Site-specific Interactions Research Articles

Breaking adsorption-energy scaling limitations of electrocatalytic nitrate reduction on intermetallic CuPd nanocubes by machine-learned insights

The electrochemical nitrate reduction reaction (NO3RR) to ammonia is an essential step toward restoring the globally disrupted nitrogen cycle. In search of highly efficient electrocatalysts, tailoring catalytic sites with ligand and strain effects in random alloys is a common approach but remains limited due to the ubiquitous energy-scaling relations. With interpretable machine learning, we unravel a mechanism of breaking adsorption-energy scaling relations through the site-specific Pauli repulsion interactions of the metal d-states with adsorbate frontier orbitals. The non-scaling behavior can be realized on (100)-type sites of ordered B2 intermetallics, in which the orbital overlap between the hollow *N and subsurface metal atoms is significant while the bridge-bidentate *NO3 is not directly affected. Among those intermetallics predicted, we synthesize monodisperse ordered B2 CuPd nanocubes that demonstrate high performance for NO3RR to ammonia with a Faradaic efficiency of 92.5% at −0.5 VRHE and a yield rate of 6.25 mol h−1 g−1 at −0.6 VRHE. This study provides machine-learned design rules besides the d-band center metrics, paving the path toward data-driven discovery of catalytic materials beyond linear scaling limitations.

AXL inhibitors selected by molecular docking: Option for reducing SARS-CoV-2 entry into cells.

The COVID-19 pandemic is ongoing and the benefit from vaccines is still insufficient since COVID-19 continues to be dia g-nosed in vaccinated individuals. It is, therefore, necessary to propose specific pharmacological treatments against COVID-19. A new therapeutic target on the human cellular membrane is AXL (anexelekto), proposed as an independent pathway by which interaction with the S protein of SARS-CoV-2 allows the virus to enter the cell, without the participation of ACE2. AXL serves as another gate through which SARS-CoV-2 can enter cells. Therefore, any stage of COVID-19 could be ameliorated by hindering the interaction between AXL and SARS-CoV-2. This study proposes ten compounds (1-10), selected by mole-cu lar docking and using a library of nearly 500,000 compounds, to develop a new drug that will decrease the interaction of AXL with the S protein of SARS-CoV-2. These compounds have a specific potential site of interaction with AXL, between Glu59, His61, Glu70 and Ser74 amino acids. This site is necessary for the interaction of AXL with the S protein. With this, we propose to develop a new adjuvant treatment against COVID-19.

CeO2 Functionalized Cobalt Layered Double Hydroxide for Efficient Catalytic Oxygen-Evolving Reaction.

Water splitting to produce hydrogen is an effective means to alleviate the energy crisis. The anodic oxygen-evolving reaction (OER) limits the overall efficiency due to its high energy barrier. To address this, layered double hydroxides (LDHs) with high catalytic activities have been widely studied, especially those modified with CeO2 , either bound to the surface or doped into interior. However, experimental evidence for the atomic-level understanding of the mechanism for the enhanced catalytic performance is conspicuously missing. Herein, anchoring CeO2 nanoparticles onto Co LDH, based on the thoughts of loading capacity and size effect to regulate the properties of the interface and to optimize the performance, is attempted. The electronic interactions are studied by X-ray photoelectron spectroscopy (XPS) and electron energy loss spectroscopy (EELS), revealing electron transfer from Co2+ to Ce4+ that leads to an increase in Co3+ . The strong Lewis acidity of Co3+ helps the binding of OH- , which is conducive to the formation and transformation of oxygen-containing intermediates. Providing evidence is the formation of one of the key intermediates Co-OOH at a sizably reduced potential as monitored by in situ Raman spectroscopy. With this work, the atomic level correlation of site-specific electronic interactions with the enhanced catalytic performance is clearly established.

Mutually Exclusive Interactions of Rifabutin with Spatially Distinct Mycobacterial Cell Envelope Membrane Layers Offer Insights into Membrane-Centric Therapy of Infectious Diseases.

