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Volumn 91, Issue 7, 2006, Pages 2636-2646

Spectral signatures of heterogeneous protein ensembles revealed by MD simulations of 2DIR spectra

Author keywords

[No Author keywords available]

Indexed keywords

AMIDE; SOLVENT;

EID: 33749438763     PISSN: 00063495     EISSN: None     Source Type: Journal    
DOI: 10.1529/biophysj.106.088070     Document Type: Article
Times cited : (93)

References (66)
  • 1
    • 36449001245 scopus 로고
    • Model calculations on the amide-I infrared bands of globular proteins
    • Torii, H., and M. Tasumi. 1992. Model calculations on the amide-I infrared bands of globular proteins. J. Chem. Phys. 96:3379-3387.
    • (1992) J. Chem. Phys. , vol.96 , pp. 3379-3387
    • Torii, H.1    Tasumi, M.2
  • 2
    • 0001326710 scopus 로고    scopus 로고
    • Structure of the amide I band of peptides measured by femtosecond nonlinear-infrared spectroscopy
    • Hamm, P., M. Lim, and R. M. Hochstrasser. 1998. Structure of the amide I band of peptides measured by femtosecond nonlinear-infrared spectroscopy. J. Phys. Chem. B. 102:6123-6138.
    • (1998) J. Phys. Chem. B. , vol.102 , pp. 6123-6138
    • Hamm, P.1    Lim, M.2    Hochstrasser, R.M.3
  • 3
    • 20544452788 scopus 로고    scopus 로고
    • Amide I vibrational dynamics of N-methylacetamide in polar solvents: The role of electrostatic interactions
    • DeCamp, M. F., L. DeFlores, J. M. McCracken, A. Tokmakoff, K. Kwac, and M. Cho. 2005. Amide I vibrational dynamics of N-methylacetamide in polar solvents: the role of electrostatic interactions. J. Phys. Chem. B. 109:11016-11026.
    • (2005) J. Phys. Chem. B. , vol.109 , pp. 11016-11026
    • DeCamp, M.F.1    DeFlores, L.2    McCracken, J.M.3    Tokmakoff, A.4    Kwac, K.5    Cho, M.6
  • 4
    • 33646196840 scopus 로고    scopus 로고
    • Evaluation of the information content in infrared spectra for protein secondary structure determination
    • Goormaghtigh, E., J.-M. Ruysschaert, and V. Raussens. 2006. Evaluation of the information content in infrared spectra for protein secondary structure determination. Biophys. J. 90:2946-2957.
    • (2006) Biophys. J. , vol.90 , pp. 2946-2957
    • Goormaghtigh, E.1    Ruysschaert, J.-M.2    Raussens, V.3
  • 5
    • 11144304496 scopus 로고    scopus 로고
    • Application of the local regression method interval partial least-squares to the elucidation of protein secondary structure
    • Navea, S., R. Taeler, and A. de Juan. 2005. Application of the local regression method interval partial least-squares to the elucidation of protein secondary structure. Anal. Biochem. 336:231-242.
    • (2005) Anal. Biochem. , vol.336 , pp. 231-242
    • Navea, S.1    Taeler, R.2    De Juan, A.3
  • 6
    • 1642297346 scopus 로고    scopus 로고
    • Core structure of amyloid fibril proposed from IR-microscope linear dichroism
    • Hiramatsu, H., Y. Goto, H. Naiki, and T. Kitagawa. 2004. Core structure of amyloid fibril proposed from IR-microscope linear dichroism. J. Am. Chem. Soc. 126:3008-3009.
