메뉴 건너뛰기




Volumn 365, Issue 1861, 2007, Pages 2799-2812

Computing protein infrared spectroscopy with quantum chemistry

Author keywords

Amide bands; Density functional theory; Infrared spectroscopy; Proteins; Quantum chemistry

Indexed keywords

AMIDES; BIOGRAPHIES; DENSITY FUNCTIONAL THEORY; INFRARED SPECTROSCOPY; PROTEINS;

EID: 38449110101     PISSN: 1364503X     EISSN: None     Source Type: Journal    
DOI: 10.1098/rsta.2007.0018     Document Type: Article
Times cited : (16)

References (43)
  • 1
    • 0032548588 scopus 로고    scopus 로고
    • Empirical density functionals
    • doi:10.1016/S0009-2614(9701282-7)
    • Adamson, R. D., Gill, P. M. W. & Pople, J. A. 1998 Empirical density functionals. Chem. Phys. Lett. 284, 6-11. (doi:10.1016/S0009-2614(97)01282-7)
    • (1998) Chem. Phys. Lett. , vol.284 , pp. 6-11
    • Adamson, R.D.1    Gill, P.M.W.2    Pople, J.A.3
  • 2
    • 10844243891 scopus 로고    scopus 로고
    • Ab initio modeling of amide vibrational bands in solutions
    • doi:10.1021/jp046073c
    • Besley, N. A. 2004a Ab initio modeling of amide vibrational bands in solutions. J. Chem. Phys. A 108, 10 794-10 800. (doi:10.1021/jp046073c)
    • (2004) J. Chem. Phys. A , vol.108 , pp. 10794-10800
    • Besley, N.A.1
  • 3
    • 2342488085 scopus 로고    scopus 로고
    • Calculation of the electronic spectra of molecules in solution and on surfaces
    • doi:10.1016/j.cplett.2004.04.004
    • Besley, N. A. 2004b Calculation of the electronic spectra of molecules in solution and on surfaces. Chem. Phys. Lett. 390, 124-129. (doi:10.1016/j. cplett.2004.04.004)
    • (2004) Chem. Phys. Lett. , vol.390 , pp. 124-129
    • Besley, N.A.1
  • 4
    • 0001517129 scopus 로고    scopus 로고
    • Ab initio study of the effect of solvation on the electronic spectra of formamide and N-methylacetamide
    • doi:10.1021/jp982645f
    • Besley, N. A. & Hirst, J. D. 1998 Ab initio study of the effect of solvation on the electronic spectra of formamide and N-methylacetamide. J. Phys. Chem. A 102, 10 791-10 797. (doi:10.1021/jp982645f)
    • (1998) J. Phys. Chem. A , vol.102 , pp. 10791-10797
    • Besley, N.A.1    Hirst, J.D.2
  • 5
    • 0032748895 scopus 로고    scopus 로고
    • Theoretical studies toward quantitative protein circular dichroism calculations
    • doi:10. 1021/ja990627l
    • Besley, N. A. & Hirst, J. D. 1999 Theoretical studies toward quantitative protein circular dichroism calculations. J. Am. Chem. Soc. 121, 9636-9644. (doi:10. 1021/ja990627l)
    • (1999) J. Am. Chem. Soc. , vol.121 , pp. 9636-9644
    • Besley, N.A.1    Hirst, J.D.2
  • 6
    • 33846432696 scopus 로고    scopus 로고
    • Computation of the amide i band of polypeptides and proteins using a partial Hessian approach
    • doi:10.1063/1.2426344
    • Besley, N. A. & Metcalf, K. A. 2007 Computation of the amide I band of polypeptides and proteins using a partial Hessian approach. J. Chem. Phys. 126, 035101. (doi:10.1063/1.2426344)
    • (2007) J. Chem. Phys. , vol.126 , pp. 035101
    • Besley, N.A.1    Metcalf, K.A.2
  • 7
    • 0001167142 scopus 로고    scopus 로고
    • Transfer of molecular property tensors in cartesian coordinates: A new algorithm for the simu lation of vibrational spectra
    • doi:10.1002/(SICI1096-987X(19970415)18:5!646:: AID-JCC6O3.0.CO;2-N)
