A molecular dynamics study of human serum albumin binding sites

Insights into the interaction of human serum albumin with ionic liquids - Thermodynamic, spectroscopic and molecular modelling studies

Human serum albumin (HSA) effectively binds different types of low-molecular-weight compounds and thus enables their distribution in living organisms. Recently, it has been reported that the protein-ligand interactions play a crucial role in bioaccumulation processes and provide an important sorption phase, especially for ionogenic compounds. Therefore, the binding interactions of such compounds with proteins are the subject of an ongoing interest in environmental and life sciences. In this paper, the influence of some counter-ions, namely [B(CN)4]- and [C(CN)3]- on the affinity of the [IM1-12]+ towards HSA has been investigated and discussed based on experimental methods (isothermal titration calorimetry and steady-state fluorescence spectroscopy) and molecular dynamics-based computational approaches. Furthermore, the thermal stability of the resulting HSA/ligand complexes was assessed using DSC and CD spectroscopy. As an outcome of the work, it has been ascertained that the protein is able to bind simultaneously the ligands under study but in different regions of HSA. Thus, the presence in the system of [IM1-12]+ does not disturb the binding of [C(CN)3]- and [B(CN)4]-. The presented results provide important information on the presence of globular proteins and some ionogenic compounds in the distribution and bioaccumulation of ILs in the environment and living organisms.

Conformational variation of site specific glycated albumin: A Molecular dynamics approach

Human serum albumin (HSA) is a major cargo protein, which undergoes glycation in hyperglycaemic conditions and results in impaired function. In physiological conditions, HSA plays a crucial role in pharmacological activities such as drug transport or delivery through its binding capacity and also by its enzymatic activity, which enables the translation of pro-drugs into active drugs. In this study, the impact of the methylglyoxal-mediated glycation on dynamic behaviour of inter-domain motion, Cys34 reactivity, binding site residual interaction and secondary structure transition were investigated through molecular dynamics simulation. The alteration in inter-domain motion reflects the effect of glycation-mediated changes on the structural conformation of albumin. The binding site residue interactions and volume analysis revealed the impact of glycation on the geometry of the binding site. We also found the correlation of Cys34 reactivity with increase of turns in the region between Ia-h4 and Ia-h5. The rise in turn formation in that region keeps Tyr84 farther away from Cys34 which could lead to higher Cys34 reactivity. In parallel, significant alterations in alpha helical content of helices in the binding sites were observed. These structural and conformational changes in glycated albumin could be the causative agents for functional impairment which leads to diabetic complications.

Glutathione, Cysteine, and D-Penicillamine Role in Exchange of Silver Metal from the Albumin Metal Complex

The purpose of this study is to investigate the exchange reaction taking place among the bovine serum albumin (BSA), 5,5'-dithiobis-(2-nitrobenzoic acid (ESSE), reduced glutathione, N-acetylcysteine, D-penicillamine (thiolates), and silver metal (AgI). For this purpose, stock solutions of BSA and Ellman's reagent were prepared by dissolving 264 mg of BSA in 5 ml of reaction buffer (0.1 M KH2PO4 at pH 7.8) and 23.8 mg of ESSE in 1.0 ml of reaction buffer which were mixed together. Mixture of BSA-AgI was prepared in a separate procedure by dissolving 0.17 mg of silver nitrate in 1 ml of reaction buffer and then dissolving BSA (200 mg) in the same solution of silver nitrate. Blocking of Cys-34 of BSA with AgI was confirmed by treating different dilutions of BSA-AgI (500 μM) solutions with the solutions of ESSE (85 μM) and ES- (85 μM) and recording the spectra (300-450) with a UV-visible spectrophotometer. The chromatographed AgI-modified BSA ((BSA-S)AgI)) samples (typically 500 μM) were subsequently mixed with thiolates (reduced glutathione, N-acetylcysteine, and D-penicillamine). AgI and modified BSA (typically 500 μM each) were treated with these low molecular weight thiolates and allowed to react overnight followed by chromatographic separation (Sephadex G25). The redox reactions of AgI-modified BSA with various low molecular weight thiols revealed a mechanically important phenomenon. In the case of reduced glutathione and N-acetylcysteine, we observed the rapid release of a commensurate amount of Ellman's anion, indicating that an exchange has taken place and low molecular weight thiols (RSH) substituted AgI species at the Cys-34 of BSA eventually forming disulfide (BSA-SSR) at Cys-34. It can be anticipated from the phase of study involving bovine serum albumin that low molecular weight thiolates (reduced glutathione and N-acetylcysteine) take off AgI which are attached to proteins elsewhere in the physiological system, making these toxic metals free for toxic action.

