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The internal mechanics of proteins—the coordinated motions of amino acids and the pattern of forces constraining these motions—connects protein structure to function. Here we describe a new method combining the application of strong electric field pulses to protein crystals with time-resolved X-ray crystallography to observe conformational changes in spatial and temporal detail. Using a human PDZ domain (LNX2 PDZ2 ) as a model system, we show that protein crystals tolerate electric field pulses strong enough to drive concerted motions on the sub-microsecond timescale. The induced motions are subtle, involve diverse physical mechanisms, and occur throughout the protein structure. The global pattern of electric-field-induced motions is consistent with both local and allosteric conformational changes naturally induced by ligand binding, including at conserved functional sites in the PDZ domain family. This work lays the foundation for comprehensive experimental study of the mechanical basis of protein function. A new method in which strong electric fields are applied to a protein crystal while collecting time-resolved X-ray diffraction patterns is able to follow the mechanical motions of all the constituent atoms, with implications for molecular biology and drug discovery. Linking protein motions and biological function X-ray crystallography can reveal the three-dimensional structures of large proteins at atomic resolution, but provides only a static view. Now Rama Ranganathan and colleagues have applied strong electric fields to a protein crystal while collecting time-resolved X-ray diffraction patterns, to follow the mechanical motions of all constituent atoms—the essence of how machine-like proteins work. Of direct interest to molecular biology and drug discovery, this approach to protein mechanics should also inspire physicists in materials science and electrical engineering.

The recycling of SNARE proteins following complex formation and membrane fusion is an essential process in eukaryotic trafficking. A highly conserved AAA+ protein, NSF (N-ethylmaleimide sensitive factor) and an adaptor protein, SNAP (soluble NSF attachment protein), disassemble the SNARE complex. We report electron-cryomicroscopy structures of the complex of NSF, αSNAP, and the full-length soluble neuronal SNARE complex (composed of syntaxin-1A, synaptobrevin-2, SNAP-25A) in the presence of ATP under non-hydrolyzing conditions at ~3.9 Å resolution. These structures reveal electrostatic interactions by which two αSNAP molecules interface with a specific surface of the SNARE complex. This interaction positions the SNAREs such that the 15 N-terminal residues of SNAP-25A are loaded into the D1 ring pore of NSF via a spiral pattern of interactions between a conserved tyrosine NSF residue and SNAP-25A backbone atoms. This loading process likely precedes ATP hydrolysis. Subsequent ATP hydrolysis then drives complete disassembly.

Synaptic vesicles containing neurotransmitters fuse with the plasma membrane upon the arrival of an action potential at the active zone. Multiple proteins organize trans-SNARE complex assembly and priming, leading to fusion. One target membrane SNARE, syntaxin, forms nanodomains at the active zone, and another, SNAP-25, enters non-fusogenic complexes with it. Here, we reveal mechanistic details of AAA+ protein NSF (N-ethylmaleimide sensitive factor) and SNAP (soluble NSF attachment protein) action before fusion. We show that syntaxin clusters are conserved, that NSF colocalizes with them, and characterize SNARE populations that may exist within or near them using cryo-EM. Supercomplexes of NSF, α-SNAP, and either a syntaxin tetramer or one of two binary complexes of syntaxin—SNAP-25 reveal atomic details of SNARE processing and show how sequential ATP hydrolysis drives disassembly. These results suggest a functional role for syntaxin clusters as reservoirs and a corresponding role for NSF in syntaxin liberation and SNARE protein quality control preceding fusion. NSF hydrolyzes ATP to disassemble SNARE complexes. Here, the authors find NSF colocalizes with syntaxin nanodomains, reveal disassembly of syntaxin oligomers and other pre-fusion cis-SNARE complexes by NSF, and show how sequential hydrolysis drives disassembly.

