| Autor: |
Shaw RA; Department of Chemistry, University of Sheffield, Sheffield S3 7HF, U.K.; Present address: ARC Centre of Excellence in Exciton Science, School of Science, RMIT University, Melbourne, VIC 3000, Australia., Johnston-Wood T; Department of Chemistry, University of Sheffield, Sheffield S3 7HF, U.K.; Present address: Department of Chemistry, Physical and Theoretical Chemistry Laboratory, University of Oxford, Oxford OX1 3QZ, U.K., Ambrose B; Department of Chemistry, University of Sheffield, Sheffield S3 7HF, U.K., Craggs TD; Department of Chemistry, University of Sheffield, Sheffield S3 7HF, U.K., Hill JG; Department of Chemistry, University of Sheffield, Sheffield S3 7HF, U.K. |
| Abstrakt: |
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. |
