Acid Interactions Research Articles

NesT-NABind: a Nested Transformer for Nucleic Acid-Binding Site Prediction on Protein Surface.

Protein-nucleic acid interactions play a crucial role in many physiological processes. Identifying the binding sites of nucleotides on the protein surface is the prerequisite for understanding the molecular recognition mechanisms between the two types of macromolecules and also provides the information to design or generate molecule modulators against these sites to manipulate biological function according to specific requirements. Existing studies mainly focus on characterizing local surfaces around sites, often neglecting the interrelationships among these sites and the global protein information. To address this gap, we propose NesT-NABind, a Nested Transformer for Nucleic Acid-Binding site prediction. This model leverages the Transformer's advanced capabilities in contextual understanding and long-range dependency capturing. Specifically, we introduce a local patch-scale Transformer to process surface information around each site and a global protein-scale transformer to integrate surface and sequence information on the entire protein. These two Transformers operate at different scales of protein, hence the term "nested". Experiments demonstrate that NesT-NABind achieves a 5.57% improvement in the F1 score and a 3.64% improvement in AUPRC compared to state-of-the-art methods. With the incorporation of global features, NesT-NABind shows an enhanced predictive capability for the challenging large proteins and therefore can be used in a much wider range of applications.

Chemical Composition, Antimicrobial, and Enzyme Inhibitory Properties of Elaeagnus angustifolia L.

Research on natural antioxidants derived from plants has surged due to their potential health benefits. In the current study, the chemical composition, enzyme inhibitory activity, and antimicrobial effects of the Elaeagnus angustifolia L. plant, including leaves, flowers, and flower stalk (FS) extracts, were analyzed. A total of 28 compounds were identified across the different plant parts, with 24 in flowers (F), 9 in FSs, and 14 in leaves (L). The antimicrobial activity of the extracts was evaluated using the disk diffusion method against two Gram-positive (Staphylococcus aureus and Bacillus cereus) and two Gram-negative bacteria (Escherichia coli and Klebsiella pneumoniae). The minimum inhibitory concentration (MIC) was determined as 3.13-12.50mg/mL. The measured zone diameters were also in the range of 5-8mm. The results indicated that the methanol extracts exhibited significant antimicrobial properties. Additionally, the extracts demonstrated strong inhibition of cholinesterases (acetylcholinesterase [AChE]: 11.14±0.11-18.11±0.12µg/mL; butyrylcholinesterase [BChE]: 32.54±0.55-44.61±0.17µg/mL) and moderate inhibition against α-glycosidase and tyrosinase enzymes. Moreover, the molecular docking interaction of trans-ferulic, shikimic, and vanillic acids, the most abundant phenolic compounds in the extracts, with AChE, BChE, α-glycosidase, and tyrosinase, was assessed using AutoDock Vina software. E. angustifolia L. possesses a high phenolic content and exhibits significant antioxidant and enzyme inhibitory capabilities, which may contribute to its extensive utilization in food and traditional medicine.

Structure-Based Discovery of MolPort-137: A Novel Autotaxin Inhibitor That Improves Paclitaxel Efficacy

The autotaxin–lysophosphatidic acid receptor (ATX-LPAR) signaling axis is pivotal in various clinical conditions, including cancer and autoimmune disorders. This axis promotes tumorigenicity by interacting with the tumor microenvironment, facilitating metastasis, and conceding antitumor immunity, thereby fostering resistance to conventional cancer therapies. Recent studies highlight the promise of ATX/LPAR inhibitors in combination with conventional chemotherapeutic drugs to overcome some forms of this resistance, representing a novel therapeutic strategy. In the current study, we employed structure-based virtual screening, integrating pharmacophore modeling and molecular docking, to identify MolPort-137 as a novel ATX inhibitor with an IC50 value of 1.6 ± 0.2 μM in an autotaxin enzyme inhibition assay. Molecular dynamics simulations and binding free energy calculations elucidated the binding mode of MolPort-137 and its critical amino acid interactions. Remarkably, MolPort-137 exhibited no cytotoxicity as a single agent but enhanced the effectiveness of paclitaxel in 4T1 murine breast carcinoma cells and resensitized taxol-resistant cells to paclitaxel treatment, which highlights its potential in combination therapy.

