Atomistic organization and characterization of tube-like assemblies comprising peptide–polymer conjugates: computer simulation studies

Abstract

The structure and stability of the nanotube obtained by assembling peptidepolymer conjugates consisting of two poly(n-butyl acrylate) blocks coupled tohave been investigated at the molecular level using atomistic molecular dynamics simulations. The effect of the wrapping polymer shells in the tube-like core, which consists of stacked b-sheet cyclopeptides, has been examined by simulating assemblies of both unsubstituted cyclopeptides, and conjugates in chloroform and N,N-dimethylformamide solutions. Furthermore, the influence of the environment has been investigated by comparing conjugate assemblies in solution with those deposited on mica. In addition, nanotubes stabilized by b-sheet-like hydrogen bonds between both parallel and antiparallel oriented cyclopeptides have been considered in all cases. The results, which have been analysed in terms of energy contributions, partial radial distribution functions, inter-subunit distances, shape of the cyclopeptide ring, internal van der Waals diameters, and both height and width of the nanostructures deposited on mica, have provided important microscopic insights. For example, analysis of both the energy terms and the structural dynamics obtained for the different assemblies indicate that the mica surface interacts more favourably with the parallel assembly than with the antiparallel ones, whereas the only configuration that is structurally stable in solution is the latter. Furthermore, adsorption onto the solid substrate produces a small deformation of the cylindrical molecular system.

Self-assembly of biomolecular soft matter

“…The paper by Aleman and co-workers at the Discussion illustrated how computational methods can contribute to the advancement of the field. 112 …”

Modeling Nanosized Single Molecule Objects: Dendronized Polymers Adsorbed onto Mica

“…[25][26][27][28][29][30] show end cap effects (results not shown) that resemble the deformability of dendrimers adsorbed on surfaces. In these DPs dendrons located at the two ends tend to use the available space and the hemispherical end caps to align in the direction of the macromolecular backbone, whereas in adsorbed dendrimers at low g dendrons tend to occupy the spherical free volume around the core 17 to form very flat structures. The observartions that dendrimers flatten more than DPs with identical number of generations is consistent with the fact that g max < 7 for DPs 4,14 while g max 12 for a typical dendrimer.…”

Elucidating the mechanism of interaction between peptides and inorganic surfaces

“…surface was represented using the force-field parameters reported by Heinz and co-workers, which successfully describes the unit cell properties of this inorganic material. 48,49 The mica super cell model, kindly supplied by Dr Heinz, was adapted to the dimensions of the simulation box: a = 76.793 Å and b = 80.009 Å. The thickness (i.e.…”