Stability of Ligand-induced Protein Conformation Influences Affinity in Maltose-binding Protein

Maltodextrin transport in the extremely thermophilic, lignocellulose degrading bacterium Anaerocellum bescii (f. Caldicellulosiruptor bescii)

Sugar transport into microbial cells is a critical, yet understudied step in the conversion of lignocellulosic biomass to metabolic products. Anaerocellum bescii (formerly Caldicellulosiruptor bescii) is an extremely thermophilic, anaerobic bacterium that readily degrades the cellulose and hemicellulose components of lignocellulosic biomass into a diversity of oligosaccharide substrates. Despite significant understanding of how this microorganism degrades lignocellulose, the mechanisms underlying its highly efficient transport of the released oligosaccharides into the cell are comparatively underexplored. Here, we identify and characterize the ATP-binding cassette (ABC) transporters in A. bescii governing maltodextrin transport. Utilizing past transcriptomic studies on Anaerocellum and Caldicellulosiruptor species, we identify two maltodextrin transporters in A. bescii and express and purify their substrate-binding proteins (Athe_2310 and Athe_2574) for characterization. Using differential scanning calorimetry and isothermal titration calorimetry, we show that Athe_2310 strongly interacts with shorter maltodextrins, such as maltose and trehalose, with dissociation constants in the micromolar range, while Athe_2574 binds longer maltodextrins, with dissociation constants in the sub-micromolar range. Using a sequence-structure-function comparison approach combined with molecular modeling, we provide context for the specificity of each of these substrate-binding proteins. We propose that A. bescii utilizes orthogonal ABC transporters to uptake malto-oligosaccharides of different lengths to maximize transport efficiency.

IMPORTANCE

Here, we reveal the biophysical and structural basis for oligosaccharide transport by two maltodextrin ATP-binding cassette (ABC) transporters in Anaerocellum bescii. This is the first biophysical characterization of carbohydrate uptake in this organism and establishes a workflow for characterizing other oligosaccharide transporters in A. bescii and similar biomass-degrading thermophiles of interest for lignocellulosic bioprocessing. By deciphering the mechanisms underlying high-affinity sugar uptake in A. bescii, we shed light on an underexplored step between extracellular lignocellulose degradation and intracellular conversion of sugars to metabolic products. This understanding will expand opportunities for harnessing sugar transport in thermophiles to reshape lignocellulose bioprocessing as part of a renewable bioeconomy.

Single-molecule visualization of ATP-induced dynamics of the subunit composition of an ECF transporter complex under turnover conditions

Energy-Coupling Factor (ECF) transporters are ATP-binding cassette (ABC) transporters essential for uptake of vitamins and cofactors in prokaryotes. They have been linked to pathogen virulence and are potential targets for antimicrobials. ECF transporters have been proposed to use a unique transport mechanism where a substrate-translocating subunit (S-component) dynamically associates with and dissociates from an ATP-hydrolyzing motor (ECF module). This model is contentious, because it is based largely on experimental conditions without compartments or continuous bilayers. Here, we used single-molecule spectroscopy to investigate the conformational dynamics of the vitamin B12 transporter ECF-CbrT in membranes under vectorial transport conditions. We observed ATP hydrolysis-dependent dissociation of the S-component CbrT from, and re-association with the ECF module, in absence and presence of vitamin B12 consistent with futile ATP hydrolysis activity. The single-molecule spectroscopy experiments suggest that S-component expulsion from and re-association with the ECF module are an integral part of the translocation mechanism.

Site-Specific Immobilization Boosts the Performance of a Galectin-1 Biosensor

The analysis of protein-bound glycans has gained significant attention due to their pivotal roles in physiological and pathological processes like cell-cell recognition, immune response, and disease progression. Routine methods for glycan analysis are challenged by the very similar physicochemical properties of their carbohydrate components. As an alternative, lectins, which are proteins that specifically bind to glycans, have been integrated into biosensors for glycan detection. However, the effectiveness of protein-based biosensors depends heavily on the immobilization of proteins on the sensor surface. To enhance the sensitivity and/or selectivity of lectin biosensors, it is crucial to immobilize the lectin in an optimal orientation for ligand binding without compromising its function. Random immobilization methods often result in arbitrary orientation and reduced sensitivity. To address this, we explored a directed immobilization strategy relying on a reactive noncanonical amino acid (ncAA) and bioorthogonal chemistry. In this study, we site-specifically incorporated the reactive noncanonical lysine derivative, Nε-((2-azidoethoxy)carbonyl)-l-lysine, into a cysteine-less single-chain variant of human galectin-1 (scCSGal-1). The reactive bioorthogonal azide group allowed the directed immobilization of the lectin on a biosensor surface using strain-promoted azide-alkyne cycloaddition. Biolayer interferometry data demonstrated that the controlled, directed attachment of scCSGal-1 to the biosensor surface enhanced the binding sensitivity to glycosylated von Willebrand factor by about 12-fold compared to random immobilization. These findings emphasize the importance of controlled protein orientation in biosensor design. They also highlight the power of single site-specific genetic encoding of reactive ncAAs and bioorthogonal chemistry to improve the performance of lectin-based diagnostic tools.