Unveiling lotus root processing under vacuum microwave: starch-malic acid interactions based on moisture, structure, and in vitro digestibility.

This study evaluated the effects of malic acid vacuum microwave preconditioning (MVMP) on lotus root (LR) by examining its moisture content, dielectric properties, microstructure, and starch characteristics, including modifications in starch structure and composition. Dielectric properties and LF-NMR indicated that the dielectric constant (ε') was closely associated to moisture content and state, while changes in water migration depended on microwave power and the dielectric loss factor (ε″). Increased microwave power and malic acid concentration resulted in microstructural damage (indentation and breakage of starch granules) and starch hydrolysis into smaller particles. MVMP preserved higher levels of phenolic and flavonoid compounds. FT-IR analysis revealed an additional absorption peak at 1740cm-1. The maximum degree of substitution was 0.131. Starch from MVMP-treated LR exhibited higher crystallinity, with a maximum resistant starch (RS) content of 68.3%. In addition, microwave power considerably influenced amylose content, solubility, swelling power, and thermal enthalpy.

Amino Acids Frequency and Interaction Trends: Comprehensive Analysis of Experimentally Validated Viral Antigen-Antibody Complexes.

Antibodies have specific binding capabilities and therapeutic potential for treating various diseases, including viral infections. The amino acid composition of the hypervariable complementarity determining regions (CDR) loops and the framework regions (FR) are the determining factors for the affinity and therapeutic efficacy of the antibodies. In this study selected and curated, 77 viral antigen-human antibody complexes from Protein data bank from the Thera-SAbdab database were analyzed. The results revealed diversity indices within specific CDR regions, amino acid frequencies, paratope-epitope interactions, bond formations, and bond types among the analyzed viral Ag-Ab complexes. The finding revealed that Ser, Gly, Tyr, Thr, and Phe are prominently present in the antibody CDRs. Analysis of CDR profiles indicated an average amino acid diversity of 60-80% in heavy chain CDRs and 45-60% in light chain CDRs. Aromatic residues, particularly Tyr, Phe, and Trp showed significant involvement in the paratope-epitope interactions in the heavy chain, while Tyr, Ser, and Thr were key contributors in the light chain. Furthermore, the study examined the occurrence of amino acids in both light and heavy chains of viral Ag- human Ab complexes, analyzing the presence of amino acids as single residues, dipeptides and tripeptides. The analysis is crucial for enhancing the antibody engineering processes including, design, optimization, affinity enhancement, and overall antibody development.

Enhanced Sampling Simulations of RNA-Peptide Binding Using Deep Learning Collective Variables.

Enhanced sampling (ES) simulations of biomolecular recognition, such as binding small molecules to proteins and nucleic acid targets, protein-protein association, and protein-nucleic acid interactions, have gained significant attention in the simulation community because of their ability to sample long-time scale processes. However, a key challenge in implementing collective variable (CV)-based enhanced sampling methods is the selection of appropriate CVs that can distinguish the system's metastable states and, when biased, can effectively sample these states. This challenge is particularly acute when the binding of a flexible molecule to a conformationally rich host molecule is simulated, such as the binding of a peptide to an RNA. In such cases, a large number of CVs are required to capture the conformations of both the host and the guest as well as the binding process. Using such a large number of descriptors is impractical in any enhanced sampling simulation method. In our work, we used the recently developed deep targeted discriminant analysis (Deep-TDA) method to design CVs to study the binding of a cyclic peptide, L22, to a TAR RNA of HIV, which is a prototypical system. The Deep-TDA CV, obtained from a nonlinear combination of important contact pairs between the L22 peptide and the host RNA backbone atoms, along with the RNA apical loop RMSD as the second CV were used in the on-the-fly probability-based enhanced sampling (OPES) simulation to sample the reversible binding and unbinding of the L22 peptide to the TAR RNA target. The OPES simulation delineated the mechanism of peptide binding and unbinding to and from the RNA and enabled the calculation of the underlying free energy landscape. Our results demonstrate the potential of the Deep-TDA method for designing CVs to study complex biomolecular recognition processes.

