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Cyan fluorescent protein: molecular dynamics, simulations, and electronic absorption spectrum
Isabelle Demachy1, Jacqueline Ridard, Hélène Laguitton-Pasquier
1Laboratoire de Chimie Physique, UMR 8000 CNRS-Université de Paris-Sud, 91405 Orsay Cedex, France.
The Journal of Physical Chemistry. B
|December 27, 2005
Summary
Molecular dynamics simulations reveal enhanced cyan fluorescent protein (ECFP) conformations remain stable. Despite differing hydrogen bonds, ECFP
Area of Science:
- Biophysics
- Computational Chemistry
- Spectroscopy
Background:
- Enhanced cyan fluorescent protein (ECFP) is a vital mutant of green fluorescent protein (GFP).
- Understanding ECFP's dynamics and spectral properties is crucial for its application in biological imaging.
- Previous studies have not fully elucidated the relationship between ECFP's structural dynamics and its electronic absorption spectrum.
Purpose of the Study:
- To investigate the molecular dynamics and electronic absorption spectrum of enhanced cyan fluorescent protein (ECFP).
- To analyze the stability of ECFP's two X-ray conformations (A' and B') under simulation conditions.
- To explore the influence of hydrogen-bond networks and protein environment on ECFP's spectral characteristics.
Main Methods:
- A 1-nanosecond molecular dynamics (MD) simulation was performed on ECFP, considering two X-ray conformations (A' and B').
- Titratable residues were set to standard protonation states at neutral pH, and the protein was solvated with water and counterions.
- Time-dependent density functional theory (TDDFT) calculations were used to determine electronic transition energies from 160 MD snapshots.
Main Results:
- Both ECFP conformations (A' and B') demonstrated stability throughout the 1 ns simulation.
- Significant differences in hydrogen-bond networks were observed between conformations A' and B', particularly around the chromophore's indolic nitrogen.
- Despite structural differences, TDDFT calculations showed that conformations A' and B' yield very similar electronic absorption spectra.
Conclusions:
- The stability of ECFP's distinct conformations suggests a robust structural framework.
- The similarity in spectra, despite varied hydrogen-bonding, indicates a limited influence of local structural changes on ECFP's electronic transition.
- Weak charge transfer and a minimal electrostatic field near the chromophore contribute to the spectral similarity in the simulated ECFP environment.