Single Molecule FRET analysis and modeling

DFG Proposal. Joint Project by Uli Nienhaus (Experiments), Helmut Grubmüller (Simulation+Modeling) and Frank Noe (Modeling+Theory).

Goals / Program


  • Establish synthesis and measurement process for the system of choice
  • Record Single-Molecule FRET data of immobilized molecules.
  • Several Conditions (Mutants, Ions, ...)
  • Perhaps Multi-Color FRET?
  • Perhaps Vesicle Immobilization?


  • Molecular Dynamics Simulations of the system in different conformations -> Modeling the Structure and Flexibility of these conformations.
  • Conformational Flooding / Metadynamics simulatinos in order to explore new conformations.
  • Simulation of the system with fluorescent dyes in order to obtain a orientational distribution of the dyes to be used in the theory.
  • FEP calculations to estimate barriers between conformations.


  • Development of statistical methods to compute the most likely dye-distance trajectory from the experimental photon count trajectory, taking dye orientation into account.
  • Development of statistical methods to identify the conformations that are hidden in the experimental data, their flexibility in terms of the dye distance, and their transition rates.
  • Suggestion of Distance constraints to be used for the dye positions in the simulation, so as to explore different conformations.
  • Combination of structural information from MD simulation + transition rates from experiment into a joint multi-state model.
  • Suggestion of new experiments in order to optimally refine the model.


  • 31 July: Helmut and Frank should suggest a number of interesting systems to work with. Uli will decide whether that is feasible in experimental practice. Ideas:
    • Simple test system with few conformations: 2 or 3 Polyproline segments with flexible linkers (e.g. Glycin) in between. This can probably have only a few conformations and will have large distance changes (good for FRET).
    • A biologically interesting large System.
  • 15 August: Agree on a detailed list of goals and the interfaces between the three groups. Agree on how to sell the proposal (Is the goal mainly biological interest in the used system, methodological/technical advance, or understanding the energy landscape?)
  • 30 August: Write Proposal


Topic revision: r3 - 15 Jun 2012, AntoniaMey
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