Revisiting ligand-induced conformational changes in proteins: essence, advancements, implications and future challenges

A mini review of polysaccharides from Zanthoxylum bungeanum maxim: Their extraction, purification, structural characteristics, bioactivity and potential applications

Zanthoxylum bungeanum Maxim (Z. bungeanum), commonly known as Sichuan pepper or Chinese prickly ash, is a deciduous shrub in the Rutaceae family, with a lengthy history of use as a food ingredient and traditional medicine in China. Z. bungeanum polysaccharides (ZBPs) represent one of the crucial bioactive components of Z. bungeanum, garnering global attention due to their potential medicinal value, culinary significance, and promising application prospects. The principal methods for extracting ZBPs are hot water extraction, ultrasound-assisted extraction, enzyme-assisted extraction and microbial fermentation extraction. However, the structural characteristics of ZBPs remain ambiguous, necessitating further exploration and elucidation of the structure-activity relationship using the advanced analytical techniques. In addition, ZBPs demonstrate diverse bioactivities, including antioxidant activity, neuroprotective effect, antibacterial activity, and the anti-fatigue effect, positioning them as promising candidates for various therapeutic and health-promoting applications. This review provides a comprehensive overview of the extraction, purification, structural characteristics, bioactivities, and potential applications of ZBPs, emphasizing the significant promise of ZBPs as valuable natural compounds with a range of bioactivities, supporting their further exploitation and application in various fields of industries and therapeutics.

Predictive toxicology of chemical mixtures using proteome-wide thermal profiling and protein target properties

Our capability to predict the impact of exposure to chemical mixtures on environmental and human health is limited in comparison to the advances on the chemical characterization of the exposome. Current approaches, such as new approach methodologies, rely on the characterization of the chemicals and the available toxicological knowledge of individual compounds. In this study, we show a new methodological approach for the assessment of chemical mixtures based on a proteome-wide identification of the protein targets and revealing the relevance of new targets based on their role in the cellular function. We applied a proteome integral solubility alteration assay to identify 24 protein targets from a chemical mixture of 2,3,7,8-tetrachlorodibenzo-p-dioxin, alpha-endosulfan, and bisphenol A among the HepG2 soluble proteome, and validated the chemical mixture-target interaction orthogonally. To define the range of interactive capability of the new targets, the data from intrinsic properties of the targets were retrieved. Introducing the target properties as criteria for a multi-criteria decision-making analysis called the analytical hierarchy process, the prioritization of targets was based on their involvement in multiple pathways. This methodological approach that we present here opens a more realistic and achievable scenario to address the impact of complex and uncharacterized chemical mixtures in biological systems.

Plumbagin accelerates serum albumin's amyloid aggregation kinetics and generates fibril polymorphism by inducing non-native β-sheet structures

The ligand-induced conformational switch of proteins has great significance in understanding the biophysics and biochemistry of their self-assembly. In this work, we have investigated the ability of plumbagin (PL), a hydroxynaphthoquinone compound found in the root of the medicinal plant Plumbago zeylanica, to modulate aggregation precursor state, aggregation kinetics and generate distinct fibril of human serum albumin (HSA). PL was found to moderately bind (binding constant Ka ∼ 10-4 M-1)) to domain-II of HSA in the stoichiometric ratio of 1:1. We found that PL-HSA complex aggregation was accelerated as compared to that of HSA aggregation and it may be through an independent pathway. We also detected that fibril produced in the presence of PL is wider in diameter, contains a higher amount of β-sheet (∼18%) and disordered (∼46%) structures, and is less stable. We concluded that the acceleration of aggregation reaction and generation of fibril polymorphism was mainly because of the higher extent of unfolding and high content of non-native β-sheet structure in the aggregation precursor state of PL-HSA complex. This study offers opportunities to explore the ability of ligand binding to modulate aggregation reactions and generate polymorphic protein fibrils.

