Cycloartenyl ferulate improves natural killer (NK) cell immunity against cancer by binding to IFNγ receptor 1.

Cycloartenyl ferulate (CF) is abundant in brown rice with multiple biologic functions. It has been reported to possess antitumor activity; however, the related mechanism of action of CF has not been clarified. Herein, we unexpectedly uncover the immunological regulation effects of CF and its molecular mechanism. We discovered that CF directly enhanced the killing capacity of natural killer (NK) cells for various cancer cells in vitro. In vivo, CF also improved cancer surveillance in mouse models of lymphoma clearance and metastatic melanoma dependent on NK cells. In addition, CF promoted anticancer efficacy of the anti-PD1 antibody with improvement of tumor immune microenvironment. Mechanistically, we first unveiled that CF acted on the canonical JAK1/2-STAT1 signaling pathway to enhance the immunity of the NK cells by selectively binding to interferon γ receptor 1. Collectively, our results indicate that CF is a promising immunoregulation agent worthy of attention in clinical application in the future. Due to broad biological significance of interferon γ, our findings also provide a capability to understand the diverse functions of CF.

Identification of a Cryptic Binding Site in CRISPR-Cas9 for Targeted Inhibition.

The need for precision control of CRISPR-Cas9 genome editing has created a demand for anti-CRISPR molecules. Recently, the first class of small-molecule Cas9 inhibitors has been identified, verifying the feasibility of regulating CRISPR-Cas9 activity using direct-acting small molecules. However, it remains enigmatic as to the location of the ligand binding site(s) on CRISPR-Cas9 and how the ligand binding leads to Cas9 functional inhibition. Here, we established an integrative computational protocol, including massive binding site mapping, molecular docking, molecular dynamics simulations, and free energy calculations. Ultimately, a Cas9 ligand binding site was discovered from the dynamics trajectories that is hidden within its carboxyl-terminal domain (CTD), a domain recognizing the protospacer adjacent motif (PAM). Using the top inhibitor BRD0539 as a probe, we demonstrated that the ligand binding induces significant CTD structural rearrangements toward an incompetent conformation for PAM DNA engagement. The revealed molecular mechanism of BRD0539 inhibiting Cas9 is in well agreement with the experimental data. This study provides a structural and mechanistic basis for the potency improvement of existing ligands and the rational discovery of novel small-molecule brakes for developing safer CRISPR-Cas9 technologies.

Selectivity Controlled Hydroamination of Alkynes to Sulfonyl Fluoride Hubs: Development and Application.

A hydroamination of unactivated alkynes and lithium bis(fluorosulfonyl)imide (LiN(SO2F)2) is described under mild conditions, affording a single regioisomer of the sulfonyl fluorides. This method features broad functional group compatibility and delivers the target vinyl fluorosulfonimides in good to excellent yields. Moreover, gram-scale hydroamination of terminal and internal alkynes is achieved. Further transformations exploiting the reactivity of the vinyl fluorosulfonimide are subsequently developed for the synthesis of fluorosulfates and diphenyl sulfate.

Molecular Mechanism of D1135E-Induced Discriminated CRISPR-Cas9 PAM Recognition.

