Dynamics Simulation Technique Research Articles

The Dissociation Process of NADP+ from NADPH-Cytochrome P450 Reductase Studied by Molecular Dynamics Simulation.

NADPH-cytochrome P450 reductase (CPR) plays a vital role as a redox partner for mammalian cytochrome P450 enzymes (P450s), facilitating the transfer of two electrons from NADPH to the P450 heme center in a sequential manner. Previous experimental studies revealed substantial domain movements of CPR, transitioning between closed and open states during the electron transfer (ET) cycle. These transitions are essential and are influenced by the binding of NADPH or the release of NADP+. However, the intricate molecular mechanisms governing the CPR-mediated ET cycle have largely remained elusive. This study employed molecular dynamics (MD) simulation techniques to explore the dissociation of NADP+ from CPR, a crucial step preceding the initial ET from CPR to a P450. Alongside the binding structure of NADP+ observed in a crystal structure (pose I), our MD simulations identified an alternative binding structure (pose II). Although pose II exhibits slightly lower stability than pose I, it can be formed through an approximate 210° counterclockwise rotation of the adenine group, with a free energy barrier of only 2.76 kcal/mol. The simulation results further suggest that NADP+ dissociation involves a tentative formation of pose II from pose I before complete dissociation, and that the binding of NADP+ to CPR is primarily governed by nonbonded interactions within the adenosine binding pocket.

Mechanisms underlying the therapeutic effects of Gang Huo Qing wen granules in the treatment of influenza based on network pharmacology, molecular docking and molecular dynamics

Influenza (Flu) is a severe health, medical, and economic problem, but no medication that has excellent outcomes and lowers the occurrence of these problems is now available. GanghuoQingwenGranules (GHQWG) is a common Chinese herbal formula for the treatment of influenza (flu). However, its methods of action remain unknown. We used network pharmacology, molecular docking, and molecular dynamics simulation techniques to investigate the pharmacological mechanism of GHQWG in flu. TCMSP and various types of literature were used to obtain active molecules and targets of GHQWG. Flu-related targets were found in the Online Mendelian Inheritance in Man (OMIM) database, the DisFeNET database, the Therapeutic Target Database (TTD), and the DrugBank database. To screen the key targets, a protein–protein interaction (PPI) network was constructed. DAVID was used to analyze GO and KEGG pathway enrichment. Target tissue and organ distribution was assessed. Molecular docking was used to evaluate interactions between possible targets and active molecules. For the ideal core protein–compound complexes obtained using molecular docking, a molecular dynamics simulation was performed. In total, 90 active molecules and 312 GHQWG targets were discovered. The PPI network's topology highlighted six key targets. GHQWG's effects are mediated via genes involved in inflammation, apoptosis, and oxidative stress, as well as the TNF and IL-17 signaling pathways, according to GO and KEGG pathway enrichment analysis. Molecular docking and molecular dynamics simulations demonstrated that the active compounds and tested targets had strong binding capabilities. This analysis accurately predicts the effective components, possible targets, and pathways involved in GHQWG flu treatment. We proposed a novel study strategy for future studies on the molecular processes of GHQWG in flu treatment. Furthermore, the possible active components provide a dependable source for flu drug screening.

Exploring α-synuclein stability under the external electrostatic field: Effect of repeat unit

