Multiscale modeling of bio-nano interactions of zero-valent silver nanoparticles.

Abstract

Understanding the specifics of interaction between protein and nanomaterial is crucial for designing efficient, safe, and selective nanoplatforms, such as biosensor or nanocarrier systems. Routing experimental screening for the most suitable complementary pair of biomolecule and nanomaterial used in such nanoplatforms might be a resource-intensive task. While a variety of computational tools is available for pre-screening libraries of small drug molecules interacting with proteins, options for high-throughput screening of protein libraries for binding affinities to new and existing nanomaterials are limited. In the current work, we present the results of a systematic computational study of protein interaction with zero-valent silver nanoparticles using a multiscale approach. A variety of blood plasma and dietary proteins, namely, bovine and human serum albumins, bovine and human hemoglobin, papain, bromelain, lysozyme, and bovine lactoferrin, were examined. Selected combinations of nanomaterial and proteins can serve as a starting model for developing noble metal-based nanocarriers and biosensors. The computed binding (adsorption) characteristics for selected proteins were validated by experimental data reported in the literature. An advanced in silico nano-QSAR/QSPR interfacial descriptor 〖log⁡P〗^NM was also introduced to characterize the relative hydrophobicity/hydrophilicity of the nanomaterial.

Multiscale Modeling of Bio-Nano Interactions of Zero-Valent Silver Nanoparticles

“…Short-Range Surface Adsorption Potentials of Carbohydrates, Lipid Fragments, and AA Side Chains. In total, 96 PMF profiles for adsorption of biomolecules were calculated to obtain SCA's short-range surface potentials, U i,s nb (h i (d i ,θ,ϕ)), for three fcc configurations (see Figure 4 and the dataset 61 ). The majority of PMFs converged within 400 ns of production run (see Arg-Ag(110) system example at Figure S2 in the Supporting Information).…”

Multiscale modeling of transferrins and bovine serum albumin adsorption on coated gold and silver nanoparticles: the role of coating density and protein’s glycosylation state.

“…The overall elevated binding affinity of glycosylated TRF at low grafting densities can be explained by an additional effect associated with stronger binding calculated for Ag and Au slabs and individual glycan fragments (see previously reported Ag values in work 39 and Figures S4 and S5 for Au values in Supplementary Materials). For example, for Au FCC (111) the adsorption energies for carbohydrates were ca.…”

“…The obtained PMFs for gold NPs are shown in Figures S4 and S5 in Supplementary material (original files can be also found on Zenodo portal 53 ). The PMFs for silver NPs employed here were previously published elsewhere.…”

“…The PMFs for silver NPs employed here were previously published elsewhere. 22,54 Parametrization of short-range nonbonded potentials for PEG polymeric shell.…”

“…After preequilibration and obtaining a proper density/pressure, production runs of duration 200 ns were performed. The resulted short-range surface potentials for UnitedAtom Multiscale model are shown at FigureS7in Supplementary materials (original files can be also found on Zenodo portal56 ). The long-range and electrostatic UA interactions were handled as for crystalline materials.…”