Cryo-EM of Helical Polymers

Abstract

While the application of cryogenic electron microscopy (cryo-EM) to helical polymers in biology has a long history, due to the huge number of helical macromolecular assemblies in viruses, bacteria, archaea, and eukaryotes, the use of cryo-EM to study synthetic soft matter noncovalent polymers has been much more limited. This has mainly been due to the lack of familiarity with cryo-EM in the materials science and chemistry communities, in contrast to the fact that cryo-EM was developed as a biological technique. Nevertheless, the relatively few structures of self-assembled peptide nanotubes and ribbons solved at near-atomic resolution by cryo-EM have demonstrated that cryo-EM should be the method of choice for a structural analysis of synthetic helical filaments. In addition, cryo-EM has also demonstrated that the self-assembly of soft matter polymers has enormous potential for polymorphism, something that may be obscured by techniques such as scattering and spectroscopy. These cryo-EM structures have revealed how far we currently are from being able to predict the structure of these polymers due to their chaotic self-assembly behavior. CONTENTS

Archaeal bundling pili of Pyrobaculum calidifontis reveal similarities between archaeal and bacterial biofilms

“…The two possible helical symmetries were calculated from an averaged power spectrum generated from the raw particles and one was found to be correct (71, 72). Typically, the hand of a cryo-EM protein reconstruction is determined by inspecting the hand of α-helices in the map (73). However, this map only has two tiny one-turn helices that were not obvious without an atomic model.…”

Structures of synthetic helical filaments and tubes based on peptide and peptido-mimetic polymers

“…This phenomenon may also apply to helical filaments derived from self-assembly of designed peptides and peptido-mimetic foldamers. Helical hand information is lost in two-dimensional (2D) projection images obtained from TEM and cryo-EM analysis and in many cases cannot be recovered through building of the atomic model into the two enantiomorphic representations of the three-dimensional (3D) volume (Wang et al ., 2022). In the absence of structural determinations at true-atomic resolution or easily resolved helical surface features, it may not be possible to unambiguously assign the helical hand of synthetic helical filaments and tubes.…”

“…SAXS and SANS, afford information on the structural features of the assemblies in solution at low-to-medium resolution in the range from 1 to 100 nm from analysis of the form factor scattering (Guilbaud and Saiani, 2011). AFM and scanning electron microscopy) (SEM) can also be employed for assignment of the helical hand of peptide assemblies for cases in which the chirality of the surface features can be resolved (Wang et al ., 2022). However, only a small set of experimental methods can give information at NAR on filamentous helical assemblies, namely X-ray and electron diffraction methods, ssNMR spectroscopy, and cryo-EM.…”

“…The details of structural determination using cryo-EM image analysis are beyond the scope of this article. However, a recent review highlights the critical considerations involved in assignment of helical symmetry in the structural analysis of synthetic peptide filaments (Wang et al ., 2022).…”

Enzymatic Noncovalent Synthesis for Targeting Subcellular Organelles

“…Since the early demonstration of the anticancer activities of peptide assemblies in cell assays [12a] and in a murine model, [31] there has been an increasing number of reports about the molecular building blocks for ENS and the identification of new functions. Future studies should pay more attention to the mechanisms of the actions of ENS of peptide assemblies inside cells, as well as the atomistic structures of the peptide assemblies [32] and in vivo (i.e., animal models) test of ENS [33] . Although the pharmacodynamic and pharmacokinetic properties of the molecules can only be assessed in animal models, the knowledge of ENS in cell assays provides a necessary understanding of molecule‐cell interactions, which is the foundation of animal model studies.…”