Repurposing Drugs to Modulate Sortilin: Structure-Guided Strategies Against Atherogenesis, Coronary Artery Disease, and Neurological Disorders

Sortilin (SORT1) is a multifunctional protein intricately involved in atherogenesis, coronary artery disease (CAD), and various neurological disorders. It has materialized as a potential pharmacological target for therapeutic development due to its diverse biological roles in pathological processes. Despite its central role under these conditions, effective therapeutic strategies targeting SORT1 remain challenging. In this study, we introduce a drug repurposing strategy guided by structural insights to identify potent SORT1 inhibitors with broad therapeutic potential. Our approach combines molecular docking, virtual screening, and molecular dynamics (MD) simulations, enabling the systematic evaluation of 3648 FDA-approved drugs for their potential to modulate SORT1. The investigation reveals a subset of repurposed drugs exhibiting highly favorable binding profiles and stable interactions within the binding site of SORT1. Notably, two hits, ergotamine and digitoxin, were carefully chosen based on their drug profiles and subjected to analyze their interactions with SORT1 and stability assessment via all-atom MD simulations spanning 300 ns (ns). The structural analyses uncover the complex binding interactions between these identified compounds and SORT1, offering essential mechanistic insights. Additionally, we explore the clinical implications of repurposing these compounds as potential therapeutic agents, emphasizing their significance in addressing atherogenesis, CAD, and neurological disorders. Overall, this study highlights the efficacy of structure-guided drug repurposing and provides a solid foundation for future research endeavors aimed at the development of effective therapies targeting SORT1 under diverse pathological conditions.

Tunability of Pickering particle features of whey protein isolate via remodeling partial unfolding during ultrasonication-assisted complexation with chitosan/chitooligosaccharide

The potential of ultrasonication-driven molecular self-assembly of whey protein isolate (WPI) with chitosan (CS)/chitooligosaccharide (COS) to stabilize Pickering emulsions was examined, based on CS/COS ligands-induced partial unfolding in remodeling the Pickering particles features. Multi-spectral analysis suggested obvious changes in conformational structures of WPI due to interaction with CS/COS, with significantly higher unfolding degrees of WPI induced by COS. Non-covalent interactions were identified as the major forces for WPI-CS/COS conjugates. Ultrasonication enhanced electrostatic interaction between CS's -NH3 groups and WPI's -COO- groups which improved emulsification activity and storability of WPI-COS stabilized Pickering emulsion. This was attributed to increased surface hydrophobicity and decreased particle size compared to WPI-CS associated with differential unfolding degrees induced by different saccharide ligands. CLSM and SEM consistently observed smaller emulsion droplets in WPI-COS complexes than WPI-CS/COS particles tightly adsorbed at the oil-water interface. The electrostatic self-assembly of WPI with CS/COS greatly enhanced the encapsulation efficiency of quercetin than those stabilized by WPI alone and ultrasound further improved encapsulation efficiency. This corresponded well with the quantitative affinity parameters between quercetin and WPI-CS/COS complexes. This investigation revealed the great potential of glycan ligands-induced conformational transitions of extrinsic physical disruption in tuning Pickering particle features.

Searching for Structure: Characterizing the Protein Conformational Landscape with Clustering-Based Algorithms

The identification and characterization of the main conformations from a protein population are a challenging and inherently high-dimensional problem. Here, we evaluate the performance of the Secondary sTructural Ensembles with machine LeArning (StELa) double-clustering method, which clusters protein structures based on the relationship between the φ and ψ dihedral angles in a protein backbone and the secondary structure of the protein, thus focusing on the local properties of protein structures. The classification of states as vectors composed of the clusters' indices arising naturally from the Ramachandran plot is followed by the hierarchical clustering of the vectors to allow for the identification of the main features of the corresponding free energy landscape (FEL). We compare the performance of StELa with the established root-mean-squared-deviation (RMSD)-based clustering algorithm, which focuses on global properties of protein structures and with Combinatorial Averaged Transient Structure (CATS), the combinatorial averaged transient structure clustering method based on distributions of the φ and ψ dihedral angle coordinates. Using ensembles of conformations from molecular dynamics simulations of intrinsically disordered proteins (IDPs) of various lengths (tau protein fragments) or short fragments from a globular protein, we show that StELa is the clustering method that identifies many of the minima and relevant energy states around the minima from the corresponding FELs. In contrast, the RMSD-based algorithm yields a large number of clusters that usually cover most of the FEL, thus being unable to distinguish between states, while CATS does not sample well the FELs for long IDPs and fragments from globular proteins.