Insights from molecular dynamics simulations of albumin adsorption on hydrophilic and hydrophobic surfaces

Protein adsorption at the surface affects the material biocompatibility directly as it is the first reaction that happens when a foreign material comes in contact with blood. In this study, the mechanism of albumin adsorption on hydrophilic and hydrophobic surfaces is investigated. Although it is studied extensively and has been of keen interest for decades, the adsorptive nature of albumin is still not fully understood with contradicting reported studies. This problem results from previous works focusing on mostly qualitative and quantitative adsorption properties of albumin, rather than the specific interaction mechanisms. The variable local surface properties across albumin can significantly impact adsorption and must be explored. In this work, the effect of hydration is found to significantly increase adsorption with minor reductions. The adsorption of albumin on hydrophilic or hydrophobic surfaces is dependent on albumin orientation, which is dictated by local charge effects. Based on these findings, an optimized material surface is proposed to minimize albumin adsorption using functional groups to limit surface availability for hydrophobic interactions while inhibiting excess electrostatic effects at hydrophilic sites. The extent of albumin adsorption and shape change are characterized herein using the heat capacity. Current study identifies interaction mechanisms previously missing in literature, which are responsible for inconsistent adsorption results.

Interaction of ionic liquids with human serum albumin in the view of bioconcentration: a preliminary study

Bioaccumulation potential is critical in PBT and risk assessment of chemicals. However, for ionic liquids (ILs), this aspect remains neglected. It is especially important to fill this gap, because for this group of compounds, existing data confirm their risk of being environmentally persistent and toxicity. Moreover, considering preliminary reports on the interactions of ILs with lipids, it may be assumed that ILs have a higher potential for bioaccumulation than indicated by previous estimations built upon octanol–water partition coefficients. Moreover, the bioconcentration of ionizable chemical compounds may also be strongly related to plasma protein contents. Therefore, in this work, the affinity of a set of imidazolium cations and organic anions, and their combination to human serum albumin (HSA) was determined. The obtained results reveal that both cations and anions can be strongly bound to HSA, and blood proteins might play an important role in overall bioaccumulation. Furthermore, it was observed that HSA binding properties towards IL cations depend on the hydrophobicity of cations. The obtained data also provide indication that cation–anion interaction may affect ILs ions affinity to HSA.

Renal Handling of Albumin-From Early Findings to Current Concepts

Albumin is the main protein of blood plasma, lymph, cerebrospinal and interstitial fluid. The protein participates in a variety of important biological functions, such as maintenance of proper colloidal osmotic pressure, transport of important metabolites and antioxidant action. Synthesis of albumin takes place mainly in the liver, and its catabolism occurs mostly in vascular endothelium of muscle, skin and liver, as well as in the kidney tubular epithelium. Long-lasting investigation in this area has delineated the principal route of its catabolism involving glomerular filtration, tubular endocytic uptake via the multiligand scavenger receptor tandem—megalin and cubilin-amnionless complex, as well as lysosomal degradation to amino acids. However, the research of the last few decades indicates that also additional mechanisms may operate in this process to some extent. Direct uptake of albumin in glomerular podocytes via receptor for crystallizable region of immunoglobulins (neonatal FC receptor) was demonstrated. Additionally, luminal recycling of short peptides into the bloodstream and/or back into tubular lumen or transcytosis of whole molecules was suggested. The article discusses the molecular aspects of these processes and presents the major findings and controversies arising in the light of the research concerning the last decade. Their better characterization is essential for further research into pathophysiology of proteinuric renal failure and development of effective therapeutic strategies.