Parkinson’s disease (PD) is a category of neurodegenerative disorders (ND) that currently lack comprehensive and definitive treatment strategies. The etiology of PD can be attributed to the presence and aggregation of a protein known as α-synuclein. Researchers have observed that the application of an external electrostatic field holds the potential to induce the separation of the fibrous structures into peptides. To comprehend this phenomenon, our investigation involved simulations conducted on the α-synuclein peptides through the application of Molecular Dynamics (MD) simulation techniques under the influence of a 0.1 V/nm electric field. The results obtained from the MD simulations revealed that in the presence of external electric field, the monomer and oligomeric forms of α-synuclein are experienced significant conformational changes which could prevent them from further aggregation. However, as the number of peptide units in the model system increases, forming trimers and tetramers, the stability against the electric field also increases. This enhanced stability in larger aggregates indicates a critical threshold in α-synuclein assembly where the electric field’s effectiveness in disrupting the aggregation diminishes. Therefore, our findings suggest that early diagnosis and intervention could be crucial in preventing PD progression. When α-synuclein predominantly exists in its monomeric or dimeric form, applying even a lower electric field could effectively disrupt the initial aggregation process. Inhibition of α-synuclein fibril formation at early stages might serve as a viable solution to combat PD by halting the formation of more stable and pathogenic α-synuclein fibrils.

Theoretical Study of the Thermal Rate Coefficients of the H3+ + C2H4 Reaction: Dynamics Study on a Full-Dimensional Potential Energy Surface.

Ion-molecular reactions play a significant role in molecular evolution within the interstellar medium. In this study, the entrance channel reaction, H3+ + C2H4 → H2 + C2H5+, was investigated using classical molecular dynamic (classical MD) and ring polymer molecular dynamic (RPMD) simulation techniques. We developed an analytical potential energy surface function with a permutationally invariant polynomial basis, specifically employing the monomial symmetrized approach. Our dynamic simulations reproduced the rate coefficient of 300 K for H3+ + C2H4 → H2 + C2H5+, aligning reasonably well with the values in the kinetic database commonly utilized in astrochemistry. The thermal rate coefficients obtained using both the classical MD and RPMD techniques exhibited an increase from 100 K to 300 K as the temperature rose. Additionally, we analyzed the excess energy distribution of the C2H5+ fragment with respect to temperature to investigate the indirect reaction pathway of C2H5+ → H2 + C2H3+. This result suggests that the indirect reaction pathway of C2H5+ → H2 + C2H3+ holds minor significance, although the distribution highly depends on the collisional temperature.

Systematic Review of Computational Fluid Dynamics Modelling and Simulation Techniques Employed in Vertical Axis Hydrokinetic Turbines

At present, Computational Fluid Dynamics (CFD) is being utilized to explore tidal and hydrokinetic turbine systems, advancing comprehension of turbulent flow phenomena and raising the accuracy of performance predictions for these fluid-driven turbines. Consequently, this utilization of CFD contributes to the optimization of efficiency in these devices. Turbines are subject to variations from the best design point due to the influence of fluctuating flow rates, despite the findings of recent research that have identified the ideal design points. In contrast to conventional literature reviews, systematic analysis offers numerous advantages. The methodological strategy applied in this study entailed cross-referencing the findings obtained from Web of Science (WOS) and Scopus databases to establish the comprehensiveness as well as reliability of researcher data. Improving the review process, elevating the prominence of the field of study, and establishing critical priorities to mitigate research bias are all potential strategies for enhancing the quality of these evaluations. This research divides its findings into three core themes: (1) Performance assessment for practical implications, (2) Numerical analysis for theoretical insights, and (3) Design parameter optimization for engineering relevance. These themes collectively provide a well-rounded examination of the research outcomes across practical, theoretical, and engineering dimensions. Finally, the research findings have the potential to act as a significant point of reference for informing the best design considerations pertaining to vertical axis turbines.

Evolution Kinetics of Stabilizing Pickering Emulsion by Brush-Modified Janus Particles: DPD Simulation and Experimental Insights.

