Measuring the forces that control protein interactions

Spectroscopic and docking studies on the interaction between pyrrolidinium based ionic liquid and bovine serum albumin

The interaction of synthesized ionic liquid, 1-butyl-1-methyl-2-oxopyrrolidinium bromide (BMOP) and bovine serum albumin (BSA) was investigated using UV-Vis, FT-IR, steady state and time resolved fluorescence measurements and docking studies. Steady state spectra revealed that BMOP strongly quenched the intrinsic fluorescence of BSA through dynamic quenching mechanism. The corresponding thermodynamic parameters; Gibbs free energy change (ΔG), entropy change (ΔS) and enthalpy change (ΔH) showed that the binding process was spontaneous and entropy driven. It is also indicated that hydrophobic forces play a key role in the binding of BMOP to BSA. The synchronous fluorescence spectroscopy reveals that the conformation of BSA changed in the presence of BMOP. The shift in amide I band of FT-IR spectrum of BSA suggested unfolding of the protein secondary structure upon the addition of BMOP. In addition, the molecular modeling study of BSA-BMOP system shows that BMOP binds with BSA at the interface between two sub domains IIA and IIIA, which is located just above the entrance of the binding pocket of IIA through hydrophobic and hydrogen bond interactions in which hydrophobic interaction are dominated.

Transition model for ricin-aptamer interactions with multiple pathways and energy barriers

We develop a transition model to interpret single-molecule ricin-aptamer interactions with multiple unbinding pathways and energy barriers measured by atomic force microscopy dynamic force spectroscopy. Molecular simulations establish the relationship between binding conformations and the corresponding unbinding pathways. Each unbinding pathway follows a Bell-Evans multiple-barrier model. Markov-type transition matrices are developed to analyze the redistribution of unbinding events among the pathways under different loading rates. Our study provides detailed information about complex behaviors in ricin-aptamer unbinding events.

Combined spectroscopy and cyclic voltammetry investigates the interaction between [(η6-p-cymene)Ru(benzaldehyde-N(4)-phenylthiosemicarbazone)Cl]Cl anticancer drug and human serum albumin

The interaction between Ru anticancer drug and HSA was investigated systematically under physiological conditions.

Study on the interaction between 4-thio-5-methyluridine and human serum albumin by spectroscopy and molecular modeling

The interaction between 4-thio-5-methyluridine and human serum albumin (HSA) under simulative physiological conditions has been studied by the methods of fluorescence, UV-VIS absorbance and circular dichroism (CD) spectroscopy. The results show that 4-thio-5-methyluridine has a static fluorescence quenching on human serum albumin (HSA). The main forces of both interactions have typical static interaction from thermodynamic data to the determination. The experimental result was in correspondence with molecular modeling theory.

Exploring the effect of the ligand design on the interactions between [Ru(η(5)-C5H5)(PPh3)(N,O)][CF3SO3] complexes and human serum albumin

Ruthenium complexes hold a great potential in chemotherapy as an alternative to the classical platinum based drugs. The organometallic compounds studied in the present work were previously found to exhibit important anticancer activities. Here we have investigated the binding of three ruthenium compounds, namely [Ru(η(5)-C5H5)(PPh3)(bopy)][CF3SO3] 1, [Ru(η(5)-C5H5)(PPh3)(2-ap)][CF3SO3] 2, and [Ru(η(5)-C5H5)(PPh3)(isoquinpk)][CF3SO3] 3 (bopy=2-benzoylpyridine; 2-ap=2-acetylpyridine; isoquinpk=1-isoquinolinyl phenyl ketone) to fatty acid human serum albumin (HSA) and fatty acid-free human serum albumin (HSA(faf)) at physiological pH7.4. The influence of the substituent groups on the heteroaromatic (N,O) coordinated ligand was also studied by fluorescence spectroscopy to get information about this binding. The Stern-Volmer quenching constants (KSV) were calculated at 293, 298 and 310K, with the corresponding thermodynamic parameters ∆G, ∆H and ∆S as well. The fluorescence quenching method was used to determine the number of binding sites (n) and association constants (Ka) at the same temperatures. The binding site to HSA was confirmed by competitive studies of the ruthenium compounds with warfarin.

Spectroscopic studies on the interaction of carteolol hydrochloride and urea-induced bovine serum albumin

The interaction of carteolol hydrochloride, to 0.2 mol L(-1) urea-induced bovine serum albumin in aqueous solution has been first investigated by fluorescence spectra and ultraviolet-visible (UV-vis) spectra at pH 7.40. The quenching mechanism, binding parameter and sites (n), the binding mode (ΔG, ΔH, and ΔS) as well as the binding distance (r) have been obtained according to the experimental results. We also use the synchronous fluorescence method to study the effect of CTL on the conformation change of urea-induced BSA.