Binding of human serum albumin with uranyl ion at various pH: an all atom molecular dynamics study

Uranium is routinely handled in various stages of nuclear fuel cycle and its association with human serum albumin (HSA) has been reported in literature, however, their binding characteristics still remains obscure. The present study aims to understand interaction of uranium with HSA by employing all atom molecular dynamics simulation of the HSA-metal ion complex. His67, His247 and Asp249 residues constitute the major binding site of HSA, which capture the uranyl ion (UO22+). A total of six sets of initial coordinates are used for Zn2+-HSA and UO22+-HSA system at pH = 4, 7.4 and 9, respectively. Enhance sampling method, namely, well-tempered meta-dynamics (WT-MtD) is employed to study the binding and un-binding processes of UO22+ and Zn2+ ions. Potential of mean force (PMF) profiles are generated for all the six sets of complexes from the converged WT-MtD run. Various basins and barriers are observed along the (un)binding pathways. Hydrogen bond dynamics and short-range Coulomb interactions are evaluated from the equilibrium run at each basins and barriers for both the ions at all pH values. The binding of UO22+ ion with HSA is the result of the dynamical balance between UO22+-HSA and UO22+-water short range Coulomb interactions. Zn2+ ion interact more strongly than UO22+ at all pH through short range Coulomb interactions. PMF values further concludes that UO22+ cannot associate to the Zn2+ bound HSA protein but can be captured by free HSA at all pH values i.e. endosomal, alkaline and physiological pH.Communicated by Ramaswamy H. Sarma.

The effect of novel tyrosine-modified polyethyleneimines on human albumin structure - Thermodynamic and spectroscopic study

The interaction of proteins with nanoparticle components are crucial for the evaluation of nanoparticle function, toxicity and biodistribution. Polyethyleneimines (PEIs) with defined tyrosine modifications are a class of novel polymers designed for improved siRNA delivery. Their interactions with biomacromolecules are still poorly described. This paper analyzes the interaction of different tyrosine-modified PEIs with human serum albumin as the most abundant serum protein. The ability of tyrosine modified, linear or branched PEIs to bind human serum albumin (HSA) was analyzed and further characterized. The interaction with hydrophobic parts of protein were studied using 1- nilinonaphthalene-8-sulfonic acid (ANS) and changes in the HSA secondary structure were evaluated using circular dichroism (CD). Complex formation and sizes were studied by transmission electron microscopy (TEM) and dynamic light scattering methods (DLS). We demonstrate that tyrosine modified PEIs are able to bind human serum albumin. Based on thermodynamic studies, van der Waals interaction, H-bonding and hydrophobic interactions are determined as main molecular forces involved in complex formation. Analysis of secondary structures revealed that the polymers decreased α-helix content, while increasing levels of randomly folded structures. Complex formation was confirmed by TEM and DLS. These findings are crucial for understanding polymer-protein interactions and the properties of nanoparticles.

Selectivity and Ranking of Tight-Binding JAK-STAT Inhibitors Using Markovian Milestoning with Voronoi Tessellations

Janus kinases (JAK), a group of proteins in the nonreceptor tyrosine kinase (NRTKs) family, play a crucial role in growth, survival, and angiogenesis. They are activated by cytokines through the Janus kinase-signal transducer and activator of a transcription (JAK-STAT) signaling pathway. JAK-STAT signaling pathways have significant roles in the regulation of cell division, apoptosis, and immunity. Identification of the V617F mutation in the Janus homology 2 (JH2) domain of JAK2 leading to myeloproliferative disorders has stimulated great interest in the drug discovery community to develop JAK2-specific inhibitors. However, such inhibitors should be selective toward JAK2 over other JAKs and display an extended residence time. Recently, novel JAK2/STAT5 axis inhibitors (N-(1H-pyrazol-3-yl)pyrimidin-2-amino derivatives) have displayed extended residence times (hours or longer) on target and adequate selectivity excluding JAK3. To facilitate a deeper understanding of the kinase-inhibitor interactions and advance the development of such inhibitors, we utilize a multiscale Markovian milestoning with Voronoi tessellations (MMVT) approach within the Simulation-Enabled Estimation of Kinetic Rates v.2 (SEEKR2) program to rank order these inhibitors based on their kinetic properties and further explain the selectivity of JAK2 inhibitors over JAK3. Our approach investigates the kinetic and thermodynamic properties of JAK-inhibitor complexes in a user-friendly, fast, efficient, and accurate manner compared to other brute force and hybrid-enhanced sampling approaches.