Exploring the structure and nucleic acid interactions of the Leishmania sp. telomerase reverse transcriptase N-terminal region.

Leishmaniasis is a neglected tropical disease caused by protozoans of the Leishmania genus, against which no effective treatment or control is available. Like other eukaryotes, parasite telomeres are maintained by telomerase, a ribonucleoprotein complex vital for genome stability. Its protein component, TERT (telomerase reverse transcriptase), presents four structural and functional domains, with the TEN (Telomerase N-terminal) and TRBD (Telomerase RNA-binding) located at its N-terminal. The enzyme also contains an RNA component that carries the template copied by the TERT during telomere elongation. Here, we show that the tertiary structure of Leishmania major TERT (LmTERT) is conserved compared to other eukaryotes. However, the LmTERT N-terminal (LmTERT-NT) portion shows structural changes not detected in the entire protein, mainly in the TEN domain. Besides the disordered elements, the TEN gains two long β-sheets but preserves the GQ motif and the residues in β-sheet 5 that interact with the TRAP motif. In both structures, a linker flanks the TEN and TRBD. The TRBD is partially conserved in both structures and contains the canonical QFP and T motifs, invariant residues, and the putative CP and two trypanosomatid-specific motifs (TSM) besides genus-specific amino acid substitutions. Despite the structural changes, the recombinant LmTERT-NT preserves a hydrophobic cavity that binds specifically and in the picomolar range to the telomeric G-rich DNA and the TER 5' end region. Thus, LmTERT-NT shares the canonical structural domains and motifs and is biochemically active. We discuss the importance of the TERT N-terminal region in the parasite's telomerase catalysis.

Analysis of interactions between amino acids and monolayers of charged side chains

The report on an analytical platform for amino acid–amino acid interactions between charged amino acids and accumulated side chains on self-assembled monolayers combined with field-effect transistors.

Single-Molecule Visualization of BLM-DNA2-Mediated DNA End Resection Using DNA Curtains.

Homologous recombination (HR) is the principal pathway undertaken by a cell for the error-free repair of DNA double-strand breaks that are frequently encountered by the cell. HR can be initiated at the sites of DNA double-strand breaks by generating long stretches of single-stranded 3' DNA overhang through a process called DNA end resection. In one DNA end resection pathway, this is achieved via the concerted effort of specialized machinery involving the RecQ family helicase BLM, the helicase/endonuclease DNA2, and a single-strand DNA binding protein complex RPA. BLM unwinds the DNA at the sites of DNA damage. The DNA unwound by BLM is cleaved in a 5' to 3' direction by DNA2 leaving behind a long single-stranded 3' DNA tail which is rapidly coated with RPA. This long single-stranded DNA provides the loading platform for recombinase proteins to form nucleoprotein filaments which initiate the homology search to undergo HR-based repair. Most of the insights into these processes have been gained using ensemble biochemical methods. However, these approaches have proven to be challenging for dissecting complex molecular mechanisms, especially because of the dynamic nature of these processes. Experiments involving single-molecule techniques have enabled us to counter these issues by allowing us to gather information on intermediates that are heterogeneous and transient in nature. We have developed a single-molecule technique called DNA curtains where we can study hundreds of protein-nucleic acid interaction events in real time. Here, we describe a method to prepare a single-tethered double-stranded DNA curtain to visualize, in combination with total internal reflection microscopy (TIRFM), the BLM- and DNA2-mediated DNA end resection in real time.

