Atomic-resolution structure of cytoskeletal bactofilin by solid-state NMR

Bactofilins are essential spatial organizers of peptidoglycan insertion in the Lyme disease spirochete Borrelia burgdorferi

The Lyme disease spirochete Borrelia burgdorferi has a distinctive pattern of growth. Newly-born cells elongate by primarily inserting peptidoglycan at mid-cell, while in longer cells, additional insertion sites form at the one-quarter and three-quarter positions along the cell length. It is not known how peptidoglycan insertion is concentrated at these locations in B. burgdorferi. In other bacteria, multi-protein complexes are known to synthesize new peptidoglycan and are often organized by cytoskeletal proteins. We show here that B. burgdorferi 's zonal concentration of peptidoglycan insertion requires BB0538 (BbbA) and BB0245 (BbbB), two members of the bactofilin class of cytoskeletal proteins. Bactofilin depletion redistributes peptidoglycan insertion along the cell length. Prolonged bactofilin depletion arrested growth in culture and induced extensive cell blebbing, indicating that B. burgdorferi bactofilins are essential for viability. Fluorescent protein fusions of BbbA and BbbB localized to areas of peptidoglycan insertion, with BbbB accumulation preceding peptidoglycan insertion at these sites. Similar to peptidoglycan insertion, BbbB localization was disrupted upon depletion of BbbA. Our results show that BbbB relies on BbbA for its localization, and that together, BbbA and BbbB direct the spatial patterning of new peptidoglycan insertion in B. burgdorferi .

IMPORTANCE

The spirochetal bacterium Borrelia burgdorferi causes Lyme disease, the most prevalent vector-borne infection in North America and Europe. Cellular replication, which requires growth and division of the peptidoglycan cell wall, facilitates B. burgdorferi transmission to, and dissemination within, new hosts. Cellular replication is therefore essential for pathogenesis. Bactofilins regulate peptidoglycan-related processes in several bacteria. However, these functions are typically non-essential for cellular replication, as bactofilin-encoding genes can be readily deleted in multiple bacterial species. In contrast, we show that the B. burgdorferi bactofilins BbbA and BbbB are essential for cellular viability and direct zonal peptidoglycan insertion. Our findings broaden the spectrum of known bactofilin functions and advance our understanding of how peptidoglycan insertion is regulated in this unusual, medically important spirochete bacterium.

Hydrogen isotope separation at exceptionally high temperature using an unsaturated organometallic complex

A new approach for hydrogen isotope separation using an unsaturated organometallic complex was proposed. Adsorption measurements of [Mn(dppe)2(CO)(N2)](BArF24) (Mn-dppe) (dppe = 1,2-bis(diphenylphosphino)ethane, BArF24 = B[C6H3(3,5-CF3)2]4) using H2 and D2 revealed a significant difference in the adsorption enthalpy of H2/D2 at much higher room temperatures than in previous studies, with D2 molecules being more strongly adsorbed on unsaturated metal sites. Mixed gas adsorption isotherms were calculated at each temperature using IAST, and it was predicted that D2 uptake was much larger than H2 uptake. Column chromatographic separation using the difference in adsorption enthalpy indicated that deuterium could be concentrated, and DFT calculations suggest that this difference in adsorption force is due to the difference in vibrational potentials involved in metal-dihydrogen bonding. This study introduces a new separation approach that could enable hydrogen isotope separation in the ambient temperature range.

Functional specialization of the subdomains of a bactofilin driving stalk morphogenesis in Asticcacaulis biprosthecum

Bactofilins are a recently discovered class of cytoskeletal protein, widely implicated in subcellular organization and morphogenesis in bacteria and archaea. Several lines of evidence suggest that bactofilins polymerize into filaments using a central β-helical core domain, flanked by variable N- and C-terminal domains that may be important for scaffolding and other functions. However, a systematic exploration of the characteristics of these domains has yet to be performed. In Asticcacaulis biprosthecum, the bactofilin BacA serves as a topological organizer of stalk synthesis, localizing to the stalk base and coordinating the synthesis of these long, thin extensions of the cell envelope. The easily distinguishable phenotypes of wild-type A. biprosthecum stalks and ΔbacA "pseudostalks" make this an ideal system for investigating how mutations in BacA affect its functions in morphogenesis. Here, we redefine the core domain of A. biprosthecum BacA using various bioinformatics and biochemical approaches to precisely delimit the N- and C- terminal domains. We then show that loss of these terminal domains leads to cells with severe morphological abnormalities, typically presenting a pseudostalk phenotype. BacA mutants lacking the N- and C- terminal domains also exhibit localization defects, implying that the terminal domains of BacA may be involved in its subcellular positioning, whether through membrane interactions through the N-terminal domain or through interactions with the stalk-specific morphological regulator SpmX through the C-terminal domain. We further show that point mutations that render BacA defective for polymerization lead to stalk synthesis defects. Overall, our study suggests that BacA's polymerization, membrane association, and interactions with other morphological factors all play a crucial role in the protein's function as a morphogenic regulator. The specialization and modularity of the terminal domains may underlie the remarkable functional versatility of the bactofilins in different species.

Halofilins as emerging bactofilin families of archaeal cell shape plasticity orchestrators

Bactofilins are rigid, nonpolar bacterial cytoskeletal filaments that link cellular processes to specific curvatures of the cytoplasmic membrane. Although homologs of bactofilins have been identified in archaea and eukaryotes, functional studies have remained confined to bacterial systems. Here, we characterize representatives of two families of archaeal bactofilins from the pleomorphic archaeon Haloferax volcanii, halofilin A (HalA) and halofilin B (HalB). HalA and HalB polymerize in vitro, assembling into straight bundles. HalA polymers are highly dynamic and accumulate at positive membrane curvatures in vivo, whereas HalB forms more static foci that localize in areas of local negative curvatures on the outer cell surface. Gene deletions and live-cell imaging show that halofilins are critical in maintaining morphological integrity during shape transition from disk (sessile) to rod (motile). Morphological defects in ΔhalA result in accumulation of highly positive curvatures in rods but not in disks. Conversely, disk-shaped cells are exclusively affected by halB deletion, resulting in flatter cells. Furthermore, while ΔhalA and ΔhalB cells imprecisely determine the future division plane, defects arise predominantly during the disk-to-rod shape remodeling. The deletion of halA in the haloarchaeon Halobacterium salinarum, whose cells are consistently rod-shaped, impacted morphogenesis but not cell division. Increased levels of halofilins enforced drastic deformations in cells devoid of the S-layer, suggesting that HalB polymers are more stable at defective S-layer lattice regions. Our results suggest that halofilins might play a significant mechanical scaffolding role in addition to possibly directing envelope synthesis.

