A coarse-grained xDLVO model for colloidal protein–protein interactions

Colloidal protein–protein interactions (PPIs) of attractive and repulsive nature modulate the solubility of proteins, their aggregation, precipitation and crystallization. Such interactions are very important for many biotechnological processes, but are complex and hard to control, therefore, difficult to be understood in terms of measurements alone. In diluted protein solutions, PPIs can be estimated from the osmotic second virial coefficient, B$_{22}$, which has been calculated using different methods and levels of theory. The most popular approach is based on the Derjaguin–Landau–Verwey–Overbeek (DLVO) theory and its extended versions, i.e. xDLVO. Despite much efforts, these models are not fully quantitative and must be fitted to experiments, which limits their predictive value. Here, we report an extended xDLVO-CG model, which extends existing models by a coarse-grained representation of proteins and the inclusion of an additional ion–protein dispersion interaction term. We demonstrate for four proteins, i.e. lysozyme (LYZ), subtilisin (Subs), bovine serum albumin (BSA) and immunoglobulin (IgG1), that semi-quantitative agreement with experimental values without the need to fit to experimental B$_{22}$ values. While most likely not the final step in the nearly hundred years of research in PPIs, xDLVO-CG is a step towards predictive PPIs calculations that are transferable to different proteins

Binding patterns of homo-peptides on bare magnetic nanoparticles: insights into environmental dependence

Magnetic nanoparticles (MNP) are intensively investigated for applications in nanomedicine, catalysis and biotechnology, where their interaction with peptides and proteins plays an important role. However, the characterisation of the interaction of individual amino acids with MNP remains challenging. Here, we classify the affinity of 20 amino acid homo-hexamers to unmodified iron oxide nanoparticles using peptide arrays in a variety of conditions as a basis to identify and rationally design selectively binding peptides. The choice of buffer system is shown to strongly influence the availability of peptide binding sites on the MNP surface. We find that under certain buffer conditions peptides of different charges can bind the MNP and that the relative strength of the interactions can be modulated by changing the buffer. We further present a model for the competition between the buffer and the MNP’s electrostatically binding to the adsorption sites. Thereby, we demonstrate that the charge distribution on the surface can be used to correlate the binding of positively and negatively charged peptides to the MNP. This analysis enables us to engineer the binding of MNP on peptides and contribute to better understand the bio-nano interactions, a step towards the design of affinity tags for advanced biomaterials

COSMO-RS-based methods for improved modelling of complex chemical systems

The conductor-like screening model for realistic solvation (COSMO-RS) is applied to study three case studies of complex chemical systems. In the first chapter, cellulose solubility in ionic liquid (IL) solvents is considered and a molecular model for cellulose is presented for the calculation of its solubility in ILs and their mixtures with organic molecular solvents. The model is based on cellobiose units which were themselves obtained by a conformation search for a cellotetraose unit. The conformations that make up the model hence can take into account interactions of a dissolved cellulose repeating unit while making sure that the conformations are so that the repeating unit resembles a unit in the middle of a cellulose chain. It is shown that the model contains representations of all of intra-molecular hydrogen bonds as well as open hydrogen bonding sites for accepting inter-molecular ones witnessed experimentally. Relative cellulose solubilities in IL systems with cations [Amim], [Apyr], [C2OHmim], [C2OHpyr], [C2OC1mim], and [C4mim] and anions [Cl], [Br], [N(CN)2], [CH3CHOHCOO], [CH3 COO], [HOCH2 COO], [(C6 H5 )COO], [H2 NCH2 COO], [C2 N3 ], [(C2 H5 )2 PO3 OH] and [HCOO] have been studied. In addition, cellulose solubility in mixtures of [C2mim][CH3COO] and 14 molecular solvents could be reproduced. Finally, a solvent screening over a large database of cation/anion pairs was carried out, providing for a design and discovery guide pertaining to novel IL systems for cellulose dissolution. Despite the complexities of the cellulose chain, particularly regarding its hydrogen bonding sites, the overall structure of its building blocks can be arguably thought of as relatively rigid due to the rigidity of the glucose rings in the cellulose backbone. The flexibility of the hydrogen bonding groups along the chain will be shown to be well captured by a heuristic and systematic conformation search algorithm (COSMOconf). However, problems may arise as the conformational space of the molecule under study increases, so that in practice a systematic approach would not be able to adequately address its relevant conformations. As an alternative method for conformational search, a hybrid modelling strategy for the prediction of octanol/water partition coefficients for alcohol ethoxylate surfactants of varying chain lengths is developed and presented in Chapter 2. The strategy makes use of molecular dynamics (MD) simulations for the generation of molecular conformations in the presence of solvent. A clustering of the conformations from the MD trajectories is then carried out based on principal component analysis of their dihedral angles. Representative conformations thus selected will be then used for COSMO-RS calculations. Each conformation will be then assigned with a weight using an equation derived based on its probability of occurrence in the MD trajectory. Experimental partition coefficients will be thus reproduced within conformation independent accuracy of COSMO-RS. Solvents may also and often are used not only for the sole purpose of dissolving but also as deliberate media in which reactions occur. In Chapter 3, we consider a case for which the significant role of the solvent medium in determining the reaction conversion has been recently attested experimentally. In this chapter, we use COSMO-RS mainly as a molecular model of the liquid phase and study the heterogeneous hydrogenolysis of diphenyl ether (a model compound for lignin itself being a long and complex molecule) on Raney Ni. This is done using the liquid-phase atomistic descriptors COSMO-RS makes available, by means of which a model for the influence of alcoholic solvents on the conversion is then presented. In order to do so, the electrostatics of OH and Ca H bonds was first calculated using in the DFT-COSMO framework. Then, hydrogen bonding donor moment and the screening charge density on the Ca atom of the solvent molecules were used as model variables and were linked to the characteristics of their interactions (adsorption and dissociation) with the catalyst surface according to the available experimental evidence in this regard. In this way, experimentally measured conversions in a series of mono-alcohols for which systematic studies were available could be successfully reproduced. Predictions are additionally done for an extended set of alcohols for which experimental data were not available. The study hence provides for a first step to quantitatively model the dependance of the conversion of this reaction on the choice of solvent using a mechanistically inspired selection of molecular descriptors and is hence a step towards the rational selection and design of solvents with applications in lignin biorefining

Dataset to "COSMO-RS-Based Methods for Improved Modelling of Complex Chemical Systems"

This dataset contains the data referred by the PhD thesis "COSMO-RS-Based Methods for Improved Modelling of Complex Chemical Systems". The archive contains the following content:Chapter 1: COSMO (.cosmo) and structure (.xyz) files for all the conformations comprising the cellulose model and the spreadsheet file (.xlsx) containing the full screening results are included along with this document.Chapter 2: The following archive (.zip) files are digitally included along with this document:COSMOconf-conformations.zip containing the conformations obtained using the application of COSMOconf algorithm,MD-conformations.zip containing the extracted representative conformations corresponding to the minima of the free energy surfaces obtained by a princi- pal component analysis of the dihedral angles of the MD trajectories,COSMOfiles-optimised-MD-conformations.zip containing the COSMOfiles of the MD-conformations.zip after the addition of hydrogen atoms and their DFT- COSMO optimisation