Isothermal Molecular Dynamics Research Articles

Cucurbit[7]uril and β-cyclodextrin as hosts for dopamine: complexation, affinity, and computational insights

Dopamine (DP), an essential neurotransmitter implicated in diverse brain functions, was investigated as a guest molecule within the host cavities of cucurbit[7]uril (CB7) and β-cyclodextrin (βCD) using isothermal titration calorimetry (ITC), UV-titration, 1H NMR, molecular dynamics (MD) and density functional theory (DFT) calculations. The experimentally estimated binding constants of the 1:1 complexes of DP with CB7 and βCD were found to be 5.3 × 105 and 2.7 × 103 M−1, respectively. 1H NMR results further confirmed the complex formation for both hosts and provided structural insights. MD simulations revealed in the case of DP–CB7 complex a more rigid structure and deeper inclusion of the catechol moiety. Furthermore, results from the Molecular-Mechanics Poisson-Boltzmann Surface Area (MM-PBSA) method supported the experimental affinity data, revealing the higher affinity of DP towards CB7, a result of ion-dipole interactions. DFT calculations further supported the affinity data. TD-DFT predicted for both complexes a red shift in the absorption peak of DP.

Insight into the interaction of serum albumin with antihypertensive peptide Val-Ala-Pro from bovine casein hydrolysate based on the biolayer interferometry, multi-spectroscopic analysis and computational evaluation

Food-derived angiotensin-converting enzyme inhibitory peptide (ACEIP) has an effect in supportive therapeutic on hypertension. Bovine serum albumin (BSA) as a model transporter protein to explore the interaction mechanisms with casein-hydrolyzed ACEIP Val-Ala-Pro (VAP) by multi-spectroscopic, biolayer interferometry (BLI), isothermal titration calorimetry (ITC), molecular docking, and molecular dynamics simulations. Multi-spectroscopic analysis showed that the non-covalent complexes formed by VAP and BSA resulted in decreased hydrophobicity and α-helix contents on BSA, revealing the unfolding of the BSA structure. BLI revealed the reversible binding process of BSA to VAP. ITC confirmed that the combination of VAP to BSA was a spontaneous process mainly driven by entropy. Molecular docking and molecular dynamic simulations showed that VAP was primarily bound in site II of BSA by hydrogen bonding, hydrophobic interactions, van der Waals force, and electrostatic force. This study provides a systematic method to reveal the structure–activity relationship of ACEIPs.

The AD3 locus of synaptotagmin-1 C2 domains modulates domain stability

Synaptotagmin-1 (syt1) functions as the Ca2+-dependent sensor that triggers the rapid and synchronous release of neurotransmitters from neurotransmitter-containing vesicles during neuronal exocytosis. The syt1 protein has two homologous tandem C2 domains that interact with phospholipids in a Ca2+-dependent manner. Despite the crucial role of syt1 in exocytosis, the precise interactions between Ca2+, syt1, and phospholipids are not fully understood. In a study involving recessive lethal mutations in the syt1 gene, a specific mutation named AD3 was generated in Drosophila syt1, resulting in a significant reduction in Ca2+-dependent exocytosis. Further investigation revealed that the AD3 mutation was a missense mutation located in a conserved consensus sequence within the C2B domain of Drosophila syt1. However, the biophysical impact of the AD3 mutation had not been analyzed. Our study uses x-ray crystallography, isothermal titration calorimetry, thermodynamic analysis, and molecular dynamics simulation to show that the primary defect caused by the AD3 mutation in the syt1 protein is reduced thermodynamic stability. This instability alters the population of Ca2+-receptive states, leading to two major consequences: decreased affinity for calcium ions and compromised stabilization of the domain normally enhanced by Ca2+. We conclude that this conserved residue acts as a structural constraint, delimiting the movement of loop 3 within the pocket and ultimately influencing the affinity of the calcium ion binding with the C2 domain.

Destabilization of the D2 domain of Thermotoga maritima arginine binding protein induced by guanidinium thiocyanate and its counteraction by stabilizing agents.