The mycobacterial cell envelope has spatially resolved inner and outer membrane layers with distinct compositions and membrane properties. However, the functional implication and relevance of this organization remain unknown. Using membrane biophysics and molecular simulations, we reveal a varied interaction profile of these layers with antibiotic Rifabutin, underlined by the structural and chemical makeup of the constituent lipids. The mycobacterial inner membrane displayed the highest partitioning of Rifabutin, which was located exclusively in the lipid head group/interfacial region. In contrast, the drug exhibited specific interaction sites in the head group/interfacial and hydrophobic acyl regions within the outer membrane. Altogether, we show that the design of membrane-active agents that selectively disrupt the mycobacterial outer membrane structure can increase drug uptake and enhance intracellular drug concentrations. Exploiting the mycobacterium-specific membrane–drug interaction profiles, chemotypes consisting of outer membrane-disruptive agents and antitubercular drugs can offer new opportunities for combinational tuberculosis (TB) therapy.

Identification of Coastal Defence Measures Best Adapted to Mitigate Hazards in Specific Coastal Systems: Development of a Dynamic Literature Meta-Analysis Methodology

The decision-making process of the coastal defence measures (CDMs) is complex and filled with uncertainties due to site-specific interactions between hydrodynamic and geomorphological conditions, which have repercussions on the ecological and social aspects of coastal communities. Scientific knowledge of the effects of CDMs contributes to the reduction in inherent uncertainties and facilitates the decision-making and design processes. The goal of this article is to present an algorithm designed to evaluate and hierarchize CDMs in relation to different coastal environments. Drawn from 411 published scientific case studies, a total of 1709 authors’ observation statements regarding the effects of CDMs on the study sites’ environmental features (type of coast, type of substrate, tidal range, and wave climate) were entered in a database, categorized, and weighted according to a qualitative scale. The algorithm processes the information by establishing a correspondence between user-selected environment features and those stocked in the database, and it evaluates user-selected CDMs in relation to the specified coastal characteristics by identifying, collating, and rating the effects as observed in similar contexts. The result is a tool able to process, structure, and concretize scientific knowledge regarding CDMs and their effects on coastal systems. It is complementary to existing tools currently used in the decision-making and design processes of the CDMs. The results present the hierarchization of CDMs according to a multilevel aggregated structure, which can be used in different ways by coastal managers, decision-makers, and engineers. The algorithm, based on standardized coastal characteristics, can be applied to any shoreline worldwide.

Enantioselective Recognition of Helicenes by a Tailored Chiral Benzo[ghi]perylene Trisimide π-Scaffold.

Enantioselective molecular recognition of chiral molecules that lack specific interaction sites for hydrogen bonding or Lewis acid–base interactions remains challenging. Here we introduce the concept of tailored chiral π‐surfaces toward the maximization of shape complementarity. As we demonstrate for helicenes it is indeed possible by pure van‐der‐Waals interactions (π–π interactions and CH–π interactions) to accomplish enantioselective binding. This is shown for a novel benzo[ghi]perylene trisimide (BPTI) receptor whose π‐scaffold is contorted into a chiral plane by functionalization with 1,1′‐bi‐2‐naphthol (BINOL). Complexation experiments of enantiopure (P)‐BPTI with (P)‐ and (M)‐[6]helicene afforded binding constants of 10 700 M−1 and 550 M−1, respectively, thereby demonstrating the pronounced enantiodifferentiation by the homochiral π‐scaffold of the BPTI host. The enantioselective recognition is even observable by the naked eye due to a specific exciplex‐type emission originating from the interacting homochiral π‐scaffolds of electron‐rich [6]helicene and electron‐poor BPTI.

Enantioselective Recognition of Helicenes by a Tailored Chiral Benzo[ghi]perylene Trisimide π‐Scaffold

AbstractEnantioselective molecular recognition of chiral molecules that lack specific interaction sites for hydrogen bonding or Lewis acid–base interactions remains challenging. Here we introduce the concept of tailored chiral π‐surfaces toward the maximization of shape complementarity. As we demonstrate for helicenes it is indeed possible by pure van‐der‐Waals interactions (π–π interactions and CH–π interactions) to accomplish enantioselective binding. This is shown for a novel benzo[ghi]perylene trisimide (BPTI) receptor whose π‐scaffold is contorted into a chiral plane by functionalization with 1,1′‐bi‐2‐naphthol (BINOL). Complexation experiments of enantiopure (P)‐BPTI with (P)‐ and (M)‐[6]helicene afforded binding constants of 10 700 M−1 and 550 M−1, respectively, thereby demonstrating the pronounced enantiodifferentiation by the homochiral π‐scaffold of the BPTI host. The enantioselective recognition is even observable by the naked eye due to a specific exciplex‐type emission originating from the interacting homochiral π‐scaffolds of electron‐rich [6]helicene and electron‐poor BPTI.

