Small Alpha Research Articles

The Crystal Structure of the Domain of Unknown Function1480 (DUF1480) From Klebsiella pneumoniae.

Domains of unknown function (DUFs) continue to comprise a significant portion of bacterial proteomes, with more than 20% of bacterial proteins remaining annotated as DUFs. The characterization of their molecular structure can provide valuable insight that is not captured by the primary sequence analysis, thus providing a segue into the identification of the molecular function of DUF representatives. Here, we present the crystal structure of KPN_02352 from Klebsiella pneumoniae subsp. pneumoniae, a DUF1480 domain-containing protein, which was determined to be 1.75 Å resolution. Representatives of the DUF1480 family are found broadly across Enterobacterales and have been previously shown to contribute to the antibiotic response. Our structural analysis suggests that DUF1480 is comprised of a six-stranded split barrel fold featuring a small alpha helix that is positioned to cap one end of the split barrel. DUF1480 was found to be monomeric in solution, and harbors structural similarity to response regulators. The crystal structure of DUF1480 is the first experimental insight into the molecular structure of this conserved protein family, revealing several conserved features that may be functionally relevant.

Crystal structure of Kunitz-type trypsin inhibitor: Entomotoxic effect of native and encapsulated protein targeting gut trypsin of Tribolium castaneum Herbst

Trypsin inhibitors are known to act against insect pests by inhibiting proteases of the digestive tract. In this study, we report structural and functional characterization of ∼ 19 kDa Albizia procera Kunitz-type trypsin inhibitor (ApKTI) protein with potential bio-insecticidal applications. Crystal structure of ApKTI protein has been refined to 1.42 Å and molecular structure (8HNR) showed highly beta sheeted conformation including 12 beta sheets, 15 loops and two small alpha helices. Docking between predicted model of Tribolium castaneum trypsin (TcPT) and 8HNR produced a stable complex (−11.3 kcal/mol) which reflects the inhibitory potential of ApKTI against insect gut trypsin. Significant mortality was observed in all life stages of T. castaneum including egg, larvae, pupae and adults with a 3.0 mg native ApKTI treatment in comparison to negative control. Although standard trypsin inhibitor (Glycine max trypsin inhibitors; GmKTI; 3.0 mg) produced maximum reduction against all above life stages; however, a non-significant mortality difference was observed in comparison to 3.0 mg native ApKTI. The study further explores the synthesis and characterization of Graphene (GNPs) and Zinc oxide (ZnONPs) nanoparticles, followed by the optimization of ApKTI and GmKTI loading on both nanoparticles to evaluate their enhanced insecticidal effectiveness. Encapsulated proteins showed significant mortality against T. castaneum across all concentrations, with GNPs proving more effective than ZnONPs. Additionally, encapsulated GmKTI produced significant mortality of eggs compared to loaded ApKTI treatments while other life stages were non-significantly affected by two proteins. This research highlights the importance of encapsulated ApKTI protein for eco-friendly pest management strategies.

Stress beliefs moderate the impact of COVID-19 related work stress on depressive, anxiety and distress symptoms in health care workers.

Health care workers are at increased risk for mental health issues due to high psychological and physical job demands. According to a recent study, stress beliefs (i.e., believing stress to be detrimental to one's health) might influence physicians' mental health in response to a naturalistic stressor (COVID-19 hospital working conditions). Due to a small sample size and high alpha error inflation, the suggested association needs to be interpreted with caution. The current study aims to replicate those findings in a larger sample. A cross-sectional survey among N=418 (64.1% female; Median age=30-39years) physicians and nurses of a large German medical centre was conducted during the COVID-19 pandemic (May/June 2021). Perception of pandemic related increase of work stress was assessed via self-report. Stress beliefs were assessed with the Beliefs About Stress Scale, and mental health symptoms were assessed with the 21-item Depression Anxiety Stress Scale. Stress beliefs moderated the association between increased work stress and mental health symptoms. Increased work stress was associated with increased depressive, anxiety and distress symptoms only in health care workers with medium (simple slope=2.22, p<.001; simple slope=1.27, p<.001; simple slope=3.19, p<.001) and high (simple slope=3.13; p<.001; simple slope=1.66, p<.05; simple slope=4.33, p<.001) negative stress beliefs. Among health care workers with low negative stress beliefs increased work stress was not associated with increased depressive, anxiety and distress symptoms. This confirms negative stress beliefs as variable of interest in research on the impact of stress on mental health in health care workers.

