B 1998, 102, 6123-6138
46. Wang, J.; Chen, J.; Hochstrasser, R. M. Local Structure of β-Hairpin Isotopomers by FTIR, 2D IR, and Ab Initio Theory J. Phys. Chem. B 2006, 110, 7545-7555
47. 10-helical Structures in Alanine Polypeptides J. Chem. Phys. 2003, 118, 3651-3659
48. Gnanakaran, S.; Hochstrasser, R. M. Conformational Preferences and Vibrational Frequency Distributions of Short Peptides in Relation to Multidimensional Infrared Spectroscopy J. Am. Chem. Soc. 2001, 123, 12886-12898
49. 2O Complexes J. Chem. Phys. 2003, 118, 3491-3498
50. Hochstrasser, R. M. Two-Dimensional Spectroscopy at Infrared and Optical Frequencies Proc. Natl. Acad. Sci. U. S. A. 2007, 104, 14190-14196
51. 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
52. Smith, A. W.; Lessing, J.; Ganim, Z.; Peng, C. S.; Tokmakoff, A.; Roy, S.; Jansen, T. L. C.; Knoester, J. Melting of a β-Hairpin Peptide Using Isotope-Edited 2D IR Spectroscopy and Simulations J. Phys. Chem. B 2010, 114, 10913-10924
53. Li, D.; Yang, F.; Han, C.; Zhao, J.; Wang, J. Correlated High-Frequency Molecular Motions in Neat Liquid Probed with Ultrafast Overtone Two-Dimensional Infrared Spectroscopy J. Phys. Chem. L 2012, 3, 3665-3670