The off-target effects of Streptococcus pyogenes Cas9 (SpCas9) pose a significant challenge to harness it as a therapeutical approach. Two major factors can result in SpCas9 off-targeting: tolerance to target DNA-guide RNA (gRNA) mismatch and less stringent recognition of protospacer adjacent motif (PAM) flanking the target DNA. Despite the abundance of engineered SpCas9-gRNA variants with improved sensitivity to target DNA-gRNA mismatch, studies focusing on enhancing SpCas9 PAM recognition stringency are quite few. A recent pioneering study identified a D1135E variant of SpCas9 that exhibits much-reduced editing activity at the noncanonical NAG/NGA PAM sites while preserving robust on-target activity at the canonical NGG-flanking sites (N is any nucleobase). Herein, we aim to clarify the molecular mechanism by which this single D1135E mutation confers on SpCas9 enhanced specificity for PAM recognition by molecular dynamics simulations. The results suggest that the variant maintains the base-specific recognition for the canonical NGG PAM via four hydrogen bonds, akin to that in the wild type (WT) SpCas9. While the noncanonical NAG PAM is engaged to the two PAM-interacting arginine residues (i.e., R1333 and R1335) in WT SpCas9 via two to three hydrogen bonds, the D1135E variant prefers to establish two hydrogen bonds with the PAM bases, accounting for its minimal editing activity on the off-target sites with an NAG PAM. The impaired NAG recognition by D1135E SpCas9 results from the PAM duplex displacement such that the hydrogen bond of R1333 to the second PAM base is disfavored. We further propose a mechanistic model to delineate how the mutation perturbs the noncanonical PAM recognition. We anticipate that the mechanistic knowledge could be leveraged for continuous optimization of SpCas9 PAM recognition specificity toward high-precision demanding applications.

Discovery and evaluation of cytisine N-isoflavones as novel EGFR/HER2 dual inhibitors.

Aberrant signaling of EGFR (ErbB) family members, in particular epidermal growth factor receptor (EGFR) and human epidermal growth factor 2 (HER2), is associated with the occurrence and development of many types of human malignancies (e.g., breast, lung, and gastric cancers), and dual targeting of EGFR/HER2 by small-molecular inhibitors has proven to be an effective therapeutic approach for treating these cancers. Herein we extracted and isolated from the medicinal plant Sophora alopecuroides L. a new natural product, dubbed Cytisine N-methylene-(4',7-dihydroxy-3'-methoxy)-isoflavone (CNI1) that features a unique molecular framework. Our biochemical kinase assay suggested that one of its derivative CNI3 exhibited the best, micromolar (µM) inhibition activities against the EGFR (IC50 of 1.1 µM; Ki of 0.6 µM) and HER2 (IC50 of 3.5 µM; Ki of 1.8 µM) kinases. By contrast, another derivative CNI4 was most potent in inhibiting the EGFR-overexpressing A431 cancer cell line (IC50 of 45.5 µM) and the HER2-overexpressing BT-474 cancer cell line (IC50 of 32.9 µM), while the respective cellular activities of Lapatinib (a marketed drug) were 24.9 and 20.3 µM under the same assay condition. Moreover, both CNI3 and CNI4 showed desirable anti-metastatic efficacy in another two breast cancer models (viz., MDA-MB-231 and 4T1). In addition, we explored the inhibitory mechanisms of the CNIs against EGFR and HER2 by molecular dynamics simulation and revealed a novel mode of action that engages the cytisine and chromone moieties in CNIs. By combining structure- and ligand-based analysis, we further rationally engineered a new CNI compound that exhibits considerably improved cytotoxicity against both types of A431 and BT-474 cancer cells. Our study demonstrates the CNI compounds as a new class of EGFR/HER2 dual inhibitors and paves a way for their further development.

Assessing the Performance of the Nonbonded Mg2+ Models in a Two-Metal-Dependent Ribonuclease.

Magnesium ions (Mg2+), abundant in living cells, are essential for biomolecular structure, dynamics, and function. The biological importance of Mg2+ has motivated continuous development and improvement of various Mg2+ models for molecular dynamics (MD) simulations during the last decades. There are four types of nonbonded Mg2+ models: the point charge models based on a 12-6 or 12-6-4 type Lennard-Jones (LJ) potential, and the multisite models based on a 12-6 or 12-6-4 LJ potential. Here, we systematically assessed the performance of these four types of nonbonded Mg2+ models (21 models in total) in terms of maintaining a challenging intermediate state configuration captured in the structure of a prototypical two-metal-ion RNase H complex with an RNA/DNA hybrid. Our data demonstrate that the 12-6-4 multisite models, which account for charge-induced dipole interactions, perform the best in reproducing all the unique coordination modes in this intermediate state and maintaining the correct carboxylate denticity. Our benchmark work provides a useful guideline for MD simulations and structural refinement of Mg2+-containing biomolecular systems.