Abstract P5-02-03: Phenotypic analysis for TNBC using a novel breast cancer microphysiological system

Abstract Breast cancer (BC) is among the most commonly diagnosed cancers in women and is the leading cause of malignant death in U.S. women. The triple negative breast cancer (TNBC) subtype is more aggressive and has a poorer prognosis compared to other subtypes. Patient derived xenografts (PDX), human tumors transplanted and grown in mice, are a newer, better model of TNBC. However, there are barriers when using mouse models: mice stroma can take over the PDX tumors, using immunocompromised mice can prevent immune responses and site-specific interaction, and mice are expensive. To overcome these barriers, a translational microphysiological system (MPS) was developed that is capable of maintaining the primary, human breast microenvironment in vitro. By seeding these MPS with breast cancer cell lines or tumor explants, we produce breast cancer MPS (BC-MPS). Here, we show the model’s capabilities of supporting PDX tumor viability through flow cytometry on multiple PDX models as well as effects of human breast tissue on TNBC cell lines viability and proliferation. After showing the BC-MPS’ stability ex vivo, the effects on the cancer stem cell (CSC) population and lipid accumulation were explored through flow cytometry. Tu-BcX-4IC was seeded alone and in BC-MPS. After 7 days of incubation, the tumor was removed and the CSC population and lipid accumulation was measured through flow cytometry, showing an increase in CSC population and lipid accumulation when the PDX tumor was cultured in BC-MPS compared to cultured in 2D. Architectural changes that occur with the PDX explants when placed in BC-MPS were also monitored. The TNBC PDX model, Tu-BcX-4IC, was excised and seeded alone or in the BC-MPS system. The human breast tissue (HBT) and a PDX tumor piece was initially fixed in formalin before placed into BC-MPS (Day 0). After 4, 7, and 14 days of incubation, the 4IC PDX tumor explants seeded alone and in BC-MPS were fixed in formalin, paraffin embedded, and sectioned for H&E staining to determine the effect of the surrounding HBT on the PDX tumor. In additions to demonstrating the model’s capabilities of supporting PDX tumor viability and examining tumor architectural changes, assays were performed to test experimental capabilities of BC-MPS. Different BC cell lines were placed into the system and treated with chemotherapeutics to determine if the microphysiological system is capable of pharmaceutical studies. Here, we focus on the TNBC cell lines which were seeded alone and in the BC-MPS, and their response to the chemotherapeutic drugs, Paclitaxel, Romidepsin, and Cobimetinib. The proliferation response was monitored by luciferase imaging, demonstrating that BC-MPS can be used for drug studies.BC-MPS is a promising new translational microphysiological system that facilitates studying long term interactions between real human breast tissue and cancer cells as well as the native tumor environment in HBT. The BC-MPS system’s ability to support the growth of established cell lines as well as PDXs has been demonstrated. Future studies will focus on showing human tumor viability in BC-MPS, developing the model for personalized medicine. Citation Format: Katherine Hebert, Khoa Nguyen, Thomas Cheng, Madlin Alzoubi, Bridgette Collins-Burow, Elizabeth Martin, Frank Lau, Matthew Burow. Phenotypic analysis for TNBC using a novel breast cancer microphysiological system [abstract]. In: Proceedings of the 2021 San Antonio Breast Cancer Symposium; 2021 Dec 7-10; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2022;82(4 Suppl):Abstract nr P5-02-03.

