Unraveling origins of the heterogeneous curvature dependence of polypeptide interactions with carbon nanostructures

Abstract

Emerging nanotechnology has rapidly broadened interfacial prospects of biological molecules with carbon nanomaterials (CNs). A prerequisite for effectively harnessing such hybrid materials is a multi-faceted understanding of their complex interfacial interactions as functions of the physico-chemical characteristics and the surface topography of the individual components. In this article, we address the origins of the curvature dependence of polypeptide adsorption on CN surfaces (CNSs), a phenomenon bearing an acute influence upon the behavior and activity of CN-protein conjugates. Our benchmark molecular dynamics (MD) simulations with the amphiphilic full-length amyloid beta (Aβ) peptide demonstrate that protein adsorption is strongest on the concave (inner) CN surface, weakest on the convex (outer) surface, and intermediary on the planar surface, in agreement with recent experimental reports. The curvature effects, however, are found to manifest non-uniformly between the amino acid subtypes. To understand the underlying interplay of the chemical nature of the amino acids and surface topography of the CNs, we performed high-level quantum chemical (QM) calculations with amino acid analogs (AAA) representing their five prominent classes, and convex, concave and planar CN fragments. Molecular electrostatic potential maps reveal pronounced curvature dependence in the mixing of electron densities, and a resulting variance in the stabilization of the non-covalently bound molecular complexes. Interestingly, our study revealed that the interaction trends of the high-level QM calculations were captured well by the empirical force field. The findings in this study have important bearing upon the design of carbon based bio-nanomaterials, and additionally, provide valuable insights into the accuracy of various computational techniques for probing non-bonded interfacial interactions.

Carbon Nanotube Based Groundwater Remediation: The Case of Trichloroethylene

“…Hindered mobility with decrease in nanoparticle size has also been seen for polystyrene chains that surround silica nanoparticles [76]. In recent work, Jana et al [77] showed that amino acid interaction with curved graphitic interfaces is very specific to their polarity, aromaticity, and molecular size. This can also be extrapolated, as laid out by the authors [77], to analogous organic molecules.…”

“…In recent work, Jana et al [77] showed that amino acid interaction with curved graphitic interfaces is very specific to their polarity, aromaticity, and molecular size. This can also be extrapolated, as laid out by the authors [77], to analogous organic molecules. Similar observations have been made for uracil adsorption on CNTs, where flexibility of the adsorbate comes into play as the curvature of the CNT is increased [78].…”

Layer-Number-Dependent Effects of Graphene Oxide on the Pluripotency of Mouse Embryonic Stem Cells Through the Regulation of the Interaction Between the Extracellular Matrix and Integrins

“…The adsorption capacity of carbon material to protein is related to the surface curvature of carbon material, and increases with a decrease in curvature. 46 , 47 Compared to MGO, the morphology of SGO would present twists and change from 2D to 3D spontaneously to reduce its own surface energy. Therefore, the folds formed on SGO were significantly larger than those on MGO, resulting in a difference in FN adsorption capacity.…”

Size Matters: A Mechanistic Model of Nanoparticle Curvature Effects on Amyloid Fibril Formation

“…The same material can result in a variety of interactions with biomolecules, as previously observed for convex and concave curved surfaces of carbon nanotubes. 53 Arkin and Janke theoretically studied a wide range of curvatures for non-grafted and end-grafted polymers on NPs. 28 Our implicit NP curvature simulations modelled a scenario where all peptide N-termini remained bound to the NP surface.…”