    • (2004) J. Am. Chem. Soc. , vol.126 , pp. 3008-3009
    • Hiramatsu, H.1    Goto, Y.2    Naiki, H.3    Kitagawa, T.4
  • 7
    • 0344305773 scopus 로고    scopus 로고
    • The structure of tri-proline in water probed by polarized Raman, Fourier transform infrared, vibrational circular dichroism, and electric ultraviolet circular dichroism spectroscopy
    • Schweitzer-Stenner, R., F. Eker, A. Perez, K. Griebenow, X. Cao, and L. A. Nafie. 2003. The structure of tri-proline in water probed by polarized Raman, Fourier transform infrared, vibrational circular dichroism, and electric ultraviolet circular dichroism spectroscopy. Biopolymers. 71:558-568.
    • (2003) Biopolymers , vol.71 , pp. 558-568
    • Schweitzer-Stenner, R.1    Eker, F.2    Perez, A.3    Griebenow, K.4    Cao, X.5    Nafie, L.A.6
  • 8
    • 0001256511 scopus 로고
    • Structure of synthetic polypeptides
    • Elliot, A., and E. J. Ambrose. 1950. Structure of synthetic polypeptides. Nature. 165:921-922.
    • (1950) Nature , vol.165 , pp. 921-922
    • Elliot, A.1    Ambrose, E.J.2
  • 9
    • 0012997810 scopus 로고
    • Frequency shift of the CO stretching band in polypeptides and proteins
    • Krimm, S. 1955. Frequency shift of the CO stretching band in polypeptides and proteins. J. Chem. Phys. 23:1371-1372.
    • (1955) J. Chem. Phys. , vol.23 , pp. 1371-1372
    • Krimm, S.1
  • 10
    • 4243898367 scopus 로고
    • Perturbation treatment of the characteristic vibrations of polypeptide chains in various configurations
    • Miyazawa, T. 1960. Perturbation treatment of the characteristic vibrations of polypeptide chains in various configurations. J. Chem. Phys. 32:1647-1652.
    • (1960) J. Chem. Phys. , vol.32 , pp. 1647-1652
    • Miyazawa, T.1
  • 11
    • 0015407488 scopus 로고
    • Intermolecular interaction effects in the amide I vibrations of β polypeptides
    • Krimm, S., and Y. Abe. 1972. Intermolecular interaction effects in the amide I vibrations of β polypeptides. Proc. Natl. Acad. Sci. USA. 69:2788-2792.
    • (1972) Proc. Natl. Acad. Sci. USA , vol.69 , pp. 2788-2792
    • Krimm, S.1    Abe, Y.2
  • 12
    • 0012269518 scopus 로고
    • Influence of water on the infrared spectrum of crystalline N-methylacetamide
    • Häseler, S., A. Poglitsch, G. Bechtold, and W. L. Peticolas. 1986. Influence of water on the infrared spectrum of crystalline N-methylacetamide. J. Chem. Phys. 84:1046-1047.
    • (1986) J. Chem. Phys. , vol.84 , pp. 1046-1047
    • Häseler, S.1    Poglitsch, A.2    Bechtold, G.3    Peticolas, W.L.4
  • 13
    • 0001313676 scopus 로고
    • Ab initio vibrational analysis of hydrogen-bonded trans- and cis-N-methylacetamide
    • Mirkin, N. G., and S. Krimm. 1991. Ab initio vibrational analysis of hydrogen-bonded trans- and cis-N-methylacetamide. J. Am. Chem. Soc. 113:9742-9747.
    • (1991) J. Am. Chem. Soc. , vol.113 , pp. 9742-9747
    • Mirkin, N.G.1    Krimm, S.2
  • 14
    • 21844447084 scopus 로고    scopus 로고
    • Ab initio vibrational analysis of isotopic derivatives of aqueous hydrogen-bonded trans-N-methylacetamide
    • Mirkin, N. G., and S. Krimm. 1996. Ab initio vibrational analysis of isotopic derivatives of aqueous hydrogen-bonded trans-N-methylacetamide. J. Mol. Struct. 377:219-234.
