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Geometry and excitation energy fluctuations of NMA in aqueous solution with CHARMM, AMBER, OPLS, and GROMOS force fields: Implications for protein ultraviolet spectra simulation

Journal Article


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Abstract


  • Molecular dynamics (MD) simulations are performed for N-methylacetamide (NMA) in water at 300 K with different force fields. Compared to the three all-atom force fields (CHARMM22, AMBER03, and OPLS-AA), the united-atom force field (GROMOS96) pre- dicts a broader distribution of the peptide OCNH dehedral angle. A map constructed by fitting the np and pp transition energies as quadratic functions of the NMA geometric variables is used to simulate the excitation energy fluctuations. GROMOS96 predicts blue shifted np and pp energies and stronger fluctuations compared to the other three force fields, which indicates that different force fields may predict different spectral lineshapes for proteins.

Authors


  •   Li, Zhenyu (external author)
  •   Yu, Haibo
  •   Zhuang, Wei (external author)
  •   Mukamel, Shaul (external author)

Publication Date


  • 2008

Citation


  • Li, Z., Yu, H., Zhuang, W. & Mukamel, S. (2008). Geometry and excitation energy fluctuations of NMA in aqueous solution with CHARMM, AMBER, OPLS, and GROMOS force fields: Implications for protein ultraviolet spectra simulation. Chemical Physics Letters, 452 (1-3), 78-83.

Scopus Eid


  • 2-s2.0-38649106130

Ro Full-text Url


  • http://ro.uow.edu.au/cgi/viewcontent.cgi?article=1879&context=scipapers

Ro Metadata Url


  • http://ro.uow.edu.au/scipapers/840

Has Global Citation Frequency


Number Of Pages


  • 5

Start Page


  • 78

End Page


  • 83

Volume


  • 452

Issue


  • 1-3

Abstract


  • Molecular dynamics (MD) simulations are performed for N-methylacetamide (NMA) in water at 300 K with different force fields. Compared to the three all-atom force fields (CHARMM22, AMBER03, and OPLS-AA), the united-atom force field (GROMOS96) pre- dicts a broader distribution of the peptide OCNH dehedral angle. A map constructed by fitting the np and pp transition energies as quadratic functions of the NMA geometric variables is used to simulate the excitation energy fluctuations. GROMOS96 predicts blue shifted np and pp energies and stronger fluctuations compared to the other three force fields, which indicates that different force fields may predict different spectral lineshapes for proteins.

Authors


  •   Li, Zhenyu (external author)
  •   Yu, Haibo
  •   Zhuang, Wei (external author)
  •   Mukamel, Shaul (external author)

Publication Date


  • 2008

Citation


  • Li, Z., Yu, H., Zhuang, W. & Mukamel, S. (2008). Geometry and excitation energy fluctuations of NMA in aqueous solution with CHARMM, AMBER, OPLS, and GROMOS force fields: Implications for protein ultraviolet spectra simulation. Chemical Physics Letters, 452 (1-3), 78-83.

Scopus Eid


  • 2-s2.0-38649106130

Ro Full-text Url


  • http://ro.uow.edu.au/cgi/viewcontent.cgi?article=1879&context=scipapers

Ro Metadata Url


  • http://ro.uow.edu.au/scipapers/840

Has Global Citation Frequency


Number Of Pages


  • 5

Start Page


  • 78

End Page


  • 83

Volume


  • 452

Issue


  • 1-3