Electron microscopy of helical filaments: rediscovering buried treasures in negative stain

Cryo-EM of Helical Polymers

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.

Optimized Negative-Staining Protocol for Lipid-Protein Interactions Investigated by Electron Microscopy

A large number of proteins are capable of inserting themselves into lipids, and interacting with membranes, such as transmembrane proteins and apolipoproteins. Insights into the lipid-protein interactions are important in understanding biological processes, and the structure of proteins at the lipid binding stage can help identify their roles and critical functions. Previously, such structural determination was challenging to obtain because the traditional methods, such as X-ray crystallography, are unable to capture the conformational and compositional heterogeneity of protein-lipid complexes. Electron microscopy (EM) is an alternative approach to determining protein structures and visualizing lipid-protein interactions directly, and negative-staining (OpNS), a subset of EM techniques, is a rapid, frequently used qualitative approach. The concern, however, is that current NS protocols often generate artifacts with lipid-related proteins, such as rouleaux formation from lipoproteins. To overcome this artifact formation, Ren and his colleagues have refined early NS protocols, and developed an optimized NS protocol that validated by comparing images of lipoproteins from cryo-electron microscopy (cryo-EM). This optimized NS protocol produces "near native-state" particle images and high contrast images of the protein in its native lipid-binding state, which can be used to create higher-quality three-dimensional (3D) reconstruction by single-particle analysis and electron tomography (e.g. IPET). This optimized protocol is thus a promising hands-on approach for examining the structure of proteins at their lipid-binding status.

Optimized negative-staining protocol for examining lipid-protein interactions by electron microscopy

A large number of proteins are capable of inserting themselves into lipids, and interacting with membranes, such as transmembrane proteins and apolipoproteins. Protein-lipid interactions have been identified as one of the keys in understanding biological processes, while the structure of proteins at the lipid-binding stage can provide evidence to help identify their roles and critical functions. However, structure determination of proteins at the lipid-binding stage is rather difficult, because conformational and compositional heterogeneities of the protein-lipid complexes are major barriers to unravel their structures using traditional methods, such as X-ray crystallography. Electron microscopy (EM) is an alternative approach to determine protein structure and has demonstrated a capability in visualizing lipid-protein interactions directly. Among various EM techniques, negative-staining (NS) is an easy, rapid, qualitative approach that is a well-established technique, frequently used in research laboratories. Conventional NS protocols, unfortunately, often generate artifacts with lipid-related proteins, such as the rouleau formation of lipoproteins. To overcome this artifact formation, Ren and his colleagues recently developed an optimized NS protocol that was validated by comparing images of lipoproteins from cryo-electron microscopy (cryo-EM). The optimized NS protocol could produce "near native-state" particle images and high contrast images of the protein in its lipid-binding state that is favorable for three-dimensional (3D) reconstruction by single-particle analysis and individual-particle electron tomography (IPET), suggesting this optimized protocol can be used widely to examine the structure of proteins at lipid-binding stage.

ParA2, a Vibrio cholerae chromosome partitioning protein, forms left-handed helical filaments on DNA

Most bacterial chromosomes contain homologs of plasmid partitioning (par) loci. These loci encode ATPases called ParA that are thought to contribute to the mechanical force required for chromosome and plasmid segregation. In Vibrio cholerae, the chromosome II (chrII) par locus is essential for chrII segregation. Here, we found that purified ParA2 had ATPase activities comparable to other ParA homologs, but, unlike many other ParA homologs, did not form high molecular weight complexes in the presence of ATP alone. Instead, formation of high molecular weight ParA2 polymers required DNA. Electron microscopy and three-dimensional reconstruction revealed that ParA2 formed bipolar helical filaments on double-stranded DNA in a sequence-independent manner. These filaments had a distinct change in pitch when ParA2 was polymerized in the presence of ATP versus in the absence of a nucleotide cofactor. Fitting a crystal structure of a ParA protein into our filament reconstruction showed how a dimer of ParA2 binds the DNA. The filaments formed with ATP are left-handed, but surprisingly these filaments exert no topological changes on the right-handed B-DNA to which they are bound. The stoichiometry of binding is one dimer for every eight base pairs, and this determines the geometry of the ParA2 filaments with 4.4 dimers per 120 A pitch left-handed turn. Our findings will be critical for understanding how ParA proteins function in plasmid and chromosome segregation.

Reconstruction of helical filaments and tubes

While Fourier-Bessel methods gave rise to the first three-dimensional reconstruction of an object from electron microscopic images, and these methods have dominated three-dimensional reconstruction of helical filaments and tubes for 30 years, single-particle approaches to helical reconstruction have emerged within the past 10 years that are now the main method being used. The Iterative Helical Real Space Reconstruction (IHRSR) approach has been the main methodology, and it surmounts many of the problems posed by real polymers that are flexible, display less than crystalline order, or are weakly scattering. The main difficulty in applying this method, or even Fourier-Bessel methods, is in determining the approximate helical symmetry. This chapter focuses on some of the intrinsic ambiguities that are present when trying to determine the helical symmetry from power spectra of images and argues that complementary techniques or some form of prior knowledge about the subunit may be needed to have confidence in the solution that is found.

An optimized negative-staining protocol of electron microscopy for apoE4 POPC lipoprotein

Apolipoprotein E (apoE), one of the major protein components of lipoproteins in the peripheral and central nervous systems, regulates cholesterol metabolism through its interaction with members of the low density lipoprotein receptor family. One key to understanding apoE function is determining the structure of lipid-bound forms of apoE. Negative-staining (NS) electron microscopy (EM) is an easy and rapid approach for studying the structure and morphology of lipid-bound forms of apoE. However, an artifact of using the conventional NS protocol is that the apoE•phospholipid particles form rouleaux. In this study, we used cryo-electron microscopy (cryo-EM) to examine apoE4•palmitoyl-oleoylphosphatidylcholine (POPC) particles in a frozen-hydrated native state. By comparing the particle sizes and shapes produced by different NS protocols to those produced by cryo-EM, we propose an optimized protocol to examine apoE4•POPC particles. Statistical analysis demonstrated that the particle sizes differ by less than 5% between the optimized protocol and the cryo-EM method, with similar shapes. The high contrast and fine detail of particle images produced using this optimized protocol lend themselves to the structural study of lipid-bound forms of apoE.