HIV-1 Intasomes Assembled with Excess Integrase C-Terminal Domain Protein Facilitate Structural Studies by Cryo-EM and Reveal the Role of the Integrase C-Terminal Tail in HIV-1 Integration.

Retroviral integration is mediated by intasome nucleoprotein complexes wherein a pair of viral DNA ends are bridged together by a multimer of integrase (IN). Atomic-resolution structures of HIV-1 intasomes provide detailed insights into the mechanism of integration and inhibition by clinical IN inhibitors. However, previously described HIV-1 intasomes are highly heterogeneous and have the tendency to form stacks, which is a limiting factor in determining high-resolution cryo-EM maps. We have assembled HIV-1 intasomes in the presence of excess IN C-terminal domain protein, which was readily incorporated into the intasomes. The purified intasomes were largely homogeneous and exhibited minimal stacking tendencies. The cryo-EM map resolution was further improved to 2.01 Å, which will greatly facilitate structural studies of IN inhibitor action and drug resistance mechanisms. The C-terminal 18 residues of HIV-1 IN, which are critical for virus replication and integration in vitro, have not been well resolved in previous intasome structures, and its function remains unclear. We show that the C-terminal tail participates in intasome assembly, resides within the intasome core, and forms a small alpha helix (residues 271-276). Mutations that disrupt alpha helix integrity impede IN activity in vitro and disrupt HIV-1 infection at the step of viral DNA integration.

Reduction of electrostatic turbulence in a quasi-helically symmetric stellarator via critical gradient optimization

We present a stellarator configuration optimized for a large threshold (‘critical gradient’) for the onset of the ion temperature gradient (ITG) driven mode, which achieves the largest critical gradient we have seen in any stellarator. Above this threshold, gyrokinetic simulations show that the configuration has low turbulence levels over an experimentally relevant range of the drive strength. The applied optimization seeks to maximize the drift curvature, leading to enhanced local-shear stabilization of toroidal ITG modes, and the associated turbulence. These benefits are combined with excellent quasi-symmetry, yielding low neoclassical transport and vanishingly small alpha particle losses. Analysis of the resulting configuration suggests a trade-off between magnetohydrodynamic (MHD) and ITG stability, as the new configuration possesses a vacuum magnetic hill.

PAX3-FOXO1 uses its activation domain to recruit CBP/P300 and shape RNA Pol2 cluster distribution

Activation of oncogenic gene expression from long-range enhancers is initiated by the assembly of DNA-binding transcription factors (TF), leading to recruitment of co-activators such as CBP/p300 to modify the local genomic context and facilitate RNA-Polymerase 2 (Pol2) binding. Yet, most TF-to-coactivator recruitment relationships remain unmapped. Here, studying the oncogenic fusion TF PAX3-FOXO1 (P3F) from alveolar rhabdomyosarcoma (aRMS), we show that a single cysteine in the activation domain (AD) of P3F is important for a small alpha helical coil that recruits CBP/p300 to chromatin. P3F driven transcription requires both this single cysteine and CBP/p300. Mutants of the cysteine reduce aRMS cell proliferation and induce cellular differentiation. Furthermore, we discover a profound dependence on CBP/p300 for clustering of Pol2 loops that connect P3F to its target genes. In the absence of CBP/p300, Pol2 long range enhancer loops collapse, Pol2 accumulates in CpG islands and fails to exit the gene body. These results reveal a potential novel axis for therapeutic interference with P3F in aRMS and clarify the molecular relationship of P3F and CBP/p300 in sustaining active Pol2 clusters essential for oncogenic transcription.