Mechanistic insights into monomer level prevention of amyloid aggregation of lysozyme by glycyrrhizic acid

As the primary bioactive compound of glycyrrhiza rhizome, the triterpene glycoside conjugate Glycyrrhizic acid (GA) has demonstrated neuroprotective effects in vivo. This study evaluates the effectiveness of GA as an inhibitor of GuHCl-induced amyloid aggregation of hen egg white lysozyme (HEWL). Fibril formation as measured by Thioflavin-T fluorescence, 90⁰ light scattering, and 8-Anilinonaphthalene-1-sulfonic acid (ANS) fluorescence illustrated ∼90 % prevention of fibrils at [GA]/[HEWL] ≥2:1. Images of Transmission electron microscopy evidence for the absence of any fibril or amorphous aggregation products. The spectral characteristics of soluble HEWL were in close resemblance to unfolded monomer. Computational and fluorescence investigations performed to analyse GA-HEWL interactions demonstrated slightly higher affinity of GA to unfolded HEWL and aggregation-prone regions. The likely mechanism of monomer level aggregation prevention by GA as dermined by computational, stability, and ANS experiments illustrated that GA modulated the compactness, solvent-accessible surface, and solvent-exposed hydrophobic surfaces of aggregation-prone state of HEWL. Our findings corroborate GA as an effective inhibitor of HEWL amyloid formation. To our knowledge, GA interaction-induced inhibition of aggregation-prone states has not been previously discussed. GA's modulation of aggregation-prone states of disease-related proteins will successfully develop GA as an amyloid inhibitor for clinical trials of amyloidosis and neurodegenerative illnesses.

Inhibition of Cancer Cell Proliferation and Bacterial Growth by Silver(I) Complexes Bearing a CH3-Substituted Thiadiazole-Based Thioamide

Ag(I) coordination compounds have recently attracted much attention as antiproliferative and antibacterial agents against a wide range of cancer cell lines and pathogens. The bioactivity potential of these complexes depends on their structural characteristics and the nature of their ligands. Herein, we present a series of four Ag(I) coordination compounds bearing as ligands the CH₃-substituted thiadiazole-based thioamide 5-methyl-1,3,4-thiadiazole-2-thiol (mtdztH) and phosphines, i.e., [AgCl(mtdztH)(PPh₃)₂] (1), [Ag(mtdzt)(PPh₃)₃] (2), [AgCl(mtdztH)(xantphos)] (3), and [AgmtdztH)(dppe)(NO₃)]_n (4), where xantphos = 4,5-bis(diphenylphosphino)-9,9-dimethylxanthene and dppe = 1,2-bis(diphenylphosphino)ethane, and the assessment of their in vitro antibacterial and anti-cancer efficiency. Among them, diphosphine-containing compounds 3 and 4 were found to exhibit broad-spectrum antibacterial activity characteristics against both Gram-(+) and Gram-(-) bacterial strains, showing high in vitro bioactivity with IC₅₀ values as low as 4.6 μΜ. In vitro cytotoxicity studies against human ovarian, pancreatic, lung, and prostate cancer cell lines revealed the strong cytotoxic potential of 2 and 4, with IC₅₀ values in the range of 3.1-24.0 μΜ, while 3 and 4 maintained the normal fibroblast cells' viability at relatively higher levels. Assessment of these results, in combination with those obtained for analogous Ag(I) complexes bearing similar heterocyclic thioamides, suggest the pivotal role of the substituent groups of the thioamide heterocyclic ring in the antibacterial and anti-cancer efficacy of the respective Ag(I) complexes. Compounds 1-4 exhibited moderate in vitro antioxidant capacity for free radicals scavenging, as well as reasonably strong ability to interact with calf-thymus DNA, suggesting the likely implication of these properties in their bioactivity mechanisms. Complementary insights into the possible mechanism of their anti-cancer activity were provided by molecular docking calculations, exploring their ability to bind to the overexpressed fibroblast growth factor receptor 1 (FGFR1), affecting cancer cells' functionalities.

