Spermine as a porcine pancreatic elastase activator: spectroscopic and molecular simulation studies

Abstract

The aim of this study was to investigate the spermine effect on the thermal denaturation, conformation and activity of elastase at three temperatures of 303, 313 and 323?K in the Tris buffer, at pH 8.5, using UV–vis spectrophotometry, spectrofluorometry and circular dichroism as well as molecular docking and molecular simulation. The increased absorption of elastase in the presence of spermine suggested a change in the environment of tryptophan. It was found that under the influence of spermine, the emission intensity of elastase extremely was reduced, and the use of the Stern-Volmer equation showed that some static quenching had occurred. The thermodynamic parameters values (enthalpy and entropy) and the molecular docking technique also revealed that van der Waals forces or hydrogen bonding interactions played an important role in the binding process. The spermine–elastase complex formation led to increasing the value of the catalytic constant (k_cat). So it could be considered as an activator. Slight changes were observed in the second structure of elastase (1.06% increase for the α-helix and 0.048% decrease the β-sheet) and the thermal stability effect. Molecular docking results also demonstrated that spermine could bind to porcine pancreatic elastase, and van der Waals forces or hydrogen bonding interactions played the major role in the binding process. Overall, our results showed that spermine could induce structural alterations in elastase, acting as a partial stabilizer and an activator for the enzyme.

Communicated by Ramaswamy H. Sarma     

Exploring the thermal stability and activity of α-chymotrypsin in the presence of spermine

Polyamines such as spermine can have interaction with protein. The aim of the present study was to investigate how spermine could influence the structure, thermal stability, and the activity of α-chymotrypsin. Kinetics, thermodynamics, molecular dynamics (MD), and docking simulations studies were conducted to investigate the effect of spermine on the activity and structure of α-Chymotrypsin (α-Chy) in 50 mM Tris–HCl buffer, with the pH 8, using different spectroscopic techniques as well as molecular docking and MD simulations. The stability and activity of α-Chy were increased in the presence of spermine. The results of the kinetic study showed that the activity of spermine was increased. Enzyme activation was accompanied by changes on the α-Chy conformation. Fluorescence intensity changes showed dynamic quenching during spermine binding. The fluorescence quenching of the α-Chy suggested the more polar location of Trp residues. Near-UV and Far-UV circular dichroism studies also demonstrated the transfer of Trp, Phe, and Tyr residues to a more flexible environment. The increase in the absorption of α-Chy in the presence of spermine was as a result of the formation of spermine–α-Chy complex. Molecular docking results revealed the presence of one binding site with a negative value for the Gibbs free energy of the binding of spermine to α-Chy. Docking study also revealed that van der Waals interactions and hydrogen bonds played a major role in stabilizing the complex.     

Interaction studies of aristolochic acid I with human serum albumin and the binding site of aristolochic acid I in subdomain IIA

Optical spectroscopy and molecular docking methods were used to examine the binding of aristolochic acid I (AAI) to human serum albumin (HSA) in this paper. By monitoring the intrinsic fluorescence of single Trp214 residue and performing displacement measurements, the specific binding of AAI in the vicinity of Sudlow's Site I of HSA has been clarified. An apparent distance of 2.53 nm between the Trp214 and AAI was obtained via fluorescence resonance energy transfer (FRET) method. In addition, the changes in the secondary structure of HSA after its complexation with the ligand were studied with circular dichroism (CD) spectroscopy, which indicated that AAI does not has remarkable effect on the structure of the protein. Moreover, thermal denaturation experiments clearly indicated that the HSA−AAI complexes are conformationally more stable. Finally, the binding details between AAI and HSA were further confirmed by molecular docking studies, which revealed that AAI was bound at subdomain IIA through multiple interactions, such as hydrophobic effect, van der Waals forces and hydrogen bonding.     