    • Bour, P., Sopkova? J., Bedna?ova? J., Malon?, P. & Keiderling, T. A. 1997 Transfer of molecular property tensors in cartesian coordinates: A new algorithm for the simu lation of vibrational spectra. J. Comput. Chem. 18, 646-659. (doi:10.1002/(SICI)1096-987X(19970415)18:5!646:: AID-JCC6O3.0.CO;2-N)
    • (1997) J. Comput. Chem. , vol.18 , pp. 646-659
    • Bour, P.1    Sopkova, J.2    Bednaova, J.3    Malon, P.4    Keiderling, T.A.5
  • 8
    • 0037026869 scopus 로고    scopus 로고
    • Ab initio quantum chemical models of peptide helices and their vibrational spectra
    • doi:10.1002/bip.10224
    • Bour, P., Kubelka, J. & Keiderling, T. A. 2002 Ab initio quantum chemical models of peptide helices and their vibrational spectra. Biopolymers 65, 45-59. (doi:10.1002/bip.10224)
    • (2002) Biopolymers , vol.65 , pp. 45-59
    • Bour, P.1    Kubelka, J.2    Keiderling, T.A.3
  • 9
    • 0032241430 scopus 로고    scopus 로고
    • Fast events in protein folding: The time evolution of primary processes
    • doi:10.1146/annurev.physchem.49.1.173
    • Callender, R. H., Dyer, R. B., Gilmanshin, R. & Woodruff, W. H. 1998 Fast events in protein folding: the time evolution of primary processes. Annu. Rev. Phys. Chem. 49, 173-202. (doi:10.1146/annurev.physchem.49.1.173)
    • (1998) Annu. Rev. Phys. Chem. , vol.49 , pp. 173-202
    • Callender, R.H.1    Dyer, R.B.2    Gilmanshin, R.3    Woodruff, W.H.4
  • 10
    • 0037044503 scopus 로고    scopus 로고
    • Inter-peptide interaction and delocalization of amide i vibrational modes in myoglobin and flavoddoxin
    • doi:10.1063/ 1.1504438
    • Choi, J.-H., Ham, S. & Cho, M. 2002 Inter-peptide interaction and delocalization of amide I vibrational modes in myoglobin and flavoddoxin. J. Chem. Phys. 117, 6821-6832. (doi:10.1063/ 1.1504438)
    • (2002) J. Chem. Phys. , vol.117 , pp. 6821-6832
    • Choi, J.-H.1    Ham, S.2    Cho, M.3
  • 11
    • 0043195838 scopus 로고    scopus 로고
    • Local amide i mode frequencies and coupling constants in polypeptides
    • doi:10.1021/jp03483 5i
    • Choi, J.-H., Ham, S. Y. & Cho, M. 2003 Local amide I mode frequencies and coupling constants in polypeptides. J. Phys. Chem. B 107, 9132-9138. (doi:10.1021/jp03483 5i)
    • (2003) J. Phys. Chem. B , vol.107 , pp. 9132-9138
    • Choi, J.-H.1    Ham, S.Y.2    Cho, M.3
  • 12
    • 33847691555 scopus 로고    scopus 로고
    • Computational spectroscopy of ubiquitin. Comparison between theory and experiment
    • doi:10. 1063/1.2424711
    • Choi, J.-H., Lee, H., Lee, K. K., Hahn, S. & Cho, M. 2007 Computational spectroscopy of ubiquitin. Comparison between theory and experiment. J. Chem. Phys. 126, 045102. (doi:10. 1063/1.2424711)
    • (2007) J. Chem. Phys. , vol.126 , pp. 045102
    • Choi, J.-H.1    Lee, H.2    Lee, K.K.3    Hahn, S.4    Cho, M.5
  • 13
    • 0000810764 scopus 로고    scopus 로고
    • Infrared studies of fast events in protein folding
    • doi:10.1021/ar970343a
    • Dyer, R. B., Gai, F., Woodruff, W. H., Gilmanshin, R. & Callender, R. H. 1998 Infrared studies of fast events in protein folding. Acc. Chem. Res. 31, 709-716. (doi:10.1021/ar970343a)
    • (1998) Acc. Chem. Res. , vol.31 , pp. 709-716