An examination of the effects of water on normal phase enantioseparations

Superficially porous silica bonded with macrocyclic glycopeptides can separate enantiomers in various chromatographic formats, including normal phase liquid chromatography (NPLC). The conventional wisdom in NPLC is to avoid intentionally adding water in the eluents. Herein we examine the effects of small quantities of water as an additive on chiral separations in NPLC with the n-hexane-ethanol system. A phase diagram (n-hexane-ethanol-water) is used to analyze the physicochemical properties of the mobile phase. The relative polarity change of solvents upon adding water was determined by using bathochromic shifts of dissolved Nile Red dye. The effectiveness of chiral NPLC with water traces is demonstrated for various pharmaceutically relevant enantiomeric compounds. It is postulated that water molecules weaken stationary phase-solute interactions, resulting in lower retention times for both enantiomers in addition to significantly higher efficiencies. Gibbs free energy changes provided an understanding of the different enantioselectivity shifts caused by water addition. Some interesting kinetic effects also were observed. Classical van Deemter curves are not observed on macrocyclic glycopeptide stationary phases due to slow mass transfer kinetics and thermal effects at high flow rates. The most significant advantage of adding water in NPLC is reducing mass transfer kinetics and altering the mass overloading properties which is highly beneficial on macrocyclic glycopeptide phases. By overloading a 10 × 0.46-cm column with up to 0.6 mg alprenolol, it was found that the relative adsorption isotherm of the first eluting enantiomer was switched from Langmuir to anti-Langmuir type by water addition. The peak shape tuning effect demonstrated the strong influence of water on specific interaction sites of the chiral stationary phases. Water addition effects were most beneficial for enantiomeric and preparative separations in NP mode.

Metalliferous habitats and seed microbes affect the seed morphology and reproductive strategy of Arabidopsis halleri.

Plant reproduction in metalliferous habitats is challenged by elevated concentrations of metal trace elements in soil. As part of their survival strategy, metal-tolerant plants have adjusted reproductive traits, including seed morphology, dormancy, and germination rate. These traits are particularly relevant, yet poorly understood, in metal hyperaccumulators that are promising candidates for phytoremediation. We assessed seed shape characteristics, dormancy, and germination rate in the hyperaccumulating model species Arabidopsis halleri. Seed morphological parameters were evaluated using seeds collected from two metalliferous and two non-metalliferous sites (~ 1000 seeds per location). We also addressed the potential influence of seed surface-associated microbes and endophytic fungi on germination success. Seeds from non-metallicolous populations were on average 18% bigger than those from metal-contaminated post-mining sites, which contrasts the general expectation about reproductive parts in metallicolous plants. Irrespective of their origin, surface-sterilized seeds had up to ~ 20% higher germination rates and germinated earlier than non-sterilized seeds, hinting at a negative effect of seed-associated microbial communities. Surface sterilization also facilitated the emergence of an endophytic fungus (Aspergillus niger) that is a known seed-borne pathogen. Interestingly, A. niger actually promoted germination in surface-sterilized seeds from some locations. Despite species-wide metal tolerance in A. halleri, metalliferous conditions seem to differently affect reproductive traits compared to non-metalliferous environments (e.g., smaller seeds). Yet, higher germination rates in these populations hint at the potential of A. halleri to successfully colonize post-mining habitats. This process is modulated by site-specific interactions with seed microbiota.

Amber Suppression Technology for Mapping Site-specific Viral-host Protein Interactions in Mammalian Cells.

Probing the molecular interactions of viral-host protein complexes to understand pathogenicity is essential in modern virology to help the development of antiviral therapies. Common binding assays, such as co-immunoprecipitation or pull-downs, are helpful in investigating intricate viral-host proteins interactions. However, such assays may miss low-affinity and favour non-specific interactions. We have recently incorporated photoreactive amino acids at defined residues of a viral protein in vivo, by introducing amber stop codons (TAG) and using a suppressor tRNA. This is followed by UV-crosslinking, to identify interacting host proteins in live mammalian cells. The affinity-purified photo-crosslinked viral-host protein complexes are further characterized by mass spectrometry following extremely stringent washes. This combinatorial site-specific incorporation of a photoreactive amino acid and affinity purification-mass spectrometry strategy allows the definition of viral-host protein contacts at single residue resolution and greatly reduces non-specific interactors, to facilitate characterization of viral-host protein interactions. Graphic abstract: Schematic overview of the virus-host interaction assay based on an amber suppression approach. Mammalian cells grown in Bpa-supplemented medium are co-transfected with plasmids encoding viral sequences carrying a Flag tag, a (TAG) stop codon at the desired position, and an amber suppressor tRNA (tRNACUA)/aminoacyl tRNA synthetase (aaRS) orthogonal pair. Cells are then exposed to UV, to generate protein-protein crosslinks, followed by immunoprecipitation with anti-Flag magnetic beads. The affinity-purified crosslinks are probed by western blot using an anti-Flag antibody and the crosslinked host proteins are characterised by mass spectrometry.

Characterization of Acetonitrile Isotopologues as Vibrational Probes of Electrolytes.

