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UBQLN1 functions in autophagy and proteasome-mediated protein degradation. It contains an N-terminal ubiquitin-like domain (UBL), a C-terminal ubiquitin-associated domain (UBA), and a flexible central region which functions as a chaperone to prevent protein aggregation. Here, we report the 1H, 15N, and 13C resonance assignments for the backbone (NH, N, C’, Cα, and Hα) and sidechain Cβ atoms of the UBQLN1 UBA and an N-terminally adjacent segment called the UBA-adjacent domain (UBAA). We find a subset of the resonances corresponding to the UBAA to have concentration-dependent chemical shifts, likely due to self-association. We also find the backbone amide nitrogen of T572 to be shifted upfield relative to the average value for a threonine amide nitrogen, a phenomenon likely caused by T572 Hγ1 engagement in a hydrogen bond with adjacent backbone carbonyl atoms. The assignments described in this manuscript can be used to study the protein dynamics of the UBQLN1 UBA and UBAA as well as the interaction of these domains with other proteins.

PRAME is a CUL2 ubiquitin ligase subunit that is normally expressed in the testis but becomes aberrantly overexpressed in many cancer types in association with aneuploidy and metastasis. Here, we show that PRAME is expressed predominantly in spermatogonia around the time of meiotic crossing-over in coordination with genes mediating DNA double strand break repair. Expression of PRAME in somatic cells upregulates pathways involved in meiosis, chromosome segregation and DNA repair, and it leads to increased DNA double strand breaks, telomere dysfunction and aneuploidy in neoplastic and non-neoplastic cells. This effect is mediated at least in part by ubiquitination of SMC1A and altered cohesin function. PRAME expression renders cells susceptible to inhibition of PARP1/2, suggesting increased dependence on alternative base excision repair pathways. These findings reveal a distinct oncogenic function of PRAME than can be targeted therapeutically in cancer.

The present study examined whether the temporal distribution of procedural category learning experiences would impact learning outcomes. Participants completed the remote category learning study on a smartphone in one of two learning conditions: Massed (control) or distributed. Consistent with expectations, distributed learners reached higher accuracy levels. This effect disappeared after accounting for reaction time differences, suggesting that it was driven by attentional mechanisms. Distribution may have made participants more likely to discover the optimal categorization strategy and more robust to sensory habituation. Counter to previous findings, participants favored distributed learning. These results suggest that adult category learning is facilitated by temporal spacing. Future work may further explore the effects of temporal and contextual distinctiveness of learning experiences on category learning outcomes.

The E3 ligase E6AP/UBE3A has a dedicated binding site in the 26S proteasome provided by the RAZUL domain of substrate receptor hRpn10/S5a/PSMD4. Guided by RAZUL sequence similarity, we test and demonstrate here that the E6AP AZUL binds transiently to the UBA of proteasomal shuttle factor UBQLN1/2. Despite a weak binding affinity, E6AP AZUL is recruited to UBQLN2 phase-separated droplets and E6AP interacts with UBQLN1/2 in cells. Steady-state and transfer NOE experiments indicate direct interaction of AZUL with the UBQLN1 UBA domain. Intermolecular contacts identified by NOESY data were combined with AlphaFold2-Multimer predictions to yield an AZUL:UBA model structure. We also identify a concentration-dependent oligomerization domain directly adjacent to UBQLN1/2 UBA (UBA-adjacent, UBAA) that is α-helical and allosterically reconfigured by AZUL binding to UBA. These data lead to a model of E6AP recruitment to UBQLN1/2 by AZUL:UBA interaction and provide fundamental information on binding requirements for interactions in droplets and cells.

Uveal melanoma (UM) is the most common primary cancer of the eye and is associated with a high rate of metastatic death. UM can be stratified into two main classes based on metastatic risk, with class 1 UM having a low metastatic risk and class 2 UM having a high metastatic risk. Class 2 UM have a distinctive genomic, transcriptomic, histopathologic, and clinical phenotype characterized by biallelic inactivation of the BAP1 tumor-suppressor gene, an immune-suppressive microenvironment enriched for M2-polarized macrophages, and poor response to checkpoint-inhibitor immunotherapy. To identify potential mechanistic links between BAP1 loss and immune suppression in class 2 UM, we performed an integrated analysis of UM samples, as well as genetically engineered UM cell lines and uveal melanocytes (UMC). Using RNA sequencing (RNA-seq), we found that the most highly upregulated gene associated with BAP1 loss across these datasets was PROS1, which encodes a ligand that triggers phosphorylation and activation of the immunosuppressive macrophage receptor MERTK. The inverse association between BAP1 and PROS1 in class 2 UM was confirmed by single-cell RNA-seq, which also revealed that MERTK was upregulated in CD163+ macrophages in class 2 UM. Using ChIP-seq, BAP1 knockdown in UM cells resulted in an accumulation of H3K27ac at the PROS1 locus, suggesting epigenetic regulation of PROS1 by BAP1. Phosphorylation of MERTK in RAW 264.7 monocyte–macrophage cells was increased upon coculture with BAP1−/− UMCs, and this phosphorylation was blocked by depletion of PROS1 in the UMCs. These findings were corroborated by multicolor immunohistochemistry, where class 2/BAP1-mutant UMs demonstrated increased PROS1 expression in tumor cells and increased MERTK phosphorylation in CD163+ macrophages compared with class 1/BAP1-wildtype UMs. Taken together, these findings provide a mechanistic link between BAP1 loss and the suppression of the tumor immune microenvironment in class 2 UMs, and they implicate the PROS1–MERTK pathway as a potential target for immunotherapy in UM.