D2 is a structural and cooperative domain of Thermotoga maritima Arginine Binding Protein, that possesses a remarkable conformational stability, with a denaturation temperature of 102.6°C, at pH 7.4. The addition of potassium thiocyanate causes a significant decrease in the D2 denaturation temperature. The interactions of thiocyanate ions with D2 have been studied by means of isothermal titration calorimetry measurements and molecular dynamics simulations. It emerged that: (a) 20-30 thiocyanate ions interact with the D2 surface and are present in its first solvation shell; (b) each of them makes several contacts with protein groups, both polar and nonpolar ones. The addition of guanidinium thiocyanate causes a marked destabilization of the D2 native state, because both the ions are denaturing agents. However, on adding to the solution containing D2 and guanidinium thiocyanate a stabilizing agent, such as TMAO, sucrose or sodium sulfate, a significant increase in denaturation temperature occurs. The present results confirm that counteraction is a general phenomenon for globular proteins.

Preliminary exploration of the anti-ovarian cancer activity of peptides derived from bovine bone collagen hydrolysate and its related mechanisms

Ovarian cancer, a malignant tumor that poses a significant threat to women's health, has seen a rise in incidence, prompting the urgent need for more effective treatment. This study primarily aimed to explore the potential of bovine collagen peptides in inhibiting ovarian cancer. The investigation in this study began with the identification of 268 peptide sequences through LC-MS/MS, followed by a screening process using molecular docking techniques to identify potential peptides capable of binding to EGFR. Subsequently, a series of experiments were performed, demonstrating the inhibitory effects of the peptide GPAGADGDRGEAGPAGPAGPAGPR on the proliferation of ovarian cancer cells. Transcriptomic analysis further revealed that this peptide can regulate cholesterol metabolism in ovarian cancer cells. Finally, a combination of time-resolved fluorescence resonance energy transfer, isothermal titration calorimetry, molecular docking, and molecular dynamics simulations were utilized to validate the ability of this peptide to bind to the epidermal growth factor receptor (EGFR) and impede the binding of epidermal growth factor (EGF) and EGFR.

Preferential binding of cucurbit[7]uril toward 2-amino-4-chlorophenol in chlorzoxazone

Chlorzoxazone (CLZ) is a centrally acting skeletal muscle relaxant synthesized from 2-amino-4-chlorophenol (ACP). However, due to the toxic side effects of ACP, its concentration in CLZ formulations is strictly regulated (0.5%). In this study, we investigate the preferential binding of cucurbit[7]uril (CB7) toward CLZ and ACP using 1H NMR, isothermal titration calorimetry (ITC) and molecular dynamics (MD) simulations, to explore ​possible future uses of CB7, either for purifying CLZ from its toxic impurity (ACP) or in sensing ACP in CLZ. ITC experiments confirm the formation of 1:1 complexes, with favorable enthalpic and entropic contributions and binding constants of 1.1 × 106 and 4.9 × 104M−1 for ACP and CLZ, respectively, while 1H NMR and MD simulations reveal the guests in the complexes are included within the cavity of CB7. Molecular Mechanics Poisson-Boltzmann Surface Area (MM-PBSA) results further confirmed the favorability of CB7 toward ACP. Additional MD simulations reveal that CB6 and CB8 preferentially bind CLZ and ACP, respectively, with CB6 forming inclusion and exclusion complexes with CLZ and ACP, respectively, while CB8 forms stable 1:1 and 1:2 inclusion complexes with each guest.

Entropy Drives Interpolymer Association in Water: Insights into Molecular Mechanisms.

Interpolymer association in aqueous solutions is essential for many industrial processes, new materials design, and the biochemistry of life. However, our understanding of the association mechanism is limited. Classical theories do not provide molecular details, creating a need for detailed mechanistic insights. This work consolidates previous literature with complementary isothermal titration calorimetry (ITC) measurements and molecular dynamics (MD) simulations to investigate molecular mechanisms to provide such insights. The large body of ITC data shows that intermolecular bonds, such as ionic or hydrogen bonds, cannot drive association. Instead, polymer association is entropy-driven due to the reorganization of water and ions. We propose a unifying entropy-driven association mechanism by generalizing previously suggested polyion association principles to include nonionic polymers, here termed polydipoles. In this mechanism, complementary charge densities of the polymers are the common denominators of association, for both polyions and polydipoles. The association of the polymers results mainly from two processes: charge exchange and amphiphilic association. MD simulations indicate that the amphiphilic assembly alone is enough for the initial association. Our proposed mechanism is a step toward a molecular understanding of the formation of complexes between synthetic and biological polymers under ambient or biological conditions.

