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.     

Binding of caffeine with caffeic acid and chlorogenic acid using fluorescence quenching,UV/vis and FTIR spectroscopic techniques

The interactions of caffeine (CF) with chlorogenic acid (CGA) and caffeic acid (CFA) were investigated by fluorescence quenching, UV/vis and Fourier transform infrared (FTIR) spectroscopic techniques. The results of the study indicated that the fluorescence quenching between caffeine and hydroxycinnamic acids could be rationalized in terms of static quenching or the formation of non‐fluorescent CF–CFA and CF–CGA complexes. From fluorescence quenching spectral analysis, the quenching constant (K_SV), quenching rate constant (k_q), number of binding sites (n), thermodynamic properties and conformational changes of the interaction were determined. The quenching constants (K_SV) between CF and CGA, CFA are 1.84 × 10⁴ and 1.04 × 10⁴ L/mol at 298 K and their binding site n is ~ 1. Thermodynamic parameters determined using the Van't Hoff equation indicated that hydrogen bonds and van der Waal's forces have a major role in the reaction of caffeine with caffeic acid and chlorogenic acid. The 3D fluorescence, UV/vis and FTIR spectra also showed that the binding of CF with CFA and CGA induces conformational changes in CFA and CGA. Copyright © 2015 John Wiley & Sons, Ltd.     

Spectroscopic analysis on the interaction of ferulic acid and tetramethylpyrazine with trypsin

The interaction of trypsin with tetramethylpyrazine (TMP) and ferulic acid (FA) was studied using fluorescence, synchronous fluorescence, UV–vis absorption, circular dichroism (CD) and three‐dimensional (3D) fluorescence spectra techniques. Using fluorescence quenching calculations, the bimolecular quenching constant (k_q), apparent quenching constant (K_SV), effective binding constant (K_a) and binding site number (n) were obtained. The distance r between donor and acceptor was found to be 2.049 and 1.281 nm for TMP–trypsin and FA–trypsin complexes. TMP and FA can quench the fluorescence intensity of trypsin by a static quenching procedure. Thermodynamic parameters calculated on the basis of different temperatures revealed that the binding of trypsin to TMP/FA mainly depended on van der Waals' forces and hydrogen bonds. The effect of TMP and FA on the conformation of trypsin was analyzed using synchronous fluorescence, CD, 3D fluorescence spectra and molecular docking studies. Copyright © 2013 John Wiley & Sons, Ltd.     

Binding of fluphenazine with human serum albumin in the presence of rutin and quercetin: An evaluation of food‐drug interaction by spectroscopic techniques

The interactions between human serum albumin (HSA) and fluphenazine (FPZ) in the presence or absence of rutin or quercetin were studied by fluorescence, absorption and circular dichroism (CD) spectroscopy and molecular modeling. The results showed that the fluorescence quenching mechanism was static quenching by the formation of an HSA–FPZ complex. Entropy change (ΔS ⁰) and enthalpy change (ΔH ⁰) values were 68.42 J/(mol? K) and ?4.637 kJ/mol, respectively, which indicated that hydrophobic interactions and hydrogen bonds played major roles in the acting forces. The interaction process was spontaneous because the Gibbs free energy change (ΔG ⁰) values were negative. The results of competitive experiments demonstrated that FPZ was mainly located within HSA site I (sub‐domain IIA). Molecular docking results were in agreement with the experimental conclusions of the thermodynamic parameters and competition experiments. Competitive binding to HSA between flavonoids and FPZ decreased the association constants and increased the binding distances of FPZ binding to HSA. The results of absorption, synchronous fluorescence, three‐dimensional fluorescence, and CD spectra showed that the binding of FPZ to HSA caused conformational changes in HSA and simultaneous effects of FPZ and flavonoids induced further HSA conformational changes.     