Hydrogen bonding-assisted interaction between amitriptyline hydrochloride and hemoglobin: spectroscopic and molecular dynamics studies

Herein, we have explored the interaction between amitriptyline hydrochloride (AMT) and hemoglobin (Hb), using steady-state and time-resolved fluorescence spectroscopy, UV–visible spectroscopy, and circular dichroism spectroscopy, in combination with molecular docking and molecular dynamic (MD) simulation methods. The steady-state fluorescence reveals the static quenching mechanism in the interaction system, which was further confirmed by UV–visible and time-resolved fluorescence spectroscopy. The binding constant, number of binding sites, and thermodynamic parameters viz. ΔG, ΔH, ΔS are also considered; result confirms that the binding of the AMT with Hb is a spontaneous process, involving hydrogen bonding and van der Waals interactions with a single binding site, as also confirmed by molecular docking study. Synchronous fluorescence, CD data, and MD simulation results contribute toward understanding the effect of AMT on Hb to interpret the conformational change in Hb upon binding in aqueous solution.     

Interaction between azo dye Acid Red 14 and pepsin by multispectral methods and docking studies

The interaction of synthetic azo dye Acid Red 14 with pepsin was studied by fluorescence spectroscopy, UV–vis spectroscopy, circular dichroism and molecular docking. Results from the fluorescence spectroscopy show that Acid Red 14 has a strong capability to quench the intrinsic fluorescence of pepsin with static quenching. Binding constant, number of the binding sites and thermodynamic parameters were measured at different temperatures. The result indicates that Acid Red 14 interact with pepsin spontaneously by hydrogen bonding and van der Waals interactions. Three‐dimensional fluorescence spectra and circular dichroism spectra reveal that Acid Red 14 could slightly change the structure of pepsin. The hydrogen bond is formed between Acid Red 14 and Tyr‐189 and Thr‐218 residues of pepsin. Furthermore, the binding between Acid Red 14 and pepsin inhibits pepsin activity. The study can provide a way to analyze the biological safety of Acid Red 14 on digestive proteases or other proteins.     

Spectroscopic and molecular docking studies on interaction of two Schiff base complexes with bovine serum albumin

Abstract

This study was designed to examine interaction of two ternary copper (II) Schiff base complexes with bovine serum albumin (BSA), using spectroscopic and molecular docking techniques. The fluorescence quenching measurements revealed that the quenching mechanism was static and the binding site of both Schiff bases to BSA was singular. Förster energy transfer measurements, synchronous fluorescence spectroscopy, and docking study showed both Schiff bases bind to the Trp residues of BSA in short distances. Docking study showed that both Schiff base molecules bind with BSA by forming several hydrogen and van der Waals bonds. In addition, molecular docking study indicated that Schiff base A and Schiff base B were located within the binding pocket of subdomain IB and subdomain IIA of BSA, respectively. Results of Fourier transform-infrared spectroscopy demonstrated that bovine serum albumin interacts with both Schiff bases and the secondary structure of BSA was changed.

Communicated by Ramaswamy H. Sarma     

Probing the Interaction between Acotiamide Hydrochloride and Pepsin by Multispectral Methods,Electrochemical Measurements,and Docking Studies

The interaction between acotiamide hydrochloride and pepsin was systematically characterized by fluorescence and electrochemical approaches. Fluorescence lifetime measurements showed that acotiamide hydrochloride quenched the intrinsic fluorescence of pepsin with a new complex formation via static mode, which was reconfirmed by cyclic voltammetry results. Both of the binding number and binding constants were calculated from differential pulse voltammetry analysis and fluorescence spectroscopy. The values obtained from the above two methods displayed a relatively high degree of consistency. Thermodynamic parameters suggested that acotiamide hydrochloride interacted with pepsin spontaneously by hydrogen bonding and van der Waals interactions. These results were consistent with the results obtained from molecular docking analysis. As revealed by synchronous fluorescence, three‐dimensional fluorescence, Fourier transform infrared spectrometry, and circular dichroism spectra, acotiamide hydrochloride could affect the microenvironment and slightly change the secondary structure of pepsin. Furthermore, acotiamide hydrochloride can inhibit pepsin activity in vitro, as explained by the molecular docking.     