    • (1996) J. Mol. Struct. , vol.377 , pp. 219-234
    • Mirkin, N.G.1    Krimm, S.2
  • 15
    • 0001443463 scopus 로고    scopus 로고
    • Effects of hydration on the structure, vibrational wavenumbers, vibrational force field and resonance Raman intensities of N-methylacetamide
    • Torii, H., T. Tatsumi, and M. Tasumi. 1998. Effects of hydration on the structure, vibrational wavenumbers, vibrational force field and resonance Raman intensities of N-methylacetamide. J. Raman Spectrosc. 29:537-546.
    • (1998) J. Raman Spectrosc. , vol.29 , pp. 537-546
    • Torii, H.1    Tatsumi, T.2    Tasumi, M.3
  • 16
    • 0031648837 scopus 로고    scopus 로고
    • Effects of intermolecular hydrogen-bonding interactions on the amide I mode of N-methylacetamide: Matrix-isolation infrared studies and ab initio molecular orbital calculations
    • Torii, H., T. Tatsumi, T. Kanazawa, and M. Tasumi. 1998. Effects of intermolecular hydrogen-bonding interactions on the amide I mode of N-methylacetamide: matrix-isolation infrared studies and ab initio molecular orbital calculations. J. Phys. Chem. B. 102:309-314.
    • (1998) J. Phys. Chem. B. , vol.102 , pp. 309-314
    • Torii, H.1    Tatsumi, T.2    Kanazawa, T.3    Tasumi, M.4
  • 17
    • 0038637862 scopus 로고    scopus 로고
    • Amide I modes in the N-methylacetamide dimer and glycine dipeptide analog: Diagonal force constants
    • Ham, S., and M. Cho. 2003. Amide I modes in the N-methylacetamide dimer and glycine dipeptide analog: diagonal force constants. J. Chem. Phys. 118:6915-6922.
    • (2003) J. Chem. Phys. , vol.118 , pp. 6915-6922
    • Ham, S.1    Cho, M.2
  • 19
    • 84961981133 scopus 로고    scopus 로고
    • Empirical modeling of the peptide amide I band IR intensity in water solution
    • Bour, P., and T. A. Keiderling. 2003. Empirical modeling of the peptide amide I band IR intensity in water solution. J. Chem. Phys. 119:11253-11262.
    • (2003) J. Chem. Phys. , vol.119 , pp. 11253-11262
    • Bour, P.1    Keiderling, T.A.2
  • 20
    • 9744273194 scopus 로고    scopus 로고
    • Ultrafast vibrational spectroscopy of water and aqueous N-methylacetamide: Comparison of different electronic structure/molecular dynamics approaches
    • Schmidt, J. R., S. A. Corcelli, and J. L. Skinner. 2004. Ultrafast vibrational spectroscopy of water and aqueous N-methylacetamide: comparison of different electronic structure/molecular dynamics approaches. J. Chem. Phys. 121:8887-8896.
    • (2004) J. Chem. Phys. , vol.121 , pp. 8887-8896
    • Schmidt, J.R.1    Corcelli, S.A.2    Skinner, J.L.3
  • 21
    • 31544436644 scopus 로고    scopus 로고
    • A transferable electrostatic map for solvation effects on amide I vibrations and its application to linear and two-dimensional spectroscopy
    • Jansen, T. l. C., and J. Knoester. 2006. A transferable electrostatic map for solvation effects on amide I vibrations and its application to linear and two-dimensional spectroscopy. J. Chem. Phys. 124:044502.
    • (2006) J. Chem. Phys. , vol.124 , pp. 044502
    • Jansen, T.L.C.1    Knoester, J.2
  • 22
    • 0035975474 scopus 로고    scopus 로고
    • Correlation effects in the two-dimensional vibrational spectroscopy of coupled vibrations
    • Demirdöven, N., M. Khalil, O. Golonzka, and A. Tokmakoff. 2001. Correlation effects in the two-dimensional vibrational spectroscopy of coupled vibrations. J. Phys. Chem. A. 105:8025-8030.
