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Höfling, Martin (2011): Simulations and Experiments: How close can we get?. Dissertation, LMU München: Faculty of Physics
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Abstract

The interactions between biomolecules and their environment can be studied by experiments and simulations. Results from experiments and simulations are often interpretations based on the raw data. For an accurate comparison of both approaches, the interpretation of the raw data from experiments and simulation have to be in compliance. The design of such simulations and interpretation of raw data is demonstrated in this thesis for two examples; fluorescence resonance energy transfer (FRET) experiments and surface adsorption of biomolecules on inorganic surfaces like gold. FRET experiments allow to probe molecular distances via the distance-dependent energy transfer efficiency from an excited donor dye to its acceptor counterpart. In single molecule settings, not only average distances, but also distance distributions or even fluctuations can be probed, providing a powerful tool to study flexibilities and structural changes in biomolecules. However, the measured energy transfer efficiency does not only depend on the distance between the two dyes, but also on their mutual orientation, which is typically inaccessible to experiments. Thus, assumptions on the orientation distributions and averages have to be employed, which severely limit the accuracy of the distance distributions extracted from FRET experiments alone. In this work, I combined efficiency distributions from FRET experiments with dye orientation statistics from molecular dynamics (MD) simulations to calculate improved estimates of the distance distributions. From the time-dependent mutual dye orientations, the FRET efficiency was calculated and the statistics of individual photo-absorption, FRET, and photo-emission events were determined from subsequent Monte Carlo (MC) simulations. All recorded emission events were then collected to bursts from which efficiencies were calculated in close resemblance to the actual FRET experiment. The feasibility of this approach has been tested by direct comparison to experimental data. As my test system, I chose a poly-proline chain with Alexa 488 and Alexa 594 dyes attached. Quantitative agreement of calculated efficiency distributions from simulations with the experimental ones was obtained. In addition, the presence of cis-isomers and specific dye conformations were identified as the sources of the experimentally observed heterogeneity. This agreement of in silico FRET with experiments allows employment of the dye orientation dynamics from simulations in the distance reconstruction. For multiple levels of approximation, the dye orientation dynamics was used in dye orientation models. At each level, fewer assumptions were applied to the dye orientation model. Each model was then used to reconstruct distance distributions from experimental efficiency distributions. Comparison of reconstructed distance distributions with those from simulations revealed a systematically improved accuracy of the reconstruction in conjunction with a reduction of model assumptions. This result demonstrates that dye orientations from MD simulations, combined with MC photon generation, can indeed be used to improve the accuracy of distance distribution reconstruction from experimental FRET efficiencies. A second example of simulations and interpretation in compliance with experiments are the studies of protein adsorption on gold surfaces. Interactions between biomolecules and inorganic surfaces, e.g. during the biomineralization of bone, are fundamental for multicellular organisms. Moreover, understanding these interactions is the basis for biotechnological applications such as biochips or nano-sensing. In the framework of the PROSURF project, a multi-scale approach for the simulation of biomolecular adsorption was implemented. First, parameters for MD simulations were derived from ab initio calculations. These parameters were then applied to simulate the adsorption of single amino acids and to calculate their adsorption free energy profiles. For the screening of adsorbed protein conformations, rigid body Brownian dynamics (BD) docking on surfaces was benchmarked with the free energy profiles from the MD simulations. Comparison of the protein adsorption rate from surface plasmon resonance experiments and BD docking yielded good agreement and therefore justifies the multi-scale approach. Additionally, MD simulations of protein adsorption on gold surfaces revealed an unexpected importance of positively charged residues on the surface for the initial adsorption steps. The multi-scale approach presented here allows the study of biomolecular interactions with inorganic surfaces consistently at multiple levels of theory: Atomistic details of the adsorption process can be studied by MD simulations whereas BD allows the extensive screening of protein libraries or adsorption geometries. In summary, compliance of simulation and experimental setup allows benchmarking of the simulation accuracy by comparison to experiments. In contrast to employing experiments alone, the combination of experiments and simulations enhances the accuracy of interpreted results from experimental raw data.