Acetonitrile has emerged as a solvent candidate for novel electrolyte formulations in metal-ion batteries and supercapacitors. It features a bright local C≡N stretch vibrational mode whose infrared (IR) signature is sensitive to battery-relevant cations (Li+, Mg2+, Zn2+, Ca2+) both in pure form and in the presence of water admixture across a full possible range of concentrations from the dilute to the superconcentrated regime. Stationary and time-resolved IR spectroscopy thus emerges as a natural tool to study site-specific intermolecular interactions from the solvent perspective without introducing an extrinsic probe that perturbs solution morphology and may not represent the intrinsic dynamics in these electrolytes. The metal-coordinated acetonitrile, water-separated metal–acetonitrile pair, and free solvent each have a distinct vibrational signature that allows their unambiguous differentiation. The IR band frequency of the metal-coordinated acetonitrile depends on the ion charge density. To study the ion transport dynamics, it is necessary to differentiate energy-transfer processes from structural interconversions in these electrolytes. Isotope labeling the solvent is a necessary prerequisite to separate these processes. We discuss the design principles and choice of the CD313CN label and characterize its vibrational spectroscopy in these electrolytes. The Fermi resonance between 13C≡N and C–D stretches complicates the spectral response but does not prevent its effective utilization. Time-resolved two-dimensional (2D) IR spectroscopy can be performed on a mixture of acetonitrile isotopologues and much can be learned about the structural dynamics of various species in these formulations.

Site-specific interactions enhanced dissolution of natural aragonite (110) surfaces in succinic acid (SUC) solutions: Implications for the oceanic aragonite dissolution fluxes

Aragonite, one of the most common biological calcium carbonate minerals, is widespread in marine plankton and neritic sediments (e.g., accounting for 89% of pelagic calcification of CaCO3 in the surface ocean). Its dissolution directly affects the export fluxes of CaCO3 in seawater. The aragonite dissolution in the ocean correlates with the increase of partial pressure of carbon dioxide and is pertinent to acidic biomolecules. However, aragonite dissolution in seawater with acidic biomolecules has been overlooked, and the interaction mechanism is unclear. In-situ atomic force microscopy (AFM) was employed to observe the dissolution features of aragonite (110) growth surfaces in succinic acid (SUC, HOOC-CH2-CH2-COOH) solutions. The results demonstrate that (1) both the morphologies and spreading rates of the etch pits formed on aragonite (110) surfaces are altered by the interactions between SUC molecules and the surfaces; (2) the [11‾1] and [1‾11] steps of the etch pits on aragonite (110) surfaces in SUC solutions are kinetically controlled; (3) dissolution rates of aragonite (110) surfaces are proportional to SUC concentrations, which is attributed to the strong complexation between SUC molecules and surface-bounded Ca atoms (≡Ca+); (4) etch pits morphologies of aragonite (110) and calcite (10.4) surfaces are different in SUC solutions, and the spreading rates of the etch pits of the former are one to two orders of magnitude lower than those of the latter. Furthermore, aragonite is found to be more sensitive to SUC molecules than calcite, suggesting that dissolving aragonitic materials could be more easily affected by circumambient biomolecules than dissolving calcitic materials. In seawater that contains organic molecules, the dissolution fluxes of aragonite could be much slower than those of calcite. These findings not only reveal the site-specific interactions between SUC molecules and the ≡Ca+ on aragonite (110) surfaces but also emphasize its implication for the oceanic aragonite dissolution fluxes.

Binding specificity of type three secretion system effector NleH2 to multi-cargo chaperone CesT and their phosphorylation.

Gram-negative pathogens like Enteropathogenic Escherichia coli (EPEC) utilize the type three secretion system (T3SS) to translocate various effector proteins that are needed to "hijack" the host system for pathogenic survival. Specialized T3SS chaperones inside bacterial cells stabilize these effector proteins and facilitate their translocation. CesT is a unique multi-cargo chaperone that interacts with and translocates ~10 different effector proteins. Here, we report the specific interaction between CesT and its key effector, NleH2, and explore the potential role of NleH2 as a kinase for CesT phosphorylation. First, we identified the chaperone-binding domain (CBD; 19-97aa) of NleH2, and mapped the specific interaction sites for both CesT and NleH2. The N- and C-terminal residues of the CBD interact with the dimeric interface of CesT. Further, we compared the CesT binding to NleH2, to that of another key effector Tir and with the global carbon regulator CsrA. Notably, the effectors have the binding regions at the β-sheet core and dimer interface of CesT, whereas the CsrA regulator interacts predominantly through the C-terminal region, which is found ~17 Å away from the effectors-binding sites. Next, we showed that NleH2 remains an active kinase even as a complex with CesT and is responsible for its autophosphorylation as well as phosphorylation of CesT at Tyr153. Collectively, our findings enhance the understanding of the role of multi-cargo chaperone CesT in orchestrating effector translocation through T3SS.