Exploring the Higher Order Structure and Conformational Transitions in Insulin Microcrystalline Biopharmaceuticals by Proton-Detected Solid-State Nuclear Magnetic Resonance at Natural Abundance

The integrity of a higher order structure (HOS) is an essential requirement to ensure the efficacy, stability, and safety of protein therapeutics. Solution-state nuclear magnetic resonance (NMR) occupies a unique niche as one of the most promising methods to access atomic-level structural information on soluble biopharmaceutical formulations. Another major class of drugs is poorly soluble, such as microcrystalline suspensions, which poses significant challenges for the characterization of the active ingredient in its native state. Here, we have demonstrated a solid-state NMR method for HOS characterization of biopharmaceutical suspensions employing a selective excitation scheme under fast magic angle spinning (MAS). The applicability of the method is shown on commercial insulin suspensions at natural isotopic abundance. Selective excitation aided with proton detection and non-uniform sampling (NUS) provides improved sensitivity and resolution. The enhanced resolution enabled us to demonstrate the first experimental evidence of a phenol-escaping pathway in insulin, leading to conformational transitions to different hexameric states. This approach has the potential to serve as a valuable means for meticulously examining microcrystalline biopharmaceutical suspensions, which was previously not attainable in their native formulation states and can be seamlessly extended to other classes of biopharmaceuticals such as mAbs and other microcrystalline proteins.

A dynamic bactofilin cytoskeleton cooperates with an M23 endopeptidase to control bacterial morphogenesis

Bactofilins have emerged as a widespread family of cytoskeletal proteins with important roles in bacterial morphogenesis, but their precise mode of action is still incompletely understood. In this study, we identify the bactofilin cytoskeleton as a key regulator of cell growth in the stalked budding alphaproteobacterium Hyphomonas neptunium. We show that, in this species, bactofilin polymers localize dynamically to the stalk base and the bud neck, with their absence leading to unconstrained growth of the stalk and bud compartments, indicating a central role in the spatial regulation of cell wall biosynthesis. Database searches reveal that bactofilin genes are often clustered with genes for cell wall hydrolases of the M23 peptidase family, suggesting a functional connection between these two types of proteins. In support of this notion, we find that the H. neptunium M23 peptidase homolog LmdC interacts directly with bactofilin in vitro and is required for proper cell shape in vivo. Complementary studies in the spiral-shaped alphaproteobacterium Rhodospirillum rubrum again reveal a close association of its bactofilin and LmdC homologs, which co-localize at the inner curve of the cell, modulating the degree of cell curvature. Collectively, these findings demonstrate that bactofilins and M23 peptidases form a conserved functional module that promotes local changes in the mode of cell wall biosynthesis, thereby driving cell shape determination in morphologically complex bacteria.

VirB, a key transcriptional regulator of Shigella virulence, requires a CTP ligand for its regulatory activities

IMPORTANCE

Shigella species cause bacillary dysentery, the second leading cause of diarrheal deaths worldwide. There is a pressing need to identify novel molecular drug targets. Shigella virulence phenotypes are controlled by the transcriptional regulator, VirB. We show that VirB belongs to a fast-evolving, plasmid-borne clade of the ParB superfamily, which has diverged from versions with a distinct cellular role-DNA partitioning. We report that, like classic members of the ParB family, VirB binds a highly unusual ligand, CTP. Mutants predicted to be defective in CTP binding are compromised in a variety of virulence attributes controlled by VirB, likely because these mutants cannot engage DNA. This study (i) reveals that VirB binds CTP, (ii) provides a link between VirB-CTP interactions and Shigella virulence phenotypes, (iii) provides new insight into VirB-CTP-DNA interactions, and (iv) broadens our understanding of the ParB superfamily, a group of bacterial proteins that play critical roles in many bacteria.

VirB, a key transcriptional regulator of Shigella virulence, requires a CTP ligand for its regulatory activities

The VirB protein, encoded by the large virulence plasmid of Shigella spp., is a key transcriptional regulator of virulence genes. Without a functional virB gene, Shigella cells are avirulent. On the virulence plasmid, VirB functions to offset transcriptional silencing mediated by the nucleoid structuring protein, H-NS, which binds and sequesters AT-rich DNA, making it inaccessible for gene expression. Thus, gaining a mechanistic understanding of how VirB counters H-NS-mediated silencing is of considerable interest. VirB is unusual in that it does not resemble classic transcription factors. Instead, its closest relatives are found in the ParB superfamily, where the best-characterized members function in faithful DNA segregation before cell division. Here, we show that VirB is a fast-evolving member of this superfamily and report for the first time that the VirB protein binds a highly unusual ligand, CTP. VirB binds this nucleoside triphosphate preferentially and with specificity. Based on alignments with the best-characterized members of the ParB family, we identify amino acids of VirB likely to bind CTP. Substitutions in these residues disrupt several well-documented activities of VirB, including its anti-silencing activity at a VirB-dependent promoter, its role in generating a Congo red positive phenotype in Shigella , and the ability of the VirB protein to form foci in the bacterial cytoplasm when fused to GFP. Thus, this work is the first to show that VirB is a bona fide CTP-binding protein and links Shigella virulence phenotypes to the nucleoside triphosphate, CTP.

Importance

Shigella species cause bacillary dysentery (shigellosis), the second leading cause of diarrheal deaths worldwide. With growing antibiotic resistance, there is a pressing need to identify novel molecular drug targets. Shigella virulence phenotypes are controlled by the transcriptional regulator, VirB. We show that VirB belongs to a fast-evolving, primarily plasmid-borne clade of the ParB superfamily, which has diverged from versions that have a distinct cellular role - DNA partitioning. We are the first to report that, like classic members of the ParB family, VirB binds a highly unusual ligand, CTP. Mutants predicted to be defective in CTP binding are compromised in a variety of virulence attributes controlled by VirB. This study i) reveals that VirB binds CTP, ii) provides a link between VirB-CTP interactions and Shigella virulence phenotypes, and iii) broadens our understanding of the ParB superfamily, a group of bacterial proteins that play critical roles in many different bacteria.

Hydrogen Isotope Separation Using Graphene-Based Membranes in Liquid Water

Hydrogen isotope separation has been effectively achieved electrochemically by passage of gaseous H₂/D₂ through graphene/Nafion composite membranes. Nevertheless, deuteron nearly does not exist in the form of gaseous D₂ in nature but as liquid water. Thus, it is a more feasible way to separate and enrich deuterium from water. Herein, we have successfully transferred monolayer graphene to a rigid and porous polymer substrate, PITEM (polyimide track-etched membrane), which could avoid the swelling problem of the Nafion substrate as well as keep the integrity of graphene. Meanwhile, defects in the large area of CVD graphene could be successfully repaired by interfacial polymerization resulting in a high separation factor. Moreover, a new model was proposed for the proton transport mechanism through monolayer graphene based on the kinetic isotope effect (KIE). In this model, graphene plays a significant role in the H/D separation process by completely breaking the O-H/O-D bond, which can maximize the KIE, leading to increased H/D separation performance. This work suggests a promising application for using monolayer graphene in the industry and proposes a pronounced understanding of proton transport in graphene.

Solid-state NMR studies of amyloids

Amyloids have special structural properties and are involved in many aspects of biological function. In particular, amyloids are the cause or hallmarks of a group of notorious and incurable neurodegenerative diseases. The extraordinary high molecular weight and aggregation states of amyloids have posed a challenge for researchers studying them. Solid-state NMR (SSNMR) has been extensively applied to study the structures and dynamics of amyloids for the past 20 or more years and brought us tremendous progress in understanding their structure and related diseases. These studies, at the same time, helped to push SSNMR technical developments in sensitivity and resolution. In this review, some interesting research studies and important technical developments are highlighted to give the reader an overview of the current state of this field.

