The effect of the allosteric regulation on the catalytic activity of fructosyltransferase studied molecular dynamics simulations.

Fructosyltransferase (FTase) is a key glycosidase with hydrolytic and transglycosylation functions that can utilize sucrose to generate oligofructose (FOS), which is extremely important in the food industry as well as in plants and microorganisms. However, there remain significant gaps in our understanding of the catalytic mechanism of FTase, particularly regarding the effect of regulatory mechanisms of residues on enzyme catalytic activity. In this study, molecular dynamics simulations and immobilized enzyme catalysis experiments were employed to investigate the structural dynamics and catalytic activity of QU10-FTase.

Fluorination of Aza-BODIPY for Cancer Cell Plasma Membrane-Targeted Imaging and Therapy.

Photodynamic therapy (PDT) holds great potential in cancer treatment, leveraging photosensitizers (PSs) to deliver targeted therapy. Fluorination can optimize the physicochemical and biological properties of PSs for better PDT performance. Here, we report some high-performance multifunctional PSs specifically designed for cancer PDT by fluorinating aza-BODIPY with perfluoro--butoxymethyl (PFBM) groups.

Aromatic-aromatic interactions drive fold switch of GA95 and GB95 with three residue difference.

Proteins typically adopt a single fold to carry out their function, but metamorphic proteins, with multiple folding states, defy this norm. Deciphering the mechanism of conformational interconversion of metamorphic proteins is challenging. Herein, we employed nuclear magnetic resonance (NMR), circular dichroism (CD), and all-atom molecular dynamics (MD) simulations to elucidate the mechanism of fold switching in proteins GA95 and GB95, which share 95% sequence homology.

The Molecular Mechanism of Fluorescence Lifetime of Fluorescent Probes in Cell Membranes.

Fluorescence probes play crucial roles in unraveling the structure and dynamics of cell membranes including membrane fluidity, polarity, and lipid molecule ordering. The fluorescence lifetime of probes describes the average duration of time that a fluorescent molecule remains in an excited state before returning to the ground state, which is sensitive to environmental changes. However, the molecular mechanism and inherent properties to determine the fluorescence lifetimes remain unexplored and inadequately studied.

Native Cellular Membranes Facilitate Channel Activity of MscL by Enhancing Slow Collective Motions of Its Transmembrane Helices.

Mechanosensitive channels of large conductance (MscL) serve as a mechanoelectrical valve of cells in response to the membrane tension. The influence of membrane environments on the MscL channel activity and the underlying mechanism remains unclear. Herein, we developed a new sample preparation protocol that allows for the detection of high-quality H-detected solid-state NMR spectra of MscL in cellular membranes, enabling site-specific analysis of its dynamics.

Residual Membrane Fluidity in Mycobacterial Cell Envelope Layers under Extreme Conditions Underlines Membrane-Centric Adaptation.

One of the routes for adaptation to extreme environments is via remodeling of cell membrane structure, composition, and biophysical properties rendering a functional membrane. Collective studies suggest some form of membrane feedback in mycobacterial species that harbor complex lipids within the outer and inner cell wall layers. Here, we study the homeostatic membrane landscape of mycobacteria in response to high hydrostatic pressure and temperature triggers using high pressure fluorescence, mass and infrared spectroscopies, NMR, SAXS, and molecular dynamics simulations.

Fast collective motions of backbone in transmembrane α helices are critical to water transfer of aquaporin.

Fast collective motions are widely present in biomolecules, but their functional relevance remains unclear. Herein, we reveal that fast collective motions of backbone are critical to the water transfer of aquaporin Z (AqpZ) by using solid-state nuclear magnetic resonance (ssNMR) spectroscopy and molecular dynamics (MD) simulations. A total of 212 residue site-specific dipolar order parameters and 158 N spin relaxation rates of the backbone are measured by combining the C- and H-detected multidimensional ssNMR spectra.

Mechanistic Insight into the Mechanical Unfolding of the Integral Membrane Diacylglycerol Kinase.

The essential forces stabilizing membrane proteins and governing their folding and unfolding are difficult to decipher. Single-molecule atomic force spectroscopy mechanically unfolds individual membrane proteins and quantifies their dynamics and energetics. However, it remains challenging to structurally assign unfolding intermediates precisely and to deduce dominant interactions between specific residues that facilitate either the localized stabilization of these intermediates or the global assembly of membrane proteins.