Investigations on the interactions of diclofenac sodium with HSA and ctDNA using molecular modeling and multispectroscopic methods

A tentative study on interaction of diclofenac sodium (DF-Na) with human serum albumin (HSA) and calf thymus DNA (ctDNA) was conducted by using multi-spectroscopic and molecular modeling techniques under simulative physiological conditions. The results of spectroscopic measurements suggested that the quenching mechanisms were static quenching. Three-dimensional fluorescence spectroscopy clearly demonstrated the occurrence of conformational changes of HSA with addition of DF-Na. In addition, competitive studies with ethidium bromide (EB) have shown that DF-Na can bind to ctDNA relatively strong via groove binding. Based on the values of thermodynamic parameters and the results of molecular modeling, it was confirmed that hydrophobic forces and hydrogen bond were the mainly binding forces in DF-Na-HSA and DF-Na-DNA systems. The binding distance between DF-Na and HSA was also determined using the theory of the Förster energy transference.

Review series: The functions and consequences of force at kinetochores

Chromosome segregation requires the generation of force at the kinetochore—the multiprotein structure that facilitates attachment of chromosomes to spindle microtubules. This force is required both to move chromosomes and to signal the formation of proper bioriented attachments. To understand the role of force in these processes, it is critical to define how force is generated at kinetochores, the contributions of this force to chromosome movement, and how the kinetochore is structured and organized to withstand and respond to force. Classical studies and recent work provide a framework to dissect the mechanisms, functions, and consequences of force at kinetochores.

Quantum dot applications endowing novelty to analytical proteomics

This review surveys all the state-of-art applications of quantum dots (QDs) in conventional and modern analytical methods in proteomic studies. A brief introduction of QDs and their properties is initially presented followed by outlining the application of QDs in fluorescence, MS, imaging, and cancer-based proteomics. The in-depth application of QDs in MALDI-MS and surface assisted laser desorption/ionization-MS has been elaborately discussed, summarizing the speculated mechanism behind the protein-QDs interactions during QD matrix applications leading to enhanced detection sensitivity.

Molecular Modeling and Spectroscopic Studies on the Interaction of Transresveratrol with Bovine Serum Albumin

The interaction of transresveratrol (TRES) with bovine serum albumin (BSA) has been investigated by ultraviolet-visible, fluorescence, Fourier transform infrared spectroscopic methods and molecular modeling techniques. The fluorescence results show that the intrinsic fluorescence of BSA is quenched by TRES through a static quenching procedure. The binding constants of TRES with BSA at 292, 297 and 302 K are calculated as10.22×104,8.71×104, and7.59×104 L mol−1, respectively, and corresponding numbers of binding sites are approximately equal to unity. The thermodynamic parameters ΔHand ΔSare estimated to be −21.82 kJ mol−1and +21.15 J mol−1 K−1, which indicates that the interaction of TRES with BSA is driven mainly by hydrophobic forces and there are also hydrogen bonds and electrostatic interactions. The competitive experiments suggest that the binding site of TRES to BSA is probably located on site II. The results of infrared spectra show that the binding of TRES with BSA leads to conformational changes of BSA, and the binding stabilizes theα-helix andβ-sheet at the cost of a corresponding loss in theβ-turn structure of BSA. The results of molecular modeling calculation clarify the binding mode and the binding sites which are in good accordance with the experiment results.

Exploring the binding mechanism of Guaijaverin to human serum albumin: fluorescence spectroscopy and computational approach

The Guaijaverin (Gua) is a polyphenolic substance which exhibits some pharmacological activities such as antibacterial and antioxidant activities. Here we have investigated the binding of Gua with human serum albumin (HSA) at physiological pH 7.0. In this study, the fluorescence spectroscopy, ab initio and molecular modeling calculations were applied. The Stern-Volmer quenching constant (K(SV)) and its modified form (K(a)) were calculated at 298, 303 and 308 K, with the corresponding thermodynamic parameters ΔH, ΔG and ΔS as well. The fluorescence quenching method was used to determine the number of binding sites (n) and binding constants (K(b)) values at 298, 303 and 308 K. The distance between donor (HSA) and acceptor (Gua) was estimated according to fluorescence resonance energy transfer. The geometry optimization of Gua was performed in its ground state by using ab initio DFT/B3LYP functional with a 6-31G(d,p) basis set used in calculations. Molecular modeling calculation indicated that the Gua is located within the hydrophobic pocket of the subdomain IIA of HSA. The theoretical results obtained by molecular modeling were corroborated by fluorescence spectroscopy data.