In the present study, we report the evolution of stabilizing Pickering emulsions using brush-modified Janus particles (JPs), utilizing the dissipative particle dynamics (DPD) simulation technique. Our results are subsequently corroborated with experimental findings. Each JP has one-half of the hydrophobic surface, with the other half embedded with hydrophilic polymer brushes grown via atom transfer radical polymerization (ATRP). Our generic simulation model analyzes the chemical kinetics of polymer brush growth on one-half of the initiator-embedded microparticle (MP) surface, resulting in the formation of JP. This involves evaluating monomer conversion and reaction rates. Our results exhibit a substantial influence of the number of JPs, grafted brush density, and brush length on oil-in-water emulsion stability. We studied the evolution kinetics and stability of emulsion formation by analyzing the growth of average domain size and corresponding scaling functions up to a late time limit. This study aims to clarify the connection between the size, quantity, and functionality of JPs and the stability of Pickering emulsions.

The intramolecular self-assembly of bidesmosidic kalopanaxsaponins

The phenomena of intramolecular self-assembly of bidesmosidic kalopanaxsaponins was identified for the first time in this paper. NMR (1H-NMR, NOESY), transmission electron microscopy (TEM), and molecular dynamics (MD) simulation techniques were used to compare the spatial structures of bidesmosidic kalopanaxsaponins and monodesmosidic kalopanaxsaponins. The results showed that the bidesmosidic kalopanaxsaponins formed a clustered and twisted structure in space, whereas the monodesmosidic kalopanaxsaponins were in an extended state. This discovery confirmed the presence of intramolecular self-assembly in bidesmosidic kalopanaxsaponins.

Discovery of Nine Dipeptidyl Peptidase-4 Inhibitors from Coptis chinensis Using Virtual Screening, Bioactivity Evaluation, and Binding Studies.

The objective of this study was to identify multiple alkaloids in Coptis chinensis that demonstrate inhibitory activity against DPP-4 and systematically evaluate their activity and binding characteristics. A combined strategy that included molecular docking, a DPP-4 inhibition assay, surface plasmon resonance (SPR), and a molecular dynamics simulation technique was employed. The results showed that nine alkaloids in Coptis chinensis directly inhibited DPP-4, with IC50 values of 3.44-53.73 μM. SPR-based binding studies revealed that these alkaloids display rapid binding and dissociation characteristics when interacting with DPP-4, with KD values ranging from 8.11 to 29.97 μM. A molecular dynamics analysis revealed that equilibrium was rapidly reached by nine DPP-4-ligand systems with minimal fluctuations, while binding free energy calculations showed that the ∆Gbind values for the nine test compounds ranged from -31.84 to -16.06 kcal/mol. The most important forces for the binding of these alkaloids with DPP-4 are electrostatic interactions and van der Waals forces. Various important amino acid residues, such as Arg125, His126, Phe357, Arg358, and Tyr547, were involved in the inhibition of DPP-4 by the compounds, revealing a mechanistic basis for the further optimization of these alkaloids as DPP-4 inhibitors. This study confirmed nine alkaloids as direct inhibitors of DPP-4 and characterized their binding features, thereby providing a basis for further research and development on novel DPP-4 inhibitors.

Analysis of Diffusion Characteristics and Influencing Factors of Particulate Matter in Ship Exhaust Plume in Arctic Environment Based on CFD

The gradual opening of the Arctic shipping route has made navigation possible. However, the harm caused by ship exhaust emissions is increasingly severe. Therefore, it is necessary to study the diffusion characteristics of ship exhaust plumes during Arctic navigation. The study focuses on a merchant vessel as the subject of investigation, employing computational fluid dynamics (CFD) simulation techniques to analyze the diffusion characteristics of particulate matter (PM) within ship exhaust plumes under Arctic environmental conditions. The diffusion law of ship exhaust plume PM is clarified, and the influence of three factors, synthetic wind speed, yaw angle and chimney angle, on the PM diffusion is analyzed. It was found that after the PM was discharged from the chimney, the majority of the PM dispersed directly backward along with the external flow field, while a minor fraction lingered at the stern of the ship for an extended period before eventually diffusing backward. Among them, 1235 particles were captured within a range of 200 m from the stern, with a capture rate of 0.6%. When the synthetic wind shows a yaw angle, the capture rate of PM in the interval increases rapidly with the increase of yaw angle, while other factors have less influence on the capture rate of PM. This study provides foundational guidance for predicting PM diffusion from ship exhaust plumes in Arctic environments, thereby enabling more effective strategies for managing such emissions.