Spectroscopic studies on the interaction of aspartame with human serum albumin

In this work the binding of artificial sweetener aspartame with human serum albumin (HSA) was studied at physiological pH. Binding studies of aspartame (APM) with HSA are useful to understand APM -HSA interaction, mechanism and providing guidance for the application and design of new and more efficient artificial sweeteners. The interaction was investigated by spectrophotometric, spectrofluorometric competition experiment and circular dichroism (CD) techniques. The results indicated that the binding of APM to HSA caused fluorescence quenching of HSA through static quenching mechanism with binding constant 1.42 × 10⁺⁴ M^-1 at 298 K and the number of binding sites is approximately one. Thermodynamic parameters, enthalpy changes (ΔH) and entropy changes (ΔS) were calculated to be -41.20 kJ mol^-1 and -58.19 J mol^-1 K^-1, respectively, according to van't Hoff equation, which indicated that reaction is enthalpically driven. Quenching of the fluorescence of HSA was found to be a static quenching process. The binding constants and number of binding sites were obtained at three different temperatures (298, 308 and 318 K). Combining above results and those of spectrofluorometric competition experiment and circular dichroism (CD), indicated that APM binds to HSA via Sudlow's site I. Furthermore, the study of molecular docking on HSA binding also indicated that APM can strongly bind to the site I (subdomain IIA) of HSA mainly by hydrophobic interaction and hydrogen bond interactions exist between APM and HSA.

In Vitro Investigations of Acetohexamide Binding to Glycated Serum Albumin in the Presence of Fatty Acid

The interaction of drugs with human serum albumin (HSA) is an important element of therapy. Albumin affects the distribution of the drug substance in the body, as well as its pharmacokinetic and pharmacodynamic properties. On the one hand, inflammation and protein glycation, directly associated with many pathological conditions and old age, can cause structural and functional modification of HSA, causing binding disorders. On the other hand, the widespread availability of various dietary supplements that affect the content of fatty acids in the body means that knowledge of the binding activity of transporting proteins, especially in people with chronic diseases, e.g., diabetes, will achieve satisfactory results of the selected therapy. Therefore, the aim of the present study was to evaluate the effect of a mixture of fatty acids (FA) with different saturated and unsaturated acids on the affinity of acetohexamide (AH), a drug with hypoglycaemic activity for glycated albumin, simulating the state of diabetes in the body. Based on fluorescence studies, we can conclude that the presence of both saturated and unsaturated FA disturbs the binding of AH to glycated albumin. Acetohexamide binds more strongly to defatted albumin than to albumin in the presence of fatty acids. The competitive binding of AH and FA to albumin may influence the concentration of free drug fraction and thus its therapeutic effect.

Are zinc oxide nanoparticles safe? A structural study on human serum albumin using in vitro and in silico methods

With due attention to adsorption of proteins on the nanoparticles surface and the formation of nanoparticle-protein corona, investigation of nanoparticles toxicity on the structure of proteins is important. Therefore, this work was done to evaluate toxicity of Zinc oxide nanoparticles (ZnO NPs) on the structure of human serum albumin (HSA) through in vitro and in silico studies. First, ZnO NPs were synthesized using hydrothermal method and their size and morphology were determined by SEM and TEM methods and then to study its toxicity on the HSA structure were used UV-Vis and fluorescence spectroscopy. Also, in order to investigate interaction mechanism of ZnO NP with HSA at the atomistic level was used molecular dynamics (MD) simulation. The obtained images from SEM and TEM showed that ZnO NPs were nanosheet with size of less than 40 nm. The results of spectroscopic studies showed ZnO NPs lead to significant conformational changes in the protein's absorption and emission spectra. Moreover, MD results indicated the minor structure changes in HSA due to interaction with ZnO NP during the 100 ns simulation, and the formation of nanoparticle-protein corona complex is mainly because of electrostatic interactions between charge groups of HSA and ZnO NP.Communicated by Ramaswamy H. Sarma.