The Omicron variant of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) introduced a relatively large number of mutations, including three mutations in the highly conserved heptad repeat 1 (HR1) region of the spike glycoprotein (S) critical for its membrane fusion activity. We show that one of these mutations, N969K induces a substantial displacement in the structure of the heptad repeat 2 (HR2) backbone in the HR1HR2 postfusion bundle. Due to this mutation, fusion-entry peptide inhibitors based on the Wuhan strain sequence are less efficacious. Here, we report an Omicron-specific peptide inhibitor designed based on the structure of the Omicron HR1HR2 postfusion bundle. Specifically, we inserted an additional residue in HR2 near the Omicron HR1 K969 residue to better accommodate the N969K mutation and relieve the distortion in the structure of the HR1HR2 postfusion bundle it introduced. The designed inhibitor recovers the loss of inhibition activity of the original longHR2_42 peptide with the Wuhan strain sequence against the Omicron variant in both a cell–cell fusion assay and a vesicular stomatitis virus (VSV)-SARS-CoV-2 chimera infection assay, suggesting that a similar approach could be used to combat future variants. From a mechanistic perspective, our work suggests the interactions in the extended region of HR2 may mediate the initial landing of HR2 onto HR1 during the transition of the S protein from the prehairpin intermediate to the postfusion state.

SNARE complex disassembly by the ATPase NSF is essential for neurotransmitter release and other membrane trafficking processes. We developed a single-molecule FRET assay to monitor repeated rounds of NSF-mediated disassembly and reassembly of individual SNARE complexes. For ternary neuronal SNARE complexes, disassembly proceeds in a single step within 100 msec. We observed short- (<0.32 s) and long-lived (≥0.32 s) disassembled states. The long-lived states represent fully disassembled SNARE complex, while the short-lived states correspond to failed disassembly or immediate reassembly. Either high ionic strength or decreased αSNAP concentration reduces the disassembly rate while increasing the frequency of short-lived states. NSF is also capable of disassembling anti-parallel ternary SNARE complexes, implicating it in quality control. Finally, complexin-1 competes with αSNAP binding to the SNARE complex; addition of complexin-1 has an effect similar to that of decreasing the αSNAP concentration, possibly differentially regulating cis and trans SNARE complexes disassembly.

Variants of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) challenge currently available COVID-19 vaccines and monoclonal antibody therapies due to structural and dynamic changes of the viral spike glycoprotein (S). The heptad repeat 1 (HR1) and heptad repeat 2 (HR2) domains of S drive virus–host membrane fusion by assembly into a six-helix bundle, resulting in delivery of viral RNA into the host cell. We surveyed mutations of currently reported SARS-CoV-2 variants and selected eight mutations, including Q954H, N969K, and L981F from the Omicron variant, in the postfusion HR1HR2 bundle for functional and structural studies. We designed a molecular scaffold to determine cryogenic electron microscopy (cryo-EM) structures of HR1HR2 at 2.2–3.8 Å resolution by linking the trimeric N termini of four HR1 fragments to four trimeric C termini of the Dps4 dodecamer from Nostoc punctiforme. This molecular scaffold enables efficient sample preparation and structure determination of the HR1HR2 bundle and its mutants by single-particle cryo-EM. Our structure of the wild-type HR1HR2 bundle resolves uncertainties in previously determined structures. The mutant structures reveal side-chain positions of the mutations and their primarily local effects on the interactions between HR1 and HR2. These mutations do not alter the global architecture of the postfusion HR1HR2 bundle, suggesting that the interfaces between HR1 and HR2 are good targets for developing antiviral inhibitors that should be efficacious against all known variants of SARS-CoV-2 to date. We also note that this work paves the way for similar studies in more distantly related viruses.

Variants of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) challenge currently available coronavirus disease 2019 vaccines and monoclonal antibody therapies through epitope change on the receptor binding domain of the viral spike glycoprotein. Hence, there is a specific urgent need for alternative antivirals that target processes less likely to be affected by mutation, such as the membrane fusion step of viral entry into the host cell. One such antiviral class includes peptide inhibitors, which block formation of the so-called heptad repeat 1 and 2 (HR1HR2) six-helix bundle of the SARS-CoV-2 spike (S) protein and thus interfere with viral membrane fusion. We performed structural studies of the HR1HR2 bundle, revealing an extended, well-folded N-terminal region of HR2 that interacts with the HR1 triple helix. Based on this structure, we designed an extended HR2 peptide that achieves single-digit nanomolar inhibition of SARS-CoV-2 in cell-based and virus-based assays without the need for modifications such as lipidation or chemical stapling. The peptide also strongly inhibits all major SARS-CoV-2 variants to date. This extended peptide is ~100-fold more potent than all previously published short, unmodified HR2 peptides, and it has a very long inhibition lifetime after washout in virus infection assays, suggesting that it targets a prehairpin intermediate of the SARS-CoV-2 S protein. Together, these results suggest that regions outside the HR2 helical region may offer new opportunities for potent peptide-derived therapeutics for SARS-CoV-2 and its variants, and even more distantly related viruses, and provide further support for the prehairpin intermediate of the S protein.

