Unraveling origins of the heterogeneous curvature dependence of polypeptide interactions with carbon nanostructuresElectronic supplementary information (ESI) available: Snapshots of initial orientations of peptide-nanotube complexes used for MD simulations; temporal evolution of peptide-nanosurface contact area and interaction strengths of individual trajectories; peptide RMSD and backbone hydrogen bonding as a function of simulation time; protein-water pair correlation functions; secondary stru
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...
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| Main Authors | , , , |
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| Format | Journal Article |
| Published |
17.02.2016
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| Online Access | Get full text |
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| Summary: | 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.
Underlying causes of the differential polypeptide interactions on carbon nanosurfaces of varying curvatures emerge from a synchronized computational study. |
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| Bibliography: | 10.1039/c5cp04675k Electronic supplementary information (ESI) available: Snapshots of initial orientations of peptide-nanotube complexes used for MD simulations; temporal evolution of peptide-nanosurface contact area and interaction strengths of individual trajectories; peptide RMSD and backbone hydrogen bonding as a function of simulation time; protein-water pair correlation functions; secondary structure fractions; schematic representations of fragmented geometries of toluene and benzene-concave surfaces of SWCNT complexes; gas phase optimized geometries of ethane and methane with the concave surface of the SWCNT and graphene and convex surfaces of the SWCNT at the M062X/6-31G** level of theory; gas phase optimized geometries of formic acid with the concave surface of the SWCNT and graphene and convex surfaces of the SWCNT; gas phase optimized geometries of toluene, ethane and propanamide with the concave surface of the SWCNT, graphene and convex surfaces of the SWCNT at the dispersion corrected B3LYP-D2/6-31G** and B3LYP/6-31G** levels of theory; molecular electrostatic potential isosurfaces of isolated nanotubes, isolated graphene, propanamide-CNS complexes, ethylammonium-CNS complexes and propanoate-CNS complexes; interaction energies of toluene and benzene with different walls of the concave surface of the SWCNT; C-O and C-N bond distances (in Å) in the amido group of propanamide in propanamide-CNS complexes and C-O bond distances (in Å) in the carboxylic group of propanoic acid in propanoic acid-CNS complexes; mulliken charges on all the atoms of the amido group of propanamide in propanamide-CNS complexes and the carboxylic group of propanoic acid in propanoic acid-CNS complexes; the interaction energy of ammonia with CNSs; interaction energies of toluene, ethane and propanamide with CNSs at the gas/B3LYP-D2/6-31G** and gas/B3LYP/6-31G** levels of theory; the difference in the HOMO-LUMO energy gap of optimized geometries of complexes and bare CNS; interaction energies of toluene, ethane, propanamide, ethylammonium and propanoate with CNSs at CPCM/M062X/6-31+G** and CPCM/M062X/6-31++G** levels of theory; coordinates of the optimized geometries. See DOI |
| ISSN: | 1463-9076 1463-9084 |
| DOI: | 10.1039/c5cp04675k |