Molecular interactions of thymol with bovine serum albumin: Spectroscopic and molecular docking studies

Thymol is the main monoterpene phenol present in the essential oils which is used in the food industry as flavoring and preservative agent. In this study, the interaction of thymol with the concentration range of 1 to 6 μM and bovine serum albumin (BSA) at fixed concentration of 1 μM was investigated by fluorescence, UV‐vis, and molecular docking methods under physiological‐like condition. Fluorescence experiments were performed at 5 different temperatures, and the results showed that the fluorescence quenching of BSA by thymol was because of a static quenching mechanism. The obtained binding parameters, K, were in the order of 10⁴ M^?1, and the binding number, n, was approximately equal to unity indicating that there is 1 binding site for thymol on BSA. Calculated thermodynamic parameters for enthalpy (ΔH), entropy (ΔS), and Gibb's free energy (ΔG) showed that the reaction was spontaneous and hydrophobic interactions were the main forces in the binding of thymol to BSA. The results of UV‐vis spectroscopy and Arrhenius' theory showed the complex formation in the interaction of thymol and BSA. Negligible conformational changes in BSA by thymol were observed in fluorescence experiments, and the same results were also obtained from UV‐vis studies. Results of molecular docking indicated that the subdomain IA of BSA was the binding site for thymol.     

Prolonged conversion of n-butyrate to n-butanol with Clostridium saccharoperbutylacetonicum in a two-stage continuous culture with in-situ product removal

n‐Butanol was produced continuously in a two‐stage fermentor system with integrated product removal from a co‐feed of n‐butyric acid and glucose. Glucose was always required as a source of ATP and electrons for the conversion of n‐butyrate to n‐butanol and for biomass growth; for the latter it also served as a carbon source. The first stage generated metabolically active planktonic cells of Clostridium saccharoperbutylacetonicum strain N1‐4 that were continuously fed into the second (production) stage; the volumetric ratio of the two fermentors was 1:10. n‐Butanol was removed continuously from the second stage via gas stripping. Implementing a two‐stage process was observed to dramatically dampen metabolic oscillations (i.e., periodical changes of solventogenic activity). Culture degeneration (i.e., an irreversible loss of solventogenic activity) was avoided by periodical heat shocking and re‐inoculating stage 1 and by maintaining the concentration of undissociated n‐butyric acid in stage 2 at 3.4 mM with a pH‐auxostat. The system was successfully operated for 42 days during which 93% of the fed n‐butyrate was converted to n‐butanol at a production rate of 0.39 g/(L × h). The molar yields Y_{n‐butanol/n‐butyrate} and Y_{n‐butanol/glucose} were 2.0, and 0.718, respectively. For the same run, the molar ratio of n‐butyrate to glucose consumed was 0.358. The molar yield of carbon in n‐butanol produced from carbon in n‐butyrate and glucose consumed (Y_{n‐butanol/carbon}) was 0.386. These data illustrate that conversion of n‐butyrate into n‐butanol by solventogenic Clostridium species is feasible and that this can be performed in a continuous system operating for longer than a month. However, our data also demonstrate that a relatively large amount of glucose is required to supply electrons and ATP for this conversion and for cell growth in a continuous culture. Biotechnol. Bioeng. 2012; 109:913–921. © 2011 Wiley Periodicals, Inc.     

Study on the interaction of β‐carotene and astaxanthin with trypsin and pepsin by spectroscopic techniques

β‐Carotene and astaxanthin are two carotenoids with powerful antioxidant properties, but the binding mechanisms of β‐carotene/astaxanthin to proteases remain unclear. In this study, the interaction of these two carotenoids with trypsin and pepsin was investigated using steady‐state and time‐resolved fluorescence measurements, synchronous fluorescence spectroscopy, UV–vis absorption spectroscopy and circular dichroism (CD) spectroscopy. The experimental results indicated that the quenching mechanisms of trypsin/pepsin by the two carotenoids are static processes. The binding constants of trypsin and pepsin with these two carotenoids are in the following order: astaxanthin–trypsin > astaxanthin–pepsin > β‐carotene–trypsin > β‐carotene–pepsin, respectively. Thermodynamic investigations revealed that the interaction between the two carotenoids and trypsin/pepsin is synergistically driven by enthalpy and entropy, and hydrophobic forces and electrostatic attraction have a significant role in the reactions. In addition, as shown by synchronous fluorescence spectroscopy, UV–vis absorption spectroscopy and CD, the two carotenoids may induce conformational and microenvironmental changes in trypsin/pepsin. The study provides an accurate and full basic data for clarifying the binding mechanisms of the two carotenoids with trypsin/pepsin and is helpful in understanding their effect on protein function and their biological activity in vivo. Copyright © 2015 John Wiley & Sons, Ltd.     

