Mechanism of interaction between urolithin A and α-glucosidase: Analysis by inhibition kinetics, fluorescence spectroscopy, isothermal titration calorimetry and molecular docking
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Isothermal Titration Calorimetry
Hydrophobic effect
AutoDock
Docking (animal)
Isothermal Titration Calorimetry
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Interaction of curcumin to dipeptydyl peptidase-4 (DPP-4) has been studied by employing docking method using Molecular Operating Environment (MOE) and AutoDock as the docking software applications. Although MOE can sample more conformational spaces that represent the original interaction poses than AutoDock, both softwares serve as valid and acceptable docking applications to study the interactions of small compound to DPP-4. The calculated free energy of binding (DGbinding) results from MOE and AutoDock shows that curcumin is needed to be optimized to reach similar or better DGbinding compare to the reference compound. Curcumin can be considered as a good lead compound in the development of new DPP-4 inhibitor. The results of these studies can serve as an initial effort of the further study. Keywords: curcumin, docking, molecular operating environment (MOE), AutoDock, dipeptydyl peptidase-4 (DPP-4)
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The interaction of chrysophanol with bovine serum albumin(BSA) was investigated by fluorescence spectroscopy,synchronous fluorescence spectroscopy and molecular modeling techniques at different temperatures.The experimental results suggested that static quenching was the main reason for the fluorescence quenching process.Thermodynamic studies showed that the change for Gibbs free energy of the binding was a large negative value,which indicated that the interaction of chrysophanol with BSA was driven mainly by hydrophobic force.The results of molecular modeling indicated that there was not only hydrophobic interaction on the binding of chrysophanol to BSA,but there was also hydrogen bonding.The results of molecular modeling are in good agreement with those of spectral and thermodynamic studies.
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Perfluorononanoic acid (PFNA) is the third most frequently detected in serum among all perfluoroalkyl acids (PFAAs) which is a kind of toxic emerging environmental contaminant. The influence of PFNA on the conformation and even function of human serum albumin (HSA) is still just at the beginning of research. The attempt of this paper was to completely elucidate the interaction mechanism of PFNA with HSA by means of multi-spectroscopic, molecular docking and isothermal titration calorimetry (ITC) techniques. The inner filter effect of all fluorescence data in the paper was eliminated to get accurate binding parameters. The results showed that the fluorescence of HSA was quenched by PFNA through a combined quenching procedure of dynamic and static quenching. Through site marker competitive experiments, subdomain IIA of HSA had been assigned to possess the high-affinity binding site of PFNA. Furthermore, molecular docking reconfirmed that PFNA was bound in subdomain IIA mainly through polar force, hydrophobic interaction and halogen-bond, and the calculated free energy was -26.54 kJ·mol(-1) which indicated that the PFNA molecule exhibited large binding affinity towards HSA. The thermodynamic characterizations of two different classes of binding sites by ITC displayed that the first class with a higher affinity constant was dominated by an enthalpic contribution due to electrostatic interactions and halogen-bond, whereas the second class with a lower affinity constant was preponderated by hydrophobic interaction. The three-dimensional fluorescence revealed that the conformation of HSA was changed and the hydrophobicity of the Trp and Tyr residues microenvironment increased after formation of PFNA-HSA complex. The alterations of the protein secondary structure were quantitatively calculated from circular dichroism (CD) spectroscopy with reduction of α-helix content about 14.3%, β-sheet 5.3%, β-turn 3.5%, and augment in random content from 14.4% to 37.5%. Above results revealed that the binding of PFNA with HSA can alter the secondary structure of HSA, further probably affecting HSA physiological function. The results can provide insights with the binding mechanism of PFNA with HSA and salient biophysical and biochemical clues on elucidating the transport and distribution of PFNA in vivo.
Isothermal Titration Calorimetry
Human serum albumin
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Hydrophobic interaction chromatography is a very popular chromatography method for purification of proteins and plasmids in all scales from analytical to industrial manufacturing. Despite this frequent use, the complex interaction mechanism and the thermodynamic aspects of adsorption in hydrophobic interaction chromatography are still not well understood. Calorimetric methods such as isothermal titration calorimetry and flow calorimetry can help to gain a deeper understanding of the adsorption strength, the influence of salt type and temperature. They can be used to study conformational changes of proteins, which are often associated with the adsorption in hydrophobic interaction chromatography. This review offers a detailed introduction into the thermodynamic fundamentals of adsorption in hydrophobic interaction chromatography with a special focus on the potential applications of isothermal titration calorimetry and flow calorimetry for studying specific problems and relationships of the adsorption behavior of proteins and its various influencing factors. Models for characterizing conformational changes upon adsorption are presented together with methods for assessing this problem for different proteins and stationary phases. All of this knowledge can contribute greatly to forming a sound basis for method development, process optimization and finding modelling strategies in hydrophobic interaction chromatography.