Evaluation of the active constituents of Nilavembu Kudineer for viral replication inhibition against SARS-CoV-2: An approach to targeting RNA-dependent RNA polymerase (RdRp)

The World Health Organization has declared the novel coronavirus (COVID-19) outbreak a global pandemic and emerging threat to people in the 21st century. SARS-CoV-2 constitutes RNA-Dependent RNA Polymerase (RdRp) viral proteins, a critical target in the viral replication process. No FDA-approved drug is currently available, and there is a high demand for therapeutic strategies against COVID-19. In search of the anti-COVID-19 compound from traditional medicine, we evaluated the active moieties from Nilavembu Kudineer (NK), a poly-herbal Siddha formulation recommended by AYUSH against COVID-19. We conducted a preliminary docking analysis of 355 phytochemicals (retrieved from PubChem and IMPPAT databases) present in NK against RdRp viral protein (PDB ID: 7B3B) using COVID-19 Docking Server and further with AutoDockTool-1.5.6. MD simulation studies confirmed that Orientin (L1), Vitexin (L2), and Kasuagamycin (L3) revealed better binding activity against RdRp (PDB ID: 7B3B) in comparison with Remdesivir. The study suggests a potential scaffold for developing drug candidates against COVID-19. PRACTICAL APPLICATIONS: Nilavembu Kudineer is a poly-herbal Siddha formulation effective against various diseases like cough, fever, breathing problems, etc. This study shows that different phytoconstituents identified from Nilavembu Kudineer were subjected to in silico and ADME analyses. Out of the former 355 phytochemical molecules, Orientin (L1), Vitexin (L2), and Kasuagamycin (L3) showed better binding activity against RdRp viral protein (PDB ID: 7B3B) in comparison with the synthetic repurposed drug. Our work explores the search for an anti-COVID-19 compound from traditional medicine like Nilavembu Kudineer, which can be a potential scaffold for developing drug candidates against COVID-19.

An insight into the interaction between Indisulam and human serum albumin: Spectroscopic method, computer simulation and in vitro cytotoxicity assay

Indisulam (IDM) is a sulfanilamide anticancer agent and has been identified as a molecular glue recently. It shows potential for novel therapies development and brings more hope for curing human diseases. The affinity between molecular glues and plasma protein makes it significant to understand the characteristics of such substances. Therefore, the interaction between IDM and human serum albumin (HSA) was explored through solvent experiments, computer simulation experiments, enzyme kinetics experiments, and cell viability assay. The results revealed that IDM and HSA spontaneously formed stable binary complex with the binding constant of the order 10⁵ M^-1. IDM inserted in the site I of HSA, resulting the change in HSA secondary structure. And π electrons in IDM's benzene rings, as well as van der Waals forces and the H-bond, all helped to stabilize the HSA-IDM complex. The results of molecular dynamic simulation (MD) corresponded with the results from solvent experiment well. For instance, there were approximately 1-5 H-bonds between IDM and HSA. Lys199 and Arg218 were crucial energy contributors in the binding process. The esterase-like activity experiment confirmed that IDM inhibited the catalytic activity of HSA. In addition, cell experiment revealed that serum albumin can significantly reduce the cytotoxicity of IDM towards human embryonic kidney 293T (HEK293T) cells.