Enantioselective binding interaction of the metolachlor pesticide enatiomers with bovine serum albumin--a spectroscopic analysis study

Enantioselective binding interaction of the pesticides, metolachlor (RAC-metolachlor) and its S-enantiomer (S-metolachlor), with bovine serum albumin (BSA) was investigated by fluorescence and UV-vis absorption spectroscopy. Both RAC- and S-metolachlors quenched the intrinsic fluorescence of BSA via a static mechanism, and various binding parameters indicated that electrostatic forces were involved in the binding of both of these compounds. Site marker competitive experiments demonstrated that S-metolachlor bound to site I of BSA, while R-metolachlor bound to site II, indicating the importance of enantiomeric factors for binding site selection. Further experiments showed that S-metolachlor had a higher binding affinity to BSA than R-metolachlor. The obtained spectral data were resolved with use of the multivariate curve resolution-alternating least squares method (MCR-ALS), and the extracted concentration profiles of the reacting species in the interaction were obtained. These profiles indicated that S-metolachlor was the main active constituent of RAC-metolachlor for binding with BSA, and these findings have significant implications in providing an explanation why S-metolachlor is the preferred herbicide in practice than RAC-metolachlor.

Spectroscopic studies on the interactions between CdTe quantum dots coated with different ligands and human serum albumin

This paper investigates the interactions between human serum albumin (HSA) and CdTe quantum dots (QDs) with nearly identical hydrodynamic size, but capped with four different ligands (MPA, NAC, and GSH are negatively charged; CA is positively charged) under physiological conditions. The investigation was carried out using fluorescence spectroscopy, circular dichroism (CD) spectra, UV-vis spectroscopy, and dynamic light scattering (DLS). The results of fluorescence quenching and UV-vis absorption spectra experiments indicated the formation of the complex of HSA and negatively charged QDs (MPA-CdTe, NAC-CdTe, and GSH-CdTe), which was also reconfirmed by the increasing of the hydrodynamic radius of QDs. The K(a) values of the three negatively charged QDs are of the same order of magnitude, indicating that the interactions are related to the nanoparticle itself rather than the ligands. ΔH<0 and ΔS>0 implied that the electrostatic interactions play predominant roles in the adsorption process. Furthermore, it was also proven that QDs can induce the conformational changes of HSA from the CD spectra and the three-dimensional fluorescence spectra of HSA. However, our results demonstrate that the interaction mechanism between the positively charged QDs (CA-CdTe) and HSA is significantly different from negatively charged QDs. For CA-CdTe QDs, both the static and dynamic quenching occur within the investigated range of concentrations. According to the DLS results, some large-size agglomeration also emerged.

Study of the interaction between bovine serum albumin and analogs of Biphenyldicarboxylate by spectrofluorimetry

This work was designed to study the interaction between bovine serum albumin (BSA) and Biphenyldicarboxylate (DDB) or analogs (I, II and III) of DDB by UV-visible and fluorescence spectroscopic methods for the first time. Results showed that both DDB and analogs had a strong ability to quench the intrinsic fluorescence of BSA through a static quenching procedure. The binding constants (K) were calculated according to the relevant fluorescence data. The thermodynamic parameters (ΔH, ΔS and ΔG) showed that the hydrophobic force played a major role in the binding interaction between BSA and DDB or analogs. Synchronous fluorescence spectra of BSA were investigated in the presence of DDB or analogs. It was showed that DDB was the strongest quencher and bound to BSA with the highest affinity among four compounds. The influence of molecular structure on the binding aspects was reported.

Spectroscopic investigation on the interaction of 9-aminoacridine with certain dyes

The fluorescence quenching of 9-Aminoacridine (9-AA) by various dyes were probed in aqueous medium using steady state and time resolved fluorescence spectroscopic techniques. From these techniques, we had rationalized the interaction of 9-AA with various dyes via ground state complex formation. The binding constant (K) and number of binding sites (n) were calculated from the relevant fluorescence quenching data. The fluorescence emission of 9-Aminoacridine was quenched by the dyes through static quenching followed by the mechanism of energy transfer. The static quenching mechanism was confirmed by lifetime measurements. The thermodynamic parameters such as free energy change (ΔG), enthalpy change (ΔH) and entropy change (ΔS), were calculated by thermodynamic equations. The results showed that Van der Waals interaction or hydrogen bond formation played a major role in the binding of 9-AA with these dyes.