Introduction The mechanism of formation of an os odontoideum is controversial and likely multifactorial. One theory states that the apex of the odontoid separates from the body because of a fracture. The intact alar and apical ligaments pull the fractured segment superiorly. The independent vascular supply of the apex allows the fractured bone to remain viable and remodel into the smooth, corticated bone characteristic of an os odontoideum. However, there are no publications with direct radiographic evidence supporting the theory. Case report In this paper, the authors present a 7-year-old child with a fracture through the apical odontoid epiphysis, extending into the body of the dens. Serial imaging studies demonstrate progressive separation of the apex from the body of the odontoid. The fractured segment begins to remodel and assume the classic form of an os. Conclusion The authors consider this case to be radiographic evidence supporting an acquired/traumatic origin of os odontoideum. Further, the mechanism of fracture through a cartilaginous epiphysis may explain the formation of an os after “normal” x-ray images or following seemingly minor trauma.

Object The distal catheter of a ventriculoatrial (VA) cerebrospinal fluid shunt is potentially exposed to bacterial seeding from a subclavian central line. The risk of blood stream infections (BSIs) from central lines increases with administration of total parenteral nutrition (TPN). The potential risks of shunt malfunction or infection in patients with a VA shunt and a concurrent subclavian central line and/or TPN administration have not been studied. Methods A retrospective review of 49 pediatric patients with placement of a VA shunt was performed. Three outcome measures were studied: shunt malfunction, shunt infection, and bacteremia/fungemia requiring shunt removal. All outcomes were measured by 1 year after shunt insertion. We analyzed the following potential risk factors: age at shunt insertion, prior ventriculoperitoneal (VP) shunt, prior shunt infection, abdominal infection/necrotizing enterocolitis (NEC), concurrent subclavian central line, and administration of TPN. The association between each risk factor and outcome was evaluated using Fisher’s exact test to generate the relative risk. Additionally, a logistic regression analysis was performed to evaluate the odds ratio of the outcomes to risk factors considering age as a covariate. Results The average age at shunt insertion was 6.3 ± 7.6 years. The most common diagnosis was posthemorrhagic hydrocephalus of prematurity (53.1 %). Fifteen patients (30.1 %) had a shunt malfunction within 1 year, 6 (12.2 %) had a shunt infection, and 3 (6.1 %) required removal of the shunt due to bacteremia/fungemia. The age at shunt insertion was not a statistically significant independent risk factor for any of the three outcomes. Prior shunt infection predicted an increased risk for both future shunt malfunction and infection in both the associative relative risk analysis and the age-dependent logistic regression analysis, although the correlation did not reach statistical significance. The presence of a subclavian central line or TPN administration did not statistically increase the risk over baseline for any of the outcomes in either analysis. Conclusions The relatively small number of patients limits the power of the study. Considering this limitation, the data suggests that the presence of a concurrent subclavian central line or administration of TPN does not increase the risk of shunt malfunction or infection over the baseline of this high-risk cohort.

Purpose The anatomy of the pedicle is complex and three-dimensional; however, there are basic dimensions important for possible screw placement. There are relatively few studies examining the pedicle anatomy in children. This study was performed to evaluate the feasibility of pedicle screw placement in children aged 5–16, based on key anatomic dimensions. A case illustration is also provided. Methods The CT scans of 102 consecutive children were studied. Patients with abnormal anatomy were excluded. The parameters of the pedicle isthmus width ( W ), estimation of screw length ( L ), and axial angle ( A ) were recorded for 1,632 pedicles from T10 through L5. Patients were divided into four age groups. Statistical analysis was performed evaluating the difference between males and females and of the particular anatomy at the thoracolumbar junction. Results The pedicles increase in both L and W from T10–T12 and from L1–L5. L1 has a consistently smaller W compared to T12 in both genders over all age ranges. Estimating a W of 4.5 mm necessary for safe screw placement, we calculate that virtually all pedicles of T12 and L3–L5 are large enough for screw placement in both genders after age 8. L4 and L5 are large enough for screw placement in both genders in the youngest age range. Conclusions Most of the pedicles of the lower lumbar spine and T12 are large enough to house the smallest commercially available screw. Understanding of the anatomy at the thoracolumbar junction is important, as the W of L1 is consistently smaller than T12.