    • (2001) J. Phys. Chem. A. , vol.105 , pp. 8025-8030
    • Demirdöven, N.1    Khalil, M.2    Golonzka, O.3    Tokmakoff, A.4
  • 23
    • 33644914712 scopus 로고    scopus 로고
    • Simulation protocols for coherent femtosecond vibrational spectra of peptides
    • Zhuang, W., D. Abramavicius, T. Hayashi, and S. Mukamel. 2006. Simulation protocols for coherent femtosecond vibrational spectra of peptides. J. Phys. Chem. B. 110:3362-3374.
    • (2006) J. Phys. Chem. B. , vol.110 , pp. 3362-3374
    • Zhuang, W.1    Abramavicius, D.2    Hayashi, T.3    Mukamel, S.4
  • 24
    • 21644447464 scopus 로고    scopus 로고
    • Simulation studies of amide I IR absorption and two-dimensional IR spectra of β-hairpins in liquid water
    • Hahn, S., S. Ham, and M. Cho. 2005. Simulation studies of amide I IR absorption and two-dimensional IR spectra of β-hairpins in liquid water. J. Phys. Chem. B. 109:11789-11801.
    • (2005) J. Phys. Chem. B. , vol.109 , pp. 11789-11801
    • Hahn, S.1    Ham, S.2    Cho, M.3
  • 25
    • 30544437694 scopus 로고    scopus 로고
    • Vibrational spectral simulation for peptides of mixed secondary structure: Method comparisons with the trpzip model hairpin
    • Bour, P., and T. A. Keiderling. 2005. Vibrational spectral simulation for peptides of mixed secondary structure: method comparisons with the trpzip model hairpin. J. Phys. Chem. B. 109:23687-23697.
    • (2005) J. Phys. Chem. B. , vol.109 , pp. 23687-23697
    • Bour, P.1    Keiderling, T.A.2
  • 26
    • 0023008334 scopus 로고
    • Vibrational spectroscopy and conformation of peptides, polypeptides, and proteins
    • C. B. Anfinsen, J. T. Edsall, and F. M. Richards, editors. Academic Press, New York
    • Krimm, S., and J. Bandekar. 1986. Vibrational spectroscopy and conformation of peptides, polypeptides, and proteins. In Advances in Protein Chemistry, Vol. 38. C. B. Anfinsen, J. T. Edsall, and F. M. Richards, editors. Academic Press, New York. 181-364.
    • (1986) Advances in Protein Chemistry , vol.38 , pp. 181-364
    • Krimm, S.1    Bandekar, J.2
  • 27
    • 0003335193 scopus 로고
    • Understanding normal modes of proteins
    • Krimm, S., and W. C. Reisdorf, Jr. 1994. Understanding normal modes of proteins. Faraday Disc. 99:181-197.
    • (1994) Faraday Disc. , vol.99 , pp. 181-197
    • Krimm, S.1    Reisdorf Jr., W.C.2
  • 28
    • 0001934802 scopus 로고    scopus 로고
    • Ab initio molecular orbital study of the amide I vibrational interactions between the peptide groups in di- and tripeptides and considerations on the conformation of the extended helix
    • Torii, H., and M. Tasumi. 1998. Ab initio molecular orbital study of the amide I vibrational interactions between the peptide groups in di- and tripeptides and considerations on the conformation of the extended helix. J. Raman Spectrosc. 29:81-86.
    • (1998) J. Raman Spectrosc. , vol.29 , pp. 81-86
    • Torii, H.1    Tasumi, M.2
  • 29
    • 0037037802 scopus 로고    scopus 로고
    • Nonlinear two-dimensional vibrational spectroscopy of peptides
    • Woutersen, S., and P. Hamm. 2002. Nonlinear two-dimensional vibrational spectroscopy of peptides. J. Phys. Condens. Matter. 14:R1035-R1062.