The study on interactions between levofloxacin and model proteins by using multi-spectroscopic and molecular docking methods

The interactions of levofloxacin (LEV) with lysozyme (LYZ), trypsin and bovine hemoglobin (BHb) were investigated, respectively, by using multi-spectral techniques and molecular docking in vitro. Fluorescence studies showed that LEV quenched LYZ/trypsin fluorescence in a combined quenching ways and BHb fluorescence in a static quenching with binding constants of .14, .51 and .20 × 10⁵ L mol^?1 at 298 K, respectively. The thermodynamic parameters demonstrated that hydrophobic forces, hydrogen bonds, and van der Waals forces played the major role in the binding process. The binding distances between LEV and the inner tryptophan residues of LYZ, trypsin, and BHb were calculated to be 4.04, 3.38, and 4.52 nm, respectively. Furthermore, the results of circular dichroism spectra (CD), UV–vis, and three-dimensional fluorescence spectra indicated that the secondary structures of LYZ, trypsin, and BHb were partially changed by LEV with the α-helix percentage of LYZ-LEV system increased while that of BHb-LEV system was decreased, the β-sheet percentage of trypsin-LEV system increased from 41.3 to 42.9%. UV–vis spectral results showed that the binding interactions could cause conformational and some micro-environmental changes of LYZ, trypsin, and BHb. The results of molecular docking revealed that in LYZ and trypsin systems, LEV bound to the active sites residues GLU 35 and ASP 52 of LYZ and trypsin at the active site SER 195, and in BHb system, LEV was located in the central cavity, which was consistent with the results of synchronous fluorescence experiment. Besides, LEV made the activity of LYZ decrease while the activity of trypsin increased.     

Multiplicity of n‐heptane oxidation pathways catalyzed by cytochrome P450

Modeling, mutagenesis, and kinetic studies have demonstrated that the substrate‐binding site of cytochrome P450 is composed of multiple interactive regions that are capable of simultaneously binding two or more xenobiotics. Substrate molecules can interact with each other after docking. Thus, substrates can compete for the activated oxygen–ferrous complex or alter the spatial orientation of other molecules. Cytochrome P450 is a unique enzyme that produces n‐heptane metabolites of different oxidation states. Metabolism of n‐heptane was investigated with rat liver microsomes and a reconstituted rat liver system. Ethanol, n‐propanol, and n‐butanol molecules interacted with the n‐heptane molecule and resulted in cytochrome P450 spectral changes as well as alterations in the n‐heptane metabolic profile. The observed modifications in the biotransformation of n‐heptane indicated that there are three distinct pathways for oxidation of n‐heptane to heptanols, heptanones, and one‐side oxygen‐oriented heptanediones. © 2009 Wiley Periodicals, Inc. J Biochem Mol Toxicol 23:287–294, 2009; Published online in Wiley InterScience ( www.interscience.wiley.com ). DOI 10.1002/jbt.20291     

Dissection of binding of trypsin to its natural inhibitor Gensenoside-Rg1 using spectroscopic methods and molecular modeling