Non-enzymatic glycation of human serum albumin modulates its binding efficacy towards bioactive flavonoid chrysin: A detailed study using multi-spectroscopic and computational methods

The non-enzymatic glycation of plasma proteins by reducing sugars have important consequences on the conformational and functional properties of protein. The formation of advanced glycation end products (AGEs) is responsible for cell death and other pathological conditions. We have synthesized the glycated human serum albumin (gHSA) and characterized the same by using differential spectroscopic measurements. The aim of the present study is to determine the effect of glycation on the binding of human serum albumin (HSA) with bioactive flavonoid chrysin, which possesses anti-cancer, anti-inflammatory and anti-oxidant activities. The interaction of chrysin with HSA and gHSA was studied using multi-spectroscopic, molecular docking and molecular dynamics (MD) simulation techniques. Chrysin quenched the intrinsic fluorescence of both HSA and gHSA by static quenching mechanism. The value of the binding constant (K_b) for the interaction of HSA-chrysin complex (4.779 ± 0.623 × 10⁵ M^-1 at 300 K) was found to be higher than that of gHSA-chrysin complex (2.206 ± 0.234 × 10⁵ M^-1 at 300 K). Hence, non-enzymatic glycation of HSA significantly reduced its binding affinity towards chrysin. The % α-helicity of HSA was found to get enhanced upon binding with chrysin, and minimal changes were observed for the gHSA-chrysin complex. Site marker probe studies indicated that chrysin binds to subdomain IIA and IIIA of both HSA and gHSA. The results from molecular docking and MD simulation studies correlated well with the experimental findings. Electrostatic interactions followed by hydrogen bonding and hydrophobic interactions played major roles in the binding process. These observations may have some useful insights into the field of pharmaceutics.

Computational prediction of interaction and pharmacokinetics profile study for polyamino-polycarboxylic ligands on binding with human serum albumin

Human serum albumin (HSA) is one of the most abundant plasma proteins available in blood and responsible for transport of fatty acids, drugs and metabolites at its binding sites which are very important for the assessment of pharmacokinetics profile of the polyamino-polycarboxylic ligands.

Influence of Piracetam on Gliclazide-Glycated Human Serum Albumin Interaction. A Spectrofluorometric Study

Advanced Glycation End-Products (AGEs) are created in the last step of protein glycation and can be a factor in aging and in the development or worsening of many degenerative diseases (diabetes, chronic kidney disease, atherosclerosis, Alzheimer’s disease, etc.). Albumin is the most susceptible to glycation plasma protein. Modified albumin by AGEs may be more resistant to enzymatic degradation, which further increases the local accumulation of AGEs in tissues. The aim of the present study was to analyze in vitro glycation of serum albumin in the presence of piracetam (PIR) and the gliclazide (GLZ)-glycated albumin interaction. The analysis of PIR as an inhibitor and GLZ interaction with nonglycated human albumin (HSA) and glycated by fructose human albumin (gHSA_FRC), in the absence and presence of piracetam (gHSA_FRC-PIR), was performed by fluorescence quenching of macromolecules. On the basis of obtained data we concluded that under the influence of glycation, association constant (Ka) of gliclazide to human serum albumin decreases and GLZ binds to HSA with less strength than under physiological conditions. PIR strongly inhibited the formation of AGEs in the system where the efficiency of HSA glycation was the largest. The analysis of piracetam influence on the GLZ-glycated albumin interaction has shown that piracetam increases the binding strength of GLZ to glycated albumin and weakens its therapeutic effect. Based on the obtained data we concluded that monitoring therapy and precautions are required in the treatment when the combinations of gliclazide and piracetam are used at the same time.

