Atomic-level engineering and imaging of polypeptoid crystal lattices

Abstract

Rational design of supramolecular nanomaterials fundamentally depends upon an atomic-level understanding of their structure and how it responds to chemical modifications. Here we studied a series of crystalline diblock copolypeptoids by a combination of sequence-controlled synthesis, cryogenic transmission electron microscopy, and molecular dynamics simulation. This family of amphiphilic polypeptoids formed free-floating 2-dimensional monolayer nanosheets, in which individual polymer chains and their relative orientations could be directly observed. Furthermore, bromine atom side-chain substituents in nanosheets were directly visualized by cryogenic transmission electron microscopy, revealing atomic details in position space inaccessible by conventional scattering techniques. While the polypeptoid backbone conformation was conserved across the set of molecules, the nanosheets exhibited different lattice packing geometries dependent on the aromatic side chain para substitutions. Peptoids are inherently achiral, yet we showed that sequences containing an asymmetric aromatic substitution pattern pack with alternating rows adopting opposite backbone chiralities. These atomic-level insights into peptoid nanosheet crystal structure provide guidance for the future design of bioinspired nanomaterials with more precisely controlled structures and properties.

Minimizing Crinkling of Soft Specimens Using Holey Gold Films on Molybdenum Grids for Cryogenic Electron Microscopy

“…The detailed protocol for polypeptoid synthesis can be found in Xuan et al (2019). Two sequence-defined di-block copolypeptoid decamers, with four hydrophilic monomers and six hydrophobic monomers, were used in this study.…”

“…They are similar to polypeptides except for the fact that the side chain is appended to the nitrogen atom rather than the α-carbon (Nam et al, 2010; Robertson et al, 2014). Crystalline polypeptoid membranes, which are only one unit-cell thick, similar to 2D protein membranes but with smaller unit cells, are generated by the self-assembly of di-block copolymers in dilute solutions (Jiang et al, 2018, 2019; Xuan et al, 2019). In a previous study, we have used images of untilted specimens to determine the structure of crystalline polypeptoid membranes with about 2 Å resolution when using vitrified specimens prepared on a holey carbon support film (Jiang et al, 2018).…”

Engineering the atomic structure of sequence-defined peptoid polymers and their assemblies

“…We demonstrated that substituents could be introduced onto the aromatic groups and varied without disrupting the packing preferences within the lattice. [76] We synthesized a series of diblock copolypeptoid decamers composed with the same hydrophilic poly(N-2(2-(2methoxyethoxy)ethoxy)ethylglycine) (pNte) block and different N-2-phenylethylglycine-based hydrophobic blocks bearing a systematic series of aromatic ring substituents, varying in size and their electron withdrawing or donating character (Figure 3A). These sequence variants all formed free-floating 2D monolayer nanosheets.…”

“…Peptoid backbones preferentially generally adopt all cis-amide conformation in peptoid crystals regardless of the chemistry of side chains, as previously reported. [52,62,76] However, free in solution, peptoids undergo cis-trans isomerization due to the similar energy of the two conformers. A common strategy to induce one conformer over the other is to utilize local non-covalent interactions, including n→π*, steric, electronic, and hydrogen bonding interactions, to regulate the amide bond rotation of peptoid backbones.…”

DNA origami protection and molecular interfacing through engineered sequence-defined peptoids

“…Peptoids, comprising N-substituted glycines, are an emerging class of peptidomimetic molecules that offer biocompatibility, low-cost synthesis, high chemical flexibility, and designable sequences and performances (42)(43)(44). In a recent study, Xuan et al (45) demonstrated that peptoid architectures could be engineered at the atomic level, resulting in a variety of atomically defined structural arrangements. Compared to peptides, peptoids possess high conformational flexibility and confer a high degree of resistance to proteolytic degradation (44,46), due to the side chains located on the nitrogen of the amide backbone instead of the α-carbon.…”