Identification, characterization and biological studies of Kinesine spindle protein inhibitor, benzo[b] [1, 4]oxazine-6-carboxamide derivative, via 3D-pharmacophore virtual screening

Kinesin spindle protein (Eg5) has been widely studied, as an important target for developing chemotherapy drugs, due to its essential role in mitotic spindle formation in mitosis. In this study, we target a promising novel allosteric site involving α4 and α6 helices, which is located 15Å from the allosteric ispinesib site. An extensive 3D-Pharmacophore structure based virtual screening was conducted. Molecular docking was carried out to explore a library of commercial molecules. Eleven compounds were identified with diversity in their chemical scaffold. Biological evaluation and MT ATPase assays revealed that compound 11 with scaffold N-(2- (2, 6 -dimethylphenoxy) phenyl) -3, 4-dihydro -3-oxo -2H-benzo[b] [1,4]oxazine-6-carboxamide inhibits Eg5 activity at (IC50=1.37±0.15µM). The chemical structure of compound 11 was confirmed by 1H-NMR and mass spectral data. The stability of compound 11 within the Eg5-ADP/ATP complex was investigated using molecular dynamic simulation technique. The free binding energy was calculated using MM/PBSA.

Unveiling the tyrosinase inhibitory potential of phenolics from Centaurium spicatum: Bridging in silico and in vitro perspectives

Phenolics, abundant in plants, constitute a significant portion of phytoconstituents consumed in the human diet. The phytochemical screening of the aerial parts of Centaurium spicatum led to the isolation of five phenolics. The anti-tyrosinase activities of the isolated compounds were assessed through a combination of in vitro experiments and multiple in silico approaches. Docking and molecular dynamics (MD) simulation techniques were utilized to figure out the binding interactions of the isolated phytochemicals with tyrosinase. The findings from molecular docking analysis revealed that the isolated phenolics were able to bind effectively to tyrosinase and potentially inhibit substrate binding, consequently diminishing the catalytic activity of tyrosinase. Among isolated compounds, cichoric acid displayed the lowest binding energy and the highest extent of polar interactions with the target enzyme. Analysis of MD simulation trajectories indicated that equilibrium was reached within 30 ns for all complexes of tyrosinase with the isolated phenolics. Among the five ligands studied, cichoric acid exhibited the lowest interaction energies, rendering its complex with tyrosinase the most stable. Considering these collective findings, cichoric acid emerges as a promising candidate for the design and development of a potential tyrosinase inhibitor. Furthermore, the in vitro anti-tyrosinase activity assay unveiled significant variations among the isolated compounds. Notably, cichoric acid exhibited the most potent inhibitory effect, as evidenced by the lowest IC50 value (7.92 ± 1.32 µg/ml), followed by isorhamnetin and gentiopicrin. In contrast, sinapic acid demonstrated the least inhibitory activity against tyrosinase, with the highest IC50 value. Moreover, cichoric acid exhibited a mixed inhibition mode against the hydrolysis of l-DOPA catalyzed by tyrosinase, with Ki value of 1.64. Remarkably, these experimental findings align well with the outcomes of docking and MD simulations, underscoring the consistency and reliability of our computational predictions with the actual inhibitory potential observed in vitro.

Comparative assessment of different anti-CD147/Basigin 2 antibodies as a potential therapeutic anticancer target by molecular modeling and dynamic simulation.