Secondary Conformational Checkpoint in CRISPR-Cas9.

A specific checkpoint between target DNA binding and cleavage primarily governs the precision of Cas9 gene editing. Although various CRISPR-Cas9 variants have been developed to improve DNA cleavage accuracy, we still lack a comprehensive understanding of how they work at the molecular level. Herein, we have focused on studying the late-stage conformational transitions of Cas9 and an evolved Cas9 mutant (evoCas9) that start from the precleavage state. Our submilliseconds of dynamic simulations reveal that the presence of base mismatches leads the HNH nuclease domain of Cas9 to alter its principal functional modes of motion, thereby impairing its conformational activation. This observation suggests the existence of a secondary conformational checkpoint that fine-tunes the final DNA cleavage activation. Remarkably, evoCas9 is prone to deviating from the normal activation pathway with base mismatches. This is characterized by a noticeable shift in the positioning of the HNH domain and a significantly perturbed allosteric communication network within the enzyme. Therefore, the mutations evolved in evoCas9 also reinforce the secondary checkpoint in addition to the previously identified primary checkpoint, collectively ensuring this variant's high gene-editing accuracy. This mechanism should also apply to other Cas9-guide RNA variants with enhanced fidelity.

Constructing Lysozyme Protective Layer via Conformational Transition for Aqueous Zn Batteries.

The practical applications for aqueous Zn ion batteries (ZIBs) are promising yet still impeded by the severe side reactions on Zn metal. Here, a lysozyme protective layer (LPL) is prepared on Zn metal surface by a simple and facile self-adsorption strategy. The LPL exhibits extremely strong adhesion on Zn metal to provide stable interface during long-term cycling. In addition, the self-adsorption strategy triggered by the hydrophobicity-induced aggregation effect endows the protective layer with a gap-free and compacted morphology which can reject free water for effective side reaction inhibition performance. More importantly, the lysozyme conformation is transformed from α-helix to ß-sheet structure before layer formation, thus abundant functional groups are exposed to interact with Zn2+ for electrical double layer (EDL) modification, desolvation energy decrease, and ion diffusion kinetics acceleration. Consequently, the LPL renders the symmetrical Zn battery with ultra-long cycling performance for more than 1200 h under high Zn depth of discharge (DOD) for 77.7%, and the Zn/Zn0.25V2O5 pouch cell with low N/P ratio of 2.1 at high Zn utilization of 48% for over 300 cycles. This study proposes a facile and low-cost method for constructing a stable protective layer of Zn metal for high Zn utilization aqueous devices.

Open Reduction and Internal Fixation for Supination-External Rotation Type IV Ankle Fractures by Means of Anterolateral and Posterolateral Approaches.

BACKGROUND: The present study aimed to analyze and compare the efficacy of the anterolateral and posterolateral approaches for surgical treatment of supination-external rotation type IV ankle fractures. METHODS: This retrospective study enrolled 60 patients (60 feet) with supination-external rotation type IV ankle fractures, including 30 patients (30 feet) treated by means of the anterolateral approach and 30 patients (30 feet) treated by means of the posterolateral approach. Postoperative clinical efficacy was compared between the groups based on operation time, intraoperative blood loss, postoperative complications, fracture healing time, visual analog scale scores, Short Form-36 Health Survey scores, and American Orthopedic Foot and Ankle Society scores. Comparisons between the two groups were performed using independent-samples t tests and analyses of variance. Intragroup differences were compared using paired t tests, and the χ2 test was used to compare categorical variables. RESULTS: All 60 included patients completed follow-up ranging from 12 to 18 months (mean duration, 14.8 ± 3.5 months). Although baseline characteristics were similar in the two groups, there were significant differences in operation time (86.73 ± 17.44 min versus 111.23 ± 10.05 min; P < .001) and intraoperative blood loss (112.60 ± 25.05 mL versus 149.47 ± 44.30 mL; P < .001). Although fracture healing time (10.90 ± 0.66 weeks versus 11.27 ± 0.94 weeks; P = .087) was shorter in the anterolateral group than in the posterolateral group, the difference was not significant. Postoperative complications occurred in one and three patients in the anterolateral and posterolateral approach groups, respectively. Visual analog scale scores were significantly lower in the anterolateral group than in the posterolateral group (1.43 ± 0.50 versus 1.83 ± 0.75; P = .019), although there was no significant difference in Short Form-36 Health Survey scores between the groups (73.63 ± 4.07 versus 72.70 ± 4.04; P = .377). However, American Orthopedic Foot and Ankle Society scores were higher in the anterolateral group than in the posterolateral group (80.43 ± 4.32 versus 75.43 ± 11.32; P = .030). CONCLUSIONS: Both the anterolateral and posterolateral approaches can achieve good results in the treatment of supination-external rotation type IV ankle fractures. Compared with the posterolateral approach, the anterolateral approach is advantageous for the treatment of supination-external rotation type IV ankle fractures given its safety and ability to reduce trauma, clear field of view revealed, and allow for exploration and repair of the inferior tibiofibular anterior syndesmosis within the same incision.