Insights into formation and stability mechanism of V7-type short amylose-resveratrol complex using molecular dynamics simulation and molecular docking

Pre-formed V-type amylose as a kind of wall material has been reported to carry polyphenols, while the interaction mechanism between V-type amylose and polyphenol is still elusive. In this work, the formation and stability mechanism of a V7-type short amylose-resveratrol complex was investigated via isothermal titration calorimetry, molecular dynamics, and molecular docking. The results presented that two stoichiometric ratios of resveratrol to short amylose were calculated to 0.120 and 0.800, and the corresponding main driving force was hydrogen bonding and hydrophobic interaction, respectively. The folding and unfolding conformation of V7-type short amylose chains appeared alternately during the simulation. Resveratrol tended to be bound in the short amylose helix between 40 ns and 80 ns to form a more stable complex. Hydrogen bonds between resveratrol molecule and O6 at the 22nd glucose molecule/O2 at the 24th glucose molecules and hydrophobic interaction between resveratrol molecule and glucose molecules (19th, 20th, 21st and 23rd) could be found.

Active sparse Bayesian committee machine potential for isothermal-isobaric molecular dynamics simulations.

Recent advancements in machine learning potentials (MLPs) have significantly impacted the fields of chemistry, physics, and biology by enabling large-scale first-principles simulations. Among different machine learning approaches, kernel-based MLPs distinguish themselves through their ability to handle small datasets, quantify uncertainties, and minimize over-fitting. Nevertheless, their extensive computational requirements present considerable challenges. To alleviate these, sparsification methods have been developed, aiming to reduce computational scaling without compromising accuracy. In the context of isothermal and isobaric ML molecular dynamics (MD) simulations, achieving precise pressure estimation is crucial for reproducing reliable system behavior under constant pressure. Despite progress, sparse kernel MLPs struggle with precise pressure prediction. Here, we introduce a virial kernel function that significantly enhances the pressure estimation accuracy of MLPs. Additionally, we propose the active sparse Bayesian committee machine (BCM) potential, an on-the-fly MLP architecture that aggregates local sparse Gaussian process regression (SGPR) MLPs. The sparse BCM potential overcomes the steep computational scaling with the kernel size, and a predefined restriction on the size of kernel allows for fast and efficient on-the-fly training. Our advancements facilitate accurate and computationally efficient machine learning-enhanced MD (MLMD) simulations across diverse systems, including ice-liquid coexisting phases, Li10Ge(PS6)2 lithium solid electrolyte, and high-pressure liquid boron nitride.

Insights into the molecular mechanism of dextran sulfate inhibiting DNA digestion by pepsin: a crucial role of sulfate group on the binding to DNA

Sulfate polysaccharides can inhibit DNA digestion in simulated gastric juice in vitro, which is important for regulating dietary nucleic acids metabolism, but the mechanism of inhibition is unclear. This study used dextran sulfate (DS) with different sulfate groups and molecular weights to explore the effect of DS on DNA digestion. Molecular interactions between DS and DNA were investigated by biolayer interferometry (BLI), isothermal titration calorimetry (ITC) and molecular dynamics simulations. Results indicated that DS with higher molecular weight and sulfate group content showed stronger inhibitory effect of DNA digestion. ITC results showed that the combined Kd value of DNA and DS was about 2.53 mM. The main reason for inhibition of DNA digestion is that the formation of hydrogen bonds between the sulfate group of DS and DNA bases hinders the binding of DNA to pepsin. This finding will facilitate new strategies for nucleic acid metabolism and oral drug delivery. Communicated by Ramaswamy H. Sarma

Gallic acid inhibits filament formation and promotes the disassembly of superoxide dismutase 1, a protein involved in the pathogenesis of amyotrophic lateral sclerosis