Cluster of differentiation 147 (CD147) is an attractive target for anticancer therapy since it is pivotal in developing and progressing several of malignant tumors in the context of its high expression levels. Although anti-CD147 antibodies by different laboratories are designed for the Ig-like domains of CD147, there is a demand to provide priority among these anti-CD147 antibodies for developing of therapeutic anti-CD147 antibody before experimental validations. This study uses molecular docking and dynamic simulation techniques to compare the binding modes and affinities of nine antibody models against the Ig-like domains of CD147. After obtaining the model antibodies by homology modeling via Robetta, we predicted the CDRs of nine antibodies and the epitopes of CD147 to reach more accurate results for antigen affinity in molecular docking. Next, from HADDOCK 2.4., we meticulously handpicked the most superior model clusters (Z-Score: - 2.5 to - 1.2) and identified that meplazumab had higher affinities according to the success rate as the percentage of a scoring scale. We achieved stable simulations of CD147-antibody interaction. Our outcomes hold hypothetical importance for further experimental cancer research on the design and development of the relevant model antibodies.

Optimization of Cabin Virus Transmission Suppression Technology Based on Hanging Curtain Physical Isolation

This study presents an innovative physical isolation measure for commercial scenarios, namely, hanging curtains, to prevent the spread of respiratory infections. Using computational fluid dynamics simulation techniques, the closed spaces within cruise cabins were modeled and numerically analyzed, focusing on the dispersion characteristics of droplets. Additionally, orthogonal methods were employed to investigate various arrangements of hanging curtains and their effects on droplet dispersion based on spatial positioning. The research findings indicated that hanging curtains can effectively alter the airflow within a space, realizing the innovative concept of localized pollutant containment. It was found that the spatial partitioning method based on the location of individuals contributes more to reducing droplet dispersion than other methods. Moreover, the sag height of curtains emerges as the most influential factor on individual infection risk, while the scheme for hanging curtain positions has the least impact. Finally, the optimal configuration recommendation is provided: a curtain bottom coordinate of Z = 2.3 m and a top coordinate of Z = 2.8 m when the infection source was positioned at the center of the space. This configuration has also been validated by varying the location of the infection source. The research findings provide valuable insights for formulating preventive measures for passengers on cruise ships and for pandemic control in similar scenarios.

Molecular dynamics study on relaxation of supercooled liquid water at different cooling rates

The relaxation in supercooled liquids is a phenomena by which the thermodynamic system starts transforming from one state to other after losing its high end thermodynamic properties (i.e. density, potential energy, enthalpy, etc.) with a significant change. Since the relaxation phenomena is quite challenging to observe, specifically near the transition region of liquid water. Hence, the thermodynamic analysis for understanding the relaxation phenomena of liquid water in supercooled region from the high density liquid (HDL) state to low density amorphous (LDA) state are important from both fundamental and as well as applied perspectives. Therefore, we focused our study on performing thermodynamic analysis on the relaxation of super-cooled liquid water by using a monatomic water (mW) potential model with an isothermal-isobaric (NPT) molecular dynamics (MD) simulation technique at zero pressure under different cooling rates. In this work, we examine the relaxation in terms of root mean square (RMS) fluctuation of two and three-body potential energy of the maximum size of four coordinated cluster under different cooling rates. The predicted data over this study shows the independency of the cooling rate, where the relaxation of the liquid state of mW water results in a sharp irreversible drop in potential energy and large fluctuation in two and three body potential energy of the maximum size of four coordinated cluster. Further, we found the relaxation of liquid state of mW water associated with the sharp and continuous increase in the fraction of four coordinated particles as a function of temperature for different cooling rates. The predicted results of this study are consistent with the literature, which helps to understand the relaxation phenomena of mW water and other such thermodynamic systems more significantly.

