Self-assembly of chiral tubules

Abstract

The efficient and controlled assembly of complex structures from macromolecular building blocks is a critical open question in both biological systems and nanoscience. Using molecular dynamics simulations we study the self-assembly of tubular structures from model macromolecular monomers with multiple binding sites on their surfaces [Cheng et al., Soft Matter, 2012, 8, 5666-5678]. In this work we add chirality to the model monomer and a lock-and-key interaction. The self-assembly of free monomers into tubules yields a pitch value that often does not match the chirality of the monomer (including achiral monomers). We show that this mismatch occurs because of a twist deformation that brings the lateral interaction sites into alignment when the tubule pitch differs from the monomer chirality. The energy cost for this deformation is small as the energy distributions substantially overlap for small differences in the pitch and chirality. In order to control the tubule pitch by preventing the twist deformation, the interaction between the vertical surfaces must be increased without resulting in kinetically trapped structures. For this purpose, we employ lock-and-key interactions and obtain good control of the self-assembled tubule pitch. These results explain some fundamental features of microtubules. The vertical interaction strength is larger than the lateral in microtubules because this yields a controlled assembly of tubules with the proper pitch. We also generally find that the control of the assembly into tubules is difficult, which explains the wide range of pitch values and protofilament numbers observed in microtubule assembly.

Molecular Dynamics Simulations of Supramolecular Anticancer Nanotubes

“…Tubular structures such as microtubules 31 or the Tobacco Mosaic Virus 32 are commonly found in nature. Self-assembly into chiral tubular structures has been suggested to be driven by a balance of both lateral and longitudinal contacts at the monomer level 33 . An in-depth understanding of the specific intermolecular forces that drive the self-assembly of tubular self-assemblies will provide insight into the molecular design of supramolecular nanotubes.…”

Computational close up on protein–protein interactions: how to unravel the invisible using molecular dynamics simulations?

“…They consist of tubular polymers of tubulin proteins. Focusing on the self‐assembly of tubular structures with multiple binding sites, Cheng et al studied the fundamentals of microtubule assembly (Figure (g)). They developed a CG model monomer that is able to self‐assemble into tubular structures and may serve as a model for microtubule studies.…”

Microtubule‐based nanomaterials: Exploiting nature's dynamic biopolymers

“…For example, molecular dynamics (MD) simulations using a wedge‐shaped monomer (Fig. a) have recently demonstrated that self‐assembly into tubule structures depends on key factors such as molecular orientation and the relative influences of both lateral (transverse to the tube) and vertical (along the tube length) molecular interaction strengths (Cheng et al, ; Cheng and Stevens ). MD has further shown that the pitch of the tubule can be controlled by the chirality of the monomer, but also that a twist deformation tends to yield a range of pitch values.…”