Superoxide dismutase 1 (SOD1) forms amyloid-like filaments in motor neurons, contributing to the pathogenesis of Amyotrophic Lateral Sclerosis (ALS) and leading to neuronal cell death. Earlier studies identified Epigallocatechin gallate (EGCG) as an effective inhibitor of SOD1 filaments. This study explored the potential of natural compounds to inhibit SOD1 filament formation as an ALS treatment strategy. Our investigation revealed that gallic acid, a soluble constituent of tannic acid and a hydrolysis product of EGCG, disrupts SOD1 filament formation, similar to EGCG. Furthermore, gallic acid demonstrated the ability to dismantle pre-existing SOD1 protein filaments. The study unveiled the inhibitory potential of red wine, a dietary source of tannic acid, and showed that tannic acid, when treated with tannase from lactobacilli, can enhance the inhibition against SOD1 filament formation. The findings were validated using isothermal titration calorimetry (ITC) and molecular dynamics (MD) simulations, suggesting that gallic acid can bind to both the soluble and filamentous forms of SOD1 protein. This interaction could elucidate the mechanism by which SOD1 filament formation is inhibited. In conclusion, the study unveils the molecular mechanism by which gallic acid inhibits the formation of SOD1 filaments. Our results suggest that gallic acid, a hydrolysis product of red wine, may be employed as a functional food ingredient to mitigate neurodegenerative diseases caused by protein filaments, such as ALS.

Discovery of anti-allergic components in Guomingkang Formula using sensitive HEMT biochips coupled with in vitro and in vivo validation

BackgroundAllergic rhinitis (AR) is a prevalent allergic disease, which seriously affects the sufferers’ life quality and increases the socioeconomic burden. Guominkang (GMK), a well-known prescription for AR treatment, showed satisfactory effects; while its anti-allergic components remain to be disclosed. AlGaN/GaN HEMT biochip is more sensitive and cost-effective than other binding equipments, indicating its great potential for screening of active ingredients from herbal medicines. MethodsAR mouse models were first established to test the anti-allergic effect of GMK and discover the ingredients absorbed into blood by ultra-high performance liquid chromatography-mass spectra (UHPLC-MS). Then, novel Syk/Lyn/Fyn-functionalized high electron mobility transistor (HEMT) biochips with high sensitivity and specificity were constructed and applied to screen the active components. Finally, the results from HEMT biochips screening were validated via in silico (molecular docking and molecular dynamics simulation), in vitro (RBL-2H3 cells), and in vivo (PCA mice model) assays. ResultsGMK showed a potent therapeutic effect on AR mice, and fifteen components were identified from the medicated plasma. Furthermore, hamaudol was firstly found to selectively inhibit the Syk and Lyn, and emodin was to selectively inhibit Lyn, which were further confirmed by isothermal titration calorimetry, molecular docking, and molecular dynamics simulation analyses. Suppression of the activation of FcεRI-MAPK signals might be the possible mechanism of the anti-allergic effect of hamaudol. ConclusionsThe targets of emodin and hamaudol were discovered by HEMT biochips for the first time. This study provided a novel and effective strategy to discover active components in a complex herbal formula by using AlGaN/GaN HEMT biochips.

Polypropylene fiber grafted calcium alginate with mesoporous silica for adsorption of Bisphenol A and Pb2+

Polypropylene grafted calcium alginate with mesoporous silica (PP-g-CaAlg@SiO2) for adsorbing Bisphenol A (BPA) and Pb2+ was prepared by calcium chloride (CaCl2) crosslinking and hydrochloric acid solution treatment. The PP-g-CaAlg@SiO2 was characterized by SEM, TEM, BET, XRD, FTIR and TG. PP-g-CaAlg@SiO2 exhibited excellent adsorption capacity for BPA and Pb2+, because the formation of reticulated nanorod structure increased its specific surface area. Subsequently, the adsorption behaviours of BPA and Pb2+, including adsorption isotherms and adsorption kinetics, were investigated. Afterward, isothermal titration calorimetry (ITC) and molecular dynamics (MD) simulation were performed to explore the adsorption mechanism. The results indicated that hydrogen bonding played the leading role in the adsorption of BPA, while the bonding of Pb2+ to carboxyl group binding sites was the focus of Pb2+ adsorption. In addition, the adsorption capacity of PP-g-CaAlg@SiO2 was stable over 10 cycles.