Expression and immobilization of novel N-glycan-binding protein for highly efficient purification and enrichment of N-glycans, N-glycopeptides, and N-glycoproteins

Comprehensive and selective enrichment of N-glycans, N-glycopeptides, and N-glycoproteins prior to analysis is of great significance in N-glycomics research, reducing sample complexity, removing impurity interference, increasing sample abundance and enhancing signal intensity. However, only an Fbs1 (F-box protein that recognizes sugar chain 1) GYR variant (Fg) can enrich these N-glycomolecules solely due to its substantial binding affinity for the core pentasaccharide motif of N-glycans. Stationary phase separation is commonly used to enrich N-glycomolecules efficiently. Herein, DNA encoding the Fg was cloned into pGEX-4T-1, and the protein was expressed with a GST tag, which facilitates the convenient and efficient immobilization of recombinant GST-tagged Fg to GSH agarose resin. The yield of the GST-tagged Fg reached to 0.05 g/L after optimization of the induction condition, and the purified protein exhibited good identification ability and excellent stability for months. In particular, the immobilized GST-tagged Fg can enrich N-glycans released by PNGase F and capture derivatized N-glycans possessing an intact terminal N-acetyl glucosamine (GlcNAc). Validation of immobilized GST-tagged Fg with standard N-glycopeptides and N-glycoproteins revealed its high loading capacity, sensitivity, and selectivity. The novel immobilized GST-tagged Fg is a convenient and efficient enrichment material specific for N-glycans, N-glycopeptides, and N-glycoproteins, suggesting excellent performance and prospects for industrial application.

Effect of non-covalent interactions on the stability and structural properties of 2,4-dioxo-4-phenylbutanoic complex: a computational analysis

CONTEXT

The 2,4-dioxo-4-phenylbutanoic acid (DPBA) is a subject of interest in pharmaceutical research, particularly in developing new drugs targeting viral and bacterial infections. Complexation with metal ions can improve the stability and solubility of organic compounds. The present study uses quantum chemical calculations to explore the structural and electronic results arising from the interaction between the metal cation (Fe2+) and the π-system of DPBA in different solvents. For this purpose, the analyses of atoms in molecules (AIM) and natural bond orbital (NBO) are employed to comprehend the interaction features and the charge delocalization during the process of complexation. The results demonstrate that the strongest/weakest interactions are evident when the complex is situated in non-polar/polar solvents, respectively. In addition, the investigated complex exhibits two intramolecular hydrogen bonds (IMHBs) characterized by the O-H···O motif. The results indicate that the HBs present in the complex fall within the category of weak to medium HBs. Moreover, the O-H···O HBs are influenced by cation-π interactions, which can increase/decrease their strength in polar/non-polar solvents. To enhance understanding of the interactions above, an examination is conducted on various physical properties including the energy gap, electronic chemical potential, chemical hardness, softness, and electrophilicity power.

METHOD

All calculations are conducted within the density functional theory (DFT) using the ωB97XD functional and 6-311 +  + G(d,p) basis set. The computations are performed using the quantum chemistry package GAMESS, and the obtained results are visualized by employing the GaussView program.

A Review of Electromagnetic Fields in Cellular Interactions and Cacao Bean Fermentation

The influence of magnetic fields on biological systems, including fermentation processes and cocoa bean fermentation, is an area of study that is under development. Mechanisms, such as magnetosensitivity, protein conformational changes, changes to cellular biophysical properties, ROS production, regulation of gene expression, and epigenetic modifications, have been identified to explain how magnetic fields affect microorganisms and cellular processes. These mechanisms can alter enzyme activity, protein stability, cell signaling, intercellular communication, and oxidative stress. In cacao fermentation, electromagnetic fields offer a potential means to enhance the sensory attributes of chocolate by modulating microbial metabolism and optimizing flavor and aroma development. This area of study offers possibilities for innovation and the creation of premium food products. In this review, these aspects will be explored systematically and illustratively.