    • Dyer, R.B.1    Gai, F.2    Woodruff, W.H.3    Gilmanshin, R.4    Callender, R.H.5
  • 14
    • 0030963424 scopus 로고    scopus 로고
    • Fast events in protein folding: Relaxation dynamics of secondary and tertiary structure in native apomyoglobin
    • doi:10.1073/pnas.94.8.3709
    • Gilmanshin, R., Williams, S., Callender, R. H., Woodruff, W. H. & Dyer, R. B. 1997 Fast events in protein folding: relaxation dynamics of secondary and tertiary structure in native apomyoglobin. Proc. Natl Acad. Sci. USA 94, 3709-3713. (doi:10.1073/pnas.94.8.3709)
    • (1997) Proc. Natl Acad. Sci. USA , vol.94 , pp. 3709-3713
    • Gilmanshin, R.1    Williams, S.2    Callender, R.H.3    Woodruff, W.H.4    Dyer, R.B.5
  • 15
    • 0037460569 scopus 로고    scopus 로고
    • Correlation between electronic and molecular structure distortions and vibrational properties II. Amide i modes of NMA-nD2O complexes
    • doi:10.1063/1.1536980
    • Ham, S., Kim, J. H., Lee, H. & Cho, M. 2003a Correlation between electronic and molecular structure distortions and vibrational properties. II. Amide I modes of NMA-nD2O complexes. J. Chem. Phys. 118, 3491-3498. (doi:10.1063/1.1536980)
    • (2003) J. Chem. Phys. , vol.118 , pp. 3491-3498
    • Ham, S.1    Kim, J.H.2    Lee, H.3    Cho, M.4
  • 16
    • 0042594667 scopus 로고    scopus 로고
    • Amide i modes of tripeptides: Hessian matrix reconstruction and isotope effects
    • doi:10.1 063/1.1581855
    • Ham, S., Cha, S., Choi, J.-H. & Cho, M. 2003b Amide I modes of tripeptides: Hessian matrix reconstruction and isotope effects. J. Chem. Phys. 119, 1451-1461. (doi:10.1 063/1.1581855)
    • (2003) J. Chem. Phys. , vol.119 , pp. 1451-1461
    • Ham, S.1    Cha, S.2    Choi, J.-H.3    Cho, M.4
  • 17
    • 3142704435 scopus 로고    scopus 로고
    • Amide i modes of a-helical polypeptides in liquid water: Conformation fluctuation, phase correlation, and linear and nonlinear vibrational spectra
    • doi:10.1021/j p048678e
    • Ham, S., Hahn, S., Lee, C., Kim, T.-K., Kwak, K. & Cho, M. 2004 Amide I modes of a-helical polypeptides in liquid water: conformation fluctuation, phase correlation, and linear and nonlinear vibrational spectra. J. Phys. Chem. B 108, 9333-9345. (doi:10.1021/j p048678e)
    • (2004) J. Phys. Chem. B , vol.108 , pp. 9333-9345
    • Ham, S.1    Hahn, S.2    Lee, C.3    Kim, T.-K.4    Kwak, K.5    Cho, M.6
  • 18
    • 0001326710 scopus 로고    scopus 로고
    • Structure of the amide i band of peptides measured by femtosecond nonlinear-infrared spectroscopy
    • doi:10.1021/jp9813286
    • Hamm, P., Lim, M. & Hochstrasser, R. M. 1998 Structure of the amide I band of peptides measured by femtosecond nonlinear-infrared spectroscopy. J. Phys. Chem . B 102, 6123-6138.(doi:10.1021/jp9813286)
    • (1998) J. Phys. Chem . B , vol.102 , pp. 6123-6138
    • Hamm, P.1    Lim, M.2    Hochstrasser, R.M.3
  • 19
    • 0000096233 scopus 로고    scopus 로고
    • Response to "comment on improving protein circular dichroism calculations in the far-ultraviolet through reparameterizing the amide chromo phore
    • 1999
    • Hirst, J. D. & Besley, N. A. 1999 Response to "Comment on improving protein circular dichroism calculations in the far-ultraviolet through reparameterizing the amide chromo phore" [J. Chem.Phys. 111, 2844 (1999)].