Histidine (an imidazole-based amino acid) is a promising building block for short aromatic peptides containing a proton donor/acceptor moiety. Previous studies have shown that polyalanine helical peptides substituted at regular intervals with histidine residues exhibit both structural stability as well as high proton affinity and high conductivity. Here, we present first-principle calculations of non-aqueous histidine-containing 310-,  and -helices and show that they are able to form hydrogen-bonded networks mimicking proton wires that have the ability to shuttle protons via the Grotthuss shuttling mechanism. The formation of these wires enhances the stability of the helices, and our structural characterizations confirm that the secondary structures are conserved despite distortions of the backbones. In all cases, the helices exhibit high proton affinity and proton transfer barriers on the order of 1~4 kcal/mol. Zero-point energy calculations suggest that for these systems, ground state vibrational energy can provide enough energy to cross the proton transport energy barrier. Additionally, ab initio molecular dynamics results suggests that the protons are transported unidirectionally through the wire at a rate of approximately 2 Å every 20 fs. These results demonstrate that efficient deprotonation-controlled proton wires can be formed using non-aqueous histidine-containing helical peptides.

Various properties of (CdSe)3n clusters (n = 1–9) were obtained using computational techniques. Using a simple force field, a simulated annealing technique was employed to explore the potential ene...

Mosquito and arbovirus surveillance is essential to the protection of public health. A majority of surveys are undertaken at ground level. However, mosquitoes shelter, breed, and quest for hosts across vertical strata, thus limiting our ability to fully describe mosquito and arboviral communities. To elucidate patterns of mosquito vertical stratification, canopy traps were constructed to sample mosquitoes at heights of 1.5, 5.0, and 8.7 m across three different landscape types in a Florida coastal conservation area. We assessed trapping efforts using individual-based rarefaction and extrapolation. The effects of height, landscape, site location, and sampling date on mosquito community composition were parsed out using permutational ANOVA on a Hellinger-transformed Bray–Curtis dissimilarity abundance matrix. Lastly, a generalized linear mixed effects model (GLMM) was used to explore species-specific vertical patterns. We observed differences in sampling effort and community composition structure across various heights and landscapes. Our GLMM revealed significant effects of trap height for Aedes taeniorhynchus, Anopheles crucians, Anopheles quadrimaculatus, and Culex coronator, but not for Culex nigripalpus, the ultra-dominant species present in this area. Together these data provide evidence that height and landscape significantly affect mosquito community structures and highlight a need to develop sampling regimes to target specific vector and nuisance species at their preferred height and across different landscape types.

The studies on the L. pectinata hemoglobins (HbI, HbII, and HbIII) are essential because of their biological roles in hydrogen sulfide transport and metabolism. Variation in the pH could also play a role in the transport of hydrogen sulfide by HbI and oxygen by HbII and HbIII, respectively. Here, fluoride binding was used to further understand the structural properties essential for the molecular mechanism of ligand stabilization as a function of pH. The data allowed us to gain insights into how the physiological roles of HbI, HbII, HbIII, adult hemoglobin (A-Hb), and horse heart myoglobin (Mb) have an impact on the heme-bound fluoride stabilization. In addition, analysis of the vibrational assignments of the met-cyano heme complexes shows varied strength interactions of the heme-bound ligand. The heme pocket composition properties differ between HbI (GlnE7 and PheB10) and HbII/HbIII (GlnE7 and TyrB10). Also, the structural GlnE7 stereo orientation changes between HbI and HbII/HbIII. In HbI, its carbonyl group orients towards the heme iron, while in HbII/HbIII, the amino group occupies this position. Therefore, in HbI, the interactions to the heme-bound fluoride ion, cyanide, and oxygen with GlnE7 via H-bonding are not probable. Still, the aromatic cage PheB10, PheCD1, and PheE11 may contribute to the observed stabilization. However, a robust H-bonding networking stabilizes HbII and HbIII, heme-bound fluoride, cyanide, and oxygen ligand with the OH and NH2 groups of TyrB10 and GlnE7, respectively. At the same time, A-Hb and Mb have moderate but similar ligand interactions controlled by their respective distal E7 histidine.

