Implementing electrostatic polarization cannot fill the gap between experimental and theoretical measurements for the ultrafast fluorescence decay of myoglobin

Bingbing Lin, Ya Gao, Yongxiu Li, John Zhang, Ye Mei

Research output: Contribution to journalArticle

Abstract

Over the past few years, time-dependent ultrafast fluorescence spectroscopy method has been applied to the study of protein dynamics. However, observations from these experiments are in a controversy with other experimental studies. Participating of theoretical methods in this debate has not reconciled the contradiction, because the predicted initial relaxation from computer simulations is one-order faster than the ultrafast fluorescence spectroscopy experiment. In those simulations, pairwise force fields are employed, which have been shown to underestimate the roughness of the free energy landscape. Therefore, the relaxation rate of protein and water molecules under pairwise force fields is falsely exaggerated. In this work, we compared the relaxations of tryptophan/environment interaction under linear response approximation employing pairwise, polarized, and polarizable force fields. Results show that although the relaxation can be slowed down to a certain extent, the large gap between experiment and theory still cannot be filled.

Original languageEnglish (US)
Article number2189
JournalJournal of Molecular Modeling
Volume20
Issue number4
DOIs
StatePublished - 2014

Fingerprint

myoglobin
Myoglobin
Electrostatics
Fluorescence
Fluorescence spectroscopy
Polarization
electrostatics
field theory (physics)
fluorescence
decay
polarization
Proteins
Experiments
proteins
Tryptophan
Free energy
tryptophan
Surface roughness
spectroscopy
Molecules

Keywords

  • Electrostatic polarization
  • Myoglobin
  • Ultrafast fluorescence decay

ASJC Scopus subject areas

  • Physical and Theoretical Chemistry
  • Computer Science Applications
  • Computational Theory and Mathematics
  • Catalysis
  • Organic Chemistry
  • Inorganic Chemistry

Cite this

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abstract = "Over the past few years, time-dependent ultrafast fluorescence spectroscopy method has been applied to the study of protein dynamics. However, observations from these experiments are in a controversy with other experimental studies. Participating of theoretical methods in this debate has not reconciled the contradiction, because the predicted initial relaxation from computer simulations is one-order faster than the ultrafast fluorescence spectroscopy experiment. In those simulations, pairwise force fields are employed, which have been shown to underestimate the roughness of the free energy landscape. Therefore, the relaxation rate of protein and water molecules under pairwise force fields is falsely exaggerated. In this work, we compared the relaxations of tryptophan/environment interaction under linear response approximation employing pairwise, polarized, and polarizable force fields. Results show that although the relaxation can be slowed down to a certain extent, the large gap between experiment and theory still cannot be filled.",
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AU - Gao, Ya

AU - Li, Yongxiu

AU - Zhang, John

AU - Mei, Ye

PY - 2014

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AB - Over the past few years, time-dependent ultrafast fluorescence spectroscopy method has been applied to the study of protein dynamics. However, observations from these experiments are in a controversy with other experimental studies. Participating of theoretical methods in this debate has not reconciled the contradiction, because the predicted initial relaxation from computer simulations is one-order faster than the ultrafast fluorescence spectroscopy experiment. In those simulations, pairwise force fields are employed, which have been shown to underestimate the roughness of the free energy landscape. Therefore, the relaxation rate of protein and water molecules under pairwise force fields is falsely exaggerated. In this work, we compared the relaxations of tryptophan/environment interaction under linear response approximation employing pairwise, polarized, and polarizable force fields. Results show that although the relaxation can be slowed down to a certain extent, the large gap between experiment and theory still cannot be filled.

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