Callistemon viminalis (Sol. ex Gaertn.) exhibiting anti-neuroblastoma activity via molecular interaction of ascorbic acid and 5-lipoxygenase: An in vitro and in silico study

Callistemon viminalis (Sol. ex Gaertn.) exhibiting anti-neuroblastoma activity via molecular interaction of ascorbic acid and 5-lipoxygenase: An in vitro and in silico study

Green synthesis of γ-Fe2O3@SiO2 magnetic nanoparticles functionalized with penciclovir drug: antiproliferative effect, and nucleic acids (DNA and RNA) interaction

This study focuses on generating single-phase maghemite (γ-Fe2O3) using Echinophora platyloba DC. (E. platyloba) extract, followed by a silica coating. Subsequently, the γ-Fe2O3@SiO2 magnetic nanoparticles (γ-Fe2O3@SiO2 MNPs) are functionalized with the antiviral drug penciclovir (PNV). The objective of this research is to produce a dual-function therapeutic agent that exhibits both antiviral and anticancer properties. Nanoparticles were characterized using FT-IR, VSM, XRD, TEM, SEM-EDX, DLS, zeta potential measurements, and ultraviolet–visible analysis. The γ-Fe2O3@SiO2-PNV MNPs exhibited lower toxicity towards normal fibroblast cells compared to cancerous MCF-7 cells. Furthermore, loading PNV onto γ-Fe2O3@SiO2 MNPs resulted in a significant increase in the anticancer and biological effects of PNV. To assess the therapeutic potential of γ-Fe2O3@SiO2-PNV MNPs, their interactions with nucleic acids (DNA and RNA) were investigated through absorption and fluorescence studies. The experimental findings showed that γ-Fe2O3@SiO2-PNV MNPs had a strong propensity for binding to nucleic acids both through the groove and intercalate (partial intercalation), indicating their promising candidacy as a targeted and specific chemotherapeutic agent.

Nanoconfined Chlorine-Substituted Monomethine Cyanine Dye with a Propionamide Function Based on the Thiazole Orange Scaffold-Use of a Fluorogenic Probe for Cell Staining and Nucleic Acid Visualization.

The development of fluorescence-based methods for bioassays and medical diagnostics requires the design and synthesis of specific markers to target biological microobjects. However, biomolecular recognition in real cellular systems is not always as selective as desired. A new concept for creating fluorescent biomolecular probes, utilizing a fluorogenic dye and biodegradable, biocompatible nanomaterials, is demonstrated. The synthesis of a new dicationic asymmetric monomethine cyanine dye with benzo[d]thiazolium-N-propionamide and chloroquinoline end groups is presented. The photophysical properties of the newly synthesized dye were examined through the combined application of spectroscopic and theoretical methods. The applicability of the dye as a fluorogenic nucleic acid probe was proven by UV-VIS spectroscopy and fluorescence titration. The dye-nucleic acid interaction mode was investigated by UV-Vis and CD spectroscopy. The newly synthesized dicationic dye, like other similar fluorogenic structures, limited permeability, which restricts its use as a probe for RNA and DNA. To enhance cellular delivery, we utilized a patented technology that employs solid, insoluble lipid nanoparticles. This method ensures the complete introduction of the dye into cells while minimizing activity outside the cells. In our study involving two human cell lines, we observed improved penetration through the cell membrane and distinctive selectivity in visualizing nucleic acids within the cytoplasm and nucleus.

Gut Microbiome and Bile Acid Interactions: Mechanistic Implications for Cholangiocarcinoma Development, Immune Resistance, and Therapy.