Mucoadhesion: mucin-polymer molecular interactions

Mucoadhesion, adhesion of a material to a mucous membrane or a mucus-covered surface, has been employed in drug delivery to prolong contact with adsorption sites and consequently a likely improvement of drug absorption. Mucoadhesion in the oral cavity also provides additional effects on tactile mouthfeel and extended flavor delivery, which impact consumer perception. The mechanisms behind mucoadhesion have not been well understood and there are contradictory literature results on the ranking of mucoadhesive properties of different polymers based on what in-vitro methods that are used. We herein examine the molecular interactions of different polymers with mucin from bovine submaxillary glands at pH 6.6 by using 1H NMR (Nuclear Magnetic Resonance) that provides atomically resolved information on conformational mobility of the mucin. Studying different types of polymers with different chemical structures and degrees of polymerization (DP), we can via the NMR linewidths and the signal intensities distinguish if the polymers interact with specific segments of the mucin or if they have a universal effect on the mobility of all the molecular segments of the mucin. The specific interaction sites on the mucin for positively charged polymer poly(ethyleneimine) are shown to be different from those for negatively and neutrally charged polymers. In addition, the interactions are also driven by the DP, the concentration of the polymers, and the dehydration. Deepened understanding of molecular effects of the different polymers on the mucin can therefore have strong impact on the development of mucoadhesive products in pharmaceutical and food applications. Finally, we raise awareness of the interpretation of rheological data in terms of mucoadhesion.

Site specific interactions of amino acids with (ZnO)12 cluster: Density functional approach

The Stability and electronic properties of bio-hybrid molecules are investigated in the framework of the first-principles density functional theory. The site-specific interactions between (ZnO)12 nano-cluster and arginine/aspartic acid are investigated. There are partially ionic and covalent bonds between the interacting atoms, higher binding energy 8.86 eV is observed at –COOH site of arginine, and 7.60 eV at –CN site of aspartic acid during the interaction with a nano-cluster. Higher HOMO-LUMO gap 4.3 eV is found in arginine, and smaller 2.6 eV in a cluster, it becomes zero with –COOH site of arginine, and 0.8 eV at –CN site of aspartic acid during the formation of bio-hybrids, i.e. highly stable amino acids arg/asp-nano-cluster (ZnO)12 bio-hybrids are formed with small forbidden energy-gap. This study will support in the formation of drugs which will improve the response in wound healing, immune functioning in burn injuries, and in the treatment of bone dysfunction. Highlights The binding energy is higher in a bio-hybrid at –COOH site of Arg, and –CN site of Asp. HOMO-LUMO gap is higher in a pristine Arg (4.3 eV), smaller in a cluster (2.6 eV), zero gap in a bio-hybrid with –COOH site of Arg, smaller 0.8 eV at –CN site of Asp. Higher binding energy is found with the small forbidden energy-gap of bio-hybrid molecules. This study will support in the formation of drugs which will improve the response in wound healing, immune functioning in burn injuries, and in the treatment of bone dysfunction. Communicated by Ramaswamy H. Sarma

Relative Affinities of Protein-Cholesterol Interactions from Equilibrium Molecular Dynamics Simulations.

Specific interactions of lipids with membrane proteins contribute to protein stability and function. Multiple lipid interactions surrounding a membrane protein are often identified in molecular dynamics (MD) simulations and are, increasingly, resolved in cryo-electron microscopy (cryo-EM) densities. Determining the relative importance of specific interaction sites is aided by determination of lipid binding affinities using experimental or simulation methods. Here, we develop a method for determining protein–lipid binding affinities from equilibrium coarse-grained MD simulations using binding saturation curves, designed to mimic experimental protocols. We apply this method to directly obtain affinities for cholesterol binding to multiple sites on a range of membrane proteins and compare our results with free energies obtained from density-based equilibrium methods and with potential of mean force calculations, getting good agreement with respect to the ranking of affinities for different sites. Thus, our binding saturation method provides a robust, high-throughput alternative for determining the relative consequence of individual sites seen in, e.g., cryo-EM derived membrane protein structures surrounded by an array of ancillary lipid densities.