SLC24A-mediated calcium exchange as an indispensable component of the diatom cell density-driven signaling pathway.

Diatom bloom is characterized by a rapid increase of population density. Perception of population density and physiological responses can significantly influence their survival strategies, subsequently impacting bloom fate. The population density itself can serve as a signal, which is perceived through chemical signals or chlorophyll fluorescence signals triggered by high cell density, and their intracellular signaling mechanisms remain to be elucidated. In this study, we focused on the model diatom, Phaeodactylum tricornutum, and designed an orthogonal experiment involving varying cell densities and light conditions, to stimulate the release of chemical signals and light-induced chlorophyll fluorescence signals. Utilizing RNA-Seq and Weighted Gene Co-expression Network Analysis, we identified four gene clusters displaying density-dependent expression patterns. Within these, a potential hub gene, PtSLC24A, encoding a Na+/Ca2+ exchanger, was identified. Based on molecular genetics, cellular physiology, computational structural biology, and in situ oceanic data, we propose a potential intracellular signaling mechanism related to cell density in marine diatoms using Ca2+: upon sensing population density signals mediated by chemical cues, the membrane-bound PtSLC24A facilitates the efflux of Ca2+ to maintain specific intracellular calcium levels, allowing the transduction of intracellular density signals, subsequently regulating physiological responses, including cell apoptosis, ultimately affecting algal blooms fate. These findings shed light on the calcium-mediated intracellular signaling mechanism of marine diatoms to changing population densities, and enhances our understanding of diatom bloom dynamics and their ecological implications.

Efficacy of two different types of island flaps for the repair of diabetic foot ulcers on the heel.

Background: Heel ulcer of diabetic foot (DF) is a difficulty in clinical repair. The current study aimed to investigate the clinical efficacy of the medial plantar island flap (MPIF) and the sural nerve nutritional artery island flap (SNNAIF) for the repair of chronic diabetic foot ulcers (DFU) on the heel. Methods: Twelve patients with chronic DFU on the heel were admitted to our department from August 2018 to August 2020. Upon admission, ulcer debridement and bone cement filling were performed for 2-3 weeks to control infection. Digital subtraction angiography (DSA) or computed tomography angiography (CTA) of the lower limb was performed to assess vascular status. Then, 5 patients were repaired with MPIF and 7 patients with SNNAIF. Results: The MPIF survived completely in 5 cases; SNNAIF was used in 7 cases, and 6 cases survived completely. Meanwhile, 1 patient who underwent SNNAIF presented with partial necrosis of the distal end of the flap. Then, it healed after debridement and dressing changes. All 12 flaps were followed up for 6-12 months. The flaps had a soft texture, and their shape was satisfactory. In 2 cases, SNNAIFs re-ruptured 8 months after surgery. However, they healed after dressing changes and weight-bearing reduction. During the 10-month follow-up, the sensory recovery of MPIF in 5 cases was satisfactory because the flap contained medial plantar cutaneous nerve. Meanwhile, 7 patients who underwent SNNAIF repair had poor sensory recovery. All patients had good dorsiflexion and plantarflexion of the ankle with satisfactory function. Conclusions: Both the MPIF and SNNAIF flaps had a high survival rate and are feasible for DFU repair with good clinical outcomes. If DSA or CTA shows that the medial plantar artery is unobstructed and the heel wound is small, MPIF can retain sensory function and wear resistance. It is the first choice for repairing diabetic foot ulcers on the heel. If the heel wound are large or DSA or CTA shows that the posterior tibial artery is occluded and the peroneal artery is unobstructed, SNNAIF repair is safer.