Adequately addressing missing data is a pervasive issue in the social sciences. Failure to correctly address missing data can lead to biased or inefficient estimation of parameters, confidence intervals, and significance tests. Multiple imputation is a statistical technique for handling missing data that involves using existing data to generate multiple datasets of plausible values for missing data that each incorporate random components to reflect their uncertainty. Each dataset is analyzed individually and identically, and parameter estimates are pooled into one set of estimates, variances, and confidence intervals. Although this technique is widely used, there is little consensus on what constitutes best practices in multiple imputation, including with regard to assessing the extent of missing data bias and reporting multiple imputation procedures in publications. This decision tree was crowdsourced at the 2021 annual meeting of the Society for the Improvement of Psychological Science (SIPS) and revised thereafter. This document is intended to provide practical guidelines for researchers to follow when examining their data for missingness and making decisions about how to handle that missingness. We primarily offer recommendations for multiple imputation, but also indicate where the same decisional guidelines are appropriate for other types of missing data procedures such as full imputation maximum likelihood (FIML).

Author(s): Burton-Pye, BP; Dembowski, M; Lukens, WW; Cruz, A; Althour, A; Lopez, GE; Salcedo, R; Gallagher, CMB; McGregor, D; Francesconi, LC | Abstract: Technetium-99, a prevalent by-product of the nuclear fuel cycle, is a transition metal with 9 accessible oxidation states and a half-life of 2.1 × 105 years. 99TcVII has been found in the environment surrounding National Lab sites and fuel reprocessing centers, and its separation and long-term storage is complicated by its extensive redox chemistry. In our prior work we have reported the synthesis and reduction of TcVO to TcIVO in α1- and α2-Wells–Dawson P2W17O6110– polyoxometalates and reported on the polyoxometalate features that promote reduction and stabilization. In this work we report on the oxidation state stabilization of TcVO, TcVIO and TcVIN within the α-Keggin PW11O397– polyoxometalate. Both Density Functional Theory and experimental results show that Tc in TBA4[TcVIN-PW11O39] can be reduced to TcV, but any subsequent electrons reduce the tungsten framework of the polyoxometalate. TBA4[TcVO-PW11O39] however, can be theoretically reduced down to TcI before reduction of the polyoxometalate occurs.

Uveal Melanoma (UM) is the most common primary ocular cancer in adults. Virtually all UM have activating mutations in the Gq signaling pathway. Metastatic risk in patients correlates with additional secondary mutations, where the lowest metastatic risk (class 1) is associated with EIF1AX and SF3B1, and the highest metastatic risk (class 2) is associated with BAP1 mutations. The interplay between the initiating Gq pathway mutations, and the secondary mutations found in all UM has not been well understood yet. Here, we utilize a multi-omics approach, to describe gene expression changes, the proteome, and phosphatome, following GNAQ mutation and BAP1 knockout in primary human uveal melanocytes. We generated human uveal melanocyte cell lines with inducible and specific mutations and analyzed via RNAseq, ATACseq, and mass spectrometry. Results reveal significant changes in pathways related to p53, chromatin regulation/modification, gene expression, and RNA processing with noted dysregulation of genes JUN, HDAC4, YAP, and SOX10, which cause senescence in melanocytes following GNAQ mutation, and are relieved through additional mutation in BAP1. Citation Format: Dawn Alexandra Owens, Stefan Kurtenbach, Jeffim N. Kuznetsoff, Daniel A. Rodriguez, Anthony Cruz, J. Harbour. Analysis of canonical uveal melanoma mutations reveals novel signaling effects [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 855.