Accurate Determination of Motional Amplitudes in Biomolecules by Solid-State NMR

Protein dynamics are an intrinsically important factor when considering a protein's biological function. Understanding these motions is often limited through the use of static structure determination methods, namely, X-ray crystallography and cryo-EM. Molecular simulations have allowed for the prediction of global and local motions of proteins from these static structures. Nevertheless, determining local dynamics at residue-specific resolution through direct measurement remains crucial. Solid-state nuclear magnetic resonance (NMR) is a powerful tool for studying dynamics in rigid or membrane-bound biomolecules without prior structural knowledge with the help of relaxation parameters such as T ₁ and T _1ρ. However, these provide only a combined result of amplitude and correlation times in the nanosecond-millisecond frequency range. Thus, direct and independent determination of the amplitude of motions might considerably improve the accuracy of dynamics studies. In an ideal situation, the use of cross-polarization would be the optimal method for measuring the dipolar couplings between chemically bound heterologous nuclei. This would unambiguously provide the amplitude of motion per residue. In practice, however, the inhomogeneity of the applied radio-frequency fields across the sample leads to significant errors. Here, we present a novel method to eliminate this issue through including the radio-frequency distribution map in the analysis. This allows for direct and accurate measurement of residue-specific amplitudes of motion. Our approach has been applied to the cytoskeletal protein BacA in filamentous form, as well as to the intramembrane protease GlpG in lipid bilayers.

Hydrogen Isotope Separation Using a Metal-Organic Cage Built from Macrocycles

Porous materials that contain ultrafine pore apertures can separate hydrogen isotopes via kinetic quantum sieving (KQS). However, it is challenging to design materials with suitably narrow pores for KQS that also show good adsorption capacities and operate at practical temperatures. Here, we investigate a metal-organic cage (MOC) assembled from organic macrocycles and ZnII ions that exhibits narrow windows (<3.0 Å). Two polymorphs, referred to as 2α and 2β, were observed. Both polymorphs exhibit D2 /H2 selectivity in the temperature range 30-100 K. At higher temperature (77 K), the D2 adsorption capacity of 2β increases to about 2.7 times that of 2α, along with a reasonable D2 /H2 selectivity. Gas sorption analysis and thermal desorption spectroscopy suggest a gate-opening effect of the MOCs pore aperture. This promotes KQS at temperatures above liquid nitrogen temperature, indicating that MOCs hold promise for hydrogen isotope separation in real industrial environments.

Thermodynamic Separation of Hydrogen Isotopes Using Hofmann-Type Metal-Organic Frameworks with High-Density Open Metal Sites

Hydrogen isotope separation with nanoporous materials is a very challenging yet promising approach. To overcome the limitation of the conventional isotope separation strategy, quantum sieving-based separation using nanoporous materials has been investigated recently. In this study, to see the thermodynamic deuterium separation phenomena attributed to the chemical affinity quantum sieving effect, we examine Hofmann-type metal-organic frameworks (MOFs), Co(pyz)[M(CN)₄] (pyz = pyrazine, M = Pd²⁺, Pt²⁺, and Ni²⁺), which have microporosity (4.0 × 3.9 Ų) and an extraordinarily high density of open metal sites (∼9 mmol/cm³). Owing to the preferential adsorption of D₂ over H₂ at strongly binding open metal sites, the Hofmann-type MOF, Co(pyz)[Pd(CN)₄] exhibited a high selectivity (S_D2/H2) of 21.7 as well as a large D₂ uptake of 10 mmol/g at 25 K. This is the first study of Hofmann-type MOFs to report high selectivity and capacity, both of which are important parameters for the practical application of porous materials toward isotope separation.

Chemical Affinity of Ag-Exchanged Zeolites for Efficient Hydrogen Isotope Separation

We report an ion-exchanged zeolite as an excellent candidate for large-scale application in hydrogen isotope separation. Ag(I)-exchanged zeolite Y has been synthesized through a standard ion-exchange procedure. The D₂/H₂ separation performance has been systematically investigated via thermal desorption spectroscopy (TDS). Undercoordinated Ag⁺ in zeolite AgY acts as a strong adsorption site and adorbs preferentially the heavier isotopologue even above liquid nitrogen temperature. The highest D₂/H₂ selectivity of 10 is found at an exposure temperature of 90 K. Furthermore, the high Al content of the zeolite structure leads to a high density of Ag sites, resulting in a high gas uptake. In the framework, approximately one-third of the total physisorbed hydrogen isotopes are adsorbed on the Ag sites, corresponding to 3 mmol/g. A density functional theory (DFT) calculation reveals that the isotopologue-selective adsorption of hydrogen at Ag sites contributes to the outstanding hydrogen isotope separation, which has been directly observed through cryogenic thermal desorption spectroscopy. The overall performance of zeolite AgY, showing good selectivity combined with high gas uptake, is very promising for future technical applications.

Silver-exchanged zeolite Y was synthesized for efficient and effective separation of hydrogen isotopes above liquid nitrogen temperature via chemical affinity sieving. The highest D₂/H₂ selectivity of 10 is achieved at 90 K combined with a high gas uptake, making zeolite AgY a promising candidate for large-scale deuterium enrichment.

1H-Detected Biomolecular NMR under Fast Magic-Angle Spinning

Since the first pioneering studies on small deuterated peptides dating more than 20 years ago, 1H detection has evolved into the most efficient approach for investigation of biomolecular structure, dynamics, and interactions by solid-state NMR. The development of faster and faster magic-angle spinning (MAS) rates (up to 150 kHz today) at ultrahigh magnetic fields has triggered a real revolution in the field. This new spinning regime reduces the 1H-1H dipolar couplings, so that a direct detection of 1H signals, for long impossible without proton dilution, has become possible at high resolution. The switch from the traditional MAS NMR approaches with 13C and 15N detection to 1H boosts the signal by more than an order of magnitude, accelerating the site-specific analysis and opening the way to more complex immobilized biological systems of higher molecular weight and available in limited amounts. This paper reviews the concepts underlying this recent leap forward in sensitivity and resolution, presents a detailed description of the experimental aspects of acquisition of multidimensional correlation spectra with fast MAS, and summarizes the most successful strategies for the assignment of the resonances and for the elucidation of protein structure and conformational dynamics. It finally outlines the many examples where 1H-detected MAS NMR has contributed to the detailed characterization of a variety of crystalline and noncrystalline biomolecular targets involved in biological processes ranging from catalysis through drug binding, viral infectivity, amyloid fibril formation, to transport across lipid membranes.

Strain-dependent motility defects and suppression by a flhO mutation for B. subtilis bactofilins

Objective

Bactofilins can assemble into polymeric structures and play important roles in cell shape maintenance, chromosome segregation and motility. Bacillus subtilis bactofilins BacE and BacF were shown to be important for swimming motility in strain PY79, and single gene deletions were reported to be lethal, in contrast to a double bacEF deletion.