Spectroscopic investigation of the effects of aqueous‐phase prepared CdTe quantum dots on protein hemoglobin at the molecular level

3‐Mercaptopropionic Acid‐modified CdTe quantum dots (QDs) were synthesized and characterized by infrared, fluorescence, and ultraviolet–visible absorption spectra and Nano‐ZetaSizer measurements. Then the interaction between QDs and hemoglobin was studied to investigate the effects of QDs on the structure and function of hemoglobin by using a variety of spectroscopy methods and isothermal titration calorimetry. The results showed van der Waals forces and hydrogen bonding predominantly played major roles in the binding. The intrinsic fluorescence of hemoglobin was quenched with changes to the microenvironment of tyrosine and tryptophan residues and complex conformational changes of hemoglobin were induced with the loosening and unfolding skeleton. However, the heme in hemoglobin was still stable, indicating that the main physiological function of hemoglobin might not be significantly inhibited. This study will provide a new strategy to study the biological toxicity of QDs at the molecular level.     

Interaction of colchicine with human serum albumin investigated by spectroscopic methods

We investigated the interaction between colchicine and human serum albumin (HSA) by fluorescence and UV-vis absorption spectroscopy. In the mechanism discussion, it was proved that the fluorescence quenching of HSA by colchicine is a result of the formation of colchicines-HSA complex; van der Waals interactions and hydrogen bonds play a major role in stabilizing the complex. The modified Stern-Volmer quenching constant K(a) and corresponding thermodynamic parameters deltaH, deltaG, deltaS at different temperatures were calculated. The distance r between donor (Trp214) and acceptor (colchicine) was obtained according to fluorescence resonance energy transfer (FRET).     

Investigation on the Interaction of Norgestrel with Human Serum Albumin Using Spectroscopy and Molecular‐Docking Method

The interaction of norgestrel with human serum albumin (HSA) was investigated by spectroscopy and molecular‐docking methods. Results of spectroscopy methods suggested that the quenching mechanism of norgestrel on HSA was static quenching and that the quenching process was spontaneous. Negative values of thermodynamic parameters (ΔG, ΔH, and ΔS) indicated that hydrogen bonding and van der Waals forces dominated the binding between norgestrel and HSA. Three‐dimensional fluorescence spectrum and circular dichroism spectrum showed that the HSA structure was slightly changed by norgestrel. Norgestrel mainly bound with Sudlow site I based on a probe study, as confirmed by molecular‐docking results. Competition among similar structures indicated that ethisterone and norethisterone affected the binding of norgestrel with HSA. CH₃ in R₁ had little effect on norgestrel binding with HSA. The surface hydrophobicity properties of HSA, investigated using 8‐anilino‐1‐naphthalenesulfonic acid, was changed with norgestrel addition.     

Interaction of (-)-epigallocatechin-3-gallate with human serum albumin: fluorescence, fourier transform infrared, circular dichroism, and docking studies

(-)-Epigallocatechin-3-gallate (EGCG), the major constituent of green tea has been reported to prevent many diseases by virtue of its antioxidant properties. The binding of EGCG with human serum albumin (HSA) has been investigated for the first time by using fluorescence, circular dichroism (CD), Fourier transform infrared (FTIR) spectroscopy, and protein-ligand docking. We observed a quenching of fluorescence of HSA in the presence of EGCG. The binding parameters were determined by a Scatchard plot and the results were found to be consistent with those obtained from a modified Stern-Volmer equation. From the thermodynamic parameters calculated according to the van't Hoff equation, the enthalpy change deltaH degrees and entropy change deltaS degrees were found to be -22.59 and 16.23 J/mol K, respectively. These values suggest that apart from an initial hydrophobic association, the complex is held together by van der Waals interactions and hydrogen bonding. Data obtained by fluorescence spectroscopy, CD, and FTIR experiments along with the docking studies suggest that EGCG binds to residues located in subdomains IIa and IIIa of HSA. Specific interactions are observed with residues Trp 214, Arg 218, Gln 221, Asn 295 and Asp 451. We have also looked at changes in the accessible surface area of the interacting residues on binding EGCG for a better understanding of the interaction.     

