Simulation of the amide i infrared spectrum in photoinduced peptide folding/unfolding transitions

Journal of Physical Chemistry B

Volumn 117, Issue 41, 2013, Pages 12383-12390

  Zanetti Polzi, Laura ^a,b   Aschi, Massimiliano ^a   Amadei, Andrea ^c   Daidone, Isabella ^a  

^a UNIVERSITY OF L'AQUILA   (Italy)

^b CNR   (Italy)

^c UNIVERSITY OF ROME TOR VERGATA   (Italy)

Author keywords

[No Author keywords available]

Indexed keywords

CALCULATED SPECTRUM; CONFORMATIONAL SAMPLINGS; HIGHER FREQUENCIES; MIXED QUANTUM MECHANICS; MOLECULAR SWITCHES; PERTURBED MATRIX METHODS; SPECTROSCOPIC BEHAVIOR; SPECTROSCOPIC DATA;

AMIDES; ISOTOPES; SPECTROSCOPY;

PEPTIDES;

AMIDE; PEPTIDE;

ARTICLE; CHEMICAL STRUCTURE; CHEMISTRY; INFRARED SPECTROPHOTOMETRY; MOLECULAR DYNAMICS; PHOTOCHEMISTRY; PROTEIN FOLDING; PROTEIN UNFOLDING; QUANTUM THEORY;

AMIDES; MODELS, MOLECULAR; MOLECULAR DYNAMICS SIMULATION; PEPTIDES; PHOTOCHEMICAL PROCESSES; PROTEIN FOLDING; PROTEIN UNFOLDING; QUANTUM THEORY; SPECTROPHOTOMETRY, INFRARED;

EID: 84886908833     PISSN: 15206106     EISSN: 15205207     Source Type: Journal    
DOI: 10.1021/jp406708p     Document Type: Article

References (74)

1. Krimm, S.; Bandekar, J. Vibrational Spectroscopy and Conformation of Peptides, Polypeptides and Proteins Adv. Protein Chem. 1986, 38, 181-364
2. Surewicz, W.; Mantsch, H. New Insight into Protein Secondary Structure from Resolution-Enhanced Infrared Spectra Biochim. Biophys. Acta 1988, 952, 115-130
3. Dong, A.; Huang, P.; Caughey, W. Protein Secondary Structure in Water from Second-Derivative Amide I Infrared Spectra Biochemistry 1990, 29, 3303-3308
4. 2O) Solution. II. Amide Absorption Bands of Polypeptide and Fibrous Protein in α -, β -, and Random Coil Conformation Biopolymers 1990, 30, 1259-1271
5. Surewicz, W. K.; Mantsch, J. H. H.; Chapman, D. Determination of Protein Secondary Structure by Fourier Transform Infrared Spectroscopy: A Critical Assessment Biochemistry 1993, 32, 389-394
6. Kumosinski, T. F.; Unruh, J. J. Quantitation of the Global Secondary Structure of Globular proteins by FTIR Spectroscopy: Comparison with X-ray Crystallographic Structure Talanta 1996, 43, 199-219
7. Barth, A. Infrared Spectroscopy of Proteins Biochim. Biophys. Acta 2007, 1767, 1073-1101
8. 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
9. Kong, J.; Yu, S. Fourier Transform Infrared Spectroscopic Analysis of Protein Secondary Structures Acta Biochim. Biophys. Sinica 2007, 39 (8) 549-559
10. Kauppinen, J.; Moffatt, D.; Mantsch, H.; Cameron, D. A Method for Resolving Intrinsically Overlapped Bands Appl. Spectrosc. 1986, 35, 271-276
11. Byler, D.; Susi, H. Examination of the Secondary Structure of Proteins by Deconvolved FTIR Spectra Biopolymers 1986, 25, 469-487
12. Lee, D.; Haris, P.; Chapman, D.; Mitchell, R. Determination of Protein Secondary Structure Using Factor Analysis of Infrared Spectra Biochemistry 1990, 29, 9185-9193
13. Sarver, R.; Krueger, W. Protein Secondary Structure from Fourier Transform Infrared Spectroscopy: a Data Base Analysis Anal. Biochem. 1991, 194, 89-100
14. Decatur, S. IR Spectroscopy of Isotope-Labeled Helical Peptides: Probing the Effect of N-acetylation on Helix Stability Biopolymers 2000, 54, 180-185
15. Ihalainen, J.; Paoli, B.; Muff, S.; Backus, E.; Bredenbeck, J.; Caflisch, G. W. A.; Hamm, P. α -Helix Folding in the Presence of Structural Constraints Proc. Natl. Acad. Sci. U.S.A. 2008, 105 (28) 9588-9593
16. Ludlam, C.; Arkin, I.; Liu, X.; Rothman, M.; Rath, P.; Aimoto, S.; Smith, S.; Engelman, D.; Rothschild, K. Fourier Transform Infrared Spectroscopy and Site-Directed Isotopelabeling as a Probe of Local Secondary Structure in the Transmembrane Domain of Phospholamban Biophys. J. 1996, 70 (4) 1728-1736
17. Decatur, S.; Antonic, J. Isotope-edited Infrared Spectroscopy of Helical Peptides J. Am. Chem. Soc. 1999, 121, 11914-11915
18. 13C Isotope Labeling of Hydrophobic Peptides. Origin of the Anomalous Intensity Distribution in the Infrared Amide I Spectral Region of β -Sheet Structures J. Am. Chem. Soc. 2000, 122 (4) 677-683
19. Huang, R.; Kubelka, J.; Barber-Armstrong, W.; Silva, R.; Decatur, S.; Keiderling, T. Nature of Vibrational Coupling in Helical Peptides:? an Isotopic Labeling Study J. Am. Chem. Soc. 2004, 126 (8) 2346-2354
20. Hiramatsu, H.; Kitagawa, T. FT-IR Approaches on Amyloid Fibril Structure Biochim. Biophys. Acta 2005, 1753 (1) 100-107
21. Decatur, S. Elucidation of Residue-Level Structure and Dynamics of Polypeptides via Isotope-Edited Infrared Spectroscopy Acc. Chem. Res. 2006, 39 (3) 169-175
22. Kumita, J.; Smart, O.; Woolley, G. Photo-Control of Helix Content in a Short Peptide Proc. Natl. Acad. Sci. U.S.A. 2000, 97 (8) 3803-3808
23. Bredenbeck, J.; Helbing, J.; Behrendt, R.; Renner, C.; Moroder, L.; Wachtveitl, J.; Hamm, P. Transient 2D-IR Spectroscopy:? Snapshots of the Nonequilibrium Ensemble during the Picosecond Conformational Transition of a Small Peptide J. Phys. Chem. B 2003, 107 (33) 8654-8660
24. Wachtveitl, J.; Sporlein, S.; Satzger, H.; Fonrobert, B.; Renner, C.; Behrendt, R.; Oesterhelt, D.; Moroder, L.; Zinth, W. Ultrafast Conformational Dynamics in Cyclic Azobenzene Peptides of Increased Flexibility Biophys. J. 2004, 86 (4) 2350-2362
25. Bredenbeck, J.; Helbing, J.; Kumita, J.; Woolley, G.; Hamm, P. α -Helix Formation in a Photoswitchable Peptide Tracked from Picoseconds to Microseconds by Time-Resolved IR Spectroscopy Proc. Natl. Acad. Sci. U.S.A. 2005, 102, 2379-2384
26. Aemissegger, A.; Krautler, V.; van Gunsteren, W.; Hilver, D. A Photoinducible β -Hairpin J. Am. Chem. Soc. 2005, 127 (9) 2929-2936
27. Dong, S.; Loweneck, M.; Schrader, T.; Schreier, W.; Zinth, W.; Moroder, L.; Renner, C. A Photocontrolled β -Hairpin Peptide Chem.-Eur. J. 2006, 12 (4) 1114-1120
28. Kolano, C.; Helbing, J.; Kozinski, M.; Sander, W.; Hamm, P. Watching Hydrogen-Bond Dynamics in a β -Turn by Transient two-Dimensional Infrared Spectroscopy Nature 2006, 444, 469-472
29. Ihalainen, J. A.; Bredenbeck, J.; Pfister, R.; Helbing, J.; Chi, L.; van Stokkum, I. H.; Woolley, G. A.; Hamm, P. Folding and Unfolding of a Photoswitchable Peptide from Picoseconds to Microseconds Proc. Natl. Acad. Sci. U.S.A. 2007, 104, 5383-5388
30. Hamm, P.; Helbing, J.; Bredenbeck, J. Two-Dimensional Infrared Spectroscopy of Photoswitchable Peptides Annu. Rev. Phys. Chem. 2008, 59, 291-317
31. Backus, E.; Bloem, R.; Donaldson, P.; Ihalainen, J.; Pfister, R.; Paoli, B.; Caflisch, A.; Hamm, P. 2D-IR Study of a Photoswitchable Isotope-Labeled α -Helix J. Phys. Chem. B 2010, 114 (10) 3735-3740
32. Sporlein, S.; Carstens, H.; Satzger, H.; Renner, C.; Behrendt, R.; Moroder, L.; Tavan, P.; Zinth, W.; Wachtveitl, J. Ultrafast Spectroscopy Reveals Subnanosecond Peptide Conformational Dynamics and Validates Molecular Dynamics Simulation Proc. Natl. Acad. Sci. U.S.A. 2002, 99, 7998-8002
33. Carstens, H.; Renner, C.; Milbradt, A.; P. Tavan, L. M. Multiple Loop Conformations of Peptides Predicted by Molecular Dynamics Simulations Are Compatible with Nuclear Magnetic Resonance Biochemistry 2005, 44 (12) 4829-4840
34. Nguyen, P.; Gorbunov, R.; Stock, G. Photoinduced Conformational Dynamics of a Photoswitchable Peptide: A Nonequilibrium Molecular Dynamics Simulation Study Biophys. J. 2006, 91 (4) 1224-1234
35. Nguyen, P.; Stock, G. Nonequilibrium Molecular Dynamics Simulation of a Photoswitchable Peptide Chem. Phys. 2006, 323, 36-44
36. Paoli, B.; Pellarin, R.; Caflisch, A. Slow Folding of Cross-Linked a-Helical Peptides Due to Steric Hindrance J. Phys. Chem. B 2010, 114, 2023-2027
37. Torii, H.; Tasumi, M. Model Calculations on the Amide I Infrared Bands of Globular Proteins J. Chem. Phys. 1992, 96, 3379-3387
38. Lee, S. H.; Krimm, S. Ab Initio-Based Vibrational Analysis of α-Poly(L-alanine) Biopolymers 1998, 46, 283-317
39. Kwac, K.; Cho, M. Molecular Dynamics Simulation Study of N-Methylacetamide in Water. I. Amide I Mode Frequency Fluctuation J. Chem. Phys. 2003, 119, 2247-2255
40. 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
41. Schmidt, J. R.; Corcelli, S. A.; Skinner, J. L. Ultrafast Vibrational Spectroscopy of Water and Aqueous N-Methylacetamide: Comparison of Different Electronic Structure/Molecular Dynamics Approaches J. Chem. Phys. 2004, 121, 8887-8896
42. 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
43. Yang, S.; Cho, M. IR Spectra of N-Methylacetamide in Water Predicted by Combined Quantum Mechanical/Molecular Mechanical Molecular Dynamics Simulations J. Chem. Phys. 2005, 123, 134503-134505
44. Bour, P.; Keiderling, T. A. Vibrational Spectral Simulation for Peptides of Mixed Secondary Structure: Method Comparisons with the Trpzip Model Hairpin J. Phys. Chem. B 2005, 109, 23687-23697
45. Gaigeot, M. P.; Vuilleumier, R.; Sprik, M.; Borgis, D. Infrared Spectroscopy of N-Methylacetamide Revisited by ab Initio Molecular Dynamics Simulations J. Chem. Theory Comput. 2005, 1, 772-789
46. Smith, A. E.; Tokmakoff, A. Amide I two-Dimensional Infrared Spectroscopy of β -Hairpin Peptides J. Chem. Phys. 2007, 126, 45108-45111
47. Gorbunov, R. D.; Nguyen, P. H.; Kobus, M.; Stock, G. Quantum-Classical Description of the Amide I Vibrational Spectrum of Trialanine J. Chem. Phys. 2007, 126, 054509-054518
48. 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
49. Hahn, S.; Ham, S.; Cho, M. Simulation Studies of Amide I IR Absorption and Two-Dimensional IR Spectra of β Hairpins in Liquid Water J. Phys. Chem. B 2005, 109, 11789-11801
50. Choi, J. H.; Lee, H.; Lee, K. K.; Hahn, S.; Cho, M. Computational Spectroscopy of Ubiquitin: Comparison between Theory and Experiments J. Chem. Phys. 2007, 126, 045102-045115
51. Aschi, M.; Spezia, R.; Di Nola, A.; Amadei, A. A First Priciples Method to Model Perturbed Electronic Wavefunctions: the Effect of an External Electric Field Chem. Phys. Lett. 2001, 344, 374-380
52. Spezia, R.; Aschi, M.; Di Nola, A.; Amadei, A. Extension of the Perturbed Matrix Method: Application to a Water Molecule Chem. Phys. Lett. 2002, 365, 450-456
53. Amadei, A.; D'Abramo, M.; Zazza, C.; Aschi, M. Electronic Properties of Formaldehyde: a Theoretical Study Chem. Phys. Lett. 2003, 381, 187-193
54. Amadei, A.; Marinelli, F.; D'Abramo, M.; D'Alessandro, M.; Anselmi, M.; Di Nola, A.; Aschi, M. Theoretical Modeling of Vibro-Electronic Quantum States in Complex Molecular Systems: Solvated Carbon Monoxide, a Test Case J. Chem. Phys. 2005, 122, 124506-124515
55. Amadei, A.; D'Alessandro, M.; D'Abramo, M.; Aschi, M. Theoretical Characterization of Electronic States in Interacting Chemical Systems J. Chem. Phys. 2009, 130, 08410-08415
56. Daidone, I.; Aschi, M.; Zanetti-Polzi, L.; Nola, A. D.; Amadei, A. On the Origin of IR Spectral Changes upon Protein Folding Chem. Phys. Lett. 2010, 488, 213-218
57. Zanetti-Polzi, L.; Daidone, I.; Anselmi, M.; Carchini, G.; Di Nola, A.; Amadei, A. Analysis of Infrared Spectra of ß-Hairpin Peptides as Derived from Molecular Dynamics Simulations J. Phys. Chem. B 2011, 115 (41) 11872-11878
58. Zanetti-Polzi, L.; Amadei, A.; Aschi, M.; Daidone, I. Insight into the IR-Spectra/Structure Relationship in Amyloid Fibrils: a Theoretical Study on a Prion Peptide J. Am. Chem. Soc. 2011, 133 (30) 11414-11417
59. Zanetti-Polzi, L.; Daidone, I.; Amadei, A. A Theoretical Reappraisal of Polylysine in the Investigation of Secondary Structure Sensitivity of Infrared Spectra J. Phys. Chem. B 2012, 116 (10) 3353-3360
60. Gao, J.; Truhlar, D. G. Quantum Mechanical Methods for Enzyme Kinetics Annu. Rev. Phys. Chem. 2002, 53, 467-505
61. Amadei, A.; Daidone, I.; Di Nola, A.; Aschi, M. Theoretical-Computational Modelling of Infrared Spectra in Peptides and Proteins: a new Frontier for Combined Theoretical-Experimental Investigations Curr. Opin. Struct. Biol. 2010, 20, 155-161
62. Amadei, A.; Daidone, I.; Zanetti-Polzi, L.; Aschi, M. Modeling Quantum Vibrational Excitations in Condensed-Phase Molecular Systems Theor. Chem. Acc. 2011, 129, 31-43
63. Vreven, T.; Morokuma, K. Chapter 3 Hybrid Methods: ONIOM(QM:MM) and QM/MM Annu. Rep. Comp. Chem. 2006, 2, 35-51
64. Senn, H. M.; Thiel, W. QM/MM Studies of Enzymes Curr. Opin. Chem. Biol. 2007, 11, 182-187
65. Schaftenaar, G.; Noordik, J. Molden: a pre- and post-Processing Program for Molecular and Electronic Structures J. Comput.-Aided Mol. Des. 2000, 14, 123-134
66. Berendsen, H. J. C.; van der Spoel, D.; van Drunen, R. GROMACS: A Message-Passing Parallel Molecular Dynamics Implementation Comput. Phys. Commun. 1995, 91, 43-56
67. Jorgensen, W.; Tirado-Rives, J. The OPLS [Optimized Potentials for Liquid Simulations] Potential Functions for Proteins, Energy Minimizations for Crystals of Cyclic Peptides and Crambin J. Am. Chem. Soc. 1988, 110 (6) 1657-1666
68. Bayly, C.; Cieplak, P.; Cornell, W.; Kollman, P. A Well-Behaved Electrostatic Potential Based Method Using Charge Restraints for Deriving Atomic Charges: the RESP Model J. Phys. Chem. 1993, 97, 10269-10280
69. Schmidt, M.; Baldridge, K.; Boatz, J.; Elbert, S.; Gordon, M.; Jensen, J.; Koseki, S.; Matsunaga, N.; Nguyen, K.; Su, S.; Windus, T.; Dupuis, M.; Montgomery, J. General Atomic and Molecular Electronic Structure System J. Comput. Chem. 1993, 14, 1347-1363
70. Berendsen, H. J. C.; Grigera, J. R.; Straatsma, T. P. The Missing Term in Effective Pair Potentials J. Phys. Chem. 1987, 91, 6269-6271
71. Darden, T.; York, D.; Pedersen, L. Particle mesh Ewald: An N-log(N) Method for Ewald Sums in Large Systems J. Chem. Phys. 1993, 98, 10089-10092
72. Hess, B.; Bekker, H.; Berendsen, H. J. C.; Fraaije, J. LINCS: A Linear Constraint Solver for Molecular Simulations J. Comput. Chem. 1997, 18, 1463-1472
73. Brown, D.; Clarke, J. A Comparison of Constant Energy, Constant Temperature and Constant Pressure Ensembles in Molecular Dynamics Simulations of Atomic Liquids Mol. Phys. 1984, 51, 1243-1252
74. Marquesee, S.; Robbins, V.; Baldwin, R. Unusually Stable Helix Formation in Short Alanine-Based Peptides Proc. Natl. Acad. Sci. U.S.A. 1989, 86, 5286-5290