    • (2002) J. Phys. Condens. Matter , vol.14
    • Woutersen, S.1    Hamm, P.2
  • 30
    • 33644767320 scopus 로고    scopus 로고
    • Visualization and characterization of the infrared active amide I vibrations of proteins
    • Chung, H. S., and A. Tokmakoff. 2006. Visualization and characterization of the infrared active amide I vibrations of proteins. J. Phys. Chem. B. 110:2888-2898.
    • (2006) J. Phys. Chem. B. , vol.110 , pp. 2888-2898
    • Chung, H.S.1    Tokmakoff, A.2
  • 31
    • 34548087522 scopus 로고    scopus 로고
    • Ab initio-based exciton model of amide I vibrations in peptides: Definition, conformational dependence, and transferability
    • Gorbunov, R. D., D. S. Kosov, and G. Stock. 2005. Ab initio-based exciton model of amide I vibrations in peptides: definition, conformational dependence, and transferability. J. Chem. Phys. 122:22490405.
    • (2005) J. Chem. Phys. , vol.122 , pp. 22490405
    • Gorbunov, R.D.1    Kosov, D.S.2    Stock, G.3
  • 32
    • 0037165471 scopus 로고    scopus 로고
    • Vibrational Stark effects of nitriles. II. Physical origins of Stark effects from experiment and perturbation models
    • Andrews, S. S., and S. G. Boxer. 2002. Vibrational Stark effects of nitriles. II. Physical origins of Stark effects from experiment and perturbation models. J. Phys. Chem. A. 106:469-477.
    • (2002) J. Phys. Chem. A. , vol.106 , pp. 469-477
    • Andrews, S.S.1    Boxer, S.G.2
  • 33
    • 0142072231 scopus 로고    scopus 로고
    • Vibrational Stark effects calibrate the sensitivity of vibrational probes for electric fields in proteins
    • Suydam, I. T., and S. G. Boxer. 2003. Vibrational Stark effects calibrate the sensitivity of vibrational probes for electric fields in proteins. Biochemistry. 42:12050-12055.
    • (2003) Biochemistry , vol.42 , pp. 12050-12055
    • Suydam, I.T.1    Boxer, S.G.2
  • 34
    • 27744553101 scopus 로고    scopus 로고
    • Electric field fluctuations drive vibrational dephasing in water
    • Eaves, J. D., A. Tokmakoff, and P. L. Geissler. 2005. Electric field fluctuations drive vibrational dephasing in water. J. Phys. Chem. A. 109:9424-9436.
    • (2005) J. Phys. Chem. A. , vol.109 , pp. 9424-9436
    • Eaves, J.D.1    Tokmakoff, A.2    Geissler, P.L.3
  • 35
    • 0036088423 scopus 로고    scopus 로고
    • Coupling of the amide I modes of the glycine dipeptide
    • Hamm, P., and S. Woutersen. 2002. Coupling of the amide I modes of the glycine dipeptide. Bull. Chem. Soc. Jpn. 75:985-988.
    • (2002) Bull. Chem. Soc. Jpn. , vol.75 , pp. 985-988
    • Hamm, P.1    Woutersen, S.2
  • 36
    • 0042594667 scopus 로고    scopus 로고
    • Amide I modes of tripeptides: Hessian matrix reconstruction and isotope effects
    • Ham, S., S. Cha, J. Choi, and M. Cho. 2003. Amide I modes of tripeptides: Hessian matrix reconstruction and isotope effects. J. Chem. Phys. 119:1451-1461.
    • (2003) J. Chem. Phys. , vol.119 , pp. 1451-1461
    • Ham, S.1    Cha, S.2    Choi, J.3    Cho, M.4
  • 38
    • 25444506927 scopus 로고    scopus 로고
    • Residual native structure in a thermally denatured β-hairpin
    • Smith, A. W., H. S. Chung, Z. Ganim, and A. Tokmakoff. 2005. Residual native structure in a thermally denatured β-hairpin. J. Phys. Chem. B. 109:17025-17027.