Highly rarefied gas flows in rough channels of finite length

Highly rarefied gas flows through a rough channel of finite length with small bumps appended to its surfaces are investigated, by varying the accommodation coefficient alpha in Maxwell’s diffuse-specular boundary condition, the characteristic size and position of the bumps, and the channel length. First, we study the influence of the surface bumps and consider the rarefied gas flow in a unit channel with periodic boundary conditions to remove the end effect. It is found that the surface bumps have a significant impact on the flow permeability. When alpha is very small (i.e., nearly specular reflection of gas molecules at the channel surface), the apparent gas permeability is dramatically reduced, even in the presence of small bumps, to a value that is almost comparable to the one when fully diffuse gas-surface scattering is assumed. This impact can be taken into account through an effective accommodation coefficient, i.e., the permeability of the rough channel is taken equivalently as that of a smooth channel without bumps but having gas-surface scattering under the effective accommodation coefficient. Second, we study the end effect by connecting a smooth channel of length L_0 to two huge gas reservoirs. It is found that (i) the end correction length is large at small alpha. Consequently, the mass flow rate barely reduces with increasing L_0 rather than scales down by a factor of 1/L_0 as predicted by the classical Knudsen diffusion theory; and (ii) the end correction is related to the channel’s aspect ratio. Finally, based on the effective accommodation coefficient and end correction, we explain the exotic flow enhancement in graphene angstrom-scale channels observed by Geim’s research group (Keerthi et al, Nature 558:420–424, 2018).

Development and a feasibility study using Gafchromic XRQA2 film as a novel passive radon measurement technique

In the present paper, a novel passive-type radon measurement technique based on Gafchromic XRQA2 film was developed. A Gafchromic XRQA2 film was modified by peeling off a polyester layer to enhance the film sensitivity to alpha particles, which were mainly emitted from radon and its progeny, and the response of the modified Gafchromic XRQA2 film to alpha particles was investigated. The results indicated that, with the increase in time-integrated alpha activity, the darkness of the exposed modified Gafchromic film increased, and only a small alpha energy dependence with less than 2% relative difference in the film response was observed. Next, the modified Gafchromic XRQA2 film was deployed with a RADUET container for radon measurement to evaluate application feasibility, and the radon response of the modified Gafchromic XRQA2 film was compared with the traditional one of a RADUET with CR-39 detector. The radon calibration was investigated using the radon exposure chamber. The obtained calibration functions showed that the net optical density of modified Gafchromic XRQA2 film was directly proportional to the accumulated radon concentration over the exposure period. From the calibration, the minimum and maximum detectable radon concentrations for a three-month measurement period were estimated to be about 390 Bq m−3 and 15,000 Bq m−3, respectively. Moreover, this technique enables to minimize the effect of thoron interference by the RADUET container design. These results suggest that this technique can be used for measuring radon, particularly in areas with potentially high radon concentrations, for example, underground mines and caves.

Advances in computational approaches to structure determination of alphaviruses and flaviviruses using cryo-electron microscopy

Advancements in the field of cryo-electron microscopy (cryo-EM) have greatly contributed to our current understanding of virus structures and life cycles. In this review, we discuss the application of single particle cryo-electron microscopy (EM) for the structure elucidation of small enveloped icosahedral viruses, namely, alpha- and flaviviruses. We focus on technical advances in cryo-EM data collection, image processing, three-dimensional reconstruction, and refinement strategies for obtaining high-resolution structures of these viruses. Each of these developments enabled new insights into the alpha- and flavivirus architecture, leading to a better understanding of their biology, pathogenesis, immune response, immunogen design, and therapeutic development.

Computational modeling and prediction of deletion mutants

In-frame deletion mutations can result in disease. The impact of these mutations on protein structure and subsequent functional changes remain understudied, partially due to the lack of comprehensive datasets including a structural readout. In addition, the recent breakthrough in structure prediction through deep learning demands an update of computational deletion mutation prediction. In this study, we deleted individually every residue of a small α-helical sterile alpha motif domain and investigated the structural and thermodynamic changes using 2D NMR spectroscopy and differential scanning fluorimetry. Then, we tested computational protocols to model and classify observed deletion mutants. We show a method using AlphaFold2 followed by RosettaRelax performs the best overall. In addition, a metric containing pLDDT values and Rosetta ΔΔG is most reliable in classifying tolerated deletion mutations. We further test this method on other datasets and show they hold for proteins known to harbor disease-causing deletion mutations.

