Effects of molecular crowding on structural and dynamical properties of biological macromolecules do depend on the concentration of crowding agents but also on the molecular mass and the structural compactness of the crowder molecules. By employing fluorescence correlation spectroscopy (FCS), we investigated the translational mobility of several biological macromolecules ranging from 17 kDa to 2.7 MDa. Polyethylene glycol and Ficoll polymers of different molecular masses were used in buffer solutions to mimic a crowded environment. The reduction in translational mobility of the biological tracer molecules was analyzed as a function of crowder volume fractions and was generally more pronounced in PEG as compared to Ficoll solutions. For several crowding conditions, we observed a molecular sieving effect, in which the diffusion coefficient of larger tracer molecules is reduced to a larger extent than predicted by the Stokes–Einstein relation. By employing a FRET-based biosensor, we also showed that a multiprotein complex is significantly compacted in the presence of macromolecular crowders. Importantly, with respect to sensor in vivo applications, ligand concentration determining sensors would need a crowding specific calibration in order to deliver correct cytosolic ligand concentration.

Understanding interactions between polymers and enzymes to boost enzymatic activity is of high importance for application of enzymes in multicomponent systems, such as laundry, food, pharmaceuticals, or cosmetics. Proteases are widely used in industries and increased performance in the presence of polymers has been reported. Boosting of enzymes activity by polymers and understanding of the molecular principles is of high interest in biomedical and biotechnological applications. A molecular understanding of the boosting effect of poly­(acrylic acid) (PAA) and poly­(l-γ-glutamic acid) (γ-PGA) for a nonspecific subtilisin protease (Protein Database (PDB) ID: 1ST3) was generated through biophysical characterization (fluorescence correlation and circular dichroism spectroscopies, isothermal titration calorimetry), molecular dynamics simulations, and protease reengineering (site-saturation mutagenesis). Our study revealed that enthalpically driven interactions via key amino acid residues close to the protease Ca2+ binding sites cause the boosting effect in protease activity. On the molecular level electrostatic interactions results in the formation of protease-polyelectrolyte complexes. Site-saturation mutagenesis on positions S76, I77, A188, V238, N242, and K245 yielded an increased proteolytic performance against a complex protein mixture (trademark CO-3; up to ∼300% and ∼70%) in the presence of PAA and γ-PGA. Being able to fine-tune interactions between proteins and negatively charged polymers through integrative use of computational design, protein re-engineering and biophysical characterization proved to be an efficient workflow to improve protease performance.

The optical properties of 3D metacrystals made of gold nanoparticles in protein nanocages are studied. These metacrystals have sizes of tens of micrometers and are of high structural and optical quality. Through microspectroscopy measurements and model calculations it is demonstrated that the metacrystals show plasmonic absorption in the green wavelength range and are largely transparent in the red and infrared ranges. By using empty nanocages as placeholders in the metacrystal lattice, it is possible to control how strongly the metamaterial absorbs. Measurements on a pyramidal metacrystal show that it deflects visible light. The deflection shows evidence for anomalous refraction at short wavelengths and normal refraction at long wavelengths. The refractive dispersion is ascribed to the optical dispersion relation of the plasmonic metamaterial.

with its ligand 1-adamantanecarboxylic acid. Our volumetric measurements showed that the binding constant is significantly greater in a solution of 5% DMSO than in pure water. Our molecular dynamics simulations provided the vision at the molecular scale of the effect of DMSO in the binding event as well as associated free energy values in the presence and absence of 5% DMSO. This work should help in providing a better rationalization in the design of potent hydrophobic ligands knowing the DMSO contribution to their binding properties.