Results

Extending this work, we show that motility defects vary between different B. subtilis strains, with strain 168 showing no defect in motility, and 3610 showing delayed induction of swimming. Generation of single gene deletions in PY79 was possible by transferring corresponding deletions from 168. In the natural isolate 3610, gene deletions also showed a negative effect on biofilm formation, revealing an additional function for BacE and BacF. A spontaneous arising suppressor mutation in PY79 was mapped to the flhO gene, a constituent of the flagellum, which obtained an 18 amino acid extension at its C-terminus. Our findings show that bactofilin gene deletions lead to different motility phenotypes dependent on the strain background, and affect biofilm formation in the natural isolate 3610. Our data reinforce the idea of a connection between bactofilins and motion via the flagellum, and suggest that they operate in a switch like manner.

Supplementary Information

The online version contains supplementary material available at 10.1186/s13104-022-06048-6.

Design Elements for Enhanced Hydrogen Isotope Separations in Barely Porous Organic Cages

Barely porous organic cages (POCs) successfully separate hydrogen isotopes (H₂/D₂) at temperatures below 100 K. Identifying the mechanisms that control the separation process is key to the design of next-generation hydrogen separation materials. Here, ab initio molecular dynamics (AIMD) simulations are used to elucidate the mechanisms that control D₂ and H₂ separation in barely POCs with varying functionalization. The temperature and pore size dependence were identified, including the selective capture of D₂ in three different CC3 structures (RCC3, CC3-S, and 6ET-RCC3). The temperature versus capture trend was reversed for the 6ET-RCC3 structure, identifying that the D₂ and H₂ escape mechanisms are unique in highly functionalized systems. Analysis of calculated isotope velocities identified effective pore sizes that extend beyond the pore opening distances, resulting in increased capture in minimally functionalized CC3-S and RCC3. In a highly functionalized POC, 6ET-RCC3, higher velocities of the H isotopes were calculated moving through the restricted pore compared to the rest of the system, identifying a unique molecular behavior in the barely nanoporous pore openings. By using AIMD, mechanisms of H₂ and D₂ separation were identified, allowing for the targeted design of future novel materials for hydrogen isotope separation.

Unambiguous Side-Chain Assignments for Solid-State NMR Structure Elucidation of Nondeuterated Proteins via a Combined 5D/4D Side-Chain-to-Backbone Experiment

Owing to fast-magic-angle-spinning technology, proton-detected solid-state NMR has been facilitating the analysis of insoluble, crystalline, sedimented, and membrane proteins. However, potential applications have been largely restricted by limited access to side-chain resonances. The recent availability of spinning frequencies exceeding 100 kHz in principle now allows direct probing of all protons without the need for partial deuteration. This potentiates both the number of accessible target proteins and possibilities to exploit side-chain protons as reporters on distances and interactions. Their low dispersion, however, has severely compromised their chemical-shift assignment, which is a prerequisite for their use in downstream applications. Herein, we show that unambiguous correlations are obtained from 5D methodology by which the side-chain resonances are directly connected with the backbone. When further concatenated with simultaneous 4D intra-side-chain correlations, this yields comprehensive assignments in the side chains and hence allows a high density of distance restraints for high-resolution structure calculation from minimal amounts of protein.

Atomic-resolution chemical characterization of (2x)72-kDa tryptophan synthase via four- and five-dimensional 1H-detected solid-state NMR

NMR chemical shifts provide detailed information on the chemical properties of molecules, thereby complementing structural data from techniques like X-ray crystallography and electron microscopy. Detailed analysis of protein NMR data, however, often hinges on comprehensive, site-specific assignment of backbone resonances, which becomes a bottleneck for molecular weights beyond 40 to 45 kDa. Here, we show that assignments for the (2x)72-kDa protein tryptophan synthase (665 amino acids per asymmetric unit) can be achieved via higher-dimensional, proton-detected, solid-state NMR using a single, 1-mg, uniformly labeled, microcrystalline sample. This framework grants access to atom-specific characterization of chemical properties and relaxation for the backbone and side chains, including those residues important for the catalytic turnover. Combined with first-principles calculations, the chemical shifts in the β-subunit active site suggest a connection between active-site chemistry, the electrostatic environment, and catalytically important dynamics of the portal to the β-subunit from solution.

Deuteration for High-Resolution Detection of Protons in Protein Magic Angle Spinning (MAS) Solid-State NMR

Proton detection developed in the last 20 years as the method of choice to study biomolecules in the solid state. In perdeuterated proteins, proton dipolar interactions are strongly attenuated, which allows yielding of high-resolution proton spectra. Perdeuteration and backsubstitution of exchangeable protons is essential if samples are rotated with MAS rotation frequencies below 60 kHz. Protonated samples can be investigated directly without spin dilution using proton detection methods in case the MAS frequency exceeds 110 kHz. This review summarizes labeling strategies and the spectroscopic methods to perform experiments that yield assignments, quantitative information on structure, and dynamics using perdeuterated samples. Techniques for solvent suppression, H/D exchange, and deuterium spectroscopy are discussed. Finally, experimental and theoretical results that allow estimation of the sensitivity of proton detected experiments as a function of the MAS frequency and the external B₀ field in a perdeuterated environment are compiled.

A Dynamic, Ring-Forming Bactofilin Critical for Maintaining Cell Size in the Obligate Intracellular Bacterium Chlamydia trachomatis

Bactofilins are polymer-forming cytoskeletal proteins that are widely conserved in bacteria. Members of this protein family have diverse functional roles such as orienting subcellular molecular processes, establishing cell polarity, and aiding in cell shape maintenance. Using sequence alignment to the conserved bactofilin domain, we identified a bactofilin ortholog, BacA_CT, in the obligate intracellular pathogen Chlamydia trachomatis. Chlamydia species are obligate intracellular bacteria that undergo a developmental cycle alternating between infectious nondividing elementary bodies (EBs) and noninfectious dividing reticulate bodies (RBs). As Chlamydia divides by a polarized division process, we hypothesized that BacA_CT may function to establish polarity in these unique bacteria. Utilizing a combination of fusion constructs and high-resolution fluorescence microscopy, we determined that BacA_CT forms dynamic, membrane-associated filament- and ring-like structures in Chlamydia's replicative RB form. Contrary to our hypothesis, these structures are distinct from the microbe's cell division machinery and do not colocalize with septal peptidoglycan or MreB, the major organizer of the bacterium's division complex. Bacterial two-hybrid assays demonstrated BacA_CT interacts homotypically but does not directly interact with proteins involved in cell division or peptidoglycan biosynthesis. To investigate the function of BacA_CT in chlamydial development, we constructed a conditional knockdown strain using a newly developed CRISPR interference system. We observed that reducing bacA_CT expression significantly increased chlamydial cell size. Normal RB morphology was restored when an additional copy of bacA_CT was expressed in trans during knockdown. These data reveal a novel function for chlamydial bactofilin in maintaining cell size in this obligate intracellular bacterium.

