Abstract
We present CHARMM-compatible force field parameters for a series of fluorescent dyes from the Alexa, Atto, and Cy families, commonly used in Förster resonance energy transfer (FRET) experiments. These dyes are routinely used in experiments to resolve the dynamics of proteins and nucleic acids at the nanoscale. However, little is known about the accuracy of the theoretical approximations used in determining the dynamics from the spectroscopic data. Molecular dynamics simulations can provide valuable insights into these dynamics at an atomistic level, but this requires accurate parameters for the dyes. The complex structure of the dyes and the importance of this in determining their spectroscopic properties mean that parameters generated by analogy to existing parameters do not give meaningful results. Through validation relative to quantum chemical calculation and experiments, the new parameters are shown to significantly outperform those that can be generated automatically, giving better agreement in both the charge distributions and structural properties. These improvements, in particular with regard to orientation of the dipole moments on the dyes, are vital for accurate simulation of FRET processes.
Highlights
The study of the structure and dynamics of biochemical systems, such as DNA and proteins, is a complex but important field of research
The procedure is highly dependent on the choice of starting guess: we found that in particular for the bonds involved in the conjugated portions of the dye, the guesses generated by CHARMM general force-field (CGenFF) are too large and lead to unphysical rigidity
There is a paucity of experimental data on Förster resonance energy transfer (FRET) dyes with which we can meaningfully compare the results from the molecular dynamics (MD) simulations
Summary
The study of the structure and dynamics of biochemical systems, such as DNA and proteins, is a complex but important field of research. Journal of Chemical Theory and Computation lifetime.[7,8] the FRET technique has been shown to give accurate distance measurements within a 3 Å precision for separations between 30 and 100 Å,9 which has allowed the use of such measurements to determine biomolecular structure and dynamics.[8,10−12] the reliability of FRET below 40 Å is unknown This is thought to be partially due to the validity of assuming the isotropic limit of κ2 in this regime.[13,14]. The fluorescent dyes used experimentally are varied and many, depending on the absorption and emission frequencies needed for the particular experiment These will usually be attached to a protein or nucleic acid via some kind of organic linker. These types were based on those generated by the CGenFF program adapted to fully exploit the similarities in structure between the different
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