Anisotropic Friction in a Ligand-Protein Complex

Cryoprotective effect of wheat starch granular surface proteins on frozen HMW and LMW glutenins: Structure, property and functionality across length scales

Although frozen dough technology has demonstrated significant benefits, the mechanisms underlying dough deterioration during freezing remain unclear. To overcome this obstacle, the effect of freezing-induced deteriorations of wheat starch granular surface proteins (SGSPs)-high/low molecular weight (HMW/LMW) glutenins complexes were analyzed from the molecular to macroscopic scales. After 7 cycles of freezing/thawing treatment, SGSPs-LMW complex showed a higher antifreeze stability than SGSPs-HMW complex. The freezable water content of SGSPs-HMW increased from 32 % to 39 %, indicating a marked migration and recrystallization of ice. In this situation, the interactions of SGSPs-HMW complex were affected and destabilized, leading to partially denatured and depolymerized molecular structures. Furthermore, the bulk protein aggregation network was also dissociated under the ice tearing and splitting, which irreversibly collapsed to small molecular protein particles. In comparison, the resistance of SGSPs-LMW complex on continued network disruption appear to be the key to maintain the quality of frozen dough.

Unfolding of von Willebrand Factor Type D Like Domains Promotes Mucin Adhesion

Mucins are the macromolecular key components of mucus. On wet epithelia of mammals, mucin solutions and gels act as powerful biolubricants and reduce friction and wear by generating a sacrificial layer and establishing hydration lubrication. Yet the structure-function relationship of mucin adhesion and lubrication remains elusive. We study the adhesion behavior of mucin using atomic force microscopy-based single molecule force spectroscopy with covalently attached, lab-purified salivary MUC5B and gastric MUC5AC. We can resolve the structural motifs mediating adhesion on chemically distinct substrates, such as highly oriented pyrolytic graphite and steel. We report on force-induced partial unfolding of the von Willebrand factor type D like domains and deliver their unfolding rates and free energy barriers. These domains serve to dissipate energy during the desorption process of mucins. Partial mucin unfolding might significantly contribute to the stability of a sacrificial mucin layer during shearing processes, enhancing the lubrication potential of mucin solutions.

Dynamics and Stability Mechanism of Lactoferrin-EPA During Emulsification Process: Insights from Macroscopic and Molecular Perspectives

Although eicosapentaenoic acid (EPA) as a functional fatty acid has shown significant benefits for human health, its susceptibility to oxidation significantly limits its application. In this study, we developed a nanoemulsion of the lactoferrin (LTF)-EPA complex and conducted a thorough investigation of its macro- and molecular properties. By characterizing the emulsion with different LTF concentrations, we found that 1.0% LTF formed the most stable complex with EPA, which benefited the formation and stability of the emulsion against storage and freezing/thawing treatment. As the foundation block of the emulsion structure, the binding mechanism and the entire dynamic reaction process of the complex have been fully revealed through various molecular simulations and theoretical calculations. This study establishes a comprehensive picture of the LTF-EPA complex across multiple length scales, providing new insights for further applications and productions of its emulsion.

Effect of Electric Fields on the Mechanical Mechanism of Regorafenib-VEGFR2 Interaction to Enhance Inhibition of Hepatocellular Carcinoma

The interaction between molecular targeted therapy drugs and target proteins is crucial with regard to the drugs' anti-tumor effects. Electric fields can change the structure of proteins, which determines the interaction between drugs and proteins. However, the regulation of the interaction between drugs and target proteins and the anti-tumor effects of electric fields have not been studied thoroughly. Here, we explored how electric fields enhance the inhibition of regorafenib with regard to the activity, invasion, and metastasis of hepatocellular carcinoma cells. We found that electric fields lead to an increase in the normal (adhesion) and transverse (friction) interaction forces between regorafenib and VEGFR2. In single molecule pair interactions, there are changes in specific and nonspecific forces. Hydrogen bonds, hydrophobic interactions, and van der Waals forces are the main influencing factors. Importantly, the increase in the adhesion force and friction force between regorafenib and VEGFR2 caused by electric fields is related to the activity and migration ability of hepatocellular carcinoma cells. The morphological changes in VEGFR2 prove that electric fields regulate protein conformation. Overall, our work proves the drug-protein mechanical mechanism by which electric fields enhance the anti-tumor effect of regorafenib and provides insights into the application of electric fields in clinical tumor treatment.

Engineering the Mechanical Stability of a Therapeutic Complex between Affibody and Programmed Death-Ligand 1 by Anchor Point Selection

Protein-protein complexes can vary in mechanical stability depending on the direction from which force is applied. Here, we investigated the mechanical stability of a complex between a binding scaffold called Affibody and an immune checkpoint protein Programmed Death-Ligand 1 (PD-L1). We used AFM single-molecule force spectroscopy with bioorthogonal clickable peptide handles, shear stress bead adhesion assays, molecular modeling, and steered molecular dynamics (SMD) to understand the pulling point dependency of the mechanostability of the Affibody:(PD-L1) complex. We observed a wide range of rupture forces depending on the anchor point. Pulling from residue #22 on Affibody generated an intermediate state attributed to partially unfolded PD-L1, while pulling from Affibody's N-terminus generated a force-activated catch bond. Pulling from residue #22 or #47 on Affibody generated high rupture forces, with the complex breaking at up to ∼190 pN under loading rates of ∼104-105 pN/s, representing a ∼4-fold increase as compared with low-force N-terminal pulling. SMD simulations showed relative tendencies in rupture forces that were consistent with experiments and, through visualization of force propagation networks, provided mechanistic insights. These results demonstrate how the mechanical properties of protein-protein interfaces can be controlled by informed choice of site-specific bioconjugation points within molecules, with implications for optimal bioconjugation strategies in drug delivery vehicles.