胡椒碱分子键合人血清白蛋白位点的表征

利用荧光光谱法、紫外光谱法并结合计算机模拟技术在分子水平上研究了胡椒碱与人血清白蛋白(human serum albumin HSA)的键合作用.同步荧光及紫外光谱图表明,胡椒碱对HSA微环境有影响.位点竞争试验证明,胡椒碱分子键合在HSA的位点Ⅱ区.通过荧光光谱滴定数据求得不同温度下(300K 310K和318 K)药物与蛋白相互作用的结合常数及结合位点数.分子模拟的结果显示了胡椒碱与HSA的键合区域和键合模式,表明药物与蛋白有较强的键合作用;维持药物与蛋白质的相互作用力主要是疏水用,兼有氢键(位于氨基酸残基Arg 257,Arg 222及Arg218位).通过实验数据计算得到的热力学参数(ΔH0与ΔS0的值分别为原33.11 kJ·mol-1和原18.90 J·mol原1·K-1)确定了胡椒碱与HSA分子的相互作用力类型主要为氢键兼范德华力.     

NMR investigations of protein-carbohydrate interactions binding studies and refined three-dimensional solution structure of the complex between the B domain of wheat germ agglutinin and N,N', N"-triacetylchitotriose.

The specific interaction of the isolated B domain of wheat germ agglutinin (WGA-B) with N,N',N"-triacetylchitotriose has been analyzed by 1H-NMR spectroscopy. The association constants for the binding of WGA-B to this trisaccharide have been determined from both 1H-NMR titration experiments and microcalorimetry methods. Entropy and enthalpy of binding have been obtained. The driving force for the binding process is provided by a negative DeltaH which is partially compensated by negative DeltaS. These negative signs indicate that hydrogen bonding and van der Waals forces are the major interactions stabilizing the complex. NOESY NMR experiments in water solution provided 327 protein proton-proton distance constraints. All the experimental constraints were used in a refinement protocol including restrained molecular dynamics in order to determine the refined solution conformation of this protein/carbohydrate complex. With regard to the NMR structure of the free protein, no important changes in the protein NOEs were observed, indicating that carbohydrate-induced conformational changes are small. The average backbone rmsd of the 35 refined structures was 1.05 A, while the heavy atom rmsd was 2.10 A. Focusing on the bound ligand, two different orientations of the trisaccharide within WGA-B binding site are possible. It can be deduced that both hydrogen bonds and van der Waals contacts confer stability to both complexes. A comparison of the three-dimensional structure of WGA-B in solution to that reported in the solid state and to those deduced for hevein and pseudohevein in solution has also been performed.     

A Minimal or Concise Set of Definition of Life is Not Useful

The binding of ciprofloxacin to lysozyme in the presence of three Ag nano-particles of varying sizes was for the first time investigated by multispectroscopic and isothermal titration calorimetry techniques at pH 7.4. The results indicated that ciprofloxacin quenched the fluorescence intensity of lysozyme through a static mechanism but in the presence of size-II Ag nano-particles, there were two kinds of interaction behaviors. The interaction between ciprofloxacin and lysozyme occurred via a second type of binding site, whereas in the presence of the Ag nano-particles, some changes occurred. The secondary structure of lysozyme–ciprofloxacin in the presence of Ag nano-particles was determined by circular dichroism. The thermodynamic parameters of the interaction between ciprofloxacin and lysozyme in the presence of Ag nano-particles were measured according to the van’t Hoff equation. The enthalpy (ΔH^○) and entropy (ΔS^○) changes were calculated to be ?49.7 (kJ?mol^?1) and ?20.1 (J?mol^?1?K^?1), respectively, which indicated that the interaction of ciprofloxacin with lysozyme was driven mainly by van der Waals forces and hydrogen bonding. In the presence of the three different-sized Ag nano-particles, the enthalpic and the entropic changes were both negative which indicated that hydrogen bonding with van der Waals forces played major roles in the binding between ciprofloxacin and lysozyme. Recent developments in nano-materials offer new pathways for controlling the protein behavior through surface interactions. These data indicate that the recent research on nano-particle/protein interactions will emphasize the importance of such interactions in biological systems with applications including the diagnosis and treatment of human diseases.     