Effects of arterial blood supply on the survival of reverse-flow island flaps: an experimental study.

OBJECTIVES: This study aimed to investigate the effect of arterial blood supply on the survival area of retrograde island flap. METHODS: The vein and saphenous artery in rabbits were selected to design the reverse-flow island flap experimental model. Forty rabbits were randomly divided into four groups: control group (group A), partial anastomosis of the saphenous artery group (group B), partial anastomosis of the vein group (group C), and no superficial vein group (group D). Flap survival was observed postoperatively, the survival area was measured, and the survival rate was compared. Blood distribution in the flap at different time points was observed by radionuclide imaging. RESULTS: The blood vessel distribution and blood cell status were observed histologically. The survival rate of flaps in group B was higher than that of the other three groups (P < 0.05). The radioactive material (RM) could be seen clearly in group B, whereas those in groups A, C, and D existed transiently. The RM in group B was higher than that in groups A, C, and D (P < 0.05). On postoperative day 10, group B had more capillary regeneration and blood cells than the other three groups (P < 0.05). CONCLUSIONS: Increasing blood supply can improve the survival rate of flaps, but simply promoting venous return has no significant effect on the survival rate of flaps.

Rational Engineering of CRISPR-Cas9 Nuclease to Attenuate Position-Dependent Off-Target Effects.

The RNA-guided Cas9 nuclease from Streptococcus pyogenes has become an important gene-editing tool. However, its intrinsic off-target activity is a major challenge for biomedical applications. Distinct from some reported engineering strategies that specifically target a single domain, we rationally introduced multiple amino acid substitutions across multiple domains in the enzyme to create potential high-fidelity variants, considering the Cas9 specificity is synergistically determined by various domains. We also exploited our previously derived atomic model of activated Cas9 complex structure for guiding new modifications. This approach has led to the identification of the HSC1.2 Cas9 variant with enhanced specificity for DNA cleavage. While the enhanced specificity associated with the HSC1.2 variant appeared to be position-dependent in the in vitro cleavage assays, the frequency of off-target DNA editing with this Cas9 variant is much less than that of the wild-type Cas9 in human cells. The potential mechanisms causing the observed position-dependent effect were investigated through molecular dynamics simulation. Our discoveries establish a solid foundation for leveraging structural and dynamic information to develop Cas9-like enzymes with high specificity in gene editing.

Repair of tophus wound of the heel with sural nerve nutrition flap with peroneal artery perforating branch: a retrospective study.