Heteronuclear and homonuclear radio-frequency-driven recoupling

The radio-frequency-driven recoupling (RFDR) pulse sequence is used in magic-angle spinning (MAS) NMR to recouple homonuclear dipolar interactions. Here we show simultaneous recoupling of both the heteronuclear and homonuclear dipolar interactions by applying RFDR pulses on two channels. We demonstrate the method, called HETeronuclear RFDR (HET-RFDR), on microcrystalline SH3 samples at 10 and 55.555 kHz MAS. Numerical simulations of both HET-RFDR and standard RFDR sequences allow for better understanding of the influence of offsets and paths of magnetization transfers for both HET-RFDR and RFDR experiments, as well as the crucial role of XY phase cycling.

Architecture of the flexible tail tube of bacteriophage SPP1

Bacteriophage SPP1 is a double-stranded DNA virus of the Siphoviridae family that infects the bacterium Bacillus subtilis. This family of phages features a long, flexible, non-contractile tail that has been difficult to characterize structurally. Here, we present the atomic structure of the tail tube of phage SPP1. Our hybrid structure is based on the integration of structural restraints from solid-state nuclear magnetic resonance (NMR) and a density map from cryo-EM. We show that the tail tube protein gp17.1 organizes into hexameric rings that are stacked by flexible linker domains and, thus, form a hollow flexible tube with a negatively charged lumen suitable for the transport of DNA. Additionally, we assess the dynamics of the system by combining relaxation measurements with variances in density maps.

Bacteriophages of the Siphoviridae family have a long, flexible, non-contractile tail that has been difficult to characterize structurally. Here, the authors present the atomic structure of the tail tube of one of these phages, showing a hollow flexible tube formed by hexameric rings stacked by flexible linkers.

A Compass To Boost Navigation: Cell Biology of Bacterial Magnetotaxis

Magnetotactic bacteria are aquatic or sediment-dwelling microorganisms able to take advantage of the Earth's magnetic field for directed motility. The source of this amazing trait is magnetosomes, unique organelles used to synthesize single nanometer-sized crystals of magnetic iron minerals that are queued up to build an intracellular compass. Most of these microorganisms cannot be cultivated under controlled conditions, much less genetically engineered, with only few exceptions. However, two of the genetically amenable Magnetospirillum species have emerged as tractable model organisms to study magnetosome formation and magnetotaxis. Recently, much has been revealed about the process of magnetosome biogenesis and dedicated structures for magnetosome dynamics and positioning, which suggest an unexpected cellular intricacy of these organisms. In this minireview, we summarize new insights and place the molecular mechanisms of magnetosome formation in the context of the complex cell biology of Magnetospirillum spp. First, we provide an overview on magnetosome vesicle synthesis and magnetite biomineralization, followed by a discussion of the perceptions of dynamic organelle positioning and its biological implications, which highlight that magnetotactic bacteria have evolved sophisticated mechanisms to construct, incorporate, and inherit a unique navigational device. Finally, we discuss the impact of magnetotaxis on motility and its interconnection with chemotaxis, showing that magnetotactic bacteria are outstandingly adapted to lifestyle and habitat.

A Division of Labor in the Recruitment and Topological Organization of a Bacterial Morphogenic Complex

Bacteria come in an array of shapes and sizes, but the mechanisms underlying diverse morphologies are poorly understood. The peptidoglycan (PG) cell wall is the primary determinant of cell shape. At the molecular level, morphological variation often results from the regulation of enzymes involved in cell elongation and division. These enzymes are spatially controlled by cytoskeletal scaffolding proteins, which both recruit and organize the PG synthesis complex. How then do cells define alternative morphogenic processes that are distinct from cell elongation and division? To address this, we have turned to the specific morphotype of Alphaproteobacterial stalks. Stalk synthesis is a specialized form of zonal growth, which requires PG synthesis in a spatially constrained zone to extend a thin cylindrical projection of the cell envelope. The morphogen SpmX defines the site of stalk PG synthesis, but SpmX is a PG hydrolase. How then does a non-cytoskeletal protein, SpmX, define and constrain PG synthesis to form stalks? Here, we report that SpmX and the bactofilin BacA act in concert to regulate stalk synthesis in Asticcacaulis biprosthecum. We show that SpmX recruits BacA to the site of stalk synthesis. BacA then serves as a stalk-specific topological organizer for PG synthesis activity, including its recruiter SpmX, at the base of the stalk. In the absence of BacA, cells produce "pseudostalks" that are the result of unconstrained PG synthesis. Therefore, the protein responsible for recruitment of a morphogenic PG remodeling complex, SpmX, is distinct from the protein that topologically organizes the complex, BacA.

Distinct cytoskeletal proteins define zones of enhanced cell wall synthesis in Helicobacter pylori

Helical cell shape is necessary for efficient stomach colonization by Helicobacter pylori, but the molecular mechanisms for generating helical shape remain unclear. The helical centerline pitch and radius of wild-type H. pylori cells dictate surface curvatures of considerably higher positive and negative Gaussian curvatures than those present in straight- or curved-rod H. pylori. Quantitative 3D microscopy analysis of short pulses with either N-acetylmuramic acid or D-alanine metabolic probes showed that cell wall growth is enhanced at both sidewall curvature extremes. Immunofluorescence revealed MreB is most abundant at negative Gaussian curvature, while the bactofilin CcmA is most abundant at positive Gaussian curvature. Strains expressing CcmA variants with altered polymerization properties lose helical shape and associated positive Gaussian curvatures. We thus propose a model where CcmA and MreB promote PG synthesis at positive and negative Gaussian curvatures, respectively, and that this patterning is one mechanism necessary for maintaining helical shape.

Round spheres, straight rods, and twisting corkscrews, bacteria come in many different shapes. The shape of bacteria is dictated by their cell wall, the strong outer barrier of the cell. As bacteria grow and multiply, they must add to their cell wall while keeping the same basic shape. The cells walls are made from long chain-like molecules via processes that are guided by protein scaffolds within the cell. Many common antibiotics, including penicillin, stop bacterial infections by interrupting the growth of cell walls.

Helicobacter pylori is a common bacterium that lives in the gut and, after many years, can cause stomach ulcers and stomach cancer. H. pylori are shaped in a twisting helix, much like a corkscrew. This shape helps H. pylori to take hold and colonize the stomach.

It remains unclear how H. pylori creates and maintains its helical shape. The helix is much more curved than other bacteria, and H. pylori does not have the same helpful proteins that other curved bacteria do. If H. pylori grows asymmetrically, adding more material to the cell wall on its long outer side to create a twisting helix, what controls the process?

To find out, Taylor et al. grew H. pylori cells and watched how the cell walls took shape. First, a fluorescent dye was attached to the building blocks of the cell wall or to underlying proteins that were thought to help direct its growth. The cells were then imaged in 3D, and images from hundreds of cells were reconstructed to analyze the growth patterns of the bacteria’s cell wall.

A protein called CcmA was found most often on the long side of the twisting H. pylori. When the CcmA protein was isolated in a dish, it spontaneously formed sheets and helical bundles, confirming its role as a structural scaffold for the cell wall. When CcmA was absent from the cell of H. pylori, Taylor et al. observed that the pattern of cell growth changed substantially.