How arginine inhibits substrate-binding domain 2 elucidated using molecular dynamics simulations

The substrate-binding domain 2 (SBD2) is an important part of the bacterial glutamine (GLN) transporter and mediates binding and delivery of GLN to the transporter translocation subunit. The SBD2 consists of two domains, D1 and D2, that bind GLN in the space between domains in a closed structure. In the absence of ligand, the SBD2 adopts an open conformation with larger space between domains. The GLN binding and closing are essential for the subsequent transport into the cell. Arginine (ARG) can also bind to SBD2 but does not induce closing and inhibits GLN transport. We use atomistic molecular dynamics (MD) simulations in explicit solvent to study ARG binding in the presence of the open SBD2 structure and observed reversible binding to the native GLN binding site with similar contacts but no transition to a closed SBD2 state. Absolute binding free energy simulations predict a considerable binding affinity of ARG and GLN to the binding site on the D1 domain. Free energy simulations to induce subsequent closing revealed a strong free energy penalty in case of ARG binding in contrast to GLN binding that favors the closed SBD2 state but still retains a free energy barrier for closing. The simulations allowed the identification of the molecular origin of the closing penalty in case of bound ARG and suggested a mutation of lysine at position 373 to alanine that strongly reduced the penalty and allowed closing even in the presence of bound ARG. The study offers an explanation of the molecular mechanism of how ARG competitively inhibits GLN from binding to SBD2 and from triggering the transition to a closed conformation. The proposed Lys373Ala mutation shows promise as a potential tool to validate whether a conformational mismatch between open SBD2 and the translocator is responsible for preventing ARG uptake to the cell.

Inhibition of IL-17 signaling in macrophages underlies the anti-arthritic effects of halofuginone hydrobromide: Network pharmacology, molecular docking, and experimental validation

BACKGROUND

Rheumatoid arthritis (RA) is a prevalent autoimmune disease marked by chronic synovitis as well as cartilage and bone destruction. Halofuginone hydrobromide (HF), a bioactive compound derived from the Chinese herbal plant Dichroa febrifuga Lour., has demonstrated substantial anti-arthritic effects in RA. Nevertheless, the molecular mechanisms responsible for the anti-RA effects of HF remain unclear.

METHODS

This study employed a combination of network pharmacology, molecular docking, and experimental validation to investigate potential targets of HF in RA.

RESULTS

Network pharmacology analyses identified 109 differentially expressed genes (DEGs) resulting from HF treatment in RA. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses unveiled a robust association between these DEGs and the IL-17 signaling pathway. Subsequently, a protein-protein interaction (PPI) network analysis revealed 10 core DEGs, that is, EGFR, MMP9, TLR4, ESR1, MMP2, PPARG, MAPK1, JAK2, STAT1, and MAPK8. Among them, MMP9 displayed the greatest binding energy for HF. In an in vitro assay, HF significantly inhibited the activity of inflammatory macrophages, and regulated the IL-17 signaling pathway by decreasing the levels of IL-17 C, p-NF-κB, and MMP9.

CONCLUSION

In summary, these findings suggest that HF has the potential to inhibit the activation of inflammatory macrophages through its regulation of the IL-17 signaling pathway, underscoring its potential in the suppression of immune-mediated inflammation in RA.

The immunomodulatory activity of Orthosiphon aristatus against atopic dermatitis: Evidence-based on network pharmacology and molecular simulations

Objectives

To explore the potential activity of Orthosiphon aristatus (OA) against atopic dermatitis (AD).

Methods

Phytocompounds from OA were identified through chromatography analysis, then continued to target identification and functional annotation to explore the potential target of OA. Then, network pharmacology from annotated proteins determined protein targets for OA phytocompounds. Protein with highest rank according to the betweenness and closeness algorithm then continued to molecular docking and validated through molecular dynamics analysis.

