The atomic-scale structure of the phosphocholine (PC) headgroup in 30 mol% propylene glycol (PG) in aqueous solution has been investigated using a combination of neutron diffraction with isotopic substitution experiments and computer simulation techniques -Molecular Dynamics and Empirical Potential Structure Refinement. Here, the hydration of the PC headgroup remains largely intact compared with the hydration of this group in a bilayer and in a bulk water solution, with the PG molecules showing limited interactions with the headgroup. When direct PG interactions with PC do occur, they are most likely to coordinate to the N(CH 3 ) + 3 motifs. Further, PG does not affect the bulk water structure and the addition of PC does not perturb the PG-solvent interactions. This suggests that the reason why PG is able to penetrate into membranes easily is that it does not form stronghydrogen bonding or electrostatic interactions with the headgroup allowing it to easily move across the membrane barrier.
We perform first-principles quantum mechanical studies of dioxygen ligand binding to the hemocyanin protein. Electronic correlation effects in the functional site of hemocyanin are investigated using a state-of-the-art approach, treating the localised copper 3d electrons with cluster dynamical mean field theory (DMFT) for the first time. This approach has enabled us to account for dynamical and multi-reference quantum mechanics, capturing valence and spin fluctuations of the 3d electrons. Our approach explains the stabilisation of the experimentally observed di-Cu singlet for the butterflied Cu 2 O 2 core, with localised charge and incoherent scattering processes across the oxo-bridge that prevent long-lived charge excitations, suggesting that the magnetic structure of hemocyanin is largely influenced by the many-body corrections. Our computational model is supported by agreement with experimental optical absorption data, and provides a revised understanding of the bonding of the peroxide to the di-Cu system in vivo.
The protein corona is an obstacle to exploiting exotic properties of nanomaterials in clinical and biotechnological settings. The atomic‐scale dynamic formation of the protein corona at the bio‐nano interface is impenetrable using conventional experimental techniques. Here, molecular dynamics simulations are used to study the effect of graphene‐oxide (GO) functionalization on apolipoprotein‐cIII (apo‐c3) adsorption. An analysis pipeline is developed, encompassing binding energy calculations to protein structure analyses employing uniform manifold approximation and projection (UMAP) dimensionality reduction and clustering. It is found that apo‐c3 is denatured by GO adsorption, driven by the large energetic contributions of electrostatic interactions; enthalpic contributions of such binding events outweigh the intraprotein bond enthalpy required to maintain the protein tertiary structure. Through denaturing and exposing buried hydrophobic residues, the protein backbone is stabilized by forming β‐bridges, which serve as binding motifs for protein–protein interactions that drive further protein aggregation on the nanomaterial surface. In contrast, adsorption on double‐clickable azide‐ and alkyne‐double functionalized GO (C2GO), apo‐c3 largely retains its tertiary structure. Binding with the nanomaterial surface is dominated by weaker van der Waals interactions that are dispersed over the protein surface, where charged protein residues are sterically hindered by azide functional groups. The apo‐c3 C‐terminus remains unchanged upon C2GO adsorption, conserving its lipid‐binding function.
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