Cholangiocarcinoma (CCA) is a rare but highly malignant carcinoma of bile duct epithelial cells with a poor prognosis. The major risk factors of CCA carcinogenesis and progression are cholestatic liver diseases. The key feature of primary sclerosing cholangitis and primary biliary cholangitis is chronic cholestasis, which means a slowdown of hepatocyte secretion of biliary lipids and metabolites into bile as well as a slowdown of enterohepatic circulation (bile acid recirculation) of bile acids with dysbiosis of the gut microbiome, which was shown to lead to enterohepatic recirculation and an increase of toxic secondary bile acids. Alterations of serum and liver bile acid compositions via the disturbed enterohepatic circulation of bile acids and the disturbance of the gut microbiome then activate a series of hepatic and cancer cell signaling pathways that promote CCA carcinogenesis and progression. This review will focus on the mechanistic roles of bile acids and the gut microbiome in the pathogenesis and progression of CCA. We will also evaluate the therapeutic potential of targeting the gut microbiome and bile acid-mediated signaling pathways for the therapy and prophylaxis of CCA.

Role of Hydration and Amino Acid Interactions on the Ion Permeation Mechanism in the hNaV1.5 Channel.

This study explores the ion selectivity and conduction mechanisms of the hNaV1.5 sodium channel using classical molecular dynamics simulations under an externally applied electric field. Our findings reveal distinct conduction mechanisms for Na+ and K+, primarily driven by differences in their hydration states when they diffuse close to the channel's selective filter (DEKA) and extracellular ring (EEDD). The Na+ ions undergo partial dehydration in the EEDD region, followed by a rehydration step in the DEKA ring, resulting in longer retention times and a deeper free energy minimum compared to K+. Conversely, the K+ ions exhibit a continuous dehydration process, facilitating a smoother passage through these key regions. These results indicate that ion selectivity and conductance are primarily governed by solvation dynamics, which, in turn, depend on the interactions with key charged residues within the channel. Additionally, we show that the delicate energetic balance between the interactions of the ions with the protein residues and with their solvation shells during the dehydration and rehydration processes is not properly captured by the force field. As a consequence, the selectivity of the channel is not well described, indicating that more accurate computational models must be applied to simulate ion conduction through eukaryotic NaV channels.

Position-Regulated Electrostatic Interactions for Single Amino Acid Revealed by Aspartic Acid-Scanning Mutagenesis.

We have examined in this contribution the electrostatic interactions between single arginine and aspartic acid by analyzing the peptide-peptide binding characteristics involving arginine-aspartic acid, arginine-glycine, arginine-tryptophan and tryptophan-glycine interactions. The results of aspartic acid mutagenesis revealed that the interactions between arginine and aspartic acid have significant dependence on the position and composition of amino acids. While the primary interaction can be attributed to arginine-tryptophan contacts originated from the indole moieties with the main chains of 14-mers containing N-H and C=O moieties, pronounced enhancement could be identified in association with the electrostatic side-chain-side-chain interactions between arginine and aspartic acid. An optimal separation of 2~4 amino acids between two adjacent aspartic acid and tryptophan binding sites can be identified to achieve maximal enhancement of binding interactions. Such observed separation dependence may be utilized to unravel cooperative effects in heterogeneous interactions between single pair of amino acids.

An amino acid-resolution interactome for motile cilia identifies the structure and function of ciliopathy protein complexes.

Motile cilia are ancient, evolutionarily conserved organelles whose dysfunction underlies motile ciliopathies, a broad class of human diseases. Motile cilia contain a myriad of different proteins that assemble into an array of distinct machines, and understanding the interactions and functional hierarchies among them presents an important challenge. Here, we defined the protein interactome of motile axonemes using cross-linking mass spectrometry in Tetrahymena thermophila. From over 19,000 cross-links, we identified over 4,700 unique amino acid interactions among over 1,100 distinct proteins, providing both macromolecular and atomic-scale insights into diverse ciliary machines, including the intraflagellar transport system, axonemal dynein arms, radial spokes, the 96-nm ruler, and microtubule inner proteins. Guided by this dataset, we used vertebrate multiciliated cells to reveal functional interactions among several poorly defined human ciliopathy proteins. This dataset provides a resource for studying the biology of an ancient organelle and the molecular etiology of human genetic disease.