BACKGROUND: This study was to investigate the clinical effect of a sural nerve nutrition flap with peroneal artery perforator for repairing tophus wound of the heel. METHODS: Over a 5-year period, 7 elderly male patients with tophus ulceration of the heel were admitted with exposed Achilles' tendon, and a chronic unhealed wound. Debridement, expansion and vacuum sealing drainage (VSD) lavage were performed initially, with simultaneous uric acid-lowering treatment. A 4×6-8×10 cm sural nerve nutrition flap with peroneal artery perforator was the secondary repair after further debridement of the wound. Preoperative Doppler ultrasound located the penetrating point of the peroneal artery perforator as the rotation point of the flap, and the line between the midpoint of the Achilles' tendon and the lateral malleolus and the midpoint of the popliteal fossa 5° above the front of Achilles' tendon was the axis. The patients were treated postoperatively with anti-inflammatory, anticoagulant and spasmolytic drugs and other rehydration therapy, and allopurinol was continued to control uric acid. The blood supply and temperature of the flap and wound healing were monitored. RESULTS: All 7 flaps survived completely after operation, with 1 case of postoperative wound discharge that finally healed after dressing change and 1 case of skin flap redness and swelling, which improved after strengthening anti-infection treatment. All 7 patients were followed up for 6-12 months (average 10 months). The skin flaps were soft in texture, with good color and appearance, and no recurrence of ulceration. The dorsal extension and plantar flexion of the ankle joint were good, and function was satisfactory. CONCLUSIONS: The sural nerve nutrition flap with peroneal artery perforator has double blood supply, strong anti-infective ability, relatively fast tissue healing process, simple operation and high survival rate, making it ideal for repairing tophus wounds of the heel.

Comparison of the modified sinus tarsi approach versus the extensile lateral approach for displaced intra-articular calcaneal fractures.

BACKGROUND: This study sought to assess and compare the clinical efficacy and complications of a modified sinus tarsi approach (MSTA) and the extensile lateral approach (ELA) in the treatment of displaced intra-articular calcaneal fractures. METHODS: This retrospective study enrolled 108 patients (117 feet) with Sanders II-IV calcaneal fractures, including 52 patients (56 feet) in the MSTA group and 56 patients (61 feet) in the ELA group. The functional and radiological results of the affected feet were analysed retrospectively. Functional evaluation included American Orthopaedic Foot and Ankle Society (AOFAS), visual analog scale (VAS), and Short Form-36 Health Survey (SF-36). Radiological evaluation included preoperative and postoperative changes in the Bohler Angle, Gissane Angle, length, width, and height of the calcaneus. The postoperative complications were also collected and analysed. The independent-samples t-test and analysis of variance (ANOVA) were employed to compare differences between the two groups. Differences within the same group were compared by paired Student's t-test, and categorical variables were compared using the chi-square test. RESULTS: The postoperative functional and radiological results showed that the mean AOFAS, VAS and physical component summary of SF-36 scores in the MSTA group were higher than those in the ELA group (P<0.05). After surgery, the Bohler and Gissane angles were significantly improved in both groups, as were the length, width, and height of the calcaneus; no statistically significant differences existed between the two groups. The incidences of wound healing complications and postoperative sural nerve injury were lower in the MSTA group than in the ELA group (P<0.000). CONCLUSIONS: The MSTA can achieve similar effects to the ELA in terms of anatomical reconstruction and functional recovery. It also can also effectively reduce the incidences of wound healing complications and postoperative sural nerve injury, and shorten the length of hospital stay.

Allosteric regulation of CRISPR-Cas9 for DNA-targeting and cleavage.

The CRISPR-Cas9 system from Streptococcus pyogenes has been exploited as a programmable RNA-guided DNA-targeting and DNA-editing platform. This evolutionary tool enables diverse genetic manipulations with unprecedented precision and ease. Cas9 is an allosteric enzyme, which is allosterically regulated in conformational activation, target recognition, and DNA cleavage. Here, we outline the underlying allosteric control over the Cas9 complex assembly and targeting specificity. We further review the strategies for mitigating intrinsic Cas9 off-target effects through allosteric modulations and the advances in engineering controllable Cas9 systems that are responsive to external allosteric signals. Future development of highly specific, tunable CRISPR-Cas9 systems through allosteric modulations would greatly benefit applications that require both conditional control and high precision.

Structural and functional insights into the bona fide catalytic state of Streptococcus pyogenes Cas9 HNH nuclease domain.

