Simulation and Analysis of Protein-Fluorophore Systems for Comparison with Fluorescence Spectroscopy Data

Proteine sind die Grundbausteine des Lebens auf molekularer Ebene und wichtig für viele biologische Funktionen wie den Transport von Molekülen, Zellbewegungen oder die Katalyse von chemischen Reaktionen. So transportiert das Protein Hämoglobin beispielsweise den Sauerstoff im menschlichen Blut. Störungen der Proteinfunktionen können schwere degenerative Krankheiten wie zum Beispiel die Parkinson-, Huntington- oder Alzheimer-Krankheit verursachen. Das Verständnis von Proteinfunktionen, ihrer Struktur und Dynamik ist daher ein wichtiges Forschungsgebiet in Biologie, Pharmakologie und Medizin. Da Proteine aufgrund ihrer geringen Größe nicht mit Lichtmikroskopie beobachtet werden können, verwendet man stattdessen indirekte Methoden. Eine dieser Methoden macht sich den Förster-Resonanzenergietransfer (FRET) zunutze, um damit Proteindynamik und andere molekulare Prozesse in vitro und in vivo zu untersuchen. Die Methode wird außerdem auch in Biosensoren zur Messung der Konzentrationen von kleinen Biomolekülen wie zum Beispiel Glukose eingesetzt. Die dabei verwendeten Systeme aus Proteinen und Fluorophoren unterliegen physikalischen Prozessen wie Molekulardynamik und Photophysik. Da man diese Mechanismen nicht direkt beobachten kann, ist die Funktionsweise vieler Systeme noch nicht vollständig verstanden. Molekulare Simulationen können diese experimentellen Messungen ergänzen. Sie ermöglichen einen Einblick in molekulare Systeme und ihre Funktion auf atomarer Ebene. Die bisherigen Modellierungsmethoden für Protein-Fluorophor-Systeme sind größtenteils Näherungen, die nur für spezielle Anwendungen verwendbar sind oder zu rechenaufwändig um alle relevanten Bewegungen zu modellieren. Diese Arbeit stellt eine neue Methode für die Simulation der Dynamik in Protein-Fluorophor-Systemen vor. Sie basiert auf recheneffizienten vereinfachten Molekulardynamiksimulationen. Mit nur wenigen Parametern bietet die Methode eine realistische Beschreibung des Systems, die quantitativ mit Experimenten übereinstimmt. Sie ermöglicht den direkten Vergleich von Simulationen mit experimentellen Daten und somit eine bessere Planung und Interpretation von Experimenten. Gleichzeitig liefert sie Informationen über die zugrundeliegende Dynamik der Systeme. Diese Arbeit präsentiert ein systematisches Simulationsprotokoll für die Modellierung von Protein-Fluorophor-Systemen in silico, welches für die Erforschung von vielen biologisch relevanten Anwendungen verwendet werden kann. Sie zeigt wie Experimente und Simulationen einander ergänzen, um neue Einblicke in Dynamik und Funktion von Biomolekülen zu erhalten

Rapid interpretation of small-angle X-ray scattering data

The fundamental aim of structural analyses in biophysics is to reveal a mutual relation between a molecule’s dynamic structure and its physiological function. Small-angle X-ray scattering (SAXS) is an experimental technique for structural characterization of macromolecules in solution and enables time-resolved analysis of conformational changes under physiological conditions. As such experiments measure spatially averaged low-resolution scattering intensities only, the sparse information obtained is not sufficient to uniquely reconstruct a three-dimensional atomistic model. Here, we integrate the information from SAXS into molecular dynamics simulations using computationally efficient native structure-based models. Dynamically fitting an initial structure towards a scattering intensity, such simulations produce atomistic models in agreement with the target data. In this way, SAXS data can be rapidly interpreted while retaining physico-chemical knowledge and sampling power of the underlying force field. We demonstrate our method’s performance using the example of three protein systems. Simulations are faster than full molecular dynamics approaches by more than two orders of magnitude and consistently achieve comparable accuracy. Computational demands are reduced sufficiently to run the simulations on commodity desktop computers instead of high-performance computing systems. These results underline that scattering-guided structure-based simulations provide a suitable framework for rapid early-stage refinement of structures towards SAXS data with particular focus on minimal computational resources and time.</div