Characteristics of COVID-19 patients with multiorgan injury across the pandemic in a large academic health system in the Bronx, New York

PurposeTo investigate the evolution of COVID-19 patient characteristics and multiorgan injury across the pandemic. MethodsThis retrospective cohort study consisted of 40,387 individuals tested positive for SARS-CoV-2 in the Montefiore Health System in Bronx, NY, between March 2020 and February 2022, of which 11,306 were hospitalized. Creatinine, troponin, and alanine aminotransferase were used to define acute kidney injury (AKI), acute cardiac injury (ACI) and acute liver injury, respectively. Demographics, comorbidities, emergency department visits, hospitalization, intensive care utilization, and mortality were analyzed across the pandemic. ResultsCOVID-19 positive cases, emergency department visits, hospitalization and mortality rate showed four distinct waves with a large first wave in April 2020, two small (Alpha and Delta) waves, and a large Omicron wave in December 2021. Omicron was more infectious but less lethal (p = 0.05). Among hospitalized COVID-19 patients, age decreased (p = 0.014), female percentage increased (p = 0.023), Hispanic (p = 0.028) and non-Hispanic Black (p = 0.05) percentages decreased, and patients with pre-existing diabetes (p = 0.002) and hypertension (p = 0.04) decreased across the pandemic. More than half (53.1%) of hospitalized patients had major organ injury. Patients with AKI, ACI and its combinations were older, more likely males, had more comorbidities, and consisted more of non-Hispanic Black and Hispanic patients (p = 0.005). Patients with AKI and its combinations had 4-9 times higher adjusted risk of mortality than those without. ConclusionsThere were shifts in demographics toward younger age and proportionally more females with COVID-19 across the pandemic. While the overall trend showed improved clinical outcomes, a substantial number of COVID-19 patients developed multi-organ injuries over time. These findings could bring awareness to at-risk patients for long-term organ injuries and help to better inform public policy and outreach initiatives.

Small Biological Preserves and Smaller Mammals: Can Protected Areas in Our Most Populous Regions Conserve Historic Community Composition?

The multi-faceted impacts of the Anthropocene are increasingly modifying natural ecosystems and threatening biodiversity. Protected spaces in and adjacent to urban landscapes may be critical in protecting species in human-modified systems. Can small, protected spaces act as reservoirs for biodiversity across dynamic spatial and temporal gradients of human impact? To address this question, we identified small mammal remains from modern raptor pellets and Holocene archaeological sites along a human modification gradient in the San Francisco Bay Area, CA. We assessed small mammal alpha and beta diversity for both modern and Holocene sites. We tested for significant differences between sites and time bins using permutational multivariate analysis of variance (PERMANOVA) and visualized these differences using non-metric multidimensional scaling (NMDS). We found that alpha diversity decreased with increasing human modification in Anthropocene sites, with no corresponding change between Holocene sites. Additionally, the alpha diversity of modern sites with moderate/high levels of human modification was significantly lower than that of protected modern sites and all Holocene sites, driven by the dominance of human-commensal and disturbance-tolerant species. On the other hand, the small mammal communities from a small, protected area (Jasper Ridge Biological Preserve) retained Holocene levels of alpha diversity. Jasper Ridge has also changed less over time in terms of overall community composition than more modified sites. Despite this, both PERMANOVA and NMDS show that Holocene and Anthropocene communities are significantly distinct regardless of collection site and level of anthropogenic modification. Our results suggest that even relatively small, protected spaces within an urbanized matrix conserve native faunal communities, highlighting their important role in urban conservation.

PLPP2: Potential therapeutic target of breast cancer in PLPP family

PLPPs (Phospholipid phosphatases) are widely expressed in different human tissues, regulate cell signal transduction, and are overexpressed in cancers such as gliomas, pancreatic adenocarcinoma, lung adenocarcinoma, and so on. As a member of the PLPP family, PLPP2 (phospholipid phosphatase 2) plays a vital role in the occurrence and development of breast cancer, but its mechanism is still unclear. Our research found that PLPP2 was overexpressed in breast cancer, and the higher expression level of PLPP2 showed a worse prognosis for breast cancer patients. Further analysis showed that overexpression of PLPP2 affected the expression of CDC34 (cell-division cycle 34), LSM7 (Like-Smith 7), and SGTA (small glutamine-rich tetratricopeptide repeat-containing protein alpha) through EMT (epigenetic-mesenchymal transition) related pathways to promote the occurrence and development of breast cancer. In vitro, silencing PLPP2 significantly reduced the proliferation, invasion, and migration abilities of human breast cancer cells MDA-MB-231. ER+ is a common subtype of breast cancer. Furthermore, we found that the overexpression of PLPP2 was significantly related to the poor prognosis of ER+ breast cancer. These results indicate that PLPP2 has value as a potential therapeutic target for breast cancer, especially for ER+ breast cancer.