The Characterization of a Low-Calorie and Lactose-Free Brown Fermented Milk by the Hydrolysis of Different Enzymatic Lactose

The adoption of brown fermented milk in the normal diet and daily beverages is accompanied by significant sugar intake and a high public health burden. To reduce the sugar content in dairy products while maintaining optimal nutritional properties, a novel low-calorie, lactose-free brown fermented milk was developed through enzymatic hydrolysis and the Maillard reaction. The optimal product was achieved using low-temperature lactase, where the lactose and glucose content were reduced 33-fold and 2.4-fold to 0.06 g/100 g and 13.32 g/L, respectively, meeting the criteria for being lactose-free (<0.5 g/100 g). Meanwhile, hazardous compounds such as 5-hydroxymethylfurfural and 3-deoxyglucosone were reduced by more than 20%. After 28 days of storage, the water-holding capacity and suspension stability remained notably stable, and the protein composition was also more enriched compared to commercial milk. It is expected that this low-calorie dairy product may promote growth in the dairy market.

Insight into the promoted recrystallization and water distribution of bread by removing starch granule - surface and - associated proteins during storage

The influence of starch granule surface proteins (SGSPs) and starch granule-associated proteins (SGAPs) on bread retrogradation was investigated in a reconstituted dough system. The removal of both SGSPs and SGAPs resulted in poor bread qualities, decreasing specific volume and crumb porosity, leading to more baking loss and compact crumb structure. Particularly, removing SGSPs was effective in promoting the bread retrogradation. After 7 days of storage, the hardness of bread without SGSPs showed an increase of 353.34 g than the bread without SGAPs. Proton population and relaxation times exhibited that the absence of SGSPs significantly decreased the content of bound water from 11.51 % to 7.03 %, indicating lower water-holding capacity due to the loosen gelling structure. Compared to the control group, bread without SGSPs accelerated the starch recrystallinity by a reduction in soluble starch content, thereby increasing the retrogradation enthalpy and relative crystallinity through promoting the molecular reassociation in starch.

Learning Protein-Ligand Unbinding Pathways via Single-Parameter Community Detection

Understanding the dynamics of biomolecular complexes, e.g., of protein-ligand (un)binding, requires the comprehension of paths such systems take between metastable states. In MD simulations, paths are usually not observable per se, but they need to be inferred from simulation trajectories. Here, we present a novel approach to cluster trajectories based on a community detection algorithm that necessitates only the definition of a single parameter. The unbinding of the streptavidin-biotin complex is used as a benchmark system and the A2a adenosine receptor in complex with the inhibitor ZM241385 as an elaborate application. We demonstrate how such clusters of trajectories correspond to pathways and how the approach helps in the identification of reaction coordinates for a considered (un)binding process.

Engineering the Mechanical Stability of a Therapeutic Affibody/PD-L1 Complex by Anchor Point Selection

Protein-protein complexes can vary in mechanical stability depending on the direction from which force is applied. Here we investigated the anisotropic mechanical stability of a molecular complex between a therapeutic non-immunoglobulin scaffold called Affibody and the extracellular domain of the immune checkpoint protein PD-L1. We used a combination of single-molecule AFM force spectroscopy (AFM-SMFS) with bioorthogonal clickable peptide handles, shear stress bead adhesion assays, molecular modeling, and steered molecular dynamics (SMD) simulations to understand the pulling point dependency of mechanostability of the Affibody:(PD-L1) complex. We observed diverse mechanical responses depending on the anchor point. For example, pulling from residue #22 on Affibody generated an intermediate unfolding event attributed to partial unfolding of PD-L1, while pulling from Affibody's N-terminus generated force-activated catch bond behavior. We found that pulling from residue #22 or #47 on Affibody generated the highest rupture forces, with the complex breaking at up to ~ 190 pN under loading rates of ~104-105 pN/sec, representing a ~4-fold increase in mechanostability as compared with low force N-terminal pulling. SMD simulations provided consistent tendencies in rupture forces, and through visualization of force propagation networks provided mechanistic insights. These results demonstrate how mechanostability of therapeutic protein-protein interfaces can be controlled by informed selection of anchor points within molecules, with implications for optimal bioconjugation strategies in drug delivery vehicles.

Effect of Environmental pH on the Mechanics of Chitin and Chitosan: A Single-Molecule Study

Chitin and chitosan are important structural macromolecules for most fungi and marine crustaceans. The functions and application areas of the two molecules are also adjacent beyond their similar molecular structure, such as tissue engineering and food safety where solution systems are involved. However, the elasticities of chitin and chitosan in solution lack comparison at the molecular level. In this study, the single-molecule elasticities of chitin and chitosan in different solutions are investigated via atomic force microscope (AFM) based single-molecule spectroscopy (SMFS). The results manifest that the two macromolecules share the similar inherent elasticity in DOSM due to their same chain backbone. However, obvious elastic deviations can be observed in aqueous conditions. Especially, a lower pH value (acid environment) is helpful to increase the elasticity of both chitin and chitosan. On the contrary, the tendency of elastic variation of chitin and chitosan in a larger pH value (alkaline environment) shows obvious diversity, which is mainly determined by the side groups. This basic study may produce enlightenment for the design of intelligent chitin and chitosan food packaging and biomedical materials.

Topology of molecular deformations induces triphasic catch bonding in selectin-ligand bonds

Among the long-standing efforts to elucidate the physical mechanisms of protein-ligand catch bonding, particular attention has been directed at the family of selectin proteins. Selectins exhibit slip, catch-slip, and slip-catch-slip bonding, with minor structural modifications causing major changes in selectins' response to force. How can a single structural mechanism allow interconversion between these various behaviors? We present a unifying theory of selectin-ligand catch bonding, using a structurally motivated free energy landscape to show how the topology of force-induced deformations of the molecular system produces the full range of observed behaviors. We find that the pathway of bond rupture deforms in non-trivial ways, such that unbinding dynamics depend sensitively on force. This implies a severe breakdown of Bell's theory-a paradigmatic theory used widely in catch bond modeling-raising questions about the suitability of Bell's theory in modeling other catch bonds. Our approach can be applied broadly to other protein-ligand systems.

Mechanism of DNA Intercalation by Chloroquine Provides Insights into Toxicity

Chloroquine has been used as a potent antimalarial, anticancer drug, and prophylactic. While chloroquine is known to interact with DNA, the details of DNA-ligand interactions have remained unclear. Here we characterize chloroquine-double-stranded DNA binding with four complementary approaches, including optical tweezers, atomic force microscopy, duplex DNA melting measurements, and isothermal titration calorimetry. We show that chloroquine intercalates into double stranded DNA (dsDNA) with a KD ~ 200 µM, and this binding is entropically driven. We propose that chloroquine-induced dsDNA intercalation, which happens in the same concentration range as its observed toxic effects on cells, is responsible for the drug's cytotoxicity.

Revealing the Control Mechanisms of pH on the Solution Properties of Chitin via Single-Molecule Studies

Chitin is one of the most common polysaccharides and is abundant in the cell walls of fungi and the shells of insects and aquatic organisms as a skeleton. The mechanism of how chitin responds to pH is essential to the precise control of brewing and the design of smart chitin materials. However, this molecular mechanism remains a mystery. Results from single-molecule studies, including single-molecule force spectroscopy (SMFS), AFM imaging, and molecular dynamic (MD) simulations, have shown that the mechanical and conformational behaviors of chitin molecules show surprising pH responsiveness. This can be compared with how, in natural aqueous solutions, chitin tends to form a more relaxed spreading conformation and show considerable elasticity under low stretching forces in acidic conditions. However, its molecular chain collapses into a rigid globule in alkaline solutions. The results show that the chain state of chitin can be regulated by the proportions of inter- and intramolecular H-bonds, which are determined via the number of water bridges on the chain under different pH values. This basic study may be helpful for understanding the cellular activities of fungi under pH stress and the design of chitin-based drug carriers.

Unusual Aspects of Charge Regulation in Flexible Weak Polyelectrolytes

This article reviews the state of the art of the studies on charge regulation (CR) effects in flexible weak polyelectrolytes (FWPE). The characteristic of FWPE is the strong coupling of ionization and conformational degrees of freedom. After introducing the necessary fundamental concepts, some unconventional aspects of the the physical chemistry of FWPE are discussed. These aspects are: (i) the extension of statistical mechanics techniques to include ionization equilibria and, in particular, the use of the recently proposed Site Binding-Rotational Isomeric State (SBRIS) model, which allows the calculation of ionization and conformational properties on the same foot; (ii) the recent progresses in the inclusion of proton equilibria in computer simulations; (iii) the possibility of mechanically induced CR in the stretching of FWPE; (iv) the non-trivial adsorption of FWPE on ionized surfaces with the same charge sign as the PE (the so-called "wrong side" of the isoelectric point); (v) the influence of macromolecular crowding on CR.

Predicting Protein-Ligand Binding and Unbinding Kinetics with Biased MD Simulations and Coarse-Graining of Dynamics: Current State and Challenges

The prediction of drug-target binding and unbinding kinetics that occur on time scales between milliseconds and several hours is a prime challenge for biased molecular dynamics simulation approaches. This Perspective gives a concise summary of the theory and the current state-of-the-art of such predictions via biased simulations, of insights into the molecular mechanisms defining binding and unbinding kinetics as well as of the extraordinary challenges predictions of ligand kinetics pose in comparison to binding free energy predictions.