On the Mobility of Macromolecules in Cells

In the first part of this thesis diffusion measurements with fluorescence correlation spectroscopy on fluorescence-labeled nanogold particles in the cytoplasm and the nucleus of living cells are presented. The nanoparticles were detected to move by subdiffusion, i.e. their mean square displacement displayed a power-law scaling ~ t^a, a < 1. This observation can be explained with the high amounts of macromolecules (such as proteins) dissolved in intracellular fluids which obstruct the motion of indiviual nanoparticles. From the diffusion behaviour of the particles the complex shear modulus G(w) ~ w^a of the intracellular fluids was calculated, which showed the cellular interior to be viscoelastic on the nanoscale. Furthermore, the efficiency of a subdiffusive molecule to approach a fixed target was quantified. Computer simulations highlighted here that the probability to reach a target is increased for a subdiffusive particle as compared to a normal diffusive particle, which suggests that a cell may benefit from the subdiffusion of macromolecules in its interior. In the second part of the thesis the two-dimensional diffusion of cylindrical objects embedded in lipid membranes is investigated. Coarse-grained molecular dynamic simulations ('dissipative particle dynamics') demonstrated that the size-dependence of the diffusion coefficients is properly described by the Saffman-Delbrück theory

Dynamic Structure Formation of Peripheral Membrane Proteins

Using coarse-grained membrane simulations we show here that peripheral membrane proteins can form a multitude of higher-order structures due to membrane-mediated interactions. Peripheral membrane proteins characteristically perturb the lipid bilayer in their vicinity which supports the formation of protein assemblies not only within the same but surprisingly also across opposing leaflets of a bilayer. In addition, we also observed the formation of lipid-protein domains on heteregeneous membranes. The clustering ability of proteins, as quantified via the potential of mean force, is enhanced when radius and hydrophobic penetration depth of the proteins increases. Based on our data, we propose that membrane-mediated cluster formation of peripheral proteins supports protein assembly in vivo and hence may play a pivotal role in the formation of templates for signaling cascades and in the emergence of transport intermediates in the secretory pathway

Time‐resolved fluorescence anisotropy with Atto 488‐labeled phytochrome Agp1 from Agrobacterium fabrum

Phytochromes are photoreceptor proteins with a bilin chromophore that undergo photoconversion between two spectrally different forms, Pr and Pfr. Three domains, termed PAS, GAF, and PHY domains, constitute the N-terminal photosensory chromophore module (PCM); the C-terminus is often a histidine kinase module. In the Agrobacterium fabrum phytochrome Agp1, the autophosphorylation activity of the histidine kinase is high in the Pr and low in the Pfr form. Crystal structure analyses of PCMs suggest flexibility around position 308 in the Pr but not in the Pfr form. Here, we performed time-resolved fluorescence anisotropy measurements with different Agp1 mutants, each with a single cysteine residue at various positions. The fluorophore label Atto-488 was attached to each mutant, and time-resolved fluorescence anisotropy was measured in the Pr and Pfr forms. Fluorescence anisotropy curves were fitted with biexponential functions. Differences in the amplitude A$_2$ of the second component between the PCM and the full-length variant indicate a mechanical coupling between position 362 and the histidine kinase. Pr-to-Pfr photoconversion induced no significant changes in the time constant t$_2$ at any position. An intermediate t$_2$ value at position 295, which is located in a compact environment, suggests flexibility around the nearby position 308 in Pr and in Pfr

Influence of Hydrophobic Mismatching on Membrane Protein Diffusion

The observation of membrane domains in vivo and in vitro has triggered a renewed interest in the size-dependent diffusion of membrane inclusions (e.g., clusters of transmembrane proteins and lipid rafts). Here, we have used coarse-grained membrane simulations to quantify the influence of a hydrophobic mismatch between the inclusion's transmembrane portion and the surrounding lipid bilayer on the diffusive mobility of the inclusion. Our data indicate only slight changes in the mobility (<30%) when altering the hydrophobic mismatch, and the scaling of the diffusion coefficient D is most consistent with previous hydrodynamic predictions, i.e., with the Saffman-Delbruck relation and the edgewise motion of a thin disk in the limit of small and large radii, respectively

Sampling the Cell with Anomalous Diffusion—The Discovery of Slowness

Diffusion-mediated searching for interaction partners is an ubiquitous process in cell biology. Transcription factors, for example, search specific DNA sequences, signaling proteins aim at interacting with specific cofactors, and peripheral membrane proteins try to dock to membrane domains. Brownian motion, however, is affected by molecular crowding that induces anomalous diffusion (so-called subdiffusion) of proteins and larger structures, thereby compromising diffusive transport and the associated sampling processes. Contrary to the naive expectation that subdiffusion obstructs cellular processes, we show here by computer simulations that subdiffusion rather increases the probability of finding a nearby target. Consequently, important events like protein complex formation and signal propagation are enhanced as compared to normal diffusion. Hence, cells indeed benefit from their crowded internal state and the associated anomalous diffusion

Engineering and Design of Polymeric Shells: Inwards Interweaving Polymers as Multilayer Nanofilm, Immobilization Matrix, or Chromatography Resins

Hydrogels with complex internal structures are required for advanced drug delivery systems and tissue engineering or used as inks for 3D printing. However, hydrogels lack the tunability and diversity of polymeric shells and require complicated postsynthesis steps to alter its structure or properties. We report on the first integrated approach to assemble and design polymeric shells to take on various complex structures and functions such as multilayer nanofilms, multidensity immobilization matrix, or multiadhesive chromatography resins via the tuning of four assembly parameters: (a) poly­(allylamine) (PA) concentration, (b) number of poly­(allylamine)/poly­(styrenesulfonic acid) (PA/PSSA) incubations, (c) poly­(allylamine) (PA) to poly­(ethylene glycol) (PEG) grafting ratio, and (d) % H₂O present during assembly. Our approach combines the complex 3D structures of hydrogels with the versatility of self-assembled polymeric layers. Polymeric shells produced from our method have a highly uniform material distribution and well-defined shell boundaries. Shell thickness, density, and adhesive properties are easily tunable. By virtue of such unique material features, we demonstrate that polymeric shells can be designed to expand beyond its conventional function as thin films and serve as immobilization matrix, chromatography resins, or even reaction compartments. This technique could also uncover interesting perspectives in the development of novel multimaterials for 3D printing to synthesize scaffolds at a higher order of complexity