Combined spectroscopy methods and molecular simulations for the binding properties of trametinib to human serum albumin

Trametinib is a novel anticancer drug for treating metastatic cutaneous melanoma. The present study probed into the binding of trametinib to human serum albumin (HSA) through spectroscopy methods and molecular simulations. Trametinib could quench the fluorescence of HSA through static quenching which could be probed via fluorescence spectroscopy and time-resolved fluorescence. Thermodynamic parameters and docking results indicated that hydrogen bonds and van der Waals forces play crucial roles in this binding process, which exerts almost no effect on the HSA conformation under synchronous fluorescence, three-dimensional fluorescence, circular dichroism spectra, and molecular dynamics simulations. Site marker displacement experiments and molecular docking reveal that trametinib primarily binds to Sudlow site I of HSA. In addition, the trametinib–HSA interaction was hardly influenced by varying amino acid (glutamine, alanine, glycine, and valine) concentrations. This study can provide useful information for the pharmacokinetic properties of trametinib.

Probing the binding properties of trametinib to human serum albumin.

Intrinsically Disordered Regions in Serum Albumin: What Are They For?

Serum albumin is a major plasma protein in mammalian blood. The importance of this protein lies in its roles in both bioregulation and transport phenomena. Serum albumin binds various metal ions and participates in the transport and storage of fatty acids, bilirubin, steroids amino acids, and many other ligands, usually with regions of hydrophobic surface. Although the primary role of serum albumin is to transport various ligand, its versatile binding capacities and high concentration mean that it can assume a number of additional functions. The major goal of this article is to show how intrinsic disorder is encoded in the amino acid sequence of serum albumin, and how intrinsic disorder is related to functions of this important serum protein.

A principal component analysis of the dynamics of subdomains and binding sites in human serum albumin

The conformational dynamics of human serum albumin (HSA) was investigated by principal component analysis (PCA) applied to three molecular dynamics trajectories of 200 ns each. The overlap of the essential subspaces spanned by the first 10 principal components (PC) of different trajectories was about 0.3 showing that the PCA based on a trajectory length of 200 ns is not completely convergent for this protein. The contributions of the relative motion of subdomains and of the subdomains (internal) distortion to the first 10 PCs were found to be comparable. Based on the distribution of the first 3 PC, 10 protein conformers are identified showing relative root mean square deviations (RMSD) between 2.3 and 4.6 Å. The main PCs are found to be delocalized over the whole protein structure indicating that the motions of different protein subdomains are coupled. This coupling is considered as being related to the allosteric effects observed upon ligand binding to HSA. On the other hand, the first PC of one of the three trajectories describes a conformational transition of the protein domain I that is close to that experimentally observed upon myristate binding. This is a theoretical support for the older hypothesis stating that changes of the protein onformation favorable to binding can precede the ligand complexation. A detailed all atoms PCA performed on the primary Sites 1 and 2 confirms the multiconformational character of the HSA binding sites as well as the significant coupling of their motions.

A Comprehensive Computational Study of the Interaction between Human Serum Albumin and Fullerenes

Human serum albumin (HSA) is the most abundant blood plasma protein, which transports fatty acids, hormones, and drugs. We consider nanoparticle-HSA interactions by investigating the binding of HSA with three fullerene analogs. Long MD simulations, quantum mechanical (fragment molecular orbital, energy decomposition analysis, atoms-in-molecules), and free energy methods elucidated the binding mechanism in these complexes. Such a systematic study is valuable due to the lack of comprehensive theoretical approaches to date. The main elements of the mechanism include the following: binding to IIA site results in allosteric modulation of the IIIA and heme binding sites with an increase in α-helical structure of IIIA. Fullerenes displayed high binding affinities for HSA; therefore, HSA can be used as a fullerene carrier, facilitating any toxic function the fullerene may exert. Complex formation is driven by hydrogen bonding, van der Waals, nonpolar, charge transfer, and dispersion energy contributions. Proper functionalization of C60 has enhanced its binding to HSA by more than an order of magnitude. This feature may be important for biological applications (e.g., photodynamic therapy of cancer). Satisfactory agreement with relevant experimental and theoretical data has been obtained.