Molecular interaction of manganese based carbon monoxide releasing molecule (MnCORM) with human serum albumin (HSA)

In the present study, the interaction between the HSA and MnCORM in vitro under physiological conditions, was investigated through ultraviolet-visible (UV-vis) absorption, fluorescence, time-resolved fluorescence, circular dichroism (CD), Fourier transform infrared (FT-IR) spectroscopic techniques and in silico molecular docking methods. Binding parameters such as the binding constant, number of binding sites and binding force were obtained from the fluorescence data. Thermodynamic interaction revealed that the reaction was spontaneous (ΔG < 0) and hydrogen bond and van der Waals interaction were primarily involved in the binding. The changes induced in the secondary structure conformation due to the MnCORM interaction were monitored using CD and FT-IR spectroscopic techniques. The results showed reduction in α-helix conformation and corresponding increase in β-sheet and unordered structures due to slight unfolding. The time-resolved fluorescence decay confirmed the static quenching mechanism of the MnCORM. The molecular docking studies revealed that the MnCORM interacted at Sudlow’s site II of domain IIIA through hydrogen bond and van der Waals interactions. In order to understand the drug distribution and elimination, studies on the drug molecule interaction with HSA are vital. Therefore, it is evident that MnCORM interacts with HSA through ground state complex formation and thus suitable for in vivo delivery.     

Investigation and comparison of the binding between tolvaptan and pepsin and trypsin: Multi‐spectroscopic approaches and molecular docking

Tolvaptan (TF), a selective arginine vasopressin V2 receptor antagonist, was approved by the Food and Drug Administration in 2009. This study mainly investigated the differences between the binding of TF with pepsin and trypsin by using a series of spectroscopy and molecular modeling methods. Thermodynamic parameters and molecular docking results suggested that the binding of TF to pepsin and trypsin were both spontaneous but driven by different forces. For pepsin, the binding was driven by hydrogen bonds and van der Waals forces; but for trypsin, it was driven by electrostatic forces and hydrophobic forces. The quenching mechanism between TF and pepsin and trypsin was investigated by fluorescence experiments and time‐resolved fluorescence spectroscopy. Synchronous fluorescence and 3‐dimensional fluorescence were used to investigate the micro‐environmental and conformational changes of pepsin and trypsin after the insertion of TF. In addition, activity‐measurement results showed that both the pepsin and trypsin activities increased with increasing TF concentration, which may help to understand the possible effect of TF on the digestion and absorption of nutrients in vivo.     

Studies on binding interactions between clenbuterol hydrochloride and two serum albumins by multispectroscopic approaches in vitro

In this study, binding properties of clenbuterol hydrochloride (CL) with human serum albumin (HSA) and bovine serum albumin (BSA) were examined using constant protein concentrations and various CL contents under physiological conditions. The binding parameters were confirmed using fluorescence quenching spectroscopy at various temperatures. The experimental results confirmed that the quenching mechanisms of CL and HSA/BSA were both static quenching processes. The thermodynamic parameters, namely, enthalpy change (ΔH) and entropy change (ΔS), were calculated according to the van't Hoff equation, which suggested that the electrostatic interactions were the predominant intermolecular forces in stabilizing the CL–HSA complex, and hydrogen bonds and van der Waals force were the predominant intermolecular forces in stabilizing the CL–BSA complex. Furthermore, the conformational changes of HSA/BSA in the presence of CL were determined using the data obtained from three‐dimensional fluorescence spectroscopy, ultraviolet‐visible absorption spectroscopy and circular dichroism spectroscopy. Copyright © 2013 John Wiley & Sons, Ltd.     