Grid Inhomogeneous Solvation Theory (GIST) maps out solvation thermodynamic properties on a fine meshed grid and provides a statistical mechanical formalism for thermodynamic end-state calculations. However, differences in how long-range non-bonded interactions are calculated in molecular dynamics engines and in the current implementation of GIST have prevented precise comparisons between free energies estimated using GIST and those from other free energy methods such as thermodynamic integration (TI). Here, we address this by presenting PME-GIST, a formalism by which particle mesh Ewald (PME) based electrostatic energies and long-range Lennard-Jones (LJ) energies are decomposed and assigned to individual atoms and the corresponding voxels they occupy in a manner consistent with the GIST approach. PME-GIST yields potential energy calculations that are precisely consistent with modern simulation engines and performs these calculations at a dramatically faster speed than prior implementations. Here, we apply PME-GIST end-states analyses to 32 small molecules whose solvation free energies are close to evenly distributed from 2 kcal/mol to -17 kcal/mol and obtain solvation energies consistent with TI calculations (R2 = 0.99, mean unsigned difference 0.8 kcal/mol). We also estimate the entropy contribution from the 2nd and higher order entropy terms that are truncated in GIST by the differences between entropies calculated in TI and GIST. With a simple correction for the high order entropy terms, PME-GIST obtains solvation free energies that are highly consistent with TI calculations (R2 = 0.99, mean unsigned difference = 0.4 kcal/mol) and experimental results (R2 = 0.88, mean unsigned difference = 1.4 kcal/mol). The precision of PME-GIST also enables us to show that the solvation free energy of small hydrophobic and hydrophilic molecules can be largely understood based on perturbations of the solvent in a region extending a few solvation shells from the solute. We have integrated PME-GIST into the open-source molecular dynamics analysis software CPPTRAJ.

SARS-CoV-2 recently jumped species and rapidly spread via human-to-human transmission to cause a global outbreak of COVID-19. The lack of effective vaccine combined with the severity of the disease necessitates attempts to develop small molecule drugs to combat the virus. COVID19_GIST_HSA is a freely available online repository to provide solvation thermodynamic maps of COVID-19-related protein small molecule drug targets. Grid inhomogeneous solvation theory maps were generated using AmberTools cpptraj-GIST, 3D reference interaction site model maps were created with AmberTools rism3d.snglpnt and hydration site analysis maps were created using SSTMap code. The resultant data can be applied to drug design efforts: scoring solvent displacement for docking, rational lead modification, prioritization of ligand- and protein- based pharmacophore elements, and creation of water-based pharmacophores. Herein, we demonstrate the use of the solvation thermodynamic mapping data. It is hoped that this freely provided data will aid in small molecule drug discovery efforts to defeat SARS-CoV-2.

In this protocal, we described the precedures to train a CNN model using DUD-E dataset. we docked all compunds to the binding site of each DUD-E target and use the docked pose as the input for model training.

Recently much effort has been invested in using convolutional neural network (CNN) models trained on 3D structural images of protein-ligand complexes to distinguish binding from non-binding ligands for virtual screening. However, the dearth of reliable protein-ligand x-ray structures and binding affinity data has required the use of constructed datasets for the training and evaluation of CNN molecular recognition models. Here, we outline various sources of bias in one such widely-used dataset, the Directory of Useful Decoys: Enhanced (DUD-E). We have constructed and performed tests to investigate whether CNN models developed using DUD-E are properly learning the underlying physics of molecular recognition, as intended, or are instead learning biases inherent in the dataset itself. We find that superior enrichment efficiency in CNN models can be attributed to the analogue and decoy bias hidden in the DUD-E dataset rather than successful generalization of the pattern of protein-ligand interactions. Comparing additional deep learning models trained on PDBbind datasets, we found that their enrichment performances using DUD-E are not superior to the performance of the docking program AutoDock Vina. Together, these results suggest that biases that could be present in constructed datasets should be thoroughly evaluated before applying them to machine learning based methodology development.

The stability of H2 molecules trapped inside a 720 carbon atoms fullerene (C720) was studied using the path integral Monte Carlo formalism. The change in free energy with respect to the free molecules as a function of H2 molecules inside the fullerene was computed using alchemy methods coupled to replica exchange algorithms. The most stable number of molecules and the maximum number of molecules that could be trapped inside C720 were obtained at T = 300 K and 200 K. Modifications in the interparticle potential were considered to increase the trapping capacity of C720. Four clearly defined concentric layers of H2 in the molecular fluid phase were observed inside the C720 at loading that are acceptable for efficient storages.

A three-dimensional structure of human IL-24 was obtained from known IL-19, IL-22, and IL-20 crystal structures. Binding free energies for IL-24 and IL-20 with IL-20R were computed and compared wit...

We have developed SSTMap, a software package for mapping structural and thermodynamic water properties in molecular dynamics trajectories. The package introduces automated analysis and mapping of local measures of frustration and enhancement of water structure. The thermodynamic calculations are based on Inhomogeneous Fluid Solvation Theory (IST), which is implemented using both site-based and grid-based approaches. The package also extends the applicability of solvation analysis calculations to multiple molecular dynamics (MD) simulation programs by using existing cross-platform tools for parsing MD parameter and trajectory files. SSTMap is implemented in Python and contains both command-line tools and a Python module to facilitate flexibility in setting up calculations and for automated generation of large data sets involving analysis of multiple solutes. Output is generated in formats compatible with popular Python data science packages. This tool will be used by the molecular modeling community for computational analysis of water in problems of biophysical interest such as ligand binding and protein function.