Study on the interaction of artificial and natural food colorants with human serum albumin: A computational point of view

Due to the high amount of artificial food colorants present in infants' diets, their adverse effects have been of major concern among the literature. Artificial food colorants have been suggested to affect children's behavior, being hyperactivity the most common disorder. In this study we compare binding affinities of a group of artificial colorants (sunset yellow, quinoline yellow, carmoisine, allura red and tartrazine) and their natural industrial equivalents (carminic acid, curcumin, peonidin-3-glucoside, cyanidin-3-glucoside) to human serum albumin (HSA) by a docking approach and further refinement through atomistic molecular dynamics simulations. Due to the protein-ligand conformational interface complexity, we used collective variable driven molecular dynamics to refine docking predictions and to score them according to a hydrogen-bond criterion. With this protocol, we were able to rank ligand affinities to HSA and to compare between the studied natural and artificial food additives. Our results show that the five artificial colorants studied bind better to HSA than their equivalent natural options, in terms of their H-bonding network, supporting the hypothesis of their potential risk to human health.

Comparative binding mechanism of lupeol compounds with plasma proteins and its pharmacological importance

Binding of lupeol compounds with plasma proteins.

Analysis of the structure and dynamics of human serum albumin

Human serum albumin (HSA) is a biologically relevant protein that binds a variety of drugs and other small molecules. No less than 50 structures are deposited in the RCSB Protein Data Bank (PDB). Based on these structures, we first performed a clustering analysis. Despite the diversity of ligands, only two well defined conformations are detected, with a deviation of 0.46 nm between the average structures of the two clusters, while deviations within each cluster are smaller than 0.08 nm. Those two conformations are representative of the apoprotein and the HSA-myristate complex already identified in previous literature. Considering the structures within each cluster as a representative sample of the dynamical states of the corresponding conformation, we scrutinize the structural and dynamical differences between both conformations. Analysis of the fluctuations within each cluster set reveals that domain II is the most rigid one and better matches both structures. Then, taking this domain as reference, we show that the structural difference between both conformations can be expressed in terms of twist and hinge motions of domains I and III, respectively. We also characterize the dynamical difference between conformations by computing correlations and principal components for each set of dynamical states. The two conformations display different collective motions. The results are compared with those obtained from the trajectories of short molecular dynamics simulations, giving consistent outcomes. Let us remark that, beyond the relevance of the results for the structural and dynamical characterization of HAS conformations, the present methodology could be extended to other proteins in the PDB archive.

About the structural role of disulfide bridges in serum albumins: evidence from protein simulated unfolding

The role of the 17 disulfide (S-S) bridges in preserving the native conformation of human serum albumin (HSA) is investigated by performing classical molecular dynamics (MD) simulations on protein structures with intact and, respectively, reduced S-S bridges. The thermal unfolding simulations predict a clear destabilization of the protein secondary structure upon reduction of the S-S bridges as well as a significant distortion of the tertiary structure that is revealed by the changes in the protein native contacts fraction. The effect of the S-S bridges reduction on the protein compactness was tested by calculating Gibbs free energy profiles with respect to the protein gyration radius. The theoretical results obtained using the OPLS-AA and the AMBER ff03 force fields are in agreement with the available experimental data. Beyond the validation of the simulation method, the results here reported provide new insights into the mechanism of the protein reductive/oxidative unfolding/folding processes. It is predicted that in the native conformation of the protein, the thiol (-SH) groups belonging to the same reduced S-S bridge are located in potential wells that maintain them in contact. The -SH pairs can be dispatched by specific conformational transitions of the peptide chain located in the neighborhood of the cysteine residues.