Nanoplastics alter the conformation and activity of human serum albumin

Nanoplastics finds its presence in most of the consumer products. Their chance of coming in contact with human cells and components is rampant. This study focuses on the interaction of polystyrene nanoplastics (PSNPs) with human serum albumin (HSA), ultimately causing structural and functional properties of the protein. Fluorescence and UV-Visible spectroscopic studies reported that PSNPs form a spontaneous ground-state complex with HSA, by hydrogen bonding, van der waal's, and hydrophobic force of attraction. This causes changes in the environment around major aromatic amino acids, especially tryptophan-214, which has a strong affinity with PSNPs. Further docking analysis confirmed hydrophobic interactions between PSNPs and aromatic amino acids in subdomain IIA of HSA. A shift in amide bands in HSA, as determined by FTIR analysis confirmed the disturbances in its secondary structure followed by reordering which will lead to the unfolding of HSA. Besides, PSNPs reduce the esterase activity of HSA by competitive inhibition. This molecular-level information such as binding energy, binding site, binding forces, reversible or irreversible binding, and structural changes of protein will shed light on the extent of toxicity in humans. This study will emphasize the urgent need for regulation of the use of nanoplastics (NPs) in consumer products, as well as the need for more research to determine the fate of NPs in the biological system.

Inclusion complex of 20(S)-protopanaxatriol with modified β-cyclodextrin: Characterization, solubility, and interaction with bovine serum albumin

20(S)-protopanaxatriol (PPT) is one of the ginsenosides isolated from Panax ginseng which have many pharmaceutical activities. However, the poor water solubility of PPT restrict its applications. Herein, a novel bridged-bis-[6-(3,3'-(ethylenedioxy) bis (propylamine))-6-deoxy-β-cyclodextrin] (EDBA-bis-β-CD) was designed and synthesized, and the inclusion complex (IC) of EDBA-bis-β-CD with PPT was successfully prepared in the solid state, and characterized by UV, ¹H NMR, 2D ROESY, FT-IR, XRD and SEM and molecular modelling methods. The continuous variation method analysis indicated that the stoichiometry of the IC was 1:1. UV-vis spectral analysis demonstrated the binding constant K_s was 995.94 M^-1, and the solubility study showed that the solubility of PPT improved 290 times. The interaction of the IC with bovine serum albumin (BSA) was investigated via fluorescence spectroscopy. The results indicated that fluorescence quenching of BSA by IC was static quenching. Thermodynamic studies showed that van der Waals forces and hydrogen bonding play significant roles in interaction. The esterase-like activity of BSA in the presence of IC showed that it reduce the esterase activity of BSA in a competitive manner. Furthermore, molecular docking and molecular dynamics simulations for EDBA-bis-β-CD/PPT and BSA/IC systems were generated to provide information on the stability and the forces in the binding.

Impact of Drug Repurposing on SARS-Cov-2 Main Protease

The recent emergence of the severe acute respiratory disease caused by a novel coronavirus remains a concern posing many challenges to public health and the global economy. The resolved crystal structure of the main protease of SARS-CoV-2 or SCV2 (M^pro) has led to its identification as an attractive target for designing potent antiviral drugs. Herein, we provide a comparative molecular impact of hydroxychloroquine (HCQ), remdesivir, and β-D-N⁴-Hydroxycytidine (NHC) binding on SCV2 M^pro using various computational approaches like molecular docking and molecular dynamics (MD) simulation. Data analyses showed that HCQ, remdesivir, and NHC binding to SARS-CoV-2 M^pro decrease the protease loop capacity to fluctuate. These binding influences the drugs’ optimum orientation in the conformational space of SCV2 M^pro and produce noticeable steric effects on the interactive residues. An increased hydrogen bond formation was observed in SCV2 M^pro–NHC complex with a decreased receptor residence time during NHC binding. The binding mode of remdesivir to SCV2 M^pro differs from other drugs having van der Waals interaction as the force stabilizing protein–remdesivir complex. Electrostatic interaction dominates in the SCV2 M^pro−HCQ and SCV2 M^pro–NHC. Residue Glu166 was highly involved in the stability of remdesivir and NHC binding at the SCV2 M^pro active site, while Asp187 provides stability for HCQ binding.

The different interactions of two anticancer drugs with bovine serum albumin based on multi-spectrum method combined with molecular dynamics simulations

Paclitaxel is the best natural anticancer drug and artemisinin also has anticancer effect. In this study, the interactions between BSA and these two drugs were determined in PBS (pH 7.40) by multi-spectroscopic method and molecular dynamics (MD) simulations. The results showed that paclitaxel and artemisinin could statically quench the BSA fluorescence when the complexes were formed and the stoichiometric ratio of BSA-drugs was 1:1. Particularly, the BSