Computational vibrational spectroscopy of peptides and proteins in one and two dimensions

Accounts of Chemical Research

Volumn 42, Issue 9, 2009, Pages 1280-1289

  Jeon, Jonggu ^a   Yang, Seongeun ^a   Choi, Jun H O ^a   Cho, Minhaeng ^a  

^a Korea University   (South Korea)

Author keywords

[No Author keywords available]

Indexed keywords

ACETAMIDE DERIVATIVE; N METHYLACETAMIDE; N-METHYLACETAMIDE; PEPTIDE; PROTEIN;

ARTICLE; CHEMICAL STRUCTURE; CHEMISTRY; CIRCULAR DICHROISM; COMPUTER SIMULATION; INFRARED SPECTROPHOTOMETRY; NONLINEAR SYSTEM; PROTEIN CONFORMATION; QUANTUM THEORY; VIBRATION;

ACETAMIDES; CIRCULAR DICHROISM; COMPUTER SIMULATION; MODELS, MOLECULAR; NONLINEAR DYNAMICS; PEPTIDES; PROTEIN CONFORMATION; PROTEINS; QUANTUM THEORY; SPECTROPHOTOMETRY, INFRARED; VIBRATION;

EID: 70349233964     PISSN: 00014842     EISSN: None     Source Type: Journal    
DOI: 10.1021/ar900014e     Document Type: Article

References (58)

1. Ernst, R. R.; Bodenhausen, G.; Wokaun, A. Nuclear Magnetic Resonance in One and Two Dimensions, Oxford University Press: Oxford, 1987.
2. Hamm, P.; Lim, M.; Hochstrasser, R. M. Structure of the amide I band of peptides measured by femtosecond nonlinear-infrared spectroscopy. J. Phvs. Chem. B1998, 702, 6123-6138.
3. Tanimura, Y.; Mukamel, S. Two-Dimensional Femtosecond Vibrational Spectroscopy of Liquids. J. Chem. Phys. 1993, 99, 9496-9511.
4. Park, K.; Cho, M. Time- and frequency-resolved coherent two-dimensional IR spectroscopy: Its complementary relationship with the coherent two-dimensional Raman scattering spectroscopy. J. Chem. Phys. 1998, 709, 10559-10569.
5. Cho, M. Two-Dimensional Vibrational Spectroscopy. In Advances in Multi-Photon Processes and Spectroscopy, Lin, S. H., Villaeys, A. A., Fujimura, Y., Eds.; Worid Scientific Publishing Co.: Singapore, 1999; Vol.12; pp 229-300.
6. Mukamel, S. Multidimensional femtosecond correlation spectroscopies of electronic and vibrational excitations. Annu. Rev. Phys. Chem. 2000, 51, 691-729.
7. Cho M. Ultrafast vibrational spectroscopy in condensed phases PhysChemComm 2002 5 40-58 http://www.rsc.org/CFCart/displayarticleeonfree.cfm? article=8%2D9%223%24%5C%5EJB%214%2E%5FL5%286%2CCZ5%3D%3C%3DS5%28%3D29%23%3C%0A DOI 10.1039/b110898k, 7 7 Cho, M. Ultralast vibrational spectroscopy in condensed phases. PhvsChemComm 2002, 40-58. (Pubitemid 40464610)
8. Cho, M. Coherent two-dimensional optical spectroscopy. Chem. Rev. 2008, 708, 1331-1418.
9. Zheng, J.; Kwak, K.; Fayer, M. D. Ultrafast 2D IR Vibrational Echo Spectroscopy. Acc. Chem. Res. 2007, 40, 75-83.
10. Ganim, Z.; Chung, H. S.; Smith, A. W.; DeFlores, L P.; Jones, K. C.; Tokmakoff, A. Amide I Two-Dimensional Infrared Spectroscopy of Proteins. Acc. Chem. Res. 2008, 47, 432-441.
11. Mukamel, S. Prindples of Nonlinear Optica Spectroscopy, Oxford University Press: Oxford, 1995.
12. 2O complexes. J. Chem. Phys. 2003, 118, 3491-3498.
13. Choi J.-H. Lee H. Lee K.-K. Hahn S. Cho M. Computational spectroscopy of ubiquitin: Comparison between theory and experiments Journal of Chemical Physics 2007 126 4 045102 DOI 10.1063/1.2424711 13 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. (Pubitemid 46372729)
14. McQuame, D. A. Statistical Mechanics, Harper & Row: New York, 1976.
15. Yang S. Cho M. IR spectra of N -methylacetamide in water predicted by combined quantum mechanical/molecular mechanical molecular dynamics simulations Journal of Chemical Physics 2005 123 13 1-5 DOI 10.1063/1.2038889, 134503 15 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. (Pubitemid 41434728)
16. Yang, S.; Cho, M. Simulations of Infrared and Vibrational Circular Dichroism Spectra Using Dynamic Partial Charges Obtained from QM/MM Molecular Dynamics: Alanine Dipeptide Analogue in Water. Submitted for publication.
17. Mukamel S. Khidekel V. Chernyak V. Classical chaos and fluctuation-dissipation relations for nonlinear response Physical Review E - Statistical Physics, Plasmas, Fluids, and Related Interdisciplinary Topics 1996 53 1 SUPPL. A R1-R4 17 Mukamel, S.; Khidekel, V.; Chernyak, V. Classical chaos and fluctuation-dissipation relations for nonlinear response. Phys. Rev. E 1996, 53, R1-R4. (Pubitemid 126583691)
18. Ma, A.; Stratt, R. M. Fifth-Order Raman Spectrum of an Atomic Liquid: Simulation and Instantaneous-Normal-Mode Calculation. Phvs. Rev. Lett 2000, 85, 1004-1007.
19. Hasegawa T. Tanimura Y. Calculating fifth-order Raman signals for various molecular liquids by equilibrium and nonequilibrium hybrid molecular dynamics simulation algorithms Journal of Chemical Physics 2006 125 7 074512 DOI 10.1063/1.2217947 19 Hasegawa, T.; Tanimura, Y. Calculating fifth-order Raman signals for various molecular liquids by equilibrium and nonequilibrium hybrid molecular dynamics simulation algorithms. J. Chem. Phys. 2006, 125, 074512. (Pubitemid 44267437)
20. Nagata, Y.; Tanimura, Y.; Mukamel, S. Two-dimensional infrared surface spectroscopy for CO on Cu(100): Detection of intermolecular coupling of adsorbates. J. Chem. Phys. 2007, 126, 204703.