Structural analysis of a genetically encoded fret biosensor by SAXS and MD simulations

Inspired by the modular architecture of natural signaling proteins, ligand binding proteins are equipped with two fluorescent proteins (FPs) in order to obtain Förster resonance energy transfer (FRET)-based biosensors. Here, we investigated a glucose sensor where the donor and acceptor FPs were attached to a glucose binding protein using a variety of different linker sequences. For three resulting sensor constructs the corresponding glucose induced conformational changes were measured by small angle X-ray scattering (SAXS) and compared to recently published single molecule FRET results (Höfig et al., ACS Sensors, 2018). For one construct which exhibits a high change in energy transfer and a large change of the radius of gyration upon ligand binding, we performed coarse-grained molecular dynamics simulations for the ligand-free and the ligand-bound state. Our analysis indicates that a carefully designed attachment of the donor FP is crucial for the proper transfer of the glucose induced conformational change of the glucose binding protein into a well pronounced FRET signal change as measured in this sensor construct. Since the other FP (acceptor) does not experience such a glucose induced alteration, it becomes apparent that only one of the FPs needs to have a well-adjusted attachment to the glucose binding protein

Modeling of Wnt-mediated tissue patterning in vertebrate embryogenesis

During embryogenesis, morphogens form a concentration gradient in responsive tissue, which is then translated into a spatial cellular pattern. The mechanisms by which morphogens spread through a tissue to establish such a morphogenetic field remain elusive. Here, we investigate by mutually complementary simulations and in vivo experiments how Wnt morphogen transport by cytonemes differs from typically assumed diffusion-based transport for patterning of highly dynamic tissue such as the neural plate in zebrafish. Stochasticity strongly influences fate acquisition at the single cell level and results in fluctuating boundaries between pattern regions. Stable patterning can be achieved by sorting through concentration dependent cell migration and apoptosis, independent of the morphogen transport mechanism. We show that Wnt transport by cytonemes achieves distinct Wnt thresholds for the brain primordia earlier compared with diffusion-based transport. We conclude that a cytoneme-mediated morphogen transport together with directed cell sorting is a potentially favored mechanism to establish morphogen gradients in rapidly expanding developmental systems

Simulation of FRET dyes allows quantitative comparison against experimental data

Fully understanding biomolecular function requires detailed insight into the systems’ structural dynamics. Powerful experimental techniques such as single molecule Förster Resonance Energy Transfer (FRET) provide access to such dynamic information yet have to be carefully interpreted. Molecular simulations can complement these experiments but typically face limits in accessing slow time scales and large or unstructured systems. Here, we introduce a coarse-grained simulation technique that tackles these challenges. While requiring only few parameters, we maintain full protein flexibility and include all heavy atoms of proteins, linkers, and dyes. We are able to sufficiently reduce computational demands to simulate large or heterogeneous structural dynamics and ensembles on slow time scales found in, e.g., protein folding. The simulations allow for calculating FRET efficiencies which quantitatively agree with experimentally determined values. By providing atomically resolved trajectories, this work supports the planning and microscopic interpretation of experiments. Overall, these results highlight how simulations and experiments can complement each other leading to new insights into biomolecular dynamics and function

FRET Dyes Significantly Affect SAXS Intensities of Proteins

Structural analyses in biophysics aim at revealing a relationship between a molecule's dynamic structure and its physiological function. Förster resonance energy transfer (FRET) and small‐angle X‐ray scattering (SAXS) are complementary experimental approaches to this. Their concomitant application in combined studies has recently opened a lively debate on how to interpret FRET measurements in the light of SAXS data with the popular example of the radius of gyration, commonly derived from both FRET and SAXS. There still is a lack of understanding in how to mutually relate and interpret quantities equally obtained from FRET or SAXS, and to what extent FRET dyes affect SAXS intensities in combined applications. In the present work, we examine the interplay of FRET and SAXS from a computational simulation perspective. Molecular simulations are a valuable complement to experimental approaches and supply instructive information on dynamics. As FRET depends not only on the mutual separation but also on the relative orientations, the dynamics, and therefore also the shapes of the dyes, we utilize a novel method for simulating FRET‐dye‐labeled proteins to investigate these aspects in atomic detail. We perform structure‐based simulations of four different proteins with and without dyes in both folded and unfolded conformations. In‐silico derived radii of gyration are different with and without dyes and depend on the chosen dye pair. The dyes apparently influence the dynamics of unfolded systems. We find that FRET dyes attached to a protein have a significant impact on theoretical SAXS intensities calculated from simulated structures, especially for small proteins. Radii of gyration from FRET and SAXS deviate systematically, which points to further underlying mechanisms beyond prevalent explanation approaches

Rapid interpretation of small-angle X-ray scattering data.