This work identifies a key component directing the growth of the cell wall of H. pylori and therefore, a new target for antibiotics. Its helical shape is essential for H. pylori to infect the gut, so blocking the action of the CcmA protein may interrupt cell wall growth and prevent stomach infections.

The structure of bactofilin filaments reveals their mode of membrane binding and lack of polarity

Bactofilins are small β-helical proteins that form cytoskeletal filaments in a range of bacteria. Bactofilins have diverse functions, from cell stalk formation in Caulobacter crescentus to chromosome segregation and motility in Myxococcus xanthus. However, the precise molecular architecture of bactofilin filaments has remained unclear. Here, sequence analysis and electron microscopy results reveal that, in addition to being widely distributed across bacteria and archaea, bactofilins are also present in a few eukaryotic lineages such as the Oomycetes. Electron cryomicroscopy analysis demonstrated that the sole bactofilin from Thermus thermophilus (TtBac) forms constitutive filaments that polymerize through end-to-end association of the β-helical domains. Using a nanobody, we determined the near-atomic filament structure, showing that the filaments are non-polar. A polymerization-impairing mutation enabled crystallization and structure determination, while reaffirming the lack of polarity and the strength of the β-stacking interface. To confirm the generality of the lack of polarity, we performed coevolutionary analysis on a large set of sequences. Finally, we determined that the widely conserved N-terminal disordered tail of TtBac is responsible for direct binding to lipid membranes, both on liposomes and in Escherichia coli cells. Membrane binding is probably a common feature of these widespread but only recently discovered filaments of the prokaryotic cytoskeleton.

A Protofilament-Protofilament Interface in the Structure of Mouse α-Synuclein Fibrils

Fibrillar α-synuclein (AS) is the major component of Lewy bodies, the pathological hallmark of Parkinson's disease. Using solid-state nuclear magnetic resonance (ssNMR), we previously reported a structural characterization of mouse AS (mAS) fibrils and found that the secondary structure of the mAS fibrils is highly similar to a form of human AS (hAS) fibrils. Recently, a three-dimensional structure of these same hAS fibrils was determined by ssNMR and scanning transmission electron microscopy. Using medium- and long-range distance restraints obtained from ssNMR spectra, we found that the single protofilament structure of mAS fibrils is also similar to that of the hAS fibrils. However, residue-specific water accessibility of mAS fibrils probed by water polarization transfer ssNMR measurements indicates that residues S42-T44 and G84-V95 are largely protected from water even though they are located at the edge of the protofilament. Some of the corresponding resonances also exhibit peak doubling. These observations suggest that these residues may be involved in, to our knowledge, a novel protofilament-protofilament interface. We propose a structural model of mAS fibrils that incorporates this dimer interface.

Biochemical characterization of the Helicobacter pylori bactofilin-homolog HP1542

The human pathogen Helicobacter pylori is known for its colonization of the upper digestive system, where it escapes the harsh acidic environment by hiding in the mucus layer. One factor promoting this colonization is the helical cell shape of H. pylori. Among shape determining proteins are cytoskeletal elements like the recently discovered bactofilins. Bactofilins constitute a widespread family of polymer-forming bacterial proteins whose biology is still poorly investigated. Here we describe the first biochemical analysis of the bactofilin HP1542 of H. pylori reference strain 26695. Purified HP1542 forms sheet-like 2D crystalline assemblies, which clearly depend on a natively structured C-terminus. Polymerization properties and protein stability were investigated. Additionally, we also could demarcate HP1542 from amyloid proteins that share similarities with the bactofilin DUF domain. By using zonal centrifugation of total H. pylori cell lysates and immunfluorescence analysis we revealed peripheral membrane association of HP1542 mostly pronounced near mid-cell. Interestingly our results indicate that H. pylori bactofilin does not contribute to cell wall stability. This study might act as a starting point for biophysical studies of the H. pylori bactofilin biology as well as for the investigation of bactofilin cell physiology in this organism. Importantly, this study is the first biochemical analysis of a bactofilin in a human pathogen.

Hydrogen Isotope Separation in Confined Nanospaces: Carbons, Zeolites, Metal-Organic Frameworks, and Covalent Organic Frameworks

One of the greatest challenges of modern separation technology is separating isotope mixtures in high purity. The separation of hydrogen isotopes can create immense economic value by producing valuable deuterium (D) and tritium (T), which are irreplaceable for various industrial and scientific applications. However, current separation methods suffer from low separation efficiency owing to the similar chemical properties of isotopes; thus, high-purity isotopes are not easily achieved. Recently, nanoporous materials have been proposed as promising candidates and are supported by a newly proposed separation mechanism, i.e., quantum effects. Herein, the fundamentals of the quantum sieving effect of hydrogen isotopes in nanoporous materials are discussed, which are mainly kinetic quantum sieving and chemical-affinity quantum sieving, including the recent advances in the analytical techniques. As examples of nanoporous materials, carbons, zeolites, metal-organic frameworks, and covalent organic frameworks are addressed from computational and experimental standpoints. Understanding the quantum sieving effect in nanospaces and the tailoring of porous materials based on it will open up new opportunities to develop a highly efficient and advanced isotope separation systems.

19F Dynamic Nuclear Polarization at Fast Magic Angle Spinning for NMR of HIV-1 Capsid Protein Assemblies

We report remarkably high, up to 100-fold, signal enhancements in 19F dynamic nuclear polarization (DNP) magic angle spinning (MAS) spectra at 14.1 T on HIV-1 capsid protein (CA) assemblies. These enhancements correspond to absolute sensitivity ratios of 12-29 and are of similar magnitude to those seen for 1H signals in the same samples. At MAS frequencies above 20 kHz, it was possible to record 2D 19F-13C HETCOR spectra, which contain long-range intra- and intermolecular correlations. Such correlations provide unique distance restraints, inaccessible in conventional experiments without DNP, for protein structure determination. Furthermore, systematic quantification of the DNP enhancements as a function of biradical concentration, MAS frequency, temperature, and microwave power is reported. Our work establishes the power of DNP-enhanced 19F MAS NMR spectroscopy for structural characterization of HIV-1 CA assemblies, and this approach is anticipated to be applicable to a wide range of large biomolecular systems.

A specialized MreB-dependent cell wall biosynthetic complex mediates the formation of stalk-specific peptidoglycan in Caulobacter crescentus

Many bacteria have complex cell shapes, but the mechanisms producing their distinctive morphologies are still poorly understood. Caulobacter crescentus, for instance, exhibits a stalk-like extension that carries an adhesive holdfast mediating surface attachment. This structure forms through zonal peptidoglycan biosynthesis at the old cell pole and elongates extensively under phosphate-limiting conditions. We analyzed the composition of cell body and stalk peptidoglycan and identified significant differences in the nature and proportion of peptide crosslinks, indicating that the stalk represents a distinct subcellular domain with specific mechanical properties. To identify factors that participate in stalk formation, we systematically inactivated and localized predicted components of the cell wall biosynthetic machinery of C. crescentus. Our results show that the biosynthesis of stalk peptidoglycan involves a dedicated peptidoglycan biosynthetic complex that combines specific components of the divisome and elongasome, suggesting that the repurposing of preexisting machinery provides a straightforward means to evolve new morphological traits.