Binding-site water is often displaced upon ligand recognition, but is commonly neglected in structure-based ligand discovery. Inhomogeneous solvation theory (IST) has become popular for treating this effect, but it has not been tested in controlled experiments at atomic resolution. To do so, we turned to a grid-based version of this method, GIST, readily implemented in molecular docking. Whereas the term only improves docking modestly in retrospective ligand enrichment, it could be added without disrupting performance. We thus turned to prospective docking of large libraries to investigate GIST's impact on ligand discovery, geometry, and water structure in a model cavity site well-suited to exploring these terms. Although top-ranked docked molecules with and without the GIST term often overlapped, many ligands were meaningfully prioritized or deprioritized; some of these were selected for testing. Experimentally, 13/14 molecules prioritized by GIST did bind, whereas none of the molecules that it deprioritized were observed to bind. Nine crystal complexes were determined. In six, the ligand geometry corresponded to that predicted by GIST, for one of these the pose without the GIST term was wrong, and three crystallographic poses differed from both predictions. Notably, in one structure, an ordered water molecule with a high GIST displacement penalty was observed to stay in place. Inclusion of this water-displacement term can substantially improve the hit rates and ligand geometries from docking screens, although the magnitude of its effects can be small and its impact in drug binding sites merits further controlled studies.

A tautomeric equilibrium exists for quinoline-2-thiol and quinoline-2(1H)-thione. Quantum mechanical calculations predict the thione is the major tautomer and this is confirmed by the absorption spectra. The utility of quinolone-2-thiol/quinoline-2(1H)-thione as a chromophore for developing fluorescent sensors is explored. No fluorescence is observed when excited at absorption maxima, however a fluorescence increase is observed when exposed to HNO, a molecule of import as a cardiovascular therapeutic. Alkylated quinoline-2-thiol derivatives are found to be fluorescent and show a reduction in fluorescence when exposed to metals and changes in pH.

By using path integral Monte Carlo simulations coupled to Replica Exchange algorithms, various phases of (p-H2)7 physically adsorbed on a model graphite surface were identified at low temperatures. At T = 0.5 K , the expected superfluid phase was observed for flat and slightly corrugated surfaces. At intermediate and high corrugations, a “supersolid” phase in C7/16 registry and a solid phase in C1/3 registry were observed, respectively. At higher temperatures, the superfluid is converted to a fluid and the “supersolid” to a solid.

Using molecular dynamics simulations, we have obtained an important insight into the structural and dynamical changes exerted by a nonaqueous solvent on the serine protease subtilisin Carlsberg. Our findings show that the structural properties of the subtilisin–acetonitrile (MeCN) system were sensitive to the amount of water present at the protein surface. A decrease or lack of water promoted the enzyme–MeCN interaction, which increased structural changes of the enzyme primarily at the surface loops. This effect caused variations on the secondary and tertiary structure of the protein and induced the opening of a pathway for the solvent to the protein core. Also, disturbance of the oxyanion hole was observed due to changes in the orientation in the Asn-155 side chain. The disruption of the oxyanion hole and the changes of the tertiary structure should affect the optimal activity of the enzyme.

Using hybrid density functional theory and a relatively large basis set, the lowest energy equilibrium structure, vibrational spectrum, and natural orbital analysis were obtained for magnesium diboride clusters [(MgB2)x for x=1,2, and 3]. For comparison, boron clusters [Bx for x=2,4, and 6] were also considered. The MgB2 and (MgB2)2 showed equilibrium structures with the boron atoms in arrangements similar to what was obtained for pure boron atoms, whereas, for (MgB2)3 a different arrangement of boron was obtained. From the population analysis, large electron density in the boron atoms forming the clusters was observed.

Haemoglobin I from Lucina pectinata is a monomeric protein consisting of 142 amino acids. Its active site contains a peculiar arrangement of phenylalanine residues (PheB10, PheCD1 and PheE11) and a distal Gln at position E7. Active site mutations at positions B10, E7 and E11 were performed in deoxy haemoglobin I (HbI), followed by 10 ns molecular dynamic simulations. The results showed that the mutations induced changes in domains far from the active site producing more flexible structures than the native HbI. Distance analyses revealed that the heme pocket amino acids at positions E7 and B10 are extremely sensitive to any heme pocket residue mutation. The high flexibility observed by the E7 position suggests an important role in the ligand binding kinetics in ferrous HbI, while both positions play a major role in the ligand stabilisation processes. Furthermore, our results showed that E11Phe plays a pivotal role in protein stability.