The CRISPR-associated endonuclease Cas9 from Streptococcus pyogenes (SpyCas9), along with a programmable single-guide RNA (sgRNA), has been exploited as a significant genome-editing tool. Despite the recent advances in determining the SpyCas9 structures and DNA cleavage mechanism, the cleavage-competent conformation of the catalytic HNH nuclease domain of SpyCas9 remains largely elusive and debatable. By integrating computational and experimental approaches, we unveiled and validated the activated Cas9-sgRNA-DNA ternary complex in which the HNH domain is neatly poised for cleaving the target DNA strand. In this catalysis model, the HNH employs the catalytic triad of D839-H840-N863 for cleavage catalysis, rather than previously implicated D839-H840-D861, D837-D839-H840, or D839-H840-D861-N863. Our study contributes critical information to defining the catalytic conformation of the HNH domain and advances the knowledge about the conformational activation underlying Cas9-mediated DNA cleavage.

Gas-phase complexation of α-/ß-cyclodextrin with amino acids studied by ion mobility-mass spectrometry and molecular dynamics simulations.

Cyclodextrins (CDs) are a class of macrocyclic molecules that have exhibited many promising applications in various fields. The knowledge of the complexation modes and recognition mechanisms of CDs with their guests are of paramount importance for rational design of more variants with controlled properties. Herein we investigated the binding conformations and the structural characteristics of α-/ß-CD with three amino acids (AA, AA=Gly, L-Leu, L-Phe) in the gas phase by a combined experimental and computational approach. Electrospray ionization-mass spectrometry suggested the formation of 1:1 anionic complexes between CDs and AAs and the complex anions were further identified by tandem mass spectrometry. Moreover, ion mobility-mass spectrometry experiments revealed the inclusion complexation adopted for [α-CD+Gly]- as well as ß-CD with either amino acid, whereas [α-CD+Leu]- and [α-CD+Phe]- favored an exclusion conformation, indicating size-dependent binding modes. The association is primarily driven by polar interactions via the formation of hydrogen bonds. Furthermore, the relative dynamic stabilities of the complex ions were observed to be in correlation with the gas-phase basicities of the deprotonated amino acid and CD anions. These above findings are well in line with our atomistic molecular dynamics simulation results. This study advances our understanding of the mechanisms underlying CD host-guest recognition.

Identification of a unique Ca2+-binding site in rat acid-sensing ion channel 3.

Acid-sensing ion channels (ASICs) evolved to sense changes in extracellular acidity with the divalent cation calcium (Ca2+) as an allosteric modulator and channel blocker. The channel-blocking activity is most apparent in ASIC3, as removing Ca2+ results in channel opening, with the site's location remaining unresolved. Here we show that a ring of rat ASIC3 (rASIC3) glutamates (Glu435), located above the channel gate, modulates proton sensitivity and contributes to the formation of the elusive Ca2+ block site. Mutation of this residue to glycine, the equivalent residue in chicken ASIC1, diminished the rASIC3 Ca2+ block effect. Atomistic molecular dynamic simulations corroborate the involvement of this acidic residue in forming a high-affinity Ca2+ site atop the channel pore. Furthermore, the reported observations provide clarity for past controversies regarding ASIC channel gating. Our findings enhance understanding of ASIC gating mechanisms and provide structural and energetic insights into this unique calcium-binding site.

Structure and Dynamics of Cas9 HNH Domain Catalytic State.

The bacterial CRISPR-Cas9 immune system has been harnessed as a powerful and versatile genome-editing tool and holds immense promise for future therapeutic applications. Despite recent advances in understanding Cas9 structures and its functional mechanism, little is known about the catalytic state of the Cas9 HNH nuclease domain, and identifying how the divalent metal ions affect the HNH domain conformational transition remains elusive. A deeper understanding of Cas9 activation and its cleavage mechanism can enable further optimization of Cas9-based genome-editing specificity and efficiency. Using two distinct molecular dynamics simulation techniques, we have obtained a cross-validated catalytically active state of Cas9 HNH domain primed for cutting the target DNA strand. Moreover, herein we demonstrate the essential roles of the catalytic Mg2+ for the active state formation and stability. Importantly, we suggest that the derived catalytic conformation of the HNH domain can be exploited for rational engineering of Cas9 variants with enhanced specificity.