Abstract

The interaction of trypsin with Gensenoside-Rg1 (G-Rg1) was studied using fluorescence, ultraviolet–visible (UV–vis), and circular dichroism (CD) spectroscopies along with enzyme activity assay and molecular docking. The enzyme activity assays showed that G-Rg1 inhibited the activity of trypsin effectively. The fluorescence experiments indicated that a complex of G-Rg1–trypsin was formed and that the fluorescence of trypsin was quenched by G-Rg1 via a mixed-quenching mechanism (both static and dynamic quenching). The thermodynamic analysis suggested that hydrophobic interaction and hydrogen bond were the major forces between G-Rg1 and trypsin. According to the theory of Förster’s non-radiation energy transfer, the binding distance between trypsin and G-Rg1 was calculated to be 2.01?nm, which implies that energy transfer occurred within the complex. The experimental results obtained from UV–vis absorption spectra, synchronous fluorescence spectra, and CD spectra indicated that G-Rg1 was mainly located on tryptophan moiety and that the interaction between G-Rg1 and trypsin led to conformational changes of trypsin with some α-helix and unordered coil structures being transformed into β-sheet structures. In addition, docking results supported the above experimental findings and suggested the possible binding location of G-Rg1 on trypsin along with the possible hydrogen bonds and hydrophobic interactions between G-Rg1 and trypsin. The experimental results from this study should be useful to minimize the antinutritional effects and make full use of Genseng extracts in the food industry and also be helpful to the design of the drugs for the diseases related to overexpression of trypsin.

Communicated by Ramaswamy H. Sarma     

Conformational selection in protein binding and function

Protein binding and function often involves conformational changes. Advanced nuclear magnetic resonance (NMR) experiments indicate that these conformational changes can occur in the absence of ligand molecules (or with bound ligands), and that the ligands may “select” protein conformations for binding (or unbinding). In this review, we argue that this conformational selection requires transition times for ligand binding and unbinding that are small compared to the dwell times of proteins in different conformations, which is plausible for small ligand molecules. Such a separation of timescales leads to a decoupling and temporal ordering of binding/unbinding events and conformational changes. We propose that conformational‐selection and induced‐change processes (such as induced fit) are two sides of the same coin, because the temporal ordering is reversed in binding and unbinding direction. Conformational‐selection processes can be characterized by a conformational excitation that occurs prior to a binding or unbinding event, while induced‐change processes exhibit a characteristic conformational relaxation that occurs after a binding or unbinding event. We discuss how the ordering of events can be determined from relaxation rates and effective on‐ and off‐rates determined in mixing experiments, and from the conformational exchange rates measured in advanced NMR or single‐molecule fluorescence resonance energy transfer experiments. For larger ligand molecules such as peptides, conformational changes and binding events can be intricately coupled and exhibit aspects of conformational‐selection and induced‐change processes in both binding and unbinding direction.     

Spectroscopy and molecular docking study on the interaction of daidzein and genistein with pepsin

The interaction of pepsin with daidzein (Dai) or genistein (Gen) was investigated using spectroscopic techniques under simulated physiological conditions. Dai and Gen can quench the fluorescence of pepsin and the quenching mechanism was a static process. The binding site number n and apparent binding constant K were measured at different temperatures. The thermodynamic parameters ΔΗ, ΔG and ΔS were calculated. The results indicated that van der Waals forces and hydrogen bond formation played major roles in the interaction of Dai or Gen with pepsin. The binding distance between pepsin and Dai or Gen was calculated according to energy transfer theory. The results of synchronous fluorescence spectra showed that the microenvironment and conformation of pepsin were changed. UV absorption and 3D fluorescence spectra showed that the binding interaction disturbed the microenvironment of amino acid residues and induced conformational changes in pepsin. Molecular docking results showed that Dai and Gen entered into the hydrophobic cavity of pepsin and two hydrogen bonds formed between Dai or Gen and pepsin. The results demonstrated that the interaction behavior between Dai and Gen with pepsin was slightly different, which denoted that the 5‐hydroxyl group of Gen, to a certain extent, had an effect on ligand binding to proteins. Copyright © 2016 John Wiley & Sons, Ltd.     