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生体分子間の相互作用解析法として等温滴定型カロリメトリー（Isothermal Titration Calorimetry; ITC）が古くから用いられている．近年，検出感度の向上と測定サンプルの微量化を達成した測定装置が市販されるようになったことから，今後その利用頻度はさらに高くなっていくものと思われる．ITC測定は，一度の測定で相互作用の熱力学的パラメータのフルセットを得ることができるという点において，表面プラズモン共鳴法やその他の分光学的方法による相互作用解析系とは一線を画している．本稿では筆者らが行った糖質加水分解酵素–基質間相互作用解析の例を中心に，ITC測定の原理と一般的な使用法に加えて，酵素の基質結合メカニズムに迫るより詳細な解析法について述べる．
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This study investigated the binding mechanism between proteins and hydrophobic adsorbents from a thermodynamics aspect. The proteins investigated here included lysozyme, myoglobin, and α-amylase. The binding isotherms were obtained for the proteins with butyl-sepharose and octyl-sepharose resins at various temperatures and salt concentrations. The binding isotherms were then analyzed using the van't Hoff equation, and the binding enthalpy and entropy of each step of the binding process are discussed. Moreover, the effects of ligand chain length and protein characteristics were also investigated. Notably, the preferential interaction model has been adopted in the discussion of the dehydration step in the binding mechanism. The analytical results show that the binding process is entropy-dominated at higher temperature and the amount of released water molecules increases with temperature. Furthermore, the binding enthalpy (ΔHvH) and heat capacity were calculated by the van't Hoff and Kirchoff equations and were compared with the directly measured enthalpy (ΔHITC) by isothermal titration calorimetry. The analytical results provide useful insights into hydrophobic interaction in biorecognition systems.
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One of the key factors of Alzheimer's disease (AD) is the conversion of amyloid β-peptide (Aβ) from its soluble random coil form into various aggregated forms. (−)-Epigallocatechin-3-gallate (EGCG) has been proved effective in preventing the aggregation of Aβ, but the thermodynamic mechanisms are still unclear. In this work, isothermal titration calorimetry (ITC) was utilized to study the interactions between Aβ42 and EGCG at different temperatures, salt concentrations, pH values, and EGCG and Aβ42 concentrations. Molecular dynamics (MD) simulations were performed to study the hydrogen bonding between Aβ42 and EGCG. The results indicate that the binding stoichiometry N is linearly related to the EGCG/Aβ42 ratio. Hydrophobic interaction and hydrogen bonding are both substantial in the binding process, but the extent of their contributions changes with experimental conditions. Namely, the predominant interaction gradually shifts from a hydrogen bonding to a hydrophobic interaction with the increase of the EGCG/Aβ42 ratio, resulting in a transition of the binding from enthalpy-driven to entropy-driven. This experimental observation is validated by the MD simulations. The binding of EGCG to Aβ42 can be promoted by increasing temperature and salt concentration and changing pH away from Aβ42′s pI. The findings have provided new insight into the molecular interactions between Aβ42 and EGCG from a thermodynamic perspective and are expected to facilitate the research on the inhibition of Aβ42 aggregation.
Isothermal Titration Calorimetry
Hydrophobic effect
Gallate
Stoichiometry
Random coil
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The interaction between dehydroeburicoic acid (DeEA), a triterpene purified from medicinal fungi and the major transport protein, human serum albumin (HSA), were systematically studied by fluorescence spectroscopy, synchronous fluorescence spectroscopy, three-dimensional fluorescence spectroscopy and molecular docking approach under simulated physiological conditions. The intrinsic fluorescence of HSA was quenched through the combination of static and dynamic quenching mechanism. DeEA cannot be stored and carried by HSA in the body at higher temperature. The hydrogen bonding, hydrophobic force and van der Waals force were major acting forces. The site II was the major binding site. The energy transfer could occur with high probability and the binding distance was 3.29 nm. The binding process slightly changed the conformation and microenvironment of HSA. The DeEA molecule entered the hydrophobic cleft of HSA and formed the hydrogen bonding with Glu-492 and Lys-545.
Human serum albumin
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