Supramolecular Study of the Interactions between Malvidin-3-O-Glucoside and Wine Phenolic Compounds: Influence on Color.

Supramolecular study of the interactions between the major wine anthocyanin, malvidin-3-O-glucoside (Mv3G) and different wine phenolic compounds (quercetin 3-O-β-glucopyranoside (QG), caffeic acid, (-)-epicatechin, (+)-catechin, and gallic acid) has been performed at two different molar ratios (1:1 and 1:2) in acidic medium where flavylium cation predominates (pH ≤ 2). Color variations have been evaluated by differential colorimetry using CIELAB color space. These studies have been complemented with isothermal titration calorimetry assays and molecular dynamics simulations. The color of Mv3G flavylium cation is modified by the interaction with QG toward more bluish and intense colors. Interaction constants between the anthocyanin and the different phenolic compounds were obtained, ranging from 9.72 × 108 M-1 for QG to 1.50 × 102 M-1 for catechin. Hydrophobic interactions and H-bonds are the main driving forces in the pigment/copigment aggregation, except for the interactions where caffeic acid is involved, in which hydrophobic interactions acquire greater preponderance.

Exploring the binding effects and inhibiting mechanism of hyperoside to lipase using multi-spectroscopic approaches, isothermal titration calorimetry, inhibition kinetics and molecular dynamics.

Hyperoside (HYP) is a flavonoid with various physiological activities. The present study examined the interaction mechanism between HYP and lipase using multi-spectrum and computer-aided techniques. Results demonstrated that the force type of HYP on lipase was mainly hydrogen bond, hydrophobic interaction force, and van der Waals force, and HYP had an excellent binding affinity with lipase at 1.576 × 105 M-1. HYP dose-dependently inhibited lipase in the inhibition experiment, and its IC50 value was 1.92 × 10-3 M. Moreover, the results suggested that HYP could inhibit the activity by binding to essential groups. Conformational studies indicated that the conformation and microenvironment of lipase were slightly changed after the addition of HYP. Computational simulations further confirmed the structural relationships of HYP to lipase. The interaction between HYP and lipase can provide ideas for the development of functional foods related to weight loss. The results of this study help comprehend the pathological significance of HYP in biological systems, as well as its mechanism.

Design, Synthesis, and Characterization of a Novel 2'-5'-Linked Amikacin-Binding Aptamer: An Experimental and MD Simulation Study.

To extend the approach of using RNA aptamers as transient protective groups for the synthesis of novel small-molecule drug derivatives from the existing aminoglycosides, we incorporated 2'-5' phosphodiester backbone modification in a structurally known neomycin RNA aptamer and studied the binding of a series of aminoglycosides using isothermal calorimetry (ITC) and molecular dynamics (MD) simulation. Experimental characterization of amikacin, a commercially available and widely used aminoglycoside for treating bacterial infections, shows that the aptamer A1 with a 2'-5' linkage between G15 and U16 exhibits a sevenfold increase in binding affinity with a lower binding energy compared to the native aptamer. Molecular dynamics (MD) simulation studies rationalize that this noncanonical linkage generates a narrower binding pocket by creating a superspiral RNA helical structure, which improves the ligand's fit in the binding pocket. These results provide new insights into applying 2'-5' linkages to diversify functional RNA aptamers as noncovalent protective groups in the synthesis of aminoglycoside derivatives, which can be further extended to other current drug molecules and complex natural compounds to make new pools of drug candidates more efficiently.

Chlorine-resistance, reswelling after drying and molecule/ions separation properties of carboxyl multi-walled carbon nanotubes/calcium alginate composite hydrogel membrane

