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A) Define secondary structure of proteins (DSSP) algorithm applied to the MD trajectory of apo‐c3 adsorption with GO and C2GO, B) the number of intramolecular hydrogen bonds per amino acid residue throughout adsorption, and C) illustration of β‐turns induced in GO‐adsorbed apo‐c3 following denaturing (residues L4‐S7, S48‐K51, and W54‐V57), pink and grey structures respectively correspond to the initial and final adsorption conformations.
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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-oxi...
Citations
... Additional future work could be directed towards analysing the involvement of the specified residues in nanoparticle interactions by examining the binding free energy for the interaction as proposed by other researchers 23 . ...
The structures of the Fc base of various IgG antibodies have been examined with a view to understanding how this region can be used to conjugate IgG to nanoparticles. The base structure is found to be largely consistent across a range of species and subtypes, comprising a hydrophobic region surrounded by hydrophilic residues, some of which are charged at physiological conditions. In addition, atomistic Molecular Dynamics simulations were performed to explore how model nanoparticles interact with the base using neutral and negatively charged gold nanoparticles. Both types of nanoparticle interacted readily with the base, leading to an adaptation of the antibody base surface to enhance the interactions. Furthermore, these interactions left the rest of the domain at the base of the Fc region structurally intact. This implies that coupling nanoparticles to the base of an IgG molecule is both feasible and desirable, since it leaves the antibody free to interact with its surroundings so that antigen-binding functionality can be retained. These results will therefore help guide future attempts to develop new nanotechnologies that exploit the unique properties of both antibodies and nanoparticles.
... This work focusses on the rapid characterisation of GO, since it is a particularly challenging GBM, produced by a range of manufacturing methods which yield wide variation of its surface chemistry, 12,17 and with many applications which depend on the effect that this has on surfaces' molecular recognition and aggregation properties. 18,19 Here we demonstrate a new approach to QC testing for graphene oxide (GO), based on the interaction of an array of probe molecules with GO surfaces, as outlined in Figure 1. The approach is similar to other supramolecular sensor/probe arrays with optical detection: [20][21][22] when molecular probes interact with aqueous GBM dispersions, their signal (absorbance or fluorescence) is quenched, providing a ready, rapid, means to measure interaction. ...
Graphene-based materials (GBMs), including graphene oxide and graphene, are atomically thin materials with great promise, but efforts to realise this promise have been hampered by inconsistent material supply and the lack of rapid, accessible, characterisation methods. Here we present a new approach, based on surface interaction with a series of probe molecules, to rapidly provide a qualitative characterisation of graphene oxide materials at low cost, using widely available instruments. We demonstrate that our method can make qualitative comparisons, allowing us to observe if batches of material differ. Furthermore, in some circumstances it can quantify systematic differences, such as surface modification. We propose this approach may prove a valuable quality control method for materials producers and users alike and, since many applications of graphene oxide ¬— and 2D materials in general — depend on surface interactions, and suggest this kind characterisation may be valuable beyond rapid QC, in GBMs and other materials.
Robust protein-nanomaterial surface analysis is important, but also a challenge. Thrombin plays an important role in the coagulant activity of protein corona mediated by Ca²⁺ ion exchanged zeolites. However, the mechanism for this modulation remains unresolved. In this study, we proposed a combined computational and experimental approach to determine the adsorbed sites and orientations of thrombin binding to Ca²⁺ -exchanged LTA-type (CaA) zeolite. Specifically, fourteen ensembles of simulated annealing molecular dynamics (SAMD) simulations and experimental surface residues microenvironment analysis were used to reduce the starting orientations needed for further molecular dynamics (MD) simulations. The combined MD simulations and procoagulant activity characterization also reveal the consequent corresponding deactivation of thrombin on CaA zeolite. It is mainly caused by two aspects: (1) the secondary structure of thrombin can change after its adsorption on the CaA zeolite. (2) The positively charged area of thrombin mediates the preferential interaction between thrombin and CaA zeolite. Some thrombin substrate sites are thus blocked by zeolite after its adsorption. This study not only provides a promising method for characterizing the protein-nanoparticle interaction, but also gives an insight into the design and application of zeolite with high procoagulant activity.