Discovery of Novel Anti-Resistance AR Antagonists Guided by Funnel Metadynamics Simulation.

Androgen receptor (AR) antagonists are widely used for the treatment of prostate cancer (PCa), but their therapeutic efficacy is usually compromised by the rapid emergence of drug resistance. However, the lack of the detailed interaction between AR and its antagonists poses a major obstacle to the design of novel AR antagonists. Here, funnel metadynamics is employed to elucidate the inherent regulation mechanisms of three AR antagonists (hydroxyflutamide, enzalutamide, and darolutamide) on AR.

Jellyfish-inspired smart tetraphenylethene lipids with unique AIE fluorescence, thermal response, and cell membrane interaction.

Smart lipids with fluorescence emission, thermal response, and polyethylene glycolation (PEGylation) functions can be highly valuable for formulation, image-traceable delivery, and targeted release of payloads. Herein, a series of jellyfish-shaped amphiphiles with a tetraphenylethene (TPE) core and four symmetrical amphiphilic side chains were conveniently synthesized and systematically investigated as smart lipids. Compared with regular amphiphilic TPE lipids and phospholipids, the unprecedented jellyfish-shaped molecular geometry was found to enable a series of valuable capabilities, including sensitive and responsive aggregation-induced emission of fluorescence (AIE FL) and real-time FL monitoring of drug uptake.

Effect of Host Cholesterol on the Membrane Dynamics of Outer Membrane Lipids of Mycobacteria.

The ability of Mycobacterium tuberculosis to remain dormant after primary infection represents the prime cause of new TB cases throughout the world. Hence, diagnosis and treatment of individuals hosting dormant mycobacterium is one of the crucial strategies to be adopted for the prevention of Tuberculosis. Among many strategies unleashed by the latent bacterium, one of them is scavenging host cholesterol for carbon source.

On the Dynamic Mechanism of Long-Flexible Fatty Acid Binding to Fatty Acid Binding Protein: Resolving the Long-Standing Debate.

Fatty acids (FAs) are one of the essential energy sources for physiological processes, and they play a vital role in regulating immune and inflammatory responses, promoting cell differentiation and apoptosis, and inhibiting tumor growth. These functions are carried out by FA binding proteins (FABPs) that recognize and transport FAs. Although the crystal structure of the FA-FABPs complex has long been characterized, the mechanism behind FA binding and dissociation from FABP remains unclear.

Fusion Landscape of Mycobacterial Envelope-Derived Lipid Vesicles with Intact Bacteria Dictates High Intracellular Drug Retention.

Membrane vesicles are critical regulators of pathogenic diseases. In tubercular infections, the use of mycobacteria derived vesicles as delivery vehicles to overcome drug resistance and complex treatment regimens has never been attempted. Here, we first address how these vesicles interact with their target cells, especially via membrane fusion.

Molecular Insights on the Conformational Transitions and Activity Regulation of the c-Met Kinase Induced by Ligand Binding.

The tyrosine-protein kinase Met (c-Met) is an important signaling molecule involved in cellular growth and division. The dysregulation of c-Met may induce many fatal diseases, including non-small cell lung cancer, gastrointestinal cancers, hepatocellular carcinoma, . The activation of the c-Met kinase is dominant by the structure and dynamics of many important functional motifs, which are regulated by adenosine triphosphate (ATP) binding.

The Conformational Transitions and Dynamics of Lipase Regulated by Water-Oil Interfaces.

Structural dynamics and conformational transitions are crucial for the activities of enzymes. As one of the most widely used industrial biocatalysts, lipase could be activated by the water-oil interfaces. The interface activations were believed to be dominated by the close-to-open transitions of the lid subdomains.

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 Conformational Transition Pathways and Hidden Intermediates in DFG-Flip Process of c-Met Kinase Revealed by Metadynamics Simulations.

Protein kinases intrinsically translate their conformations between active and inactive states, which is key to their enzymatic activities. The conformational flipping of the three-residue conservative motif, Asp-Phe-Gly (DFG), is crucial for many kinases' biological functions. Obtaining a detailed demonstration of the DFG flipping process and its corresponding dynamical and thermodynamical features could broaden our understanding of kinases' conformation-activity relationship.