In practice sodium hypochlorite (NaClO) is often used to clean biological contamination from membrane surfaces. It is worth thinking about how to balance the mechanical strength and chlorine resistance of calcium alginate (CaAlg) hydrogel membrane during cleaning. In this study, carboxyl multi-walled carbon nanotubes/calcium alginate (CMWCNT/CaAlg) composite hydrogel membrane with chlorine-resistance ability was prepared. Performance of CMWCNT/CaAlg membrane in various aspects, including morphology and chlorine resistance, were characterized. In addition, vacuum drying and reswelling method enhanced the mechanical strength of the membrane. Moreover, the interactions mechanism between CMWCNT and NaAlg were investigated by isothermal titration calorimetry (ITC) and molecular dynamics (MD) simulation. Subsequently, the factors influencing membrane separation efficiency towards dye molecule/salt ions were analyzed. It turns out that the composite membrane could achieve nearly 100% high efficiency in the rejection of dye molecules with large molecular weight (Mw > 700 Da), while the rejection of salt was below 8%. Our findings demonstrated CMWCNT/CaAlg composite membrane not only has excellent anti-fouling and chlorine resistance, but also has a very broad application prospect in the separation of dye and salt.

A novel CRISPR/Cas14a1-Exo III aptasensor for melamine detection coupled with systematically studied binding mechanism of truncated aptamer

In this work, the aptamer of melamine was truncated and mutated. Based on isothermal titration calorimetry, circular dichroism and molecular dynamics, the thermodynamic information, structural changes and binding pocket of the truncated aptamer SJs32 with 32 bases to melamine were systematically studied. Meanwhile, a novel aptasensor coupled with CRISPR/Cas14a1 and Exo III was developed for melamine detection. SJs32 was first hybridized with the complementary DNA (cDNA) to form SJs32-cDNA. In the presence of melamine, SJs32 recognized melamine to form SJs32-melamine and performed structural transformation, which resulted in the releasing of cDNA into the solution. Exo III digested the SJs32-melamine and the released melamine led to the dissociation of more cDNA from SJs32-cDNA complex. Finally, the combination of cDNA and sgRNA activated the trans-cleavage activity of Cas14a1. According to the change of fluorescence intensity, the sensitive and rapid detection of melamine was realized with the linear detection range of 4 nmol/L-1 µmol/L. The developed strategy broadened the application of melamine aptamer in food safety and provided a new insight for the development of CRISPR/Cas14a1 aptasensor.

When mechanisms of coalescence and sintering at the nanoscale fundamentally differ: Molecular dynamics study.

Employing classical isothermal molecular dynamics, we simulated coalescence of mesoscopic Au nanodroplets, containing from several thousands to several hundred thousands of atoms, and sintering of mesoscopic solid Au nanoparticles. For our atomistic simulations, we used the embedded atom method. The employed open access program large-scale atomic/molecular massively parallel simulator makes it possible to realize parallel graphical processing unit calculations. We have made a conclusion that the regularities and mechanisms of the nanodroplet coalescence (temperature is higher than the nanoparticle melting temperature) and of the solid nanoparticle sintering differ from each other. We have also concluded that the nanodroplet coalescence may be interpreted as a hydrodynamic phenomenon at the nanoscale whereas sintering of solid nanoparticles is a much more complex phenomenon related to different mechanisms, including collective rearrangements of atoms, the surface diffusion, and other types of diffusion. At the same time, collective rearrangements of atoms relate not only to the solid nanoparticle sintering but also to the nanodroplet coalescence. In general, our molecular dynamics results on sintering of Au nanoparticles consisting of 10 000-30 000 atoms agree with the Ferrando-Minnai kinetic trapping concept that was earlier confirmed in molecular dynamics experiments on Au nanoclusters consisting of about 100 atoms.

Modulation of beta-amyloid aggregation using ascorbic acid

Studies have shown that the level of ascorbic acid (AA) is reduced in the brain of Alzheimer's disease (AD) patients. However, its effect on amyloid-β 1–42 (Aβ42) aggregation has not yet been elucidated. Here we investigated for the first time the effect of AA on Aβ42 aggregation using fluorescence assay, circular dichroism, atomic force microscopy, isothermal titration calorimetry, ligand docking, and molecular dynamics. Our results showed that the fibril content decreases in the growth phase when the peptides are co-incubated with AA. AA molecules bind to Aβ42 peptides with high binding affinity and a binding site for AA between the β-strands of Aβ42 oligomers prevents the stack of adjacent strands. We demonstrate the inhibitory effect of AA on the aggregation of Aβ42 and its molecular interactions, which can contribute to the development of an accessible therapy for AD and also to the design of novel drugs for other amyloidogenic diseases.