    • (2005) J. Phys. Chem. B. , vol.109 , pp. 17025-17027
    • Smith, A.W.1    Chung, H.S.2    Ganim, Z.3    Tokmakoff, A.4
  • 39
    • 0038502170 scopus 로고    scopus 로고
    • Folding dynamics and mechanism of β-hairpin formation
    • Muñoz, V., P. A. Thompson, J. Hofrichter, and W. A. Eaton. 1997. Folding dynamics and mechanism of β-hairpin formation. Nature. 390:196-199.
    • (1997) Nature , vol.390 , pp. 196-199
    • Muñoz, V.1    Thompson, P.A.2    Hofrichter, J.3    Eaton, W.A.4
  • 42
    • 0142116251 scopus 로고    scopus 로고
    • Sampling the complex energy landscape of a simple β-hairpin
    • Wei, G., P. Derreumaux, and N. Mousseau. 2003. Sampling the complex energy landscape of a simple β-hairpin. J. Chem. Phys. 119:6403-6406.
    • (2003) J. Chem. Phys. , vol.119 , pp. 6403-6406
    • Wei, G.1    Derreumaux, P.2    Mousseau, N.3
  • 44
    • 33749050872 scopus 로고    scopus 로고
    • Absence of reptation in the high-temperature folding of the trpzip2 β-hairpin peptide
    • Pitera, J. W., I. Haque, and W. C. Swope. 2006. Absence of reptation in the high-temperature folding of the trpzip2 β-hairpin peptide. J. Chem. Phys. 124:141102.
    • (2006) J. Chem. Phys. , vol.124 , pp. 141102
    • Pitera, J.W.1    Haque, I.2    Swope, W.C.3
  • 45
    • 0035955148 scopus 로고    scopus 로고
    • Temperature-dependent helix-coil transition of an alanine based peptide
    • Huang, C. Y., J. W. Klemke, Z. Getahun, W. F. DeGrado, and F. Gai. 2001. Temperature-dependent helix-coil transition of an alanine based peptide. J. Am. Chem. Soc. 123:9235-9238.
    • (2001) J. Am. Chem. Soc. , vol.123 , pp. 9235-9238
    • Huang, C.Y.1    Klemke, J.W.2    Getahun, Z.3    DeGrado, W.F.4    Gai, F.5
  • 46
    • 0024707204 scopus 로고
    • Unusually stable helix formation in short alanine-based peptides
    • Marqusee, S., V. H. Robbins, and R. L. Baldwin. 1989. Unusually stable helix formation in short alanine-based peptides. Proc. Natl. Acad. Sci. USA. 86:5286-5290.
    • (1989) Proc. Natl. Acad. Sci. USA , vol.86 , pp. 5286-5290
    • Marqusee, S.1    Robbins, V.H.2    Baldwin, R.L.3
  • 48
    • 0031965674 scopus 로고    scopus 로고
    • Molecular dynamics simulations of hydrophobic collapse of ubiquitin
    • Alonso, D. O. V., and V. Daggett. 1998. Molecular dynamics simulations of hydrophobic collapse of ubiquitin. Protein Sci. 7:860-874.
    • (1998) Protein Sci. , vol.7 , pp. 860-874
    • Alonso, D.O.V.1    Daggett, V.2
  • 49
    • 2442589387 scopus 로고    scopus 로고
    • Signatures of β-sheet secondary structures in linear and two-dimensional infrared spectroscopy
    • Cheatum, C. M., A. Tokmakoff, and J. Knoester. 2004. Signatures of β-sheet secondary structures in linear and two-dimensional infrared spectroscopy. J. Chem. Phys. 120:8201-8215.
    • (2004) J. Chem. Phys. , vol.120 , pp. 8201-8215
    • Cheatum, C.M.1    Tokmakoff, A.2    Knoester, J.3
  • 50
    • 6344235637 scopus 로고    scopus 로고
    • Nonlinear infrared spectroscopy of protein conformational change during thermal unfolding
    • Chung, H. S., M. Khalil, and A. Tokmakoff. 2004. Nonlinear infrared spectroscopy of protein conformational change during thermal unfolding. J. Phys. Chem. B. 108:15332-15342.