    • (1999) J. Chem.Phys. , vol.111 , pp. 2844
    • Hirst, J.D.1    Besley, N.A.2
  • 20
    • 0000096233 scopus 로고    scopus 로고
    • doi:10.1063/1.479563
    • J. Chem. Phys. 111, 2846-2847. (doi:10.1063/1.479563)
    • J. Chem. Phys. , vol.111 , pp. 2846-2847
  • 21
    • 10644250257 scopus 로고
    • Inhomogeneous electron gas
    • doi:10. 1103/PhysRev.136.B864
    • Hohenberg, P. & Kohn, W. 1964 Inhomogeneous electron gas. Phys. Rev. A 136, 864-871. (doi:10. 1103/PhysRev.136.B864)
    • (1964) Phys. Rev. A , vol.136 , pp. 864-871
    • Hohenberg, P.1    Kohn, W.2
  • 24
    • 33746216303 scopus 로고    scopus 로고
    • R12 methods in explicitly correlated molecular orbital theory
    • doi:10.1080/ 01442350600799921
    • Klopper, W., Manby, F. R., Ten-no, S. & Valeev, E. F. 2006 R12 methods in explicitly correlated molecular orbital theory. Int. Rev. Phys. Chem. 25, 427-468. (doi:10.1080/ 01442350600799921)
    • (2006) Int. Rev. Phys. Chem. , vol.25 , pp. 427-468
    • Klopper, W.1    Manby, F.R.2    Ten-No, S.3    Valeev, E.F.4
  • 26
    • 33751313515 scopus 로고    scopus 로고
    • Watching hydrogen-bond dynamics in a b-turn by transient two-dimensional infrared spectroscopy
    • doi:10.1038/nature05352
    • Kolano, C., Helbing, J., Kozinski, M., Sander, S. & Hamm, P. 2006 Watching hydrogen-bond dynamics in a b-turn by transient two-dimensional infrared spectroscopy. Nature 44, 469-472. (doi:10.1038/nature05352)
    • (2006) Nature , vol.44 , pp. 469-472
    • Kolano, C.1    Helbing, J.2    Kozinski, M.3    Sander, S.4    Hamm, P.5
  • 27
    • 80051733811 scopus 로고    scopus 로고
    • Advances in quantum chemical methods in the Q-CHEM 3.0 program package
    • Kong, J. et al. 2006 Advances in quantum chemical methods in the Q-CHEM 3.0 program package. Phys. Chem. Chem. Phys. 8, 3172-3191.