Scapular morphology of great apes and humans: A three-dimensional computed tomography-based comparative study.

The primate scapula has been studied widely since its shape has been shown to correlate with how the forelimb is used in daily activities. In this study, we expand on the existing literature and use an image-based methodology that was originally developed for orthopaedic practice to quantify and compare the three-dimensional (3D) morphology of the scapula across humans and great apes. We expect that this image-based approach will allow us to identify differences between great apes and humans that can be related to differences in mobility and loading regime of the shoulder. We hypothesize that gorillas and chimpanzees will have a similar scapular morphology, geared towards stability and weight-bearing in knuckle-walking, whilst the scapular morphology of orangutans is expected to be more similar to that of humans given their high glenohumeral mobility associated with their suspensory lifestyle. We made 3D reconstructions of computed tomography scans of 69 scapulae from four hominid genera (Pongo, Gorilla, Pan and Homo). On these 3D bone meshes, the inferior glenoid plane was determined, and subsequently, a set of bony landmarks on the scapular body, coracoid, and acromion were defined. These landmarks allowed us to measure a set of functionally relevant angles which represent acromial overhang, subacromial space and coracoacromial space. The angles that were measured are: the delto-fulcral triangle (DFT), comprising the alpha, beta, and delta angle, the acromion-glenoid angle (AGA), the coracoid-glenoid centre-posterior acromial angle (CGA), the anterior tilt (TA CGA) and the posterior tilt of the CGA (PT CGA). Three observers placed the landmarks on the 3D bone meshes, allowing us to calculate the inter-observer error. The main differences in the DFT were found between humans and the great apes, with small differences between the great apes. The DFT of humans was significantly lower compared to that of the great apes, with the smallest alpha (32.7°), smallest delta (45.7°) and highest beta angle (101.6°) of all genera. The DFT of chimpanzees was significantly higher compared to that of humans (p < 0.01), with a larger alpha (37.6°) and delta angle (54.5°) and smaller beta angle (87.9°). The mean AGA of humans (59.1°) was significantly smaller (p < 0.001) than that of gorillas (68.8°). The mean CGA of humans (110.1°) was significantly higher (p < 0.001) than in orangutans (92.9°). Humans and gorillas showed mainly a posterior tilt of their coracoacromial complex whilst chimpanzees showed mainly an anterior tilt. The coracoacromial complex of the orangutans was not tilted anteriorly or posteriorly. With our image-based method, we were able to identify morphological features of the scapula that differed significantly between hominid genera. However, we did not find an overall dichotomy in scapular morphology geared towards high stability (Pan/Gorilla) or high mobility (Homo/Pongo). Further research is needed to investigate the functional implications of these differences in scapular morphology.

Core localized alpha-channeling via low frequency Alfvén mode generation in reversed shear scenarios

A novel channel for fuel ions heating in tokamak core plasma is proposed and analyzed using nonlinear gyrokinetic theory. The channel is achieved via spontaneous decay of reversed shear Alfvén eigenmode (RSAE) into low frequency Alfvén modes, which then heat fuel ions via collisionless ion Landau damping. The conditions for RSAE spontaneous decay are investigated, and the saturation level and the consequent fuel ion heating rate are also derived. The channel is expected to be crucial for future reactors operating under reversed shear configurations, where fusion alpha particles are generated in the tokamak core with the magnetic shear being, typically, reversed, and there is a dense RSAE spectrum due to the small alpha particle characteristic dimensionless orbits.

A novel family of small molecule HIF-1 alpha stabilizers for the treatment of diabetic wounds; an integrated in silico, in vitro, and in vivo strategy.