21. Okumura K. Tanimura Y. Femtosecond two-dimensional spectroscopy from anharmonic vibrational modes of molecules in the condensed phase Journal of Chemical Physics 1997 107 7 2267-2283 21 Okumura, K.; Tanimura, Y. Femtosecond two-dimensional spectroscopy from anharmonic vibrational modes of molecules in the condensed phase. J. Chem. Phys. 1997, 707, 2267-2283. (Pubitemid 127603608)
22. Combined Quantum Mechanical and Molecular Mechanical Methods, Gao, J., Thompson, M. A., Eds.: ACS Symposium Series 712; American Chemical Society: Washington, DC, 1998.
23. Kim, Y. S.; Liu, L; Axelsen, P. H.; Hochstrasser, R. M. Two-dimensional infrared spectra of isotopicalfy diluted amyloid fibrils from Aβ340. Proc. Nati. Acad. Sd. U.S.A 2008, 705, 7720-7725.
24. Schweitzer-Stenner, R. Advances in vibrational spectroscopy as a sensitive probe of peptide and protein structure: A critical review. Wb. Spectrosc. 2006, 42, 98-117.
25. Mukherjee P. Kass I. Arkin I. Zanni M.T. Picosecond dynamics of a membrane protein revealed by 2D IR Proceedings of the National Academy of Sciences of the United States of America 2006 103 10 3528-3533 DOI 10.1073/pnas.0508833103 25 Mukherjee, P.; Kass, I.; Arkin, I. T.; Zanni, M. T. Picosecond dynamics of a membrane protein revealed by 2D IR. Proc. Natl. Acad. Sci. U.S.A. 2006, 103, 3528-3533. (Pubitemid 43376589)
26. Ham, S.; Cha, S.; Choi, J.-H.; Cho, M. Amide I modes of fripeptides: Hessian matrix reconstruction and isotope effects. J. Chem. Phys. 2003, 119, 1451-1461.
27. Choi, J.-H.; Kim, J.-S.; Cho, M. Amide I vibrational circular dichroism of polypeptides: Generalized fragmentation approximation method. J. Chem. Phys. 2005, 722, 174903.
28. Liptay, W. Dipole moments and polarizabilities of molecules in excited states. In Excited States, Lim, E. C., Ed.; Academic Press: New York, 1974; Vol.1 ; pp 129229.
29. Bublitz, G. U.; Boxer, S. G. STARK SPECTROSCOPY: Applications in Chemistry, Biology, and Materials Science. Annu. Rev. Phys. Chem. 1997, 48, 213-242.
30. Cho, M. Vibrational sotvatochromism and electrochromism: Coarse-grained models and their relationships. J. Chem. Phys. 2009, 730, 094505.
31. Ham, S.; Cho, M. Amide I modes in the N-methylacetamide dimer and glycine dipeptide analog: Diagonal force constants. J. Chem. Phys. 2003, 776, 6915-6922.
32. 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. Ctem. Phys. 2004, 121, 8887-8896.
33. Jansen, T. I. C.; Knoster, 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.
34. Zhuang, W.; Abramavicius, D.; Hayashi, T.; Mukamel, S. Simulation Protocols for Coherent Femtosecond Vibrational Spectra of Peptides. J. Phys. Chem. B 2006, 770, 3362-3374.
35. Hush, N. S.; Reimers, J. R. Vibrational Stark Spectroscopy. 1. Basic Theory and Application to the CO Stretch. J. Phys. Chem. 1995, 99, 15798-15805.
36. Suydam, I. T.; Boxer, S. G. Vibrational Stark Effects Calibrate the Sensitivity of Vibrational Probes for Electric Fields in Proteins. Biochemistry 2003. 42, 12050-12055.
37. Andrews, S. S.; Boxer, S. G. Vibrational Stark Effects of Nitriles I. Methods and Experimental Results. J. Phys. Chem. A 12000, 104, 11853-11863.
38. Suydam, I. T; Snow, C. D.; Pande, V. S.; Boxer, S. G. Electric Fields at the Active Site of an Enzyme: Direct Comparison of Experiment with Theory. Science 2006, 313, 200-204.
39. Choi, J.-H.; Oh, K.I.; Lee, H.; Lee, C.; Cho, M. Nitrile and thiocyanate IR probes: Quantum chemistry calculation studies and multivariate least-square fitting analysis. J. Chem. Phys. 2008, 728, 134506.
40. Choi, J.-H.; Oh, K.-L; Cho, M. Azido-derivatized compounds as IR probes of local electrostatic environment: Theoretical studies. J. Chem. Phys. 2008, 129, 174512.
41. This experimental value was obtained with azidotrimerhylsilane, not methylazide.