The fundamental aim of structural analyses in biophysics is to reveal a mutual relation between a molecule's dynamic structure and its physiological function. Small-angle X-ray scattering (SAXS) is an experimental technique for structural characterization of macromolecules in solution and enables time-resolved analysis of conformational changes under physiological conditions. As such experiments measure spatially averaged low-resolution scattering intensities only, the sparse information obtained is not sufficient to uniquely reconstruct a three-dimensional atomistic model. Here, we integrate the information from SAXS into molecular dynamics simulations using computationally efficient native structure-based models. Dynamically fitting an initial structure towards a scattering intensity, such simulations produce atomistic models in agreement with the target data. In this way, SAXS data can be rapidly interpreted while retaining physico-chemical knowledge and sampling power of the underlying force field. We demonstrate our method's performance using the example of three protein systems. Simulations are faster than full molecular dynamics approaches by more than two orders of magnitude and consistently achieve comparable accuracy. Computational demands are reduced sufficiently to run the simulations on commodity desktop computers instead of high-performance computing systems. These results underline that scattering-guided structure-based simulations provide a suitable framework for rapid early-stage refinement of structures towards SAXS data with particular focus on minimal computational resources and time

diSTruct v1.0: generating biomolecular structures from distance constraints

The distance geometry problem is often encountered in molecular biology and the life sciences at large, as a host of experimental methods produce ambiguous and noisy distance data. In this note, we present diSTruct; an adaptation of the generic MaxEnt-Stress graph drawing algorithm to the domain of biological macromolecules. diSTruct is fast, provides reliable structural models even from incomplete or noisy distance data and integrates access to graph analysis tools

Simulation of FRET dyes allows quantitative comparison against experimental data

Fully understanding biomolecular function requires detailed insight into the systems’ structural dynamics. Powerful experimental techniques such as single molecule Förster Resonance Energy Transfer (FRET) provide access to such dynamic information yet have to be carefully interpreted. Molecular simulations can complement these experiments but typically face limits in accessing slow time scales and large or unstructured systems. Here, we introduce a coarse-grained simulation technique that tackles these challenges. While requiring only few parameters, we maintain full protein flexibility and include all heavy atoms of proteins, linkers, and dyes. We are able to sufficiently reduce computational demands to simulate large or heterogeneous structural dynamics and ensembles on slow time scales found in, e.g., protein folding. The simulations allow for calculating FRET efficiencies which quantitatively agree with experimentally determined values. By providing atomically resolved trajectories, this work supports the planning and microscopic interpretation of experiments. Overall, these results highlight how simulations and experiments can complement each other leading to new insights into biomolecular dynamics and function

Modeling of Wnt-mediated tissue patterning in vertebrate embryogenesis

During embryogenesis, morphogens form a concentration gradient in responsive tissue, which is then translated into a spatial cellular pattern. The mechanisms by which morphogens spread through a tissue to establish such a morphogenetic field remain elusive. Here, we investigate by mutually complementary simulations and in vivo experiments how Wnt morphogen transport by cytonemes differs from typically assumed diffusion-based transport for patterning of highly dynamic tissue such as the neural plate in zebrafish. Stochasticity strongly influences fate acquisition at the single cell level and results in fluctuating boundaries between pattern regions. Stable patterning can be achieved by sorting through concentration dependent cell migration and apoptosis, independent of the morphogen transport mechanism. We show that Wnt transport by cytonemes achieves distinct Wnt thresholds for the brain primordia earlier compared with diffusion-based transport. We conclude that a cytoneme-mediated morphogen transport together with directed cell sorting is a potentially favored mechanism to establish morphogen gradients in rapidly expanding developmental systems