    • (2004) J. Phys. Chem. B. , vol.108 , pp. 15332-15342
    • Chung, H.S.1    Khalil, M.2    Tokmakoff, A.3
  • 51
    • 0030040589 scopus 로고    scopus 로고
    • Structure of bovine pancreatic trypsin inhibitor at 125 K definition of carboxyl-terminal residues Gly-57 and Ala-58
    • Parkin, S., B. Rupp, and H. Hope. 1996. Structure of bovine pancreatic trypsin inhibitor at 125 K definition of carboxyl-terminal residues Gly-57 and Ala-58. Acta Crystallogr. D52:18-29.
    • (1996) Acta Crystallogr. , vol.D52 , pp. 18-29
    • Parkin, S.1    Rupp, B.2    Hope, H.3
  • 52
    • 19944365233 scopus 로고    scopus 로고
    • Collective oscillations and the linear and two-dimensional infrared spectra of inhomogeneous β-sheets
    • Dijkstra, A. G., and J. Knoester. 2005. Collective oscillations and the linear and two-dimensional infrared spectra of inhomogeneous β-sheets. J. Phys. Chem. B. 109:9787-9798.
    • (2005) J. Phys. Chem. B. , vol.109 , pp. 9787-9798
    • Dijkstra, A.G.1    Knoester, J.2
  • 53
    • 0003871536 scopus 로고    scopus 로고
    • Becker, O. M., A. D. MacKerell, Jr., B. Roux, and M. Watanabe (editors). Marcel Dekker, New York
    • Becker, O. M., A. D. MacKerell, Jr., B. Roux, and M. Watanabe (editors). 2001. Computational Biochemistry and Biophysics. Marcel Dekker, New York.
    • (2001) Computational Biochemistry and Biophysics
  • 54
    • 4444351490 scopus 로고    scopus 로고
    • Empirical force fields for biological macromolecules: Overview and issues
    • MacKerell, A. D., Jr. 2004. Empirical force fields for biological macromolecules: overview and issues. J. Comput. Chem. 25:1584-1604.
    • (2004) J. Comput. Chem. , vol.25 , pp. 1584-1604
    • MacKerell Jr., A.D.1
  • 55
    • 31944442794 scopus 로고    scopus 로고
    • Folding mechanism of β-hairpins studied by replica exchange molecular simulations
    • Zhang, J., M. Qin, and W. Wang. 2006. Folding mechanism of β-hairpins studied by replica exchange molecular simulations. Proteins. 62:672-685.
    • (2006) Proteins , vol.62 , pp. 672-685
    • Zhang, J.1    Qin, M.2    Wang, W.3
  • 56
    • 11244289252 scopus 로고    scopus 로고
    • Kinetic pathways of β-hairpin (un)folding in explicit solvent
    • Bolhuis, P. G. 2005. Kinetic pathways of β-hairpin (un)folding in explicit solvent. Biophys. J. 88:50-61.
    • (2005) Biophys. J. , vol.88 , pp. 50-61
    • Bolhuis, P.G.1
  • 57
    • 0037059017 scopus 로고    scopus 로고
    • Evidence of turn and salt bridge contributions to β-hairpin stability: MD simulations of C-terminal fragment from the B1 domain of protein G
    • Tsai, J., and M. Levitt. 2002. Evidence of turn and salt bridge contributions to β-hairpin stability: MD simulations of C-terminal fragment from the B1 domain of protein G. Biophys. Chem. 101-102:187-201.
    • (2002) Biophys. Chem. , vol.101-102 , pp. 187-201
    • Tsai, J.1    Levitt, M.2
  • 58
    • 0037076337 scopus 로고    scopus 로고
    • Drying-induced hydrophobic polymer collapse
    • ten Wolde, P. R., and D. Chandler. 2002. Drying-induced hydrophobic polymer collapse. Proc. Natl. Acad. Sci. USA. 99:6539-6543.