Unveiling the anticancer potential of the ethanolic extract from Pometia pinnata: Molecular dynamics targeting CHK1 and cytotoxicity study on MCF-7 cells

Cancer remains one of the most lethal diseases globally, with CHK1 being a critical pathway frequently altered in cancer progression. This study evaluated the anticancer and cytotoxic properties of the ethanol extract of Matoa (Pometia pinnata) leaves in silico and in vitro. Maceration was conducted to obtain the ethanol extract with physicochemical, pharmacokinetic, and toxicity predictions conducted using Lipinski’s Rule of Five, pkCSM, and Pro-Tox II. Molecular docking was performed using Autodock Vina and DOCK6.2, followed by molecular dynamic simulations using GROMACS. Cytotoxicity assays on MCF-7 cells were carried out using the MTT methods. The results demonstrated that the extract tested positive for flavonoids, alkaloids, tannins, saponins, glycosides, and steroids. The extract also shows potential inhibitory activity against CHK1, supported by favorable binding affinities and critical amino acid interactions. Additionally, the extract exhibited a moderate cytotoxic effect on cell MCF-7 with an IC50 of 139 µg/mL.

Improving α-amylase inhibitory activity of simulated gastrointestinal digested pea protein by pH shifting assisted proteolysis

To mitigate postprandial hyperglycemia, α-amylase inhibitory peptides have been casually prepared by various pretreatments and proteolysis without exploring their impacting mechanisms and digestive stabilities. In this study, pea protein treated by pH 2 shifting followed by flavourzyme hydrolysis (PS2-PF) expressed excellent protein recovery rate (40.06 %) and α-amylase inhibitory activity (IC50 of 6.75 mg/mL) after simulated gastrointestinal digestion. A moderate decrease of α-helix structure (by 10.80 %) but increases of β conformations (by ~17.75 %) and small molecules (< 5 kDa, 94.73 %) on the pea protein were beneficial to enhance α-amylase inhibition of the digested PS2-PF. 13 of potential α-amylase inhibitory peptides were identified from the digested PS2-PF to inactivate α-amylase via hydrogen bonding, Pi-Alkyl, Pi-Pi and attractive interactions of phenylalanine, proline, leucine, arginine, glutamic acid and lysine. Overall, pH 2 shifting assisted flavourzyme hydrolysis could be a valuable strategy to enhance α-amylase inhibition of in vitro digested pea protein for diabetes mellitus.

The stability of PCV2 virus-like particles from mammalian cells and challenges for biotechnological applications

Porcine circovirus type 2 (PCV2) is a highly damaging pathogen for pig farming, causing significant economic losses. Despite the availability of vaccines based on different technologies, the virus steadily infects the world's pig population. In this context, virus-like particles (VLPs) constitute appealing alternatives for vaccine development as they lack the viral genome but present intact external surfaces.Using PCV2 VLPs expressed and purified from Expi293F cells, we demonstrate the potential to generate high-purity VLPs with excellent antigenic properties through biochemical, biophysical, and immunological characterization. Using different techniques, we also determined the melting temperature of these VLPs at nearly 55 °C.Furthermore, we conducted multiscale simulations of whole VLPs combined with multiple sequence analyses to provide a new perspective into the stability determinants. Computational results support our findings and underscore the importance of protein-nucleic acid interactions in stabilizing the VLP structure. Moreover, we spotted an unforeseen correlation between amino acid conservation, solvent exposure, and flexibility, revealing a link to viral assembly and immune evasion. These novel insights are crucial to guide the development of stabilized VLP for new vaccine prototypes to respond to the emergence of new PCV2 genotypes.

Unraveling boric acid interactions with macrocyclic hosts: DFT insights into the key role of hydrogen bonding in complex stabilization

Unraveling boric acid interactions with macrocyclic hosts: DFT insights into the key role of hydrogen bonding in complex stabilization