Spectroscopic and computational approaches to unravel the mode of binding between a isoflavone,biochanin-A and calf thymus DNA

In the present study, attempt was made to explore the interaction between biochanin-A (BioA) and calf thymus DNA (ctDNA) by employing fluorescence spectroscopy, absorption spectroscopy, circular dichroism (CD), DNA melting studies, viscosity measurements, and molecular modeling methods. A well-known fluorescence probe, acridine orange (AO) was used in the present study in order to enhance the emission intensity of weakly fluorescent ctDNA. Quenching in emission intensity of ctDNA-AO system was observed in the presence of different concentrations of BioA, suggesting that BioA has interacted with ctDNA. The hyperchromic effect observed upon the addition of BioA in the absorption spectra of ctDNA-AO without any shift in its absorption maximum revealed that BioA was bound to ctDNA through groove mode of binding. Further the groove mode of binding of BioA to ctDNA was confirmed by DNA melting studies, viscosity measurements, and molecular docking studies. The results of fluorescence measurements that were carried out at different temperature indicated that the BioA has quenched the emission intensity of ctDNA-AO through static mode of quenching mechanism. Thermodynamic parameters revealed that the BioA-ctDNA-AO system was stabilized by van der Waals forces and hydrogen bonding. The effect of binding of BioA on the conformation of ctDNA was examined by circular dichroism studies.     

Binding mechanism of trans-N-caffeoyltyramine and human serum albumin: Investigation by multi-spectroscopy and docking simulation

trans-N-Caffeoyltyramine (TNC), which was isolated from the Cortex Lycii in our laboratory, is a phenolic amide compound with multiple pharmacological activities. The interaction between TNC and human serum albumin (HSA) was studied by Nuclear magnetic resonance (NMR) relaxation experiment, fluorescence spectroscopy, and docking simulation. NMR methodology is based on the analysis of selective and non-selective spin-lattice relaxation rate enhancements of TNC protons in the presence of the HSA. Result indicated that the interaction occurred between HSA and TNC, and changed the proton magnetic environment of TNC. Fluorescence spectroscopy confirmed that TNC displayed a strong capability to quench the fluorescence of HSA, and the acting forces for binding were hydrogen bonds and van der Waals forces. Furthermore, the circular dichroism, synchronous, and three-dimensional fluorescence spectra, which were employed to determine the conformation of protein, revealed that binding of TNC with HSA could induce conformational changes in HSA. In addition, the molecular modeling results exhibited that TNC mainly bonded to site I in sub-domain IIA of HSA.     

Investigation of binding properties of dicationic styrylimidazo[1,2‐a]pyridinium dyes to human serum albumin by spectroscopic techniques

The binding interaction between two dicationic styrylimidazo[1,2‐a]pyridinium dyes and human serum albumin (HSA) was investigated at physiological conditions using fluorescence, UV–vis absorption, and circular dichroism (CD) spectroscopies. Analysis of the fluorescence titration data at different temperatures suggested that the fluorescence quenching mechanism of HSA by these dyes was static. The calculated thermodynamic parameters (ΔG°, ΔH° and ΔS°) indicated that hydrogen bonding and van der Waals forces played a major role in the formation of the dye–HSA complex. Binding distances (r) between dyes and HSA were calculated according to Förster's non‐radiative energy transfer theory. Studies of conformational changes of HSA using CD measurements indicate that the α‐helical content of the protein decreased upon binding of the dyes. Copyright © 2016 John Wiley & Sons, Ltd.