    • (2002) Proc. Natl. Acad. Sci. USA , vol.99 , pp. 6539-6543
    • Ten Wolde, P.R.1    Chandler, D.2
  • 59
    • 0037154268 scopus 로고    scopus 로고
    • Protein folding mediated by solvation: Water expulsion and formation of the hydrophobic core occur after the structural collapse
    • Cheung, M. S., A. E. Garća, and J. N. Onuchic. 2002. Protein folding mediated by solvation: water expulsion and formation of the hydrophobic core occur after the structural collapse. Proc. Natl. Acad. Sci. USA. 99:685-690.
    • (2002) Proc. Natl. Acad. Sci. USA , vol.99 , pp. 685-690
    • Cheung, M.S.1    Garća, A.E.2    Onuchic, J.N.3
  • 61
    • 24144479792 scopus 로고    scopus 로고
    • Solvation free energies of amino acid side chain analogs for common molecular mechanics water models
    • Shirts, M. R., and V. S. Pande. 2005. Solvation free energies of amino acid side chain analogs for common molecular mechanics water models. J. Chem. Phys. 122:134508.
    • (2005) J. Chem. Phys. , vol.122 , pp. 134508
    • Shirts, M.R.1    Pande, V.S.2
  • 62
    • 0033917135 scopus 로고    scopus 로고
    • The key event in force-induced unfolding of titin's immunoglobulin domains
    • Lu, H., and K. Schulten. 2000. The key event in force-induced unfolding of titin's immunoglobulin domains. Biophys. J. 79:51-65.
    • (2000) Biophys. J. , vol.79 , pp. 51-65
    • Lu, H.1    Schulten, K.2
  • 63
    • 0346034894 scopus 로고    scopus 로고
    • Vibrational spectroscopy and the development of new force fields for biological molecules
    • Gerber, R. B., G. M. Chaban, S. K. Gregurick, and B. Brauer. 2003. Vibrational spectroscopy and the development of new force fields for biological molecules. Biopolymers. 68:370-382.
    • (2003) Biopolymers , vol.68 , pp. 370-382
    • Gerber, R.B.1    Chaban, G.M.2    Gregurick, S.K.3    Brauer, B.4
  • 64
    • 10844273996 scopus 로고    scopus 로고
    • Stochastic Liouville equation simulation of multidimensional vibrational line shapes of trialanine
    • Jansen, T. l. C., W. Zhuang, and S. Mukamel. 2004. Stochastic Liouville equation simulation of multidimensional vibrational line shapes of trialanine. J. Chem. Phys. 121:10577-10598.
    • (2004) J. Chem. Phys. , vol.121 , pp. 10577-10598
    • Jansen, T.L.C.1    Zhuang, W.2    Mukamel, S.3
  • 65
    • 27744526374 scopus 로고    scopus 로고
    • Electrostatic DFT map for the complete vibrational amide band of NMA
    • Hayashi, T., W. Zhuang, and S. Mukamel. 2005. Electrostatic DFT map for the complete vibrational amide band of NMA. J. Phys. Chem. A. 109:9747-9759.
    • (2005) J. Phys. Chem. A. , vol.109 , pp. 9747-9759
    • Hayashi, T.1    Zhuang, W.2    Mukamel, S.3
  • 66
    • 27944457288 scopus 로고    scopus 로고
    • Theoretical studies of the amide I vibrational frequencies of [Leu]-enkephalin
    • Watson, T. M., and J. D. Hirst. 2005. Theoretical studies of the amide I vibrational frequencies of [Leu]-enkephalin. Mol. Phys. 103:1531-1546.
    • (2005) Mol. Phys. , vol.103 , pp. 1531-1546
    • Watson, T.M.1    Hirst, J.D.2


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.