Experimental screening and molecular dynamics simulation study on wetting agent in dry suspension

Suspension is the common preparation whose absorption rate is second only to the solution. However, problems like the difficulty in screening excipients and the complicated screening process limit its application to a certain extent. In this study, trimethoprim (TMP) was used as the research object. Compound sulfachlorpyridazine sodium Powder(CSSP) containing TMP was used as the research vector to explore the effects of wetting agent(WA), mixing processes between excipients and drug on the preparation stability from the perspectives of the change of the surface free energy between the drug powder and solvent, the reduction of the particle size of the drug, and the interaction between the drug and the excipients, serving the contact angle, sedimentation volume ratio, re-dispersibility, particle size, and appearance as indicators. In addition to that, taking the number density distribution, mean square displacement (MSD), and van der Waals force (VDW) as indicators, the molecular dynamics (MD) simulation technique was employed to explore the differences in the wetting ability of wetting agents (WAs) and the wetting mechanism of WAs on drug molecules. Suitable indicators were screened to provide new ideas for the initial screening of wetting agents from the simulation level and other solutions in tedious and time-consuming problems of experimental excipients screening.

Linking clean energy consumption, globalization, and financial development to the ecological footprint in a developing country: Insights from the novel dynamic ARDL simulation techniques

Developing countries have been facing economic difficulties for over three and a half decades due to numerous factors, including fossil fuel consumption and dwindling biocapacity. It is necessary to pinpoint the factors that may be culpable for poor environmental quality leading to a rising ecological footprint (EFP). This study explores the effect of clean energy, financial development (FDV), and globalization on the EFP in a developing country using the novel dynamic ARDL simulation techniques and the bootstrap causality test. The findings suggest that green energy has no meaningful impact on the EFP. Globalization and FDV significantly reduce the EFP by 0.25% and 0.08%, respectively. Besides, the findings confirm the existence of the EKC hypothesis. Furthermore, the causality results affirm a unidirectional causality from globalization and FDV to EFP, while economic growth drives globalization. Also, a one-way causality flows from globalization to FDV, just as FDV Granger causes green energy. In line with the findings, the study recommends that public policies focus on funding environmental-friendly technologies and green innovations. The funding must be on recently developed energy-saving technologies that can ensure complementarity between increased economic growth and environmental deterioration.

Molecular modeling studies of Indoline Scaffold derivatives as PD‐1/PD‐L1 pathway inhibitors by QSAR, molecular docking and molecular dynamics simulation techniques

AbstractIn recent years, blocking the interaction of programmed cell death receptor‐1 (PD‐1) and programmed cell death ligand‐1 (PD‐L1) has been recognized as one of the promising cancer therapies. Due to the many limitations of monoclonal antibodies, the development of small molecule inhibitors targeting PD‐1/PD‐L1 is imminent. This study aims to systematically investigate the interaction mechanisms of novel PD‐1/PD‐L1 inhibitors containing indoline backbone structures using 3D/2D‐QSAR modeling, molecular docking, molecular dynamics (MD) simulation, and ADMET prediction. The performance and predictive ability of the constructed QSAR models were evaluated by internal and external validation techniques. Topomer CoMFA and HQSAR models showed good reliability and predictive capability. By searching for R‐groups in the Topomer search module and combining the existing molecules with high activity contribution values, 24 new compounds with theoretically high activity were obtained, which showed desirable docking scores, appropriate ADMET properties, and good stability. This work not only provides a reliable QSAR model as a valuable screening tool for the development of future drugs targeting PD‐1/PD‐L1, but also makes the newly designed inhibitors expected to be potential PD‐1/PD‐L1 inhibitors that can be used for further synthesis and characterization to obtain novel anti‐cancer drugs targeting PD‐1/PD‐L1.

Dynamical arrest transition of a bidisperse two-patchy colloidal dispersion: A dynamic Monte Carlo study.