Results

Chromatography data analysis revealed thirty-six compounds, predominantly classified as carboxylic acid, fatty acyls, and polyphenols. Upon identifying these compounds, network biology-based target identification revealed their potential bioactivity in modulating inflammation in AD. Tumour Necrosis Factor-alpha (TNF-α) and Prostaglandin G/H synthase 2 (PTGS2) emerged as the most probable targets based on hub centrality in the protein-protein interaction network. Later, molecular docking analyses highlighted sixteen compounds with good inhibitory activity against these two proteins. Notably, molecular dynamics simulation revealed that three compounds out of the previous sixteen potential compounds were more likely to act as the TNF-α and PTGS2 inhibitor as well as their native inhibitor. Those compounds are (1R,9R)-5-Cyclohexyl-11- (propylsulfonyl)-7,11- diazatricyclo[7.3.1.02,7]trideca- 2,4-dien-6-one, also known as ZINC8297940, as the best TNF-α inhibitor along with dl-Leucineamide and Benazol P as the potential inhibitor of PTGS2.

Conclusions

These findings suggest that OA may exert therapeutic effects against AD by controlling inflammation through TNF-α and PTGS2 signalling pathways.

Large-Scale Ligand Perturbations of the Protein Conformational Landscape Reveal State-Specific Interaction Hotspots

Protein flexibility is important for ligand binding but often ignored in drug design. Considering proteins as ensembles rather than static snapshots creates opportunities to target dynamic proteins that lack FDA-approved drugs, such as the human chaperone, heat shock protein 90 (Hsp90). Hsp90α accommodates ligands with a dynamic lid domain, yet no comprehensive analysis relating lid conformations to ligand properties is available. To date, ∼300 ligand-bound Hsp90α crystal structures are deposited in the Protein Data Bank, which enables us to consider ligand binding as a perturbation of the protein conformational landscape. By estimating binding site volumes, we classified structures into distinct major and minor lid conformations. Supported by retrospective docking, each conformation creates unique hotspots that bind chemically distinguishable ligands. Clustering revealed insightful exceptions and the impact of crystal packing. Overall, Hsp90α’s plasticity provides a cautionary tale of overinterpreting individual crystal structures and motivates an ensemble-based view of drug design.

Dual-Inhibition of Human N-Myristoyltransferase Subtypes Halts Common Cold Pathogenesis: Atomistic Perspectives from the Case of IMP-1088

The pharmacological inhibition of human N-myristoyltransferase (HsNMT) has emerged as an efficient strategy to completely prevent the replication process of rhinoviruses, a potential treatment for the common cold. This was corroborated by the recent discovery of compound IMP-1088, a novel inhibitor that demonstrated a dual-inhibitory activity against the two HsNMT subtypes 1 and 2 without inducing cytotoxicity. However, the molecular and structural basis for the dual-inhibitory potential of IMP-1088 has not been investigated. As such, we employ molecular modelling techniques to resolve the structural mechanisms that account for the dual-inhibitory prowess of IMP-1088. Sequence and nanosecond-based analyses identified Tyr296, Phe190, Tyr420, Leu453, Gln496, Val181, Leu474, Glu182, and Asn246 as residues common within the binding pockets of both HsNMT1 and HsNMT2 subtypes whose consistent interactions with IMP-1088 underpin the basis for its dual inhibitory potency. Nano-second-based assessment of interaction dynamics revealed that Tyr296 consistently elicited high-affinity π-π stacked interaction with IMP-1088, thus further highlighting its cruciality corroborating previous report. An exploration of resulting structural changes upon IMP-1088 binding further revealed a characteristic impeding of residue fluctuations, structural compactness, and a consequential burial of crucial hydrophobic residues, features required for HsNMT1/2 functionality. Findings present essential structural perspectives that augment previous experimental efforts and could also advance drug development for treating respiratory tract infections, especially those mediated by rhinoviruses.

An updated classification and mechanistic insights into ligand binding of the substrate-binding proteins

Substrate-binding proteins (SBPs) mediate ligand translocation and have been classified into seven clusters (A-G). Although the substrate specificities of these clusters are known to some extent, their ligand-binding mechanism(s) remain(s) incompletely understood. In this study, the list of SBPs belonging to different clusters was updated (764 SBPs) compared to the previously reported study (504 SBPs). Furthermore, a new cluster referred to as cluster H was identified. Results reveal that SBPs follow different ligand-binding mechanisms. Intriguingly, the majority of the SBPs follow the "one domain movement" rather than the well-known "Venus Fly-trap" mechanism. Moreover, SBPs of a few clusters display subdomain conformational movement rather than the complete movement of the N- and C-terminal domains.