Spectroscopic studies on the interaction of bovine serum albumin with surfactants and apigenin

The binding of apigenin (Ap) to bovine serum albumin (BSA) has been studied using the methods of fluorescence spectroscopy and UV-vis absorption spectroscopy. The spectroscopic analysis of the quenching mechanism indicates that the quenching constants are inversely correlated with the temperatures and the quenching process could result from a static interaction. The type of interaction force was discussed and the binding site of Ap was in site I (subdomain IIA) of BSA. The thermodynamic parameters ΔH and ΔS are -42.02kJ mol(-1) and -48.31J mol(-1)K(-1), respectively and the negative ΔG implying that the binding interaction was spontaneous. The distance r between BSA and Ap was calculated according to Förster's theory and the value is 3.44nm. The synchronous and three-dimensional fluorescence spectra show that the binding of Ap to BSA could lead to the changes in the conformation and microenvironment of BSA. At the same time, the effects of ionic surfactants on the interaction of Ap and BSA have also been investigated.

Study on the interaction of silver(I) complex with bovine serum albumin by spectroscopic techniques

The interaction of silver(I) complex, [Ag (2,9-dimethyl-1,10-phenanthroline)(2)](NO(3))·H(2)O, and bovine serum albumin (BSA) was investigated by spectrophotometry, spectrofluorimetry and circular dichroism (CD) techniques. The experimental results indicated that the quenching mechanism of BSA by the complex was a static procedure. Various binding parameters were evaluated. The negative value of ΔH, negative value of ΔS and the negative value of ΔG indicated that van der Waals force and hydrogen bonding play major roles in the binding of the complex and BSA. Based on Forster's theory of non-radiation energy transfer, the binding distance, r, between the donor (BSA) and acceptor (Ag(I) complex) was evaluated. The results of CD and UV-vis spectroscopy showed that the binding of this complex could bind to BSA and be effectively transported and eliminated in the body.

A spectroscopic investigations of anticancer drugs binding to bovine serum albumin

The binding of anticancer drugs (i) Uracil (U), (ii) 5-Fluorouracil (5FU) and (iii) 5-Chlorouracil (5ClU), to bovine serum albumin (BSA) at two levels of temperature was studied by the fluorescence of quenching method. UV/Vis, time-resolved fluorescence, Fourier transform infrared spectroscopy (FTIR), proton nuclear magnetic resonance ((1)H NMR) and scanning electron microscope (SEM) analyses were also made. Binding constants (K(a)) and binding sites (n) at various levels of temperature were calculated. The obtained binding sites were found to be equal to one for all the three quenchers (U, 5FU and 5ClU) at two different temperature levels. Thermodynamic parameters ΔH, ΔG and ΔS have been calculated and were presented in tables. Change in FTIR absorption intensity shows strong binding of anticancer drugs to BSA. Changes in chemical shifts of NMR and fluorescence lifetimes of the drugs indicate the presence of interaction and binding of BSA to anticancer drugs. (1)H NMR spectra and SEM photographs also conform this binding.

Impact of halogen substituents on interactions between 2-phenyl-2,3-dihydroqulinazolin-4(1H)-one derivatives and human serum albumin

A novel type of 2-(un)substituted phenyl-2,3-dihydroquinazolin-4(1H)-one (DQL) derivatives were designed and synthesized to study the impact of halogen substituents on interactions between DQL and human serum albumin (HSA) by comparison methodology. The interactions between DQL and HSA were studied by fluorescence spectroscopy. The intrinsic fluorescence of human serum albumin was quenched by DQL through a static quenching mechanism. Site marker competitive experiments showed that DQL bound to HSA in site II (subdomain IIIA). The binding constants, the numbers of binding sites and the thermodynamic parameters were measured too. The results indicated that the interactions were spontaneous, mainly through hydrophobic forces, and the substitution by halogen atoms in the benzene ring could increase the interactions between DQL and HSA. Furthermore, the binding affinity was enhanced gradually with the increasing of halogen atomic number.

Time dependence of lysozyme adsorption on end-grafted polymer layers of variable grafting density and length

A combined experimental and theoretical approach establishes the long-lived nature of protein adsorption on surfaces coated with chemically grafted macromolecules. Specifically, we monitor the time dependence of adsorption of lysozyme on surfaces comprising polymer assemblies made of poly(2-hydroxyethyl methacrylate) brushes grafted onto flat silica surfaces such that they produce patterns featuring orthogonal and gradual variation of the chain length (N) and grafting density (σ). We show that in the kinetically controlled regime, the amount of adsorbed protein scales universally with the product σN, while at equilibrium the amount of adsorbed protein is governed solely by σ. Surprisingly, for moderate concentrations of protein in solution, adsorption takes more than 72 h to reach an equilibrium, or steady state. Our experimental findings are corroborated with predictions using molecular theory that provides further insight into the protein adsorption phenomenon. The theory predicts that the universal behavior observed experimentally should be applicable to polymers in poor and theta solvents and to a limited extent also to good solvent conditions. Our combined experimental and theoretical findings reveal that protein adsorption is a long-lived phenomenon, much longer than generally assumed. Our studies confirm the previously predicted important differences in behavior for the kinetic versus thermodynamic control of protein adsorption.