During the last few years, patchy colloidal dispersions have emerged as ideal candidates of glass-formers of systems composed of particles that interact with non-isotropic potentials. However, from the computational point of view, the characterization of their dynamical properties close to the glass transition via any kind of molecular dynamics simulation technique can be very difficult due to the slowing down of both the rotational and translational dynamics. Although a plethora of dynamical techniques have been developed to account for the dynamics of patchy colloids, new and complementary simulation techniques are required to explore, much faster and more efficiently, the dynamical arrest transition of patchy colloidal dispersions when computer simulation consists of a large number of particles and, due to the slow particle dynamics at the glass transition, an extended time window is explicitly required. Then, in this contribution, by means of the so-called dynamic-Monte Carlo method, we report on the dynamical arrest transition, both rotational and translational, of a bidisperse patchy colloidal dispersion, following three different paths along the density-temperature plane, including high densities and low temperatures. Although this method has not been extensively tested at extreme thermodynamic conditions, we show that even at the dynamical arrest transition, it allows us to extract good dynamical data from a complex system. Therefore, it turns out to be a promising technique to explore the onset of vitrification of anisotropic colloidal particles.

FEM dynamic simulation technique for membrane structure deployment and model evaluation

This study developed a finite element method (FEM) dynamic simulation to visualize the deployment behavior of thin membrane structures in the space environment. The proliferation of space debris resulting from accelerated space development threatens the future of space. Numerous researchers have explored strategies to prevent artificial structures from remaining in space and becoming space debris. One such method involves utilizing a drag sail device to de-orbit artificial structures, which reduces their kinetic energy by inducing additional atmospheric drag, allowing them to re-enter the Earth's atmosphere. Tohoku University and Nakashimada Engineering Works, Ltd. have successfully developed a deployable membrane structure for de-orbit purposes and demonstrated its effectiveness in space. Space structures, such as membranes, exhibit highly nonlinear behavior due to their flexible properties, and ground tests by actual devices cannot fully demonstrate their deployment stability in a microgravity environment. Therefore, evaluating the deployment behavior using simulation methods instead of relying solely on hardware development is crucial. In this study, we employed FEM to establish a simulation environment, which enables us to consider nonlinear oscillations of flexible structures, such as the membrane. The simulation results closely reproduce the deployment motion observed in ground tests by appropriately incorporating constraint conditions related to deployment forces and hardware interactions, such as a hub component initially wrapped by the membrane. The simulation facilitated an assessment of the impact of membrane properties on deployment without the need for physically developing an actual hardware device. We proposed evaluation methods for determining membrane properties in terms of the trend of propagation of deployed surface area and the tendency of deployment motion. This established simulation technique can be utilized to develop future flexible space structures.

Investigation on the molecular interaction between dietary flavone luteolin and alpha-2-macroglobulin using multi-spectroscopic, calorimetric and molecular dynamics simulation techniques

The current study examined the mechanism of interaction between luteolin and human αlpha-2-macroglobulin (α2M) to determine the binding mode and the interaction of the ligand using biophysical and molecular modelling methods. The UV-absorbance confirmed the formation of a complex between α2M and luteolin. Luteolin considerably reduced the intrinsic fluorescence of α2M via dynamic quenching determined by fluorescence quenching. The binding process was spontaneous and moderate (Kb = 0.70 × 104 M−1, 300 K), and the hydrophobic interaction was a significant factor in their interaction. With increasing luteolin concentration, the anti-proteolytic activity of α2M declines by approximately 35 % of its native functional activity. Förster energy was used to determine the energy transfer and the binding distance between the ligand and the protein which was found to be 2.77 nm for the α2M-luteolin complex in accordance with fluorescence resonance energy transfer (FRET). Synchronous fluorescence and red-edge excitation shift (REES) data were used to determine the changes in the microenvironment around Tyr and Trp residues in the presence of luteolin. The circular dichroism (CD) showed changes in conformation upon binding of luteolin to α2M. The Fourier transform infrared spectroscopy (FTIR) spectra provided additional evidence that the secondary structure of α2M was considerably altered by the addition of luteolin. The molecular docking simulation revealed that, in addition to hydrophobic interactions, the hydrogen bonds were involved in the interaction of α2M-luteolin complex.