Hypoxia-inducible factor-1 alpha (HIF-1α) is a crucial regulator of wound healing, which includes epithelialization, angiogenesis, granulation, tissue development, and wound contraction. Even though diabetic wounds are hypoxic, HIF-1α levels are decreased during healing. Diabetic wound healing necessitates the modulation of hypoxia-induced responses by VHL-HIF-1α protein-protein inhibition. Our proposed hypothesis is to increase HIF-1α levels by inhibiting VHL and HIF-1α interactions by novel small bioactive molecules, accelerating diabetic wound healing. A three features (two aromatic rings and one hydrogen bond acceptor) pharmacophore hypothesis was generated from the existing HIF-1α modulators. Virtual screening was done based on the generated pharmacophore, and a library consisting of the top 20 out of 3728 compounds was selected using ZINCPharmer. Of the top 20 molecules, the pyrazole moiety was identified as the top "HIT". Five analogues of pyrazole were designed, and Scifinder ascertained the novelty. The designed compounds were synthesized and characterized by IR, Mass, and NMR. Preliminarily, we have carried out a scratch wound assay using 3T3L1 cell lines. All the synthesized compounds showed significant wound healing activity. Further, to validate the in vitro assay, the compound CI, which showed effective in vitro results was used for in vivo study. Using the diabetes mouse model, comprising streptozotocin-induced (STZ) diabetic mice and scratch wound assay, we demonstrated that inhibiting the VHL and HIF-1α connection is a promising strategy for treating diabetic ulcers. Molecules CI and CP were found to have substantial in silico, in vitro, and in vivo outcomes.

Dothidea kunmingensis, a novel asexual species of Dothideaceae on Jasminum nudiflorum (winter jasmine) from Southwestern China

During a survey of saprobic microfungi in Southwest China, a coelomycetous fungus was found on dead twigs of Jasminum nudiflorum in Kunming, Yunnan Province. Based on a detailed morphological characterization coupled with multi-locus phylogenetic analyses, the fungus was identified as a new species in the genus Dothidea. Phylogenetic analyses using a combined matrix consisting of internal transcribed spacer (ITS), large subunit rRNA (LSU), small subunit rRNA (SSU), beta tubulin (tub2) and translation elongation factor-1 alpha (tef1-α) confirmed its placement in Dothideaceae and revealed a sister relationship to Dothidea eucalypti. The new species is characterized by pycnidial conidiomata, ampulliform or doliiform conidiogenous cells as well as aseptate, subglobose to ovoid, hyaline to pale-brown conidia. Comprehensive descriptions and illustrations are provided. Morphological characteristics of asexual morph taxa in Dothideaceae are also summarized and discussed.

Distribution of preoperative angle alpha and angle kappa values in patients undergoing multifocal refractive lens surgery based on a positive contact lens test

PurposeTo assess the preoperative objective angle alpha and angle kappa measurements of patients deciding to undergo multifocal refractive lens surgery based on a subjective positive multifocal contact lens test (MCLT).MethodsRetrospective, consecutive case series. Alpha and kappa angles were measured using the iTrace aberrometer. All patients also performed a 1-week MCLT. Only patients with a positive MCLT underwent surgery. Visual outcome (UCVA) was obtained in the 1-year follow-up. We assessed the preoperative distribution of angle values within MCLT positive and negative patient groups.ResultsTwo hundred seventeen eyes (111 patients) were included. Mean age was 56.4 years (SD 5.6) and 46.9% were female. In 71 eyes (38 patients), MCLT was positive. Of them, 12 eyes (17%) had an angle alpha and angle kappa ≥ 0.5mm. Of 146 eyes (73 patients) who refrained from surgery due to a negative MCLT, 71 eyes (48.6%) had both angles small (<0.5mm). In the 1-year follow-up, UCVA improved by 0.68 logMAR (SD 0.51; p<0.001) from baseline. Eyes with both small angle alpha and kappa sizes improved by 0.78 logMAR (SD 0.56), as did eyes with high (≥0.5mm) angle sizes (0.82 logMAR (SD 0.53). UCVA of eyes (n=24) with high alpha but low kappa sizes improved less (−0.31 logMAR (SD 0.13; p=0.019)).ConclusionFour out of five patients with a positive MCLT also had correspondingly small angle values. One-half of patients with low preoperative angle values refrained from surgery due to a negative MCLT result. One-year visual acuity improvement was substantial and independent from angle sizes.