Efficient Ion Sieving in Covalent Organic Framework Membranes with Sub-2-Nanometer Channels.

Membranes of sub-2-nanometer channels show high ion transport rates, but it remains a great challenge to design such membranes with desirable ion selectivities for ion separation applications. Here, covalent organic framework (COF) membranes with a channel size of ≈1.4nm and abundant hydrogen bonding sites, exhibiting efficient ion sieving properties are demonstrated. The COF membranes have high monovalent cation permeation rates of 0.1-0.2mol m-2 h-1 and extremely low multivalent cation permeabilities, leading to high monovalent over divalent ion selectivities for K+ /Mg2+ of ≈765, Na+ /Mg2+ of ≈680, and Li+ /Mg2+ of ≈217. Experimental measurements and theoretical simulations reveal that the hydrogen bonding interaction between hydrated cations and the COF channel wall governs the high selectivity, and divalent cations transport through the channel needs to overcome higher energy barriers than monovalent cations. These findings provide an effective strategy for developing sub-2-nanometer sized membranes with specific interaction sites for high-efficiency ionic separation.

High-throughput chromosome conformation capture-based analysis of higher-order chromatin structure in nasopharyngeal carcinoma.

BackgroundFirstly, we aimed to compare the differences of higher-order chromatin structure between nasopharyngeal carcinoma (NPC) and normal nasopharyngeal tissues. The second objective was to analyze the specific chromatin interaction site of NPC and the NPC-related genes regulated by this interaction site.MethodsWe included 6 NPC patients and 6 healthy controls to obtain the sequencing results of highest-throughput chromosome conformation capture (Hi-C) technique, followed by further analysis of the specific chromatin interaction sites in NPC.ResultsWe found an abnormal ultra-long distance interaction site on the chromosome 7p in the CNE210 sample, which was caused by a fusion gene SEPT7P2-PSPH. Additionally, a significant interaction site between chromosome 8q and 3p was revealed in the samples CNE25, CNE29, and CNE211, which was the interaction between 1.5 kb downstream of ASAP1 and 0.8 kb upstream of CTNNB1 gene. Further quantitative polymerase chain reaction (qPCR) revealed that ASAP1 and CTNNB1 genes were more highly expressed in CNE25, CNE29, and CNE211 than in the Np group, preliminarily indicating that this interaction site was likely related to the high expression of ASAP1 and CTNNB1 in NPC.ConclusionsThrough Hi-C analysis, we analyzed the specific chromatin interaction sites associated with NPC, and found the chromosomal translocation and chromatin interaction sites associated with NPC based on statistical analysis. This study has certain guiding significance for in-depth study of the mechanism of NPC occurrence and development.

Substituents effect on the methanol-assisted excited-state intermolecular proton transfer of 7-Aminoquinoline: A theoretical study

Studies have shown that changing the substituted groups applied to the amine can effectively affect the strength of the excited state hydrogen bond. However, it is not common to study the mechanism of how to effectively control the hydrogen bond strength of the excited state through the substituted group. Here, we have taken 7-Aminoquinoline and its various derivatives, the TDDFT method is used to study the influence of its R substitution on the hydrogen bond strength of the excited state and the mechanism of solvent-assisted excited-state multiple proton transfer (ESMPT) reaction. We have utilized bond length, IR vibrational spectra, atomic polar tensors (APT) charge analysis and potential energy curves to depict the relationship between hydrogen bond strength and substituted groups in excited state. We have modulated deliberately the number of methanol molecules involved in the ESMPT processes based on the site-specificity of hydrogen-bonding interactions, the potential energy curves indicate that the proton transfer process is more likely to happen in 7AQs·(MeOH)3 tetramer than in 7AQs·(MeOH)2 trimer, which is conflict with previous experimental conclusion. Meanwhile, the transition state structure during the ESMPT reaction indicates that the process is concerted. Our study demonstrates well the fluorescence behavior of 7AQs molecules regulated by different R substituents and extends the boundaries of site-specific hydrogen-bonding interactions research slightly.