Conformational and adsorptive characteristics of albumin affect interfacial protein boundary lubrication: from experimental to molecular dynamics simulation approaches

The lifetime of artificial joints is mainly determined by their biotribological properties. Synovial fluid which consists of various biological molecules acts as the lubricant. Among the compositions of synovial fluid, albumin is the most abundant protein. Under high load and low sliding speed articulation of artificial joint, it is believed the lubricants form protective layers on the sliding surfaces under the boundary lubrication mechanism. The protective molecular layer keeps two surfaces from direct collision and thus decreases the possibility of wear damage. However, the lubricating ability of the molecular layer may vary due to the conformational change of albumin in the process. In this study, we investigated the influence of albumin conformation on the adsorption behaviors on the articulating surfaces and discuss the relationship between adsorbed albumin and its tribological behaviors. We performed the friction tests to study the effects of albumin unfolding on the frictional behaviors. The novelty of this research is to further carry out molecular dynamics simulation, and protein adsorption experiments to investigate the mechanisms of the albumin-mediated boundary lubrication of arthroplastic materials. It was observed that the thermal processes induce the loss of secondary structure of albumin. The compactness of the unfolded structure leads to a higher adsorption rate onto the articulating material surface and results in the increase of friction coefficient.

Studies on the Interaction of Cinnamic Acid with Bovine Serum Albumin

The interaction between cinnamic acid and bovine serum albumin (BSA) have been studied at three temperatures, 296, 303 and 310 K. Fluorescence quenching spectra in combination with Fourier transform infrared (FT-IR) spectroscopy and circular dichroism (CD) spectroscopy was used to investigate the drug-binding mode, the binding constant and the protein structure changes in the presence of cinnamic acid in aqueous solution at pH 7.40. The fluorescence quenching constant K(q), K(sv) and the binding constant K were calculated according to Stern-Volmer equation based on the quenching of the fluorescence of BSA in the presence of cinnamic acid. The thermodynamic parameters, the enthalpy (DeltaH) and the entropy change (DeltaS) were estimated to be -16.457 kJ mol(-1) and 38.028 J mol(-1) K(-1) according to the van't Hoff equation. The displacement experiment shows that cinnamic acid can bind to the subdomain IIA (corresponding to Sudlow's drug binding site I). The distance between the tryptophan residues in BSA and cinnamic acid bound to site I was estimated to be 1.63 nm using Föster's equation on the basis of fluorescence energy transfer. The decreased binding constant in the presence of common ions indicates that common ions have effect on drug-BSA system.

Molecular dynamics study of conformational changes in human serum albumin by binding of fatty acids

Human serum albumin (HSA) binds with fatty acids under normal physiologic conditions. To date, there is little published information on the tertiary structure of HSA-fatty acid complex in aqueous solution. In the present study, we used molecular dynamics (MD) simulations to elucidate possible structural changes of HSA brought about by the binding of fatty acids. Both unliganded HSA and HSA-fatty acid complex models for MD calculations were constructed based on the X-ray crystal structures. Five myristates (MYRs) were bound in the HSA-fatty acid complex model. In the present MD study, the motion of domains I and III caused by the binding of MYR molecules increased the radius of gyration of HSA. Root-mean-square fluctuations from the MD simulations revealed that the atomic fluctuations of the specific amino acids at drug-binding site I that can regulate the drug-binding affinity were increased by the binding of MYR molecules. Primary internal motions, characterized by the first three principal components, were observed mainly at domains I and III in the principal component analysis for trajectory data. The directional motion projected on the first principal component of unliganded HSA was conserved in HSA-MYR complex as the third principal directional motion with higher frequency. However, the third principal directional motion in unliganded HSA turned into the first principal directional motion with lower frequency in the HSA-MYR complex. Thus, the present MD study provides insights into the possible conformational changes of HSA caused by the binding of fatty acids.