&lt;title&gt;Simulation of solvent dynamics effects on the fluorescence of 3-methylindole in water&lt;/title&gt;

Muíño, Pedro L.; Harris, D. G.; Berryhill, Jerome; Hudson, Bruce S.; Callis, Patrik R.

doi:10.1117/12.58282

Cited by 12 publications

(19 citation statements)

References 12 publications

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“…INDO/S-CIS has proven effective in a large number of cases, including our previous studies (Muiño et al, 1992;Muiño and Callis, 1994b, c;Sreerama et al, 1994) and in several impressive applications to large systems, some similar to ours. Some examples include hybrid simulations of the photosynthetic reaction center (Gehlen et al, 1994;Marchi et al, 1993;Thompson and Zerner, 1991;Thompson and Schenter, 1995), path integral molecular dynamics simulations of tryptophan in water (using CNDO/S) (Simonson et al, 1997), electronic spectra of uracils (Broo et al, 1997), and inorganic charge-transfer spectra (Zeng et al, 1994).…”

Section: How Realistic Is the Model?supporting

confidence: 68%

Mechanisms of Tryptophan Fluorescence Shifts in Proteins

Vivian

Callis

2001

Biophysical Journal

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Tryptophan fluorescence wavelength is widely used as a tool to monitor changes in proteins and to make inferences regarding local structure and dynamics. We have predicted the fluorescence wavelengths of 19 tryptophans in 16 proteins, starting with crystal structures and using a hybrid quantum mechanical-classical molecular dynamics method with the assumption that only electrostatic interactions of the tryptophan ring electron density with the surrounding protein and solvent affect the transition energy. With only one adjustable parameter, the scaling of the quantum mechanical atomic charges as seen by the protein/solvent environment, the mean absolute deviation between predicted and observed fluorescence maximum wavelength is 6 nm. The modeling of electrostatic interactions, including hydration, in proteins is vital to understanding function and structure, and this study helps to assess the effectiveness of current electrostatic models.

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Section: How Realistic Is the Model?supporting

confidence: 68%

Mechanisms of Tryptophan Fluorescence Shifts in Proteins

Vivian

Callis

2001

Biophysical Journal

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1,268

1,128

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“…7 They have low polarity in the ground state and also have two excited states with similar node structure (L a and L b ) and relatively small separation. The upper of these states † ETH Zürich.…”

Section: Experimental and Computational Methodsmentioning

confidence: 99%

Vibronic Coupling and Microscopic Solvation of 1-Naphthol

1996

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Vibronic structure in the S 1 T S 0 absorption and fluorescence spectra of jet-cooled 1-naphthol is reexamined. Selective excitation of bands 410 or 414 cm -1 above the S 1 ( 1 L b ) origin leads to atypical, highly structured fluorescence, indicating that strong vibrational mixing occurs. From the intensity patterns and the appearance of otherwise dark modes, a large normal coordinate (Duschinsky) rotation is inferred. Vibronic coupling with the second electronic excited state ( 1 L a ) is proposed as the cause of the rotation, as supported by absorption/ emission mirror asymmetry, rotationally resolved spectra, and calculations. Coupled molecular dynamics and semiempirical simulations suggest that this vibronic coupling plays a major role in the solvent-controlled excited state proton transfer of naphthol in water by increasing the solvent-solute interaction. With vibronic mixing, L a /L b state inversion is predicted correctly as a result of coupled evolution of the solvent and solute. The excited naphthol charge distribution and the orientation of nearby water molecules change together, leading to large naphthol dipole moments. The model results are supported by the relevant data on 1-naphthol in water and water clusters.

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“…24 Charge assignments for the Phe side chain were taken from studies of Phe-water interactions. 25 The total energy is the sum of all pairwise electrostatic and van der Waals interactions.…”

Section: Hydrogen Bond Energeticsmentioning

confidence: 99%

Aromatic interactions in homeodomains contribute to the low quantum yield of a conserved, buried tryptophan

Nanda

Brand

2000

Proteins

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Trp 48, a conserved, buried residue commonly found in the hydrophobic core of homeodomains, has an unusually low fluorescence quantum yield. Chemical denaturation of Drosophila homeodomains Engrailed and Antennapedia(C39S) result in a four-fold increase in quantum yield, while unfolding of Ultrabithorax causes a twenty-fold enhancement. Global analysis of time-resolved fluorescence decay monitored at multiple emission wavelengths reveals sub-nanosecond lifetime components which dominate the overall intensity. Based on structure and sequence analysis of several homeodomains, we deduce that quenching is due to a transient, excited-state NH ellipsis pi hydrogen bond involving Trp 48 and a conserved aromatic residue at position 8. Additionally, both time-resolved fluorescence of indole-benzene mixtures and an electrostatic model of the proposed tryptophan-aromatic interaction substantiate different aspects of this mechanism. A survey of the Protein Data Bank reveals many proteins with tryptophan-aromatic pairs where the indole nitrogen participates in a NH ellipsis pi hydrogen bond with the ring of another aromatic residue. Chemical denaturation of one protein found in this survey, human fibronectin type III module 10, causes an enhancement of the fluorescence quantum yield. This unique interaction has implications for many other systems and may be useful for studying larger, multi-tryptophan containing proteins.

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<title>Simulation of solvent dynamics effects on the fluorescence of 3-methylindole in water</title>

Cited by 12 publications

References 12 publications

Mechanisms of Tryptophan Fluorescence Shifts in Proteins

Mechanisms of Tryptophan Fluorescence Shifts in Proteins

Vibronic Coupling and Microscopic Solvation of 1-Naphthol

Aromatic interactions in homeodomains contribute to the low quantum yield of a conserved, buried tryptophan

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