Fast Magic-Angle Spinning 19 F NMR Spectroscopy of HIV-1 Capsid Protein Assemblies

19 F NMR spectroscopy is an attractive and growing area of research with broad applications in biochemistry, chemical biology, medicinal chemistry, and materials science. We have explored fast magic angle spinning (MAS) 19 F solid-state NMR spectroscopy in assemblies of HIV-1 capsid protein. Tryptophan residues with fluorine substitution at the 5-position of the indole ring were used as the reporters. The 19 F chemical shifts for the five tryptophan residues are distinct, reflecting differences in their local environment. Spin-diffusion and radio-frequency-driven-recoupling experiments were performed at MAS frequencies of 35 kHz and 40-60 kHz, respectively. Fast MAS frequencies of 40-60 kHz are essential for consistently establishing 19 F-19 F correlations, yielding interatomic distances of the order of 20 Å. Our results demonstrate the potential of fast MAS 19 F NMR spectroscopy for structural analysis in large biological assemblies.

Structural assembly of the megadalton-sized receptor for intestinal vitamin B12 uptake and kidney protein reabsorption

The endocytic receptor cubam formed by the 460-kDa protein cubilin and the 45-kDa transmembrane protein amnionless (AMN), is essential for intestinal vitamin B₁₂ (B₁₂) uptake and for protein (e.g. albumin) reabsorption from the kidney filtrate. Loss of function of any of the two components ultimately leads to serious B₁₂ deficiency and urinary protein loss in humans (Imerslund-Gräsbeck’s syndrome, IGS). Here, we present the crystal structure of AMN in complex with the amino-terminal region of cubilin, revealing a sophisticated assembly of three cubilin subunits combining into a single intertwined β-helix domain that docks to a corresponding three-faced β-helix domain in AMN. This β-helix-β-helix association thereby anchors three ligand-binding cubilin subunits to the transmembrane AMN. Electron microscopy of full-length cubam reveals a 700–800 Å long tree-like structure with the potential of dimerization into an even larger complex. Furthermore, effects of known human mutations causing IGS are explained by the structural information.

Cubilin and the transmembrane protein amnionless (AMN) form the endocytic receptor cubam that is essential for intestinal vitamin B₁₂ uptake. Here the authors present the 2.3 Å crystal structure of AMN in complex with the amino-terminal region of cubilin and discuss cubam architecture and disease causing mutations.

Automated projection spectroscopy in solid-state NMR

Given that solid-state NMR is being used for protein samples of increasing molecular weight and complexity, higher-dimensionality methods are likely to be more and more indispensable for unambiguous chemical shift assignments in the near future. In addition, solid-state NMR spectral properties are increasingly comparable with solution NMR, allowing adaptation of more sophisticated solution NMR strategies for the solid state in addition to the conventional methodology. Assessing first principles, here we demonstrate the application of automated projection spectroscopy for a micro-crystalline protein in the solid state.

Protein-Protein Interfaces Probed by Methyl Labeling and Proton-Detected Solid-State NMR Spectroscopy

Proton detection and fast magic-angle spinning have advanced biological solid-state NMR, allowing for the backbone assignment of complex protein assemblies with high sensitivity and resolution. However, so far no method has been proposed to detect intermolecular interfaces in these assemblies by proton detection. Herein, we introduce a concept based on methyl labeling that allows for the assignment of these moieties and for the study of protein-protein interfaces at atomic resolution.

Protons as Versatile Reporters in Solid-State NMR Spectroscopy

Solid-state nuclear magnetic resonance (ssNMR) is a spectroscopic technique that is used for characterization of molecular properties in the solid phase at atomic resolution. In particular, using the approach of magic-angle spinning (MAS), ssNMR has seen widespread applications for topics ranging from material sciences to catalysis, metabolomics, and structural biology, where both isotropic and anisotropic parameters can be exploited for a detailed assessment of molecular properties. High-resolution detection of protons long represented the holy grail of the field. With its high natural abundance and high gyromagnetic ratio, ¹H has naturally been the most important nucleus type for the solution counterpart of NMR spectroscopy. In the solid state, similar benefits are obtained over detection of heteronuclei, however, a rocky road led to its success as their high gyromagnetic ratio has also been associated with various detrimental effects. Two exciting approaches have been developed in recent years that enable proton detection: After partial deuteration of the sample to reduce the proton spin density, the exploitation of protons could begin. Also, faster MAS, nowadays using tiny rotors with frequencies up to 130 kHz, has relieved the need for expensive deuteration. Apart from the sheer gain in sensitivity from choosing protons as the detection nucleus, the proton chemical shift and several other useful aspects of protons have revolutionized the field. In this Account, we are describing the fundamentals of proton detection as well as the arising possibilities for characterization of biomolecules as associated with the developments in our own lab. In particular, we focus on facilitated chemical-shift assignment, structure calculation based on protons, and on assessment of dynamics in solid proteins. For example, the proton chemical-shift dimension adds additional information for resonance assignments in the protein backbone and side chains. Chemical shifts and high gyromagnetic ratio of protons enable direct readout of spatial information over large distances. Dynamics in the protein backbone or side chains can be characterized efficiently using protons as reporters. For all of this, the sample amounts necessary for a given signal-to-noise have drastically shrunk, and new methodology enables assessment of molecules with increasing monomer molecular weight and complexity. Taken together, protons are able to overcome previous limitations, by speeding up processes, enhancing accuracies, and increasing the accessible ranges of ssNMR spectroscopy, as we shall discuss in detail in the following. In particular, these methodological developments have been pushing solid-state NMR into a new regime of biological topics as they realistically allow access to complex cellular molecules, elucidating their functions and interactions in a multitude of ways.

Dynamics and Rigidity of an Intact Filamentous Bacteriophage Virus Probed by Magic Angle Spinning NMR

The capsid dynamics of filamentous bacteriophages is related to their function, stability, and interactions with the genome, and can be assessed by measuring the chemical shift anisotropy (CSA) of ¹⁵ N amides, which are sensitive to large amplitude motions. In this study, CSA recoupling experiments under magic-angle spinning NMR were used to probe the dynamics of the y21m capsid mutant of fd bacteriophage. Based on fitting the generated CSA lineshapes, residues located in the N-terminus undergo increased motional amplitudes suggesting its global motion, whereas other backbone residues are rigid, and imply a tight hydrophobic packing of the phage.

Comparison of the 3D structures of mouse and human α-synuclein fibrils by solid-state NMR and STEM

Intra-neuronal aggregation of α-synuclein into fibrils is the molecular basis for α-synucleinopathies, such as Parkinson's disease. The atomic structure of human α-synuclein (hAS) fibrils was recently determined by Tuttle et al. using solid-state NMR (ssNMR). The previous study found that hAS fibrils are composed of a single protofilament. Here, we have investigated the structure of mouse α-synuclein (mAS) fibrils by STEM and isotope-dilution ssNMR experiments. We found that in contrast to hAS, mAS fibrils consist of two or even three protofilaments which are connected by rather weak interactions in between them. Although the number of protofilaments appears to be different between hAS and mAS, we found that they have a remarkably similar secondary structure and protofilament 3D structure as judged by secondary chemical shifts and intra-molecular distance restraints. We conclude that the two mutant sites between hAS and mAS (positions 53 and 87) in the fibril core region are crucial for determining the quaternary structure of α-synuclein fibrils.