Defects in the STIM1 SOAR\u03b12 domain affect multiple steps in the CRAC channel activation cascade

The calcium release-activated calcium (CRAC) channel consists of STIM1, a Ca2+ sensor in the endoplasmic reticulum (ER), and Orai1, the Ca2+ ion channel in the plasma membrane. Ca2+ store depletion triggers conformational changes and oligomerization of STIM1 proteins and their direct interaction with Orai1. Structural alterations include the transition of STIM1 C-terminus from a folded to an extended conformation thereby exposing CAD (CRAC activation domain)/SOAR (STIM1-Orai1 activation region) for coupling to Orai1. In this study, we discovered that different point mutations of F394 in the small alpha helical segment (STIM1 α2) within the CAD/SOAR apex entail a rich plethora of effects on diverse STIM1 activation steps. An alanine substitution (STIM1 F394A) destabilized the STIM1 quiescent state, as evident from its constitutive activity. Single point mutation to hydrophilic, charged amino acids (STIM1 F394D, STIM1 F394K) impaired STIM1 homomerization and subsequent Orai1 activation. MD simulations suggest that their loss of homomerization may arise from altered formation of the CC1α1-SOAR/CAD interface and potential electrostatic interactions with lipid headgroups in the ER membrane. Consistent with these findings, we provide experimental evidence that the perturbing effects of F394D depend on the distance of the apex from the ER membrane. Taken together, our results suggest that the CAD/SOAR apex is in the immediate vicinity of the ER membrane in the STIM1 quiescent state and that different mutations therein can impact the STIM1/Orai1 activation cascade in various manners. Graphic abstractLegend: Upon intracellular Ca2+ store depletion of the endoplasmic reticulum (ER), Ca2+ dissociates from STIM1. As a result, STIM1 adopts an elongated conformation and elicits Ca2+ influx from the extracellular matrix (EM) into the cell due to binding to and activation of Ca2+-selective Orai1 channels (left). The effects of three point mutations within the SOARα2 domain highlight the manifold roles of this region in the STIM1/Orai1 activation cascade: STIM1 F394A is active irrespective of the intracellular ER Ca2+ store level, but activates Orai1 channels to a reduced extent (middle). On the other hand, STIM1 F394D/K cannot adopt an elongated conformation upon Ca2+ store-depletion due to altered formation of the CC1α1-SOAR/CAD interface and/or electrostatic interaction of the respective side-chain charge with corresponding opposite charges on lipid headgroups in the ER membrane (right).

Cutoff Thermalization for Ornstein\u2013Uhlenbeck Systems with Small L\xe9vy Noise in the Wasserstein Distance

This article establishes cutoff thermalization (also known as the cutoff phenomenon) for a class of generalized Ornstein–Uhlenbeck systems (X^varepsilon _t(x))_{tgeqslant 0} with varepsilon -small additive Lévy noise and initial value x. The driving noise processes include Brownian motion, alpha -stable Lévy flights, finite intensity compound Poisson processes, and red noises, and may be highly degenerate. Window cutoff thermalization is shown under mild generic assumptions; that is, we see an asymptotically sharp infty /0-collapse of the renormalized Wasserstein distance from the current state to the equilibrium measure mu ^varepsilon along a time window centered on a precise varepsilon -dependent time scale mathfrak {t}_varepsilon . In many interesting situations such as reversible (Lévy) diffusions it is possible to prove the existence of an explicit, universal, deterministic cutoff thermalization profile. That is, for generic initial data x we obtain the stronger result mathcal {W}_p(X^varepsilon _{t_varepsilon + r}(x), mu ^varepsilon ) cdot varepsilon ^{-1} rightarrow Kcdot e^{-q r} for any rin mathbb {R} as varepsilon rightarrow 0 for some spectral constants K, q>0 and any pgeqslant 1 whenever the distance is finite. The existence of this limit is characterized by the absence of non-normal growth patterns in terms of an orthogonality condition on a computable family of generalized eigenvectors of mathcal {Q}. Precise error bounds are given. Using these results, this article provides a complete discussion of the cutoff phenomenon for the classical linear oscillator with friction subject to varepsilon -small Brownian motion or alpha -stable Lévy flights. Furthermore, we cover the highly degenerate case of a linear chain of oscillators in a generalized heat bath at low temperature.