Ferryl compounds [Fe(IV)=O] in living organisms play an essential role in the radical catalytic cycle and degradation processes of hemeproteins. We studied the reactions between H2O2 and hemoglobin II (HbII) (GlnE7, TyrB10, PheCD1, PheE11), recombinant hemoglobin I (HbI) (GlnE7, PheB10, PheCD1, PheE11), and the HbI PheB10Tyr mutant of L. pectinata. We found that the tyrosine residue in the B10 position tailors, in two very distinct ways, the reactivity of the ferryl species, compounds I and II. First, increasing the reaction pH from 4.86 to 7.50, and then to 11.2, caused the the second-order rate constant for HbII to decrease from 141.60 to 77.78 M-1 s-1, and to 2.96 M-1 s-1, respectively. This pH dependence is associated with the disruption of the heme-tyrosine (603 nm) protein moiety, which controls the access of the H2O2 to the hemeprotein active center, thus regulating the formation of the ferryl species. Second, the presence of compound I was evident in the UV-vis spectra (648-nm band) in the reactions of HbI and recombinant HbI with H2O2, This band, however, is completely absent in the analogous reaction with HbII and the HbI PheB10Tyr mutant. Therefore, the existence of a hydrogen-bonding network between the heme pocket amino acids (i.e., TyrB10) and the ferryl compound I created a path much faster than 3.0x10(-2) s-1 for the decay of compound I to compound II. Furthermore, the decay of the heme ferryl compound I to compound II was independent of the proximal HisF8 trans-ligand strength. Thus, the pH dependence of the heme-tyrosine moiety complex determined the overall reaction rate of the oxidative reaction limiting the interaction with H2O2 at neutral pH. The hydrogen-bonding strength between the TyrB10 and the heme ferryl species suggests the presence of a cycle where the ferryl consumption by the ferric heme increases significantly the pseudoperoxidase activity of these hemeproteins.

The TNF receptor Fas (CD95, TNFRSF6) is known for inducing apoptosis in primary cells via binding with Fas ligand (FasL) and activation of caspase-8 through the adapter protein FADD. In addition, recent research showed that the apoptotic signaling requires palmitoylation of Fas near its transmembrane region to localize on the lipid rafts. Fas palmitoylation-defective mutant is unable to induce apoptosis in primary cells but continues to enhance T cell differentiation into effector memory cells (CD44hiCD62Llo), indicating that Fas can also trigger non-apoptotic signaling in primary T cells. Fas non-apoptotic signaling has unexpected roles in modulating T cell tumor immunotherapy and autoimmunity (Klebanoff et al. 2016; Cruz et al. 2016). We have investigated the signaling pathways underlying non-apoptotic Fas signaling in T cells. Co-stimulation with oligomerized Fas Ligand activates Akt and ribosomal S6 protein phosphorylation, and Fas induced T cell differentiation is blocked by Akt or mTOR inhibitors. Further studies showed that T cells from RIP3−/− and Caspase-8−/− double deficient mice, but not mice deficient in RIP3, were refractory to Fas-induced differentiation, indicating that Caspase 8 is essential for Fas non-apoptotic signaling. Similar results were obtained with FADD. Our findings suggest that in addition to apoptotic functions, Fas also promotes non-apoptotic signaling via Caspase-8 and induces T cell differentiation by activating the Akt pathway. These results reveal a common role for Caspase-8 in non-apoptotic and apoptotic functions of Fas, with potentially different caspase-8 substrates mediating these diverse functions of a single receptor.

The TNF-cytokine family receptor Fas (CD95) mediates T cell apoptosis by recruiting a death-inducing signaling complex (DISC) composed of the adaptor protein (FADD) and Caspase-8. Recently, it has been shown that Fas is also directs non-death signaling and enhances effector cell differentiation in T cells. Mutations which reduce the ability of Fas to localize to lipid raft microdomains and cluster upon activation abrogate the death-inducing potential of Fas while preserving non-apoptotic signaling. Caspase-8, a key mediator of both apoptotic and non-apoptotic signal, has been shown to form filamentous structures in vitro and upon overexpression in mammalian cells, but it is unknown if this process occurs in vivo to facilitate signaling. To investigate these supramolecular phenomena, we developed Fas and Caspase-8 fused to photoactivatable fluorescent proteins to be expressed in both primary T cells and T cell lines for super resolution imaging. Additionally, we have produced supported planar lipid bilayers presenting Fas ligand (FasL) and T cell stimulatory ligands to mimic a physiologic signaling environment. Photoactivatable localization microscopy (PALM) is used to observe and quantify clustering Fas molecules and formation of caspase-8 containing signaling complexes at nanometer scale resolution. Structure illuminated microscopy (SIM) and PALM will be used to observe the behavior of Fas relative to cellular-scale actin remodeling and TCR clustering. Our findings will reveal the behavior of supramolecular complexes mediating apoptosis and non-apoptotic signaling by Fas in the plasma membrane of living cells.