Prokaryotic cytoskeletons: protein filaments organizing small cells

Most, if not all, bacterial and archaeal cells contain at least one protein filament system. Although these filament systems in some cases form structures that are very similar to eukaryotic cytoskeletons, the term 'prokaryotic cytoskeletons' is used to refer to many different kinds of protein filaments. Cytoskeletons achieve their functions through polymerization of protein monomers and the resulting ability to access length scales larger than the size of the monomer. Prokaryotic cytoskeletons are involved in many fundamental aspects of prokaryotic cell biology and have important roles in cell shape determination, cell division and nonchromosomal DNA segregation. Some of the filament-forming proteins have been classified into a small number of conserved protein families, for example, the almost ubiquitous tubulin and actin superfamilies. To understand what makes filaments special and how the cytoskeletons they form enable cells to perform essential functions, the structure and function of cytoskeletal molecules and their filaments have been investigated in diverse bacteria and archaea. In this Review, we bring these data together to highlight the diverse ways that linear protein polymers can be used to organize other molecules and structures in bacteria and archaea.

NMR of Macromolecular Assemblies and Machines at 1 GHz and Beyond: New Transformative Opportunities for Molecular Structural Biology

As a result of profound gains in sensitivity and resolution afforded by ultrahigh magnetic fields, transformative applications in the fields of structural biology and materials science are being realized. The development of dual low temperature superconducting (LTS)/high-temperature superconducting (HTS) magnets has enabled the achievement of magnetic fields above 1 GHz (23.5 T), which will open doors to an unprecedented new range of applications. In this contribution, we discuss the promise of ultrahigh field magnetic resonance. We highlight several methodological developments pertinent at high-magnetic fields including measurement of 1H-1H distances and 1H chemical shift anisotropy in the solid state as well as studies of quadrupolar nuclei such as 17O. Higher magnetic fields have advanced heteronuclear detection in solution NMR, valuable for applications including metabolomics and disordered proteins, as well as expanded use of proton detection in the solid state in conjunction with ultrafast magic angle spinning. We also present several recent applications to structural studies of the AP205 bacteriophage, the M2 channel from Influenza A, and biomaterials such as human bone. Gains in sensitivity and resolution from increased field strengths will enable advanced applications of NMR spectroscopy including in vivo studies of whole cells and intact virions.

Bactofilin-mediated organization of the ParABS chromosome segregation system in Myxococcus xanthus

In bacteria, homologs of actin, tubulin, and intermediate filament proteins often act in concert with bacteria-specific scaffolding proteins to ensure the proper arrangement of cellular components. Among the bacteria-specific factors are the bactofilins, a widespread family of polymer-forming proteins whose biology is poorly investigated. Here, we study the three bactofilins BacNOP in the rod-shaped bacterium Myxococcus xanthus. We show that BacNOP co-assemble into elongated scaffolds that restrain the ParABS chromosome segregation machinery to the subpolar regions of the cell. The centromere (parS)-binding protein ParB associates with the pole-distal ends of these structures, whereas the DNA partitioning ATPase ParA binds along their entire length, using the newly identified protein PadC (MXAN_4634) as an adapter. The integrity of these complexes is critical for proper nucleoid morphology and chromosome segregation. BacNOP thus mediate a previously unknown mechanism of subcellular organization that recruits proteins to defined sites within the cytoplasm, far off the cell poles.

The roles played by bactofilins, a widespread type of bacterial cytoskeletal elements, are unclear. Here, the authors show that the bactofilins BacNOP facilitate proper subcellular localization of the ParABS chromosome segregation system in the model organism Myxococcus xanthus.

Solid-state NMR spectroscopic trends for supramolecular assemblies and protein aggregates

Solid-state NMR is able to generate structural data on sample preparations that are explicitly non-crystalline. In particular, for amyloid fibril samples, which can comprise significant degrees of sample disorder, solid-state NMR has been used very successfully. But also solid-state NMR studies of other supramolecular assemblies that have resisted assessment by more standard methods are being performed with increasing ease and biological impact, many of which are briefly reviewed here. New technical trends with respect to structure calculation, protein dynamics and smaller sample amounts have reshaped the field of solid-state NMR recently. In particular, proton-detected approaches based on fast Magic-Angle Spinning (MAS) were demonstrated for crystalline systems initially. Currently, such approaches are being expanded to the above-mentioned non-crystalline targets, the characterization of which can now be pursued with sample amounts on the order of a milligram. In this Trends article, I am giving a brief overview about achievements of the last years as well as the directions that the field has been heading into and delineate some satisfactory perspectives for solid-state NMR's future striving.

Bacteriophage Tail-Tube Assembly Studied by Proton-Detected 4D Solid-State NMR

Obtaining unambiguous resonance assignments remains a major bottleneck in solid-state NMR studies of protein structure and dynamics. Particularly for supramolecular assemblies with large subunits (>150 residues), the analysis of crowded spectral data presents a challenge, even if three-dimensional (3D) spectra are used. Here, we present a proton-detected 4D solid-state NMR assignment procedure that is tailored for large assemblies. The key to recording 4D spectra with three indirect carbon or nitrogen dimensions with their inherently large chemical shift dispersion lies in the use of sparse non-uniform sampling (as low as 2 %). As a proof of principle, we acquired 4D (H)COCANH, (H)CACONH, and (H)CBCANH spectra of the 20 kDa bacteriophage tail-tube protein gp17.1 in a total time of two and a half weeks. These spectra were sufficient to obtain complete resonance assignments in a straightforward manner without use of previous solution NMR data.

Structure of the Bacterial Cytoskeleton Protein Bactofilin by NMR Chemical Shifts and Sequence Variation

Bactofilins constitute a recently discovered class of bacterial proteins that form cytoskeletal filaments. They share a highly conserved domain (DUF583) of which the structure remains unknown, in part due to the large size and noncrystalline nature of the filaments. Here, we describe the atomic structure of a bactofilin domain from Caulobacter crescentus. To determine the structure, we developed an approach that combines a biophysical model for proteins with recently obtained solid-state NMR spectroscopy data and amino acid contacts predicted from a detailed analysis of the evolutionary history of bactofilins. Our structure reveals a triangular β-helical (solenoid) conformation with conserved residues forming the tightly packed core and polar residues lining the surface. The repetitive structure explains the presence of internal repeats as well as strongly conserved positions, and is reminiscent of other fibrillar proteins. Our work provides a structural basis for future studies of bactofilin biology and for designing molecules that target them, as well as a starting point for determining the organization of the entire bactofilin filament. Finally, our approach presents new avenues for determining structures that are difficult to obtain by traditional means.