Self-Assembled Oligopeptide (FK) as a Chiral Alignment Medium for the Anisotropic NMR Analysis of Organic Compounds.

Anisotropic NMR parameters have been proven to be powerful for the structural elucidation of organic molecules. Herein, we present an alignment medium based on the self-assembled (FK) oligopeptide, showing excellent properties in measurements of anisotropic NMR parameters in both DO and CDOD. The preparation of the (FK)-based alignment medium is simple and rapid.

Lipid Clustering in Mycobacterial Cell Envelope Layers Governs Spatially Resolved Solvation Dynamics.

The mycobacterial cell envelope acts as a multilayered barrier to drugs. However, the role of lipid composition in the properties of different mycobacterial membranes, otherwise dictating their interactions with drugs, is poorly understood. In this study, we found that hydration states, solvation relaxation kinetics, rotational lipid mobility, and lateral lipid diffusion differed between inner and outer mycobacterial membranes.

The auto-inhibition mechanism of transcription factor Ets-1 induced by phosphorylation on the intrinsically disordered region.

As the most abundant post-translation modifications (PTMs), the phosphorylation usually occurred on the intrinsically disordered regions (IDRs). The regulation on the structures and interactions of IDRs induced by phosphorylation is critical to the function performing. The eukaryotic transcription factor 1 (Ets-1) is a member of transcription factor family, which participates in many important biological processes.

Metadynamics Simulations to Study the Structural Ensembles and Binding Processes of Intrinsically Disordered Proteins.

The structures of intrinsically disordered proteins (IDPs) are highly dynamic. It is hard to characterize the structures of these proteins experimentally. Molecular dynamics (MD) simulation is a powerful tool in the understanding of protein dynamic structures and function.

Phosphorylation Regulation on the Homo-Dimeric Binding of Transactive Response DNA-Binding Protein.

The dimerization of transactive response DNA-binding protein of 43 kDa (TDP-43) is crucial for the RNA metabolism, and the higher-order aggregation of TDP-43 would induce several neurodegenerative diseases. The dimerization and aggregation of TDP-43 are regulated by the phosphorylation on its N-terminal domain (NTD). Understanding the regulation mechanism of TDP-43 NTD dimerization is crucial for the preventing of harmful aggregation and the associated diseases.

Discovery of Novel GR Ligands toward Druggable GR Antagonist Conformations Identified by MD Simulations and Markov State Model Analysis.

Binding of different ligands to glucocorticoid receptor (GR) may induce different conformational changes and even trigger completely opposite biological functions. To understand the allosteric communication within the GR ligand binding domain, the folding pathway of helix 12 (H12) induced by the binding of the agonist dexamethasone (DEX), antagonist RU486, and modulator AZD9567 are explored by molecular dynamics simulations and Markov state model analysis. The ligands can regulate the volume of the activation function-2 through the residues Phe737 and Gln738.

Discovery of a Novel Androgen Receptor Antagonist Manifesting Evidence to Disrupt the Dimerization of the Ligand-Binding Domain via Attenuating the Hydrogen-Bonding Network Between the Two Monomers.

Androgen receptor (AR) has proved to be a vital drug target for treating prostate cancer. Here, we reported the discovery of a novel AR antagonist targeting the AR ligand-binding pocket, but distinct from the marketed drug enzalutamide (Enz), demonstrated inhibition on the AR ligand-binding domain (LBD) dimerization, which is a novel mechanism reported for the first time. First, a novel hit (, IC = 5.

Molecular View on the Dissociation Pathways and Transactivation Regulation Mechanism of Nonsteroidal GR Ligands.

As a major drug target for anti-inflammatory therapy, the glucocorticoid receptor (GR) regulates a wide range of physiological processes through transactivation (TA) or transrepression. GR TA is involved in many adverse effects of GR-targeting drugs, and therefore, the discovery of novel GR ligands with lower TA activity and longer residence time is quite urgent. Undoubtedly, understanding the ligand dissociation mechanisms and the structural basis of the TA regulation is crucial for the development of novel GR-targeting drugs.