Influence of the Fluorophore Mobility on Distance Measurements by Gas-Phase FRET

Abstract

Gas-phase Forster resonance energy transfer (FRET) combines mass spectrometry and fluorescence spectroscopy for the conformational analysis of mass-selected biomolecular ions. In FRET, fluorophore pairs are typically covalently attached to a biomolecule using short linkers, which affect the mobility of the dye and the relative orientation of the transition dipole moments of the donor and acceptor. Intramolecular interactions may further influence the range of motion. Yet, little is known about this factor, despite the importance of intramolecular interactions in the absence of a solvent. In this study, we applied transition metal ion FRET (tmFRET) to probe the mobility of a single chromophore pair (Rhodamine 110 and Cu 2+ ) as a function of linker lengths to assess the relevance of intramolecular interactions. Increasing FRET efficiencies were observed with increasing linker length, ranging from 5% (2 atoms) to 28% (13 atoms). To rationalize this trend, we profiled the conformational landscape of each model system using molecular dynamics (MD) simulations. We captured intramolecular interactions that promote a population shift toward smaller donor−acceptor separation for longer linker lengths and induce a significant increase in the acceptor's transition dipole moment. The presented methodology is a first step toward the explicit consideration of a fluorophore's range of motion in the interpretation of gas-phase FRET experiments.

General Graph Neural Network Based Implicit Solvation Model for Organic Molecules in Water

“…Molecular dynamics (MD) is a widely used approach that employs Newton's equation of motion to gain insights into the dynamical processes of molecules, ultimately allowing to rationalize experimental findings and to support drug discovery in general (for examples see Refs. [1][2][3]). Much progress has been made to efficiently explore the conformational space of molecules in a given environment.…”

A general graph neural network based implicit solvation model for organic molecules in water

“…Classical molecular dynamics (MD) is a widely used approach that employs Newton's equation of motion to provide insights into the dynamical processes of molecules, ultimately allowing rationalization of experimental findings and supporting drug discovery in general (for examples see ref. 1–3). Much progress has been made in efficiently exploring the conformational space of molecules in a given environment.…”

Probing the Stability of a β-Hairpin Scaffold after Desolvation

“…In their recent work, Metternich et al developed a novel simulation and analysis pipeline for the prediction of FRET efficiencies in the gas phase . Because the system studied here is similar, we were able to use the optimized procedure found by Metternich et al to further investigate GB1p in silico .…”

“…The estimation of the FRET efficiencies was performed using identical parameters. Notably also the theoretical R 0 , a fitting parameter, was kept the same . Hence, applying this procedure did not involve any fine-tuning of parameters and is an unbiased way of estimating the FRET efficiencies.…”