Water molecules in the active site of an enzyme occupy a complex, heterogeneous environment, and the thermodynamic properties of active-site water are functions of position. As a consequence, it is thought that an enzyme inhibitor can gain affinity by extending into a region occupied by unfavorable water or lose affinity by displacing water from a region where it was relatively stable. Recent advances in the characterization of binding-site water, based on the analysis of molecular simulations with explicit water molecules, have focused largely on simplified representations of water as occupying well-defined hydration sites. Our grid-based treatment of hydration, GIST, offers a more complete picture of the complex distributions of water properties, but it has not yet been applied to proteins. This first application of GIST to protein–ligand modeling, for the case of Coagulation Factor Xa, shows that ligand scoring functions based on GIST perform at least as well as scoring functions based on a hydration-site approach (HSA), when applied to exactly the same simulation data. Interestingly, the displacement of energetically unfavorable water emerges as the dominant factor in the fitted scoring functions, for both GIST and HSA methods, while water entropy plays a secondary role, at least in the present context.

Streptomyces tsukubaensis is a well-established industrial tacrolimus producer strain, but its molecular genetics is very poorly known. This information shortage prevents the development of tailored mutants in the regulatory pathways. A region (named bul) contains several genes involved in the synthesis and control of the gamma-butyrolactone autoregulator molecules. This region contains ten genes (bulA, bulZ, bulY, bulR2, bulS2, bulR1, bulW, bluB, bulS1, bulC) including two γ-butyrolactone receptor homologues (bulR1, bulR2), two putative gamma-butyrolactone synthetase homologues (bulS1, bulS2) and two SARP regulatory genes (bulY, bulZ). Analysis of the autoregulatory element (ARE)-like sequences by electrophoretic mobility shift assays and footprinting using the purified BulR1 and BulR2 recombinant proteins revealed six ARE regulatory sequences distributed along the bul cluster. These sequences showed specific binding of both BulR1 (the gamma-butyrolactone receptor) and BulR2, a possible pseudo γ-butyrolactone receptor. The protected region in all cases covered a 28-nt sequence with a palindromic structure. Optimal docking area analysis of BulR1 proved that this protein can be presented as either monomer or dimer but not oligomers and that it binds to the conserved ARE sequence in both strands. The effect on tacrolimus production was analysed by deletion of the bulR1 gene, which resulted in a strong decrease of tacrolimus production. Meanwhile, the ΔbulR2 mutation did not affect the biosynthesis of this immunosuppressant.

Nature Communications 4: Article number: 1403 (2013); Published: 29 January 2013; Updated: 29 July 2013. The original version of this Article contained a typographical error in the spelling of the author Mian M. K. Shahzad, which was incorrectly given as Mian M. K. Shazhad. This has now been corrected in both the PDF and HTML versions of the Article.

We report gas-phase electronic structure calculations on helical peptides that act as scaffolds for imidazole-based hydrogen-bonding networks (proton wires). We have modeled various 21-residue polyalanine peptides substituted at regular intervals with histidines (imidazole-bearing amino acids), using a hybrid approach with a semiempirical method (AM1) for peptide scaffolds and density functional theory (B3LYP) for proton wires. We have computed energy landscapes including barriers for Grotthuss-shuttling-type proton motions though wires supported on 3(10)-, α- and π-helical structures, showing the 3(10)- and α-helices to be attractive targets in terms of high proton affinities, low Grotthuss shuttling barriers, and high stabilities. Moreover, bias forces provided by the helical dipole moments were found to promote unidirectional proton translocation.

By implementing a simple reduced dimensionality model to describe the interactions in finite systems composed of two seven-amino-acid peptides, the thermodynamic properties of ordered and disordered aggregates were computed. Within this model, the hydrophobicity of each amino acid was varied, and the stability of the systems computed. Accurate averages in the canonical ensemble were obtained using various replica exchange Monte Carlo algorithms. Low and high temperature regions were encountered where the ordered and disordered aggregates were stabilized. It was observed that as the degree of hydrophobicity increased, the stability of the aggregates increased, with a significant energetic stabilization obtained for the ordered aggregates. Upon decreasing the concentration of the solution, the stability of the amorphous aggregates increased when compared to the ordered systems.