    • (2006) Phys. Chem. Chem. Phys. , vol.8 , pp. 3172-3191
    • Kong, J.1
  • 28
    • 0037054684 scopus 로고    scopus 로고
    • Parallelization of analytical Hartree-Fock and density functional theory Hessian calculations, Part, 1: Parallelization of coupled-perturbed Hartree-Fock equations
    • doi:10.1080/ 00268970110109466
    • Korambath, P. P., Kong, J., Furlani, T. R. & Head-Gordon, M. 2002 Parallelization of analytical Hartree-Fock and density functional theory Hessian calculations. Part 1: parallelization of coupled-perturbed Hartree-Fock equations. Mol. Phys. 100, 1755-1761. (doi:10.1080/ 00268970110109466)
    • (2002) Mol. Phys. , vol.100 , pp. 1755-1761
    • Korambath, P.P.1    Kong, J.2    Furlani, T.R.3    Head-Gordon, M.4
  • 29
    • 0015407488 scopus 로고
    • Intermolecular interaction effects in the amide i vibrations of b polypeptides
    • doi:10.1073/pnas.69.10.2788
    • Krimm, S. & Abe, Y. 1972 Intermolecular interaction effects in the amide I vibrations of b polypeptides. Proc. Natl Acad. Sci. USA 69, 2788-2792. (doi:10.1073/pnas.69.10.2788)
    • (1972) Proc. Natl Acad. Sci. USA , vol.69 , pp. 2788-2792
    • Krimm, S.1    Abe, Y.2
  • 30
    • 0035814332 scopus 로고    scopus 로고
    • Differentiation of b-sheet forming structures: Ab initio based simulations of IR absorption and vibrational CD for model peptide and protein b-sheets
    • doi:10.1021/ja0116627
    • Kubelka, J. & Keiderling, T. A. 2001 Differentiation of b-sheet forming structures: ab initio based simulations of IR absorption and vibrational CD for model peptide and protein b-sheets. J. Am.Chem. Soc. 123, 12 048-12 058. (doi:10.1021/ja0116627)
    • (2001) J. Am.Chem. Soc. , vol.123 , pp. 12048-12058
    • Kubelka, J.1    Keiderling, T.A.2
  • 31
    • 33749635854 scopus 로고    scopus 로고
    • Contribution of transition dipole coupling to amide coupling in IR spectra or peptide secondary structures
    • Kubelka, J., Kim, J., Bour, P. & Keiderling, T. A. 2006 Contribution of transition dipole coupling to amide coupling in IR spectra or peptide secondary structures. Vib. Spectr. 42, 63-73.
    • (2006) Vib. Spectr. , vol.42 , pp. 63-73
    • Kubelka, J.1    Kim, J.2    Bour, P.3    Keiderling, T.A.4
  • 32
    • 11344272213 scopus 로고    scopus 로고
    • Local amide i mode frequencies and coupling constants in multiple stranded antiparallel b-sheet polypeptide
    • doi:10.1021/ jp0471204
    • Lee, C. & Cho, M. 2004 Local amide I mode frequencies and coupling constants in multiple stranded antiparallel b-sheet polypeptide. J. Phys. Chem. B 108, 20 397-20 407. (doi:10.1021/ jp0471204)
    • (2004) J. Phys. Chem. B , vol.108 , pp. 20397-20407
    • Lee, C.1    Cho, M.2
  • 33
    • 1942532839 scopus 로고    scopus 로고
    • EDF2: A density functional for predicting molecular vibrational frequencies
    • doi:10.1071/CH03263
    • Lin, C. Y., George, M. W. & Gill, P. M. W. 2004 EDF2: A density functional for predicting molecular vibrational frequencies. Aust. J. Chem. 57, 365-370. (doi:10.1071/CH03263)
    • (2004) Aust. J. Chem. , vol.57 , pp. 365-370
    • Lin, C.Y.1    George, M.W.2    Gill, P.M.W.3
  • 34
    • 0347004718 scopus 로고    scopus 로고
    • The origin of vibrational mode couplings in various secondary structure motifs of polypeptides
    • doi:10.1073/pnas. 2533089100
    • Moran, A. & Mukamel, S. 2002 The origin of vibrational mode couplings in various secondary structure motifs of polypeptides. Proc. Natl Acad. Sci. USA 101, 506-510. (doi:10.1073/pnas. 2533089100)
    • (2002) Proc. Natl Acad. Sci. USA , vol.101 , pp. 506-510
    • Moran, A.1    Mukamel, S.2
  • 35
    • 0035005366 scopus 로고    scopus 로고
