Activated nanoscale actin-binding domain motion in the catenin-cadherin complex revealed by neutron spin echo spectroscopy.

As the core component of the adherens junction in cell-cell adhesion, the cadherin-catenin complex transduces mechanical tension between neighboring cells. Structural studies have shown that the cadherin-catenin complex exists as an ensemble of flexible conformations, with the actin-binding domain (ABD) of α-catenin adopting a variety of configurations. Here, we have determined the nanoscale protein domain dynamics of the cadherin-catenin complex using neutron spin echo spectroscopy (NSE), selective deuteration, and theoretical physics analyses. NSE reveals that, in the cadherin-catenin complex, the motion of the entire ABD becomes activated on nanosecond to submicrosecond timescales. By contrast, in the α-catenin homodimer, only the smaller disordered C-terminal tail of ABD is moving. Molecular dynamics (MD) simulations also show increased mobility of ABD in the cadherin-catenin complex, compared to the α-catenin homodimer. Biased MD simulations further reveal that the applied external forces promote the transition of ABD in the cadherin-catenin complex from an ensemble of diverse conformational states to specific states that resemble the actin-bound structure. The activated motion and an ensemble of flexible configurations of the mechanosensory ABD suggest the formation of an entropic trap in the cadherin-catenin complex, serving as negative allosteric regulation that impedes the complex from binding to actin under zero force. Mechanical tension facilitates the reduction in dynamics and narrows the conformational ensemble of ABD to specific configurations that are well suited to bind F-actin. Our results provide a protein dynamics and entropic explanation for the observed force-sensitive binding behavior of a mechanosensitive protein complex.

Distribution and characteristics of bacteria on the hand during oropharyngeal swab collection: Which handwashing points are affected?

AIMS: To identify the contaminated areas of the hand collection and analyse the distribution characteristics of bacteria in the hand after swab collection. DESIGN: This study used a cross-sectional design. METHODS: A cross-sectional study sampling 50 pairs of hands (sampling hand and auxiliary hand) of healthcare workers was performed. Ten samples were collected from each participant. The optimal hand hygiene rates and bacterial colony counts of the whole hand and different hand sections without hand hygiene were identified as the primary outcomes. RESULTS: The optimal hand hygiene rates of the sampling hand and auxiliary hand were 88.8% (222/250) and 91.6% (229/250), respectively. The lowest optimal hand hygiene rates for the sampling hand and the auxiliary hand were both on the dorsal side of the finger and the dorsum of the hand (86.0%, 86.0% vs. 90.0%, 86.0%); the optimal hand hygiene rates for both sites of the sampling hand were 86.0% (43/50), and the optimal hand hygiene rates for the auxiliary hand were 90.0% (45/50) and 86.0% (43/50). The bacteria colony counts did not differ between the sampling hands and auxiliary hand. CONCLUSIONS: The dorsal side of the finger and dorsum of the hand were the most likely to be contaminated during oropharyngeal swab collection. Therefore, it is essential to pay extra attention to hand hygiene care of these two sites during the collection process to minimize the risk of cross-contamination. REPORTING METHOD: The Strengthening the Reporting of Observational Studies in Epidemiology (STROBE) guidelines were adopted in this study.

Engineering of Halide Methyltransferase BxHMT through Dynamic Cross-Correlation Network Analysis.

Halide methyltransferases (HMTs) provide an effective way to regenerate S-adenosyl methionine (SAM) from S-adenosyl homocysteine and reactive electrophiles, such as methyl iodide (MeI) and methyl toluene sulfonate (MeOTs). As compared with MeI, the cost-effective unnatural substrate MeOTs can be accessed directly from cheap and abundant alcohols, but shows only limited reactivity in SAM production. In this study, we developed a dynamic cross-correlation network analysis (DCCNA) strategy for quickly identifying hot spots influencing the catalytic efficiency of the enzyme, and applied it to the evolution of HMT from Paraburkholderia xenovorans. Finally, the optimal mutant, M4 (V55T/C125S/L127T/L129P), exhibited remarkable improvement, with a specific activity of 4.08 U/mg towards MeOTs, representing an 82-fold increase as compared to the wild-type (WT) enzyme. Notably, M4 also demonstrated a positive impact on the catalytic ability with other methyl donors. The structural mechanism behind the enhanced enzyme activity was uncovered by molecular dynamics simulations. Our work not only contributes a promising biocatalyst for the regeneration of SAM, but also offers a strategy for efficient enzyme engineering.

Molecular Dynamics Refinement of Open State Serotonin 5-HT3A Receptor Structures.

Pentameric ligand-gated ion channels play an important role in mediating fast neurotransmissions. As a member of this receptor family, cation-selective 5-HT3 receptors are a clinical target for treating nausea and vomiting associated with chemotherapy and radiation therapy (Thompson and Lummis, 2006). Multiple cryo-electron microscopy (cryo-EM) structures of 5-HT3 receptors have been determined in distinct functional states (e.g., open, closed, etc.) (Basak et al., 2018; Basak et al., 2018; Polovinkin et al., 2018; Zhang et al., 2015). However, recent work has shown that the transmembrane pores of the open 5-HT3 receptor structures rapidly collapse and become artificially asymmetric in molecular dynamics (MD) simulations. To avoid this hydrophobic collapse, Dämgen and Biggin developed an equilibration protocol that led to a stable open state structure of the glycine receptor in MD simulations (Dämgen and Biggin, 2020). However, the protocol failed to yield open-like structures of the 5-HT3 receptor in our simulations. Here, we present a refined equilibration protocol that involves the rearrangement of the transmembrane helices to achieve stable open state structures of the 5-HT3 receptor that allow both water and ion permeation through the channel. Notably, channel gating is mediated through collective movement of the transmembrane helices, involving not only pore lining M2 helices but also their cross-talk with the adjacent M1 and M3 helices. Thus, the successful application of our refined equilibration protocol underscores the importance of the conformational coupling between the transmembrane helices in stabilizing open-like structures of the 5-HT3 receptor.

Exploring the effect of novel six moments on hand hygiene compliance among hospital cleaning staff members: a quasi-experimental study.

My 5 moments (M5M) was used less frequently among cleaning staff members, suggesting that a poor compliance score in this group may not indicate deficient handwashing. This quasi-experimental study compared hand hygiene compliance (HHC), hand hygiene (HH) moments, and HH time distribution in the control group (no HH intervention; n = 21), case group 1 (normal M5M intervention; n = 26), case group 2 (extensive novel six moments (NSM) training; n = 24), and case group 3 (refined NSM training; n = 18). The intervention's effect was evaluated after 3 months. The HHC gap among the four groups gradually increased in the second intervention month (control group, 31.43%; case group 1, 38.74%; case group 2, 40.19%; case group 3, 52.21%; p < 0.05). After the intervention period, the HHC of case groups 2 and 3 improved significantly from the baseline (23.85% vs. 59.22%, 27.41% vs. 83.62%, respectively; p < 0.05). 'After transferring medical waste from the site' had the highest HHC in case group 3, 90.72% (95% confidence interval, 0.1926-0.3967). HH peak hours were from 6 AM to 9 AM and 2 PM to 3 PM. The study showed that the implementation of an NSM practice can serve as an HHC monitoring indicator and direct relevant training interventions to improve HH among hospital cleaning staff.

The Cytotoxic Cardiac Glycoside (-)-Cryptanoside A from the Stems of Cryptolepis dubia and Its Molecular Targets.

A cardiac glycoside epoxide, (-)-cryptanoside A (1), was isolated from the stems of Cryptolepis dubia collected in Laos, for which the complete structure was confirmed by analysis of its spectroscopic and single-crystal X-ray diffraction data, using copper radiation at a low temperature. This cardiac glycoside epoxide exhibited potent cytotoxicity against several human cancer cell lines tested, including HT-29 colon, MDA-MB-231 breast, OVCAR3 and OVCAR5 ovarian cancer, and MDA-MB-435 melanoma cells, with the IC50 values found to be in the range 0.1-0.5 µM, which is comparable with that observed for digoxin. However, it exhibited less potent activity (IC50 1.1 µM) against FT194 benign/nonmalignant human fallopian tube secretory epithelial cells when compared with digoxin (IC50 0.16 µM), indicating its more selective activity toward human cancer versus benign/nonmalignant cells. (-)-Cryptanoside A (1) also inhibited Na+/K+-ATPase activity and increased the expression of Akt and the p65 subunit of NF-κB but did not show any effects on the expression of PI3K. A molecular docking profile showed that (-)-cryptanoside A (1) binds to Na+/K+-ATPase, and thus 1 may directly target Na+/K+-ATPase to mediate its cancer cell cytotoxicity.

Covalent inhibition of hAChE by organophosphates causes homodimer dissociation through long-range allosteric effects.

Acetylcholinesterase (EC 3.1.1.7), a key acetylcholine-hydrolyzing enzyme in cholinergic neurotransmission, is present in a variety of states in situ, including monomers, C-terminally disulfide-linked homodimers, homotetramers, and up to three tetramers covalently attached to structural subunits. Could oligomerization that ensures high local concentrations of catalytic sites necessary for efficient neurotransmission be affected by environmental factors? Using small-angle X-ray scattering (SAXS) and cryo-EM, we demonstrate that homodimerization of recombinant monomeric human acetylcholinesterase (hAChE) in solution occurs through a C-terminal four-helix bundle at micromolar concentrations. We show that diethylphosphorylation of the active serine in the catalytic gorge or isopropylmethylphosphonylation by the RP enantiomer of sarin promotes a 10-fold increase in homodimer dissociation. We also demonstrate the dissociation of organophosphate (OP)-conjugated dimers is reversed by structurally diverse oximes 2PAM, HI6, or RS194B, as demonstrated by SAXS of diethylphosphoryl-hAChE. However, binding of oximes to the native ligand-free hAChE, binding of high-affinity reversible ligands, or formation of an SP-sarin-hAChE conjugate had no effect on homodimerization. Dissociation monitored by time-resolved SAXS occurs in milliseconds, consistent with rates of hAChE covalent inhibition. OP-induced dissociation was not observed in the SAXS profiles of the double-mutant Y337A/F338A, where the active center gorge volume is larger than in wildtype hAChE. These observations suggest a key role of the tightly packed acyl pocket in allosterically triggered OP-induced dimer dissociation, with the potential for local reduction of acetylcholine-hydrolytic power in situ. Computational models predict allosteric correlated motions extending from the acyl pocket toward the four-helix bundle dimerization interface 25 Å away.

Generation of the configurational ensemble of an intrinsically disordered protein from unbiased molecular dynamics simulation.

Intrinsically disordered proteins (IDPs) are abundant in eukaryotic proteomes, play a major role in cell signaling, and are associated with human diseases. To understand IDP function it is critical to determine their configurational ensemble, i.e., the collection of 3-dimensional structures they adopt, and this remains an immense challenge in structural biology. Attempts to determine this ensemble computationally have been hitherto hampered by the necessity of reweighting molecular dynamics (MD) results or biasing simulation in order to match ensemble-averaged experimental observables, operations that reduce the precision of the generated model because different structural ensembles may yield the same experimental observable. Here, by employing enhanced sampling MD we reproduce the experimental small-angle neutron and X-ray scattering profiles and the NMR chemical shifts of the disordered N terminal (SH4UD) of c-Src kinase without reweighting or constraining the simulations. The unbiased simulation results reveal a weakly funneled and rugged free energy landscape of SH4UD, which gives rise to a heterogeneous ensemble of structures that cannot be described by simple polymer theory. SH4UD adopts transient helices, which are found away from known phosphorylation sites and could play a key role in the stabilization of structural regions necessary for phosphorylation. Our findings indicate that adequately sampled molecular simulations can be performed to provide accurate physical models of flexible biosystems, thus rationalizing their biological function.

Nurses' perceptions of barriers and supportive behaviors in end-of-life care in the intensive care unit: a cross-sectional study.

BACKGROUND AND AIM: Patient deaths are common in the intensive care unit, and a nurse's perception of barriers to and supportive behaviors in end-of-life care varies widely depending upon their cultural background. The aim of this study was to describe the perceptions of intensive care nurses regarding barriers to and supportive behaviors in providing end-of-life care in a Chinese cultural context. METHODS: A cross-sectional survey was conducted among intensive care nurses in 20 intensive care units in 11 general hospitals in central and eastern China. Instruments used in this study were general survey and Beckstrand's questionnaire. Data were collected via online survey platform. Descriptive analysis was used to describe general characteristics of participants and mean and standard deviations of the barriers and supportive behaviors. The mean and standard deviation were used to describe the intensity and frequency of each barrier or supportive behavior following Beckstrand's method to calculate the score of barriers and supportive behaviors. Content analysis was used to analyze the responses to open-ended questions. RESULTS: The response rate was 53% (n = 368/700). Five of the top six barriers related to families and the other was the nurse's lack of time. Supportive behaviors included three related to families and three related to healthcare providers. Nurses in the intensive care unit felt that families should be present at the bedside of a dying patient, there is a need to provide a quiet, independent environment and psychological support should be provided to the patient and family. Nurses believe that if possible, families can be given flexibility to visit dying patients, such as increasing the number of visits, rather than limiting visiting hours altogether. Families need to be given enough time to perform the final rites on the dying patient. Moreover, it is remarkable that nurses' supportive behaviors almost all concern care after death. CONCLUSIONS: According to ICU-nurses family-related factors, such as accompany of the dying patients and acceptence of patient's imminent death, were found the major factors affecting the quality of end-of-life care. These findings identify the most prominent current barriers and supportive behaviors, which may provide a basis for addressing these issues in the future to improve the quality of end-of-life care.

Structural Insights into gp16 ATPase in the Bacteriophage ϕ29 DNA Packaging Motor.

Biological motors, ubiquitous in living systems, convert chemical energy into different kinds of mechanical motions critical to cellular functions. Gene product 16 (gp16) in bacteriophage ϕ29 is among the most powerful biomotors known, which adopts a multisubunit ring-shaped structure and hydrolyzes ATP to package double-stranded DNA (dsDNA) into a preformed procapsid. Here we report the crystal structure of the C-terminal domain of gp16 (gp16-CTD). Structure-based alignment and molecular dynamics simulations revealed an essential binding surface of gp16-CTD for prohead RNA, a unique component of the motor complex. Furthermore, our simulations highlighted a dynamic interplay between the N-terminal domain and the CTD of gp16, which may play a role in driving movement of DNA into the procapsid. Lastly, we assembled an atomic structural model of the complete ϕ29 dsDNA packaging motor complex by integrating structural and experimental data from multiple sources. Collectively, our findings provided a refined inchworm-revolution model for dsDNA translocation in bacteriophage ϕ29 and suggested how the individual domains of gp16 work together to power such translocation.

Rational design, synthesis, and evaluation of uncharged, "smart" bis-oxime antidotes of organophosphate-inhibited human acetylcholinesterase.

Organophosphate (OP) intoxications from nerve agent and OP pesticide exposures are managed with pyridinium aldoxime-based therapies whose success rates are currently limited. The pyridinium cation hampers uptake of OPs into the central nervous system (CNS). Furthermore, it frequently binds to aromatic residues of OP-inhibited acetylcholinesterase (AChE) in orientations that are nonproductive for AChE reactivation, and the structural diversity of OPs impedes efficient reactivation. Improvements of OP antidotes need to include much better access of AChE reactivators to the CNS and optimized orientation of the antidotes' nucleophile within the AChE active-center gorge. On the basis of X-ray structures of a CNS-penetrating reactivator, monoxime RS194B, reversibly bound to native and venomous agent X (VX)-inhibited human AChE, here we created seven uncharged acetamido bis-oximes as candidate antidotes. Both oxime groups in these bis-oximes were attached to the same central, saturated heterocyclic core. Diverse protonation of the heterocyclic amines and oxime groups of the bis-oximes resulted in equilibration among up to 16 distinct ionization forms, including uncharged forms capable of diffusing into the CNS and multiple zwitterionic forms optimal for reactivation reactions. Conformationally diverse zwitterions that could act as structural antidote variants significantly improved in vitro reactivation of diverse OP-human AChE conjugates. Oxime group reorientation of one of the bis-oximes, forcing it to point into the active center for reactivation, was confirmed by X-ray structural analysis. Our findings provide detailed structure-activity properties of several CNS-directed, uncharged aliphatic bis-oximes holding promise for use as protonation-dependent, conformationally adaptive, "smart" accelerated antidotes against OP toxicity.

Mechanistic Insights into the Allosteric Inhibition of Androgen Receptors by Binding Function 3 Antagonists from an Integrated Molecular Modeling Study.

An androgen receptor (AR) is an intensively studied treatment target for castration-resistant prostate cancer that is irresponsive to conventional antiandrogen therapeutics. Binding function 3 (BF3) inhibitors with alternative modes of action have emerged as a promising approach to overcoming antiandrogen resistance. However, how these BF3 inhibitors modulate AR function remains elusive, hindering the development of BF3-targeting agents. Here, we performed an integrated computational study to interrogate the binding mechanism of several known BF3 inhibitors with ARs. Our results show that the inhibitory effect of the BF3 antagonists arises from their allosteric modulation of the activation function (AF2) site, which alters the dynamic coupling between the BF3 and AF2 sites as well as the AF2-coactivator (SRC2-3) interaction. Moreover, the per-residue binding energy analyses reveal the "anchor" role of the linker connecting the phenyl ring and benzimidazole/indole in these BF3 inhibitors. Furthermore, the allosteric driver-interacting residues are found to include both "positive", e.g., Phe673 and Asn833, and "negative" ones, e.g., Phe826, and the differential interactions with these residues provide an explanation why stronger binding does not necessarily result in higher inhibitory activities. Finally, our allosteric communication pathway analyses delineate how the allosteric signals triggered by BF3 binding are propagated to the AF2 pocket through multiple short- and/or long-ranged transmission pathways. Collectively, our combined computational study provides a comprehensive structural mechanism underlying how the selected set of BF3 inhibitors modulate AR function, which will help guide future development of BF3 antagonists.

Biological Membrane Organization and Cellular Signaling.

To execute their many vital functions, cell membranes are highly organized. Here, we review how membrane structure shapes signal transduction across membranes. Recent experimental and computational advances have shed significant light on mechanisms linking the function of membrane signaling proteins to the composition and physical properties of the membrane lateral structures in which they are embedded. We provide an overview of the structural characteristics of membranes containing heterogeneous mixtures of lipids and other molecules and summarize work on "raft" domains in model and cell membranes, as determined by microscopy, spectroscopy, neutron scattering, and computer simulations. We discuss the principles of partitioning of proteins into membranes and how the structure, dynamics, and function of membrane-embedded and peripheral proteins can be modulated by specific membrane components and physical properties of membranes and raft domains. Finally, we discuss challenges and future directions toward a molecular-level understanding of how membrane organization gives rise to various context-dependent cellular signaling.

Computational investigation of the binding of a designed peptide to λ light chain amyloid fibril.

Systemic light chain amyloidosis (AL) causes a malignant pathology associated with the formation of amyloid fibrils that deposit in human organs and tissues, leading to dysfunction and severe morbidity. Amyloid fibril-reactive antibodies have been used to remove amyloid from organs and are effective in restoring organ function in patients with AL amyloidosis. Unfortunately, antibodies do not bind amyloid in all AL patients, nor do they efficiently bind many other forms of amyloid. Recently, a synthetic peptide P62 was developed, which binds many forms of systemic amyloidosis and can be further modified and fused to a high-affinity peptide epitope to expand its utility as a novel amyloid immunotherapeutic. However, the molecular-level details of P62-fibril binding mechanisms, critical for future peptide design, are unclear. Here, we combine protein docking, all-atom molecular dynamics simulation and umbrella sampling to study the dynamical interactions between peptide P62 and a structural model of the λ light chain in systemic amyloidosis. We found that P62 only binds to the canonical interface of the fibril where the peptide inserts into the fibril groove and its two termini are more mobile than the helix core. Our results also revealed an important role of the lysine residues of P62 in the binding process by forming initial contacts with aspartic acids on the fibril surface. Collectively, our computational study provided molecular-level insights into the binding mechanism between an amyloid fibril model and peptide P62, which could lay a foundation for rational design of peptides for improved amyloid diagnosis and immunotherapy.

An Improved Weighted Gradient Projection Method for Inverse Kinematics of Redundant Surgical Manipulators.

Different from traditional redundant manipulators, the redundant manipulators used in the surgical environment require the end effector (EE) to have high pose (position and orientation) accuracy to ensure the smooth progress of the operation. When analyzing the inverse kinematics (IK) of traditional redundant manipulators, gradient-projection method (GPM) and weighted least-norm (WLN) method are commonly used methods to avoid joint position limits. However, for the traditional GPM and WLN method, when joints are close to their limits, they stop moving, which greatly reduces the accuracy of the IK solution. When robotic manipulators enter a singular region, although traditional damped least-squares (DLS) algorithms are used to handle singularities effectively, motion errors of the EE will be introduced. Furthermore, selecting singular region through trial and error may cause some joint velocities exceed their corresponding limits. More importantly, traditional DLS algorithms cannot guide robotic manipulators away from singular regions. Inspired by the merits of GPM, WLN, and DLS methods, an improved weighted gradient projection method (IWGPM) is proposed to solve the IK problem of redundant manipulators used in the surgical environment with avoiding joint position limits and singularities. The weighted matrix of the WLN method and the damping factor of the DLS algorithm have been improved, and a joint limit repulsive potential field function and singular repulsive potential field function belong to the null space are introduced to completely keep joints away from the damping interval and redundant manipulators away from the unsafe region. To verify the validity of the proposed IWGPM, simulations on a 7 degree of freedom (DOF) redundant manipulator used in laparoscopic surgery indicate that the proposed method can not only achieve higher accuracy IK solution but also avoid joint position limits and singularities effectively by comparing them with the results of the traditional GPM and WLN method, respectively. Furthermore, based on the proposed IWGPM, simulation tests in two cases show that joint position limits have a great impact on the orientation accuracy, and singular potential energy function has a great impact on the position accuracy.

Structural Insights into the Interactions of Digoxin and Na+/K+-ATPase and Other Targets for the Inhibition of Cancer Cell Proliferation.

Digoxin is a cardiac glycoside long used to treat congestive heart failure and found recently to show antitumor potential. The hydroxy groups connected at the C-12, C-14, and C-3'a positions; the C-17 unsaturated lactone unit; the conformation of the steroid core; and the C-3 saccharide moiety have been demonstrated as being important for digoxin's cytotoxicity and interactions with Na+/K+-ATPase. The docking profiles for digoxin and several derivatives and Na+/K+-ATPase were investigated; an additional small Asn130 side pocket was revealed, which could be useful in the design of novel digoxin-like antitumor agents. In addition, the docking scores for digoxin and its derivatives were found to correlate with their cytotoxicity, indicating a potential use of these values in the prediction of the cancer cell cytotoxicity of other cardiac glycosides. Moreover, in these docking studies, digoxin was found to bind to FIH-1 and NF-κB but not HDAC, IAP, and PI3K, suggesting that this cardiac glycoside directly targets FIH-1, Na+/K+-ATPase, and NF-κB to mediate its antitumor potential. Differentially, digoxigenin, the aglycon of digoxin, binds to HDAC and PI3K, but not FIH-1, IAP, Na+/K+-ATPase, and NF-κB, indicating that this compound may target tumor autophagy and metabolism to mediate its antitumor propensity.

Interaction of (+)-Strebloside and Its Derivatives with Na+/K+-ATPase and Other Targets.

Docking profiles for (+)-strebloside, a cytotoxic cardiac glycoside identified from Streblus asper, and some of its derivatives and Na+/K+-ATPase have been investigated. In addition, binding between (+)-strebloside and its aglycone, strophanthidin, and several of their other molecular targets, including FIH-1, HDAC, KEAP1 and MDM2 (negative regulators of Nrf2 and p53, respectively), NF-κB, and PI3K and Akt1, have been inspected and compared with those for digoxin and its aglycone, digoxigenin. The results showed that (+)-strebloside, digoxin, and their aglycones bind to KEAP1 and MDM2, while (+)-strebloside, strophanthidin, and digoxigenin dock to the active pocket of PI3K, and (+)-strebloside and digoxin interact with FIH-1. Thus, these cardiac glycosides could directly target HIF-1, Nrf2, and p53 protein-protein interactions, Na+/K+-ATPase, and PI3K to mediate their antitumor activity. Overall, (+)-strebloside seems more promising than digoxin for the development of potential anticancer agents.

Productive reorientation of a bound oxime reactivator revealed in room temperature X-ray structures of native and VX-inhibited human acetylcholinesterase.

Exposure to organophosphorus compounds (OPs) may be fatal if untreated, and a clear and present danger posed by nerve agent OPs has become palpable in recent years. OPs inactivate acetylcholinesterase (AChE) by covalently modifying its catalytic serine. Inhibited AChE cannot hydrolyze the neurotransmitter acetylcholine leading to its build-up at the cholinergic synapses and creating an acute cholinergic crisis. Current antidotes, including oxime reactivators that attack the OP-AChE conjugate to free the active enzyme, are inefficient. Better reactivators are sought, but their design is hampered by a conformationally rigid portrait of AChE extracted exclusively from 100K X-ray crystallography and scarcity of structural knowledge on human AChE (hAChE). Here, we present room temperature X-ray structures of native and VX-phosphonylated hAChE with an imidazole-based oxime reactivator, RS-170B. We discovered that inhibition with VX triggers substantial conformational changes in bound RS-170B from a "nonproductive" pose (the reactive aldoxime group points away from the VX-bound serine) in the reactivator-only complex to a "semi-productive" orientation in the VX-modified complex. This observation, supported by concurrent molecular simulations, suggested that the narrow active-site gorge of hAChE may be significantly more dynamic than previously thought, allowing RS-170B to reorient inside the gorge. Furthermore, we found that small molecules can bind in the choline-binding site hindering approach to the phosphorous of VX-bound serine. Our results provide structural and mechanistic perspectives on the reactivation of OP-inhibited hAChE and demonstrate that structural studies at physiologically relevant temperatures can deliver previously overlooked insights applicable for designing next-generation antidotes.

Rational Design of Small Molecules to Enhance Genome Editing Efficiency by Selectively Targeting Distinct Functional States of CRISPR-Cas12a.

CRISPR-Cas12a, a type-V CRISPR-Cas endonuclease, is an effective genome editing platform. To improve the gene editing efficiency of Cas12a, we rationally designed small molecule enhancers through a combined computational approach. First, we used extensive molecular dynamics (MD) simulations to explore the conformational landscape of Cas12a from Acidaminococcus (AsCas12a), revealing distinct conformational states that could be targeted by small molecules to modulate its genome editing function. We then identified 57 compounds that showed different binding behavior and stabilizing effects on these distinct conformational states using molecular docking. After experimental testing 6 of these 57 compounds, compound 1, quinazoline-2,4(1H,3H)-dione, was found particularly promising in enhancing the AsCas12a-mediated genome editing efficiency in human cells. Compound 1 was shown to act like a molecular "glue" at the interface between AsCas12a and crRNA near the 5'-handle region, thus specifically stabilizing the enzyme-crRNA complex. These results provide a new paradigm for future design of small molecules to modulate the genome editing of the CRISPR-Cas systems.

Heterohexamers Formed by CcmK3 and CcmK4 Increase the Complexity of Beta Carboxysome Shells.

Bacterial microcompartments (BMCs) encapsulate enzymes within a selectively permeable, proteinaceous shell. Carboxysomes are BMCs containing ribulose-1,5-bisphosphate carboxylase oxygenase and carbonic anhydrase that enhance carbon dioxide fixation. The carboxysome shell consists of three structurally characterized protein types, each named after the oligomer they form: BMC-H (hexamer), BMC-P (pentamer), and BMC-T (trimer). These three protein types form cyclic homooligomers with pores at the center of symmetry that enable metabolite transport across the shell. Carboxysome shells contain multiple BMC-H paralogs, each with distinctly conserved residues surrounding the pore, which are assumed to be associated with specific metabolites. We studied the regulation of ß-carboxysome shell composition by investigating the BMC-H genes ccmK3 and ccmK4 situated in a locus remote from other carboxysome genes. We made single and double deletion mutants of ccmK3 and ccmK4 in Synechococcus elongatus PCC7942 and show that, unlike CcmK3, CcmK4 is necessary for optimal growth. In contrast to other CcmK proteins, CcmK3 does not form homohexamers; instead CcmK3 forms heterohexamers with CcmK4 with a 1:2 stoichiometry. The CcmK3-CcmK4 heterohexamers form stacked dodecamers in a pH-dependent manner. Our results indicate that CcmK3-CcmK4 heterohexamers potentially expand the range of permeability properties of metabolite channels in carboxysome shells. Moreover, the observed facultative formation of dodecamers in solution suggests that carboxysome shell permeability may be dynamically attenuated by "capping" facet-embedded hexamers with a second hexamer. Because ß-carboxysomes are obligately expressed, heterohexamer formation and capping could provide a rapid and reversible means to alter metabolite flux across the shell in response to environmental/growth conditions.