42. Choi J.-H. Hahn S. Cho M. Vibrational spectroscopic characteristics of secondary structure polypeptides in liquid water: Constrained MD simulation studies Biopolymers 2006 83 5 519-536 DOI 10.1002/bip.20583 42 Choi, J.-H.; Hahn, S.; Cho, M. Vibrational spectroscopic characteristics of secondary structure polypeptides in liquid water Constrained MD simulation studies. Biopolvmers 2006. 83, 519-536. (Pubitemid 44851665)
43. Jansen, T. I. C.; Knoester, J. Nonadiabatic Effects in the Two-Dimensional Infrared Spectra of Peptides: Application to Alanine Dipeptide. J. Phys. Chem. B 2006, 770, 22910-22916.
44. Gorbunov R.D. Nguyen P.H. Kobus M. Stock G. Quantum-classical description of the amide I vibrational spectrum of trialanine Journal of Chemical Physics 2007 126 5 054509 DOI 10.1063/1.2431803 44 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. (Pubitemid 46251307)
45. Choi, J.-H.; Cheon, S.; Lee, H.; Cho, M. Two-dimensional nonlinear optical activity spectroscopy of coupled multi-chromophore system. Phys. Chem. Chem. Phys. 2008, 70, 3839-3856.
46. Huang, R.; Kubelka, J.; Barber-Armstrong, W.; Silva, R. A. G. D.; Decatur, S. M.; Keideriing, T. A. Nature of vibrational coupling in helical peptides: An isotopic labeling study. J.Am. Chem. Soc. 2004, 126, 2346-2354.
47. Woutersen S. Hamm P. Time-resolved two-dimensional vibrational spectroscopy of a short α-helix in water Journal of Chemical Physics 2001 115 16 7737-7743 DOI 10.1063/1.1407842 47 Woutersen, S.; Hamm, P. Time-resolved two-dimensional vibrational spectroscopy of a short a helix in water. J. Chem. Phys. 2001, 115, 7737-7743. (Pubitemid 33047866)
48. Zanni, M. T.; Ge, N.-H.; Kim, Y. S.; Hochstrasser, R. M. Two-dimensional IR spectroscopy can be designed to eliminate the diagonal peaks and expose only the crosspeaks needed for structure determination. Proc. Natl. Acad. sci. U.S.A 2001. 98, 11265-11270.
49. Hahn S. Kim S.-S. Lee C. Cho M. Characteristic two-dimensional IR spectroscopic features of antiparallel and parallel β -sheet polypeptides: Simulation studies Journal of Chemical Physics 2005 123 8 1-10 DOI 10.1063/1.1997151, 084905 49 Hahn, S.; Kim, S.-S.; Lee, C.; Cho, M. Characteristic two-dimensional IR spectroscopic features of antiparallel and parallel beta-sheet polypeptides: Simulation studies. J. Chem. Phys. 2005, 723, 084905. (Pubitemid 41285464)
50. Abramavicius D. Mukamel S. Chirality-induced signals in coherent multidimensional spectroscopy of excitons Journal of Chemical Physics 2006 124 3 1-17 DOI 10.1063/1.2104527, 034113 50 Abramavicius, D.; Mukamel, S. Chirality-induced signals in coherent multidimensional spectroscopy of excitons. J. Chem. Phys. 2006, 724, 034113. (Pubitemid 43133756)
51. Gao, J. Methods and applications of combined quantum mechanical and molecular mechanical potentials. In Rev. Comput Chem.; Lipkowitz, K. B., Boyd, D. B., Eds.; VCH Publishers, Inc.: New York, 1996; Vol.7; pp 119-185.
52. Rhee, H.; Ha, J.-H.; Jeon, S.-J.; Cho, M. Femtosecond spectral interferometry of optical activity: Theory. J Chem. Phys. 2008, 729, 094507.
53. Bour P.; Keiderling, T A. Ab initio simulations of the vibrational circular dichroism of coupled peptides. J. Am. Chem. Soc. 1993, 115, 9602-9607.
54. Williams, R. B.; Loring, R. F. Classical mechanical photon echo of a solvated anharmonic vibration. J. Chem. Phys. 2000, 113, 1932-1941.
55. Jeon, J.; Cho, M. In preparation.
56. Noid, W. G.; Ezra, G. S.; Loring, R. F. Vibrational Echoes: Dephasing, Rephasing, and the Stability of Classical Trajectories. J. Phys. Chem. B 2004, 108, 6536-6543.
57. Kryvohuz M. Cao J. Classical divergence of nonlinear response functions Physical Review Letters 2006 96 3 030403 http://oai.aps.org/oai/?verb= ListRecords&metadataPrefix=oai-apsmeta-2&set=journal:PRL:96 DOI 10.1103/PhysRevLett.96.030403 57 Kryvohuz, M.; Cao, J. Classical Divergence of Nonlinear Response Functions. Phys. Rev. Lett. 2006, 96, 030403. (Pubitemid 43248080)
58. Dellago, C.; Mukamel, S. Simulation algorithms for multidimensional nonlinear response of classical many-body systems. J. Chem. Phys. 2003, 119, 9344-9354.