    • Preorganized secondary structure as an important determinant of fast protein folding
    • doi:10.1038/88626
    • Myers, J. K. & Oas, T. G. 2001 Preorganized secondary structure as an important determinant of fast protein folding. Nat. Struct. Biol. 8, 552-558. (doi:10.1038/88626)
    • (2001) Nat. Struct. Biol. , vol.8 , pp. 552-558
    • Myers, J.K.1    Oas, T.G.2
  • 37
    • 9744273194 scopus 로고    scopus 로고
    • Ultrafast vibrational spectroscopy of water and aqueous N-methylacetamide: Comparison of different electronic structure/molecular dynamics approaches
    • doi:10.1063/1.1791632
    • Schmidt, J. R., Corcelli, S. A. & Skinner, J. L. 2004 Ultrafast vibrational spectroscopy of water and aqueous N-methylacetamide: comparison of different electronic structure/molecular dynamics approaches. J. Chem. Phys. 121, 8887-8896. (doi:10.1063/1.1791632)
    • (2004) J. Chem. Phys. , vol.121 , pp. 8887-8896
    • Schmidt, J.R.1    Corcelli, S.A.2    Skinner, J.L.3
  • 38
    • 0011083273 scopus 로고    scopus 로고
    • Harmonic vibrational frequencies: An evaluation of Hartree-Fock, Moller-Plesset, quadratic configuration interaction, density functional theory, and semiempirical scale factors
    • doi:10.1021/jp960976r
    • Scott, A. P. & Radom, L. 1996 Harmonic vibrational frequencies: an evaluation of Hartree-Fock, Moller-Plesset, quadratic configuration interaction, density functional theory, and semiempirical scale factors. J. Phys. Chem. 100, 16 502-16 513. (doi:10.1021/jp960976r)
    • (1996) J. Phys. Chem. , vol.100 , pp. 16502-16513
    • Scott, A.P.1    Radom, L.2
  • 39
    • 36449001245 scopus 로고
    • Model calculations on the amide-I infrared bands of globular proteins
    • doi:10.1063/1.461939
    • Torii, H. & Tasumi, M. 1992 Model calculations on the amide-I infrared bands of globular proteins. J. Chem. Phys. 96, 3379-3387. (doi:10.1063/1.461939)
    • (1992) J. Chem. Phys. , vol.96 , pp. 3379-3387
    • Torii, H.1    Tasumi, M.2
  • 40
    • 3042511820 scopus 로고    scopus 로고
    • Vibrational analysis of capped [Leu]enkephalin
    • doi:10.1039/b315501c
    • Watson, T. M. & Hirst, J. D. 2004 Vibrational analysis of capped [Leu]enkephalin. Phys. Chem. Chem. Phys. 6, 2580-2587. (doi:10.1039/b315501c)
    • (2004) Phys. Chem. Chem. Phys. , vol.6 , pp. 2580-2587
    • Watson, T.M.1    Hirst, J.D.2
  • 41
    • 0037037802 scopus 로고    scopus 로고
    • Nonlinear two-dimensional spectroscopy of peptides
    • doi:10.1088/0953-8984/14/39/202
    • Woutersen, S. & Hamm, P. 2002a Nonlinear two-dimensional spectroscopy of peptides. J. Phys. Condens. Matter 14, R1035-R1062. (doi:10.1088/0953-8984/ 14/39/202)
    • (2002) J. Phys. Condens. Matter , vol.14
    • Woutersen, S.1    Hamm, P.2
  • 42
    • 0036088423 scopus 로고    scopus 로고
    • Coupling of the amide i modes of the glycine dipeptide
    • doi:10.1246/bcsj.75.985
    • Woutersen, S. & Hamm, P. 2002b Coupling of the amide I modes of the glycine dipeptide. Bull. Chem. Soc. Jpn 75, 985-988. (doi:10.1246/bcsj.75.985)
    • (2002) Bull. Chem. Soc. Jpn , vol.75 , pp. 985-988
    • Woutersen, S.1    Hamm, P.2
  • 43
    • 0001547817 scopus 로고
    • Nanosecond circulardichroism spectral measurements-extension to the far-ultraviolet region
    • doi:10.1021/j100123a009
    • Zhang, C.-F., Lewis, J. W., Cerpa, R., Kuntz, I. D. & Kliger, D. S. 1993 Nanosecond circulardichroism spectral measurements-extension to the far-ultraviolet region. J. Phys. Chem. 97, 5499-5505. (doi:10.1021/j100123a009)
    • (1993) J. Phys. Chem. , vol.97 , pp. 5499-5505
    • Zhang, C.-F.1    Lewis, J.W.2    Cerpa, R.3    Kuntz, I.D.4    Kliger, D.S.5


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.