The study of Langmuir monolayers has generated the attention of researchers because of their unique properties and their not well understood phase equilibrium. These monolayers exhibit interesting phase diagrams where the unusual liquid-liquid equilibrium can be observed for a single component monolayer. Monte Carlo computer simulations in the virtual Gibbs ensemble were used to obtain the phase diagram of Langmuir monolayers. The liquid-vapor and liquid-liquid phase equilibria were considered by constructing the Cailletet-Mathias phase diagrams. By using the Ising model and the rectilinear approximations the identification of the critical properties for both equilibria was determined. These critical parameters were calculated as a function of the strength of the interaction between the surfactant molecules and the aqueous subphase. As a result, we have identified the coexistence between a liquid expanded state (LES)-vapor and the liquid condensed state-LES, in agreement with experimental and theoretical evidence in the literature. We obtained a clear separation of phases and a strong dependence on the strength of the solvent used. Namely, as the interaction between the solvent and the head of the surfactant increases, the critical properties also increase. Equilibrium states were characterized by computing thermodynamic quantities as a function of temperature and solvent strength.

Udgivelsesdato: 2006-Apr-15 Surfactant protein C (SP-C) is a membrane-associated protein essential for normal respiration. It has been found that the alpha-helix form of SP-C can undergo, under certain conditions, a transformation from an alpha-helix to a beta-strand conformation that closely resembles amyloid fibrils, which are possible contributors to the pathogenesis of pulmonary alveolar proteinosis. Molecular dynamics simulations using the NAMD2 package were performed for systems containing from one to seven SP-C molecules to study their behavior in water. The results of our simulations show that unfolding of the protein occurs at the amino terminal, and despite this unfolding, no transition from alpha-helix to beta-strand was observed.

The distal pocket of hemoglobin II (HbII) from Lucina pectinata is characterized by the presence of a GlnE7 and a TyrB10. To elucidate the functional properties of HbII, biophysical studies were conducted on HbII and a HbI PheB10Tyr site-directed mutant. The pH titration data at neutral conditions showed visible bands at 486, 541, 577 and 605 nm for both proteins. This suggests the possible existence of a conformational equilibrium between an open and closed configuration due to the interactions of the TyrB10, ligand, and heme iron. The kinetic behavior for the reaction of both ferric proteins with H2O2 indicates that the rate for the formation of the ferryl intermediates species varies with pH, suggesting that the reaction is strongly dependent on the conformational states. At basic pH values, the barrier for the reaction increases as the tyrosine adopts a closed conformation and the ferric hydroxyl replaces the met-aquo species. The existence of these conformers is further supported by resonance Raman (RR) data, which indicate that in a neutral environment, the ferric HbII species is present as a possible mixture of coordination and spin states, with values at 1558 and 1580 cm(-1) for the nu2 marker, and 1479, 1492, and 1503 cm(-1) for the nu3 mode. Moreover, the presence of the A3 and A(o) conformers at 1924 and 1964 cm(-1) in the HbII-CO infrared spectra confirms the existence of an open and closed conformation due to the orientation of the TyrB10 with respect to the heme active center.

The TNF family cytokine TL1A (Tnfsf15) costimulates T cells through its receptor DR3 (Tnfrsf25). Currently known effects of TL1A on T cell differentiation or systemic immune responses cannot account for the resistance of Tnfrsf25-/- mice to diverse animal models of autoimmune and allergic inflammation. IL-9 is a cytokine that promotes inflammatory and allergic immune responses and is expressed by a distinct subset of T cells early after T cell activation or restimulation. We have found that TL1A potently promotes generation of T cells producing IL-9 (Th9) by signaling through DR3 in a cell-intrinsic manner. Unlike the TNF family member OX40 ligand, TL1A increases Th9 differentiation independently of STAT6 and the TNF-signaling adaptor TRAF6. Instead, TL1A affects Th9 differentiation through enhancing IL-2-dependent STAT5 activation and allowing increased binding to the IL-9 promoter. In two models of allergic asthma, we demonstrate that Tnfrsf25-/- mice have reduced disease severity accompanied by fewer IL-9 producing T cells in the lung. In addition to promoting Th9 differentiation, we find that TL1A enhances pathogenicity in Th9 transfer models of both uveitis and allergic asthma, where endogenous TL1A signaling is required for maximal pathology and IL-9 production at the site of inflammation. Taken together, these data identify TL1A as a novel cytokine that promotes Th9 differentiation and pathogenicity and as a possible therapeutic target in diseases dependent on IL-9.