Urea‐induced binding between diclofenac sodium and bovine serum albumin: a spectroscopic insight

We investigated the interaction of diclofenac sodium (Dic.Na) with bovine serum albumin (BSA) in the absence and presence of urea using different spectroscopic techniques. A fluorescence quenching study revealed that the Stern–Volmer quenching constant decreases in the presence of urea, decreasing further at higher urea concentrations. The binding constant and number of binding sites were also evaluated for the BSA–Dic.Na interaction system in the absence and presence of urea using a modified Stern–Volmer equation. The binding constant is greater at high urea concentrations, as shown by the fluorescence results. In addition, for the BSA–Dic.Na interaction system, a static quenching mechanism was observed, which was further confirmed using time‐resolved fluorescence spectroscopy. UV–vis spectroscopy provided information about the formation of a complex between BSA and Dic.Na. Circular dichroism was carried out to explain the conformational changes in BSA induced by Dic.Na in the absence and presence of urea. The presence of urea reduced the α‐helical content of BSA as the Dic.Na concentration varied. The distance r between the donor (BSA) and acceptor (Dic.Na) was also obtained in the absence and presence of urea, using fluorescence resonance energy transfer. Copyright © 2015 John Wiley & Sons, Ltd.     

Fluorescence spectroscopic analysis on interaction of fleroxacin with pepsin

The interaction between fleroxacin (FLX) and pepsin was investigated by spectrofluorimetry. The effects of FLX on pepsin showed that the microenvironment of tryptophan residues and molecular conformation of pepsin were changed based on fluorescence quenching and synchronous fluorescence spectroscopy in combination with three‐dimensional fluorescence spectroscopy. Static quenching was suggested and it was proved that the fluorescence quenching of pepsin by FLX was related to the formation of a new complex and a non‐radiation energy transfer. The quenching constants K_SV, binding constants K and binding sites n were calculated at different temperatures. The molecular interaction distance (r = 6.71) and energy transfer efficiency (E = 0.216) between pepsin and FLX were obtained according to the Forster mechanism of non‐radiation energy transfer. Hydrophobic and electrostatic interaction played a major role in FLX–pepsin association. In addition, the hydrophobic interaction and binding free energy were further tested by molecular modeling study. Copyright © 2013 John Wiley & Sons, Ltd.     

Comprehensive study of interaction between biocompatible PEG‐InP/ZnS QDs and bovine serum albumin

Polyethylene glycol (PEG) surface modified biocompatible InP/ZnS quantum dots (QDs) act as a potential alternative for conventional carcinogenic cadmium‐based quantum dots for in vivo and in vitro studies. Comprehensively, we studied the interaction between a model protein bovine serum albumin (BSA) and PEGylated toxic free InP/ZnS QDs using various spectroscopic tools such as absorption, fluorescence quenching, time resolved and synchronous fluorescence spectroscopic measurements. These studies principally show that tryptophan (Trp) residues of BSA have preferable binding affinity towards PEG‐InP/ZnS QDs surface and a blue shift in Trp fluorescence emission is a signature of conformational changes in its hydrophobic microenvironment. Photoluminescence (PL) intensity of Trp is quenched by ground state complex formation (static quenching) at room temperature. However, InP/ZnS@BSA conjugates become unstable with increasing temperature and PL intensity of Trp is quenched via dynamic quenching by PEG‐InP/ZnS QDs. Experimentally determined thermodynamic parameters for these conjugates have shown spontaneity, entropy driven and exothermic nature of bio‐conjugation. The calculated binding affinity (n ? 1, Hill coefficient) suggest that the affinity of InP/ZnS QDs for a BSA protein is not dependent on whether or not other BSA proteins are already bound to the QD surface. Energy transfer efficiency (E), Trp residue to InP/ZnS QDs distances and energy transfer rate (k_T) were all obtained from FÖrster resonance energy.     

Study of the interaction between ofloxacin and human serum albumin by spectroscopic methods

The binding of ofloxacin (OFLX) to human serum albumin (HSA) was investigated by fluorescence and circular dichroism (CD) techniques. The binding parameters have been evaluated by a fluorescence quenching method. Competitive binding measurements were performed in the presence of warfarin and ibuprofen and suggest binding to the warfarin site I of HSA. The distance r between donor (HSA) and acceptor (OFLX) was estimated according to the Forster's theory of non‐radiatiative energy transfer. CD spectra revealed that the binding of OFLX to HSA induced conformational changes in HSA. Molecular docking was performed and shows that for the lowest energy complex OFLX is located in site I of HSA, which correlate to the competitive binding experiments. Copyright © 2011 John Wiley & Sons, Ltd.     

A study on the interaction between 3‐spiro‐piperidones and bovine serum albumin using spectroscopic approaches

The interaction between 3‐spiro‐2′‐pyrrolidine‐3′‐spiro‐3″‐piperidine‐2,3″‐dione (PPD) and bovine serum albumin (BSA) in aqueous solution was studied using fluorescence and UV–vis spectroscopy. Fluorescence emission data revealed that BSA (1.00 × 10^‐5 mol/L) fluorescence was statically quenched by PPD at various concentrations, which implies that a PPD–BSA complex was formed. The binding constant (K_A), the number of binding sites (n) and the specific binding site of the PPD with BSA were determined. Energy‐transfer efficiency parameters were determined and the mechanism of the interaction discussed. The thermodynamic parameters, ΔG, ΔH and ΔS, were obtained according to van't Hoff's equation, showing the involvement of hydrophobic forces in these interactions. The effect of PPD acting on the BSA conformation was detected by synchronous fluorescence. Copyright © 2012 John Wiley & Sons, Ltd.     

The lack of chiral specificity in a termite queen pheromone

The queens of many social insects produce pheromones that influence the behaviour and physiology of colony members. Pheromones produced by queens have long been considered as the prime factor inhibiting the differentiation of new reproductive individuals. A volatile pheromone consisting of a blend of n‐butyl‐n‐butyrate and 2‐methyl‐1‐butanol comprises a queen pheromone that inhibits the differentiation of female neotenic reproductives (secondary queens) of a termite Reticulitermes speratus. 2‐Methyl‐1‐butanol is the first chiral molecule to be identified as a primer pheromone in social insects, which presents the intriguing question of whether enantiomeric composition plays a role in caste regulation. In the present study, we report that the (R)‐ and (S)‐enantiomers and the racemic mixture of 2‐methyl‐1‐butanol show significant inhibitory effects on the differentiation of new female neotenics in combination with n‐butyl‐n‐butyrate, whereas no significant difference in inhibitory activity is observed among them. These results suggests that termites recognize 2‐methyl‐1‐butanol as a queen signal but they do not distinguish between the stereostructures of the enantiomers.     

Binding of hydroxylated polybrominated diphenyl ethers with human serum albumin: Spectroscopic characterization and molecular modeling

Three hydroxylated polybrominated diphenyl ethers (OH‐PBDEs), 3‐OH‐BDE‐47, 5‐OH‐BDE‐47, and 6‐OH‐BDE‐47, were selected to investigate the interactions between OH‐PBDEs with human serum albumin (HSA) under physiological conditions. The observed fluorescence quenching can be attributed to the formation of complexes between HSA and OH‐PBDEs. The thermodynamic parameters at different temperatures indicate that the binding was caused by hydrophobic forces and hydrogen bonds. Molecular modeling and three‐dimensional fluorescence spectrum showed conformational and microenvironmental changes in HSA. Circular dichroism analysis showed that the addition of OH‐PBDEs changed the conformation of HSA with a minor reduction in α‐helix content and increase in β‐sheet content. Furthermore, binding distance r between the donor (HSA) and acceptor (three OH‐PBDEs) calculated using Förster's nonradiative energy transfer theory was <7 nm; therefore, the quenching mechanisms for the binding between HSA and OH‐PBDEs involve static quenching and energy transfer. Combined with molecular dynamics simulations, the binding free energies (ΔG _bind ) were calculated using molecular mechanics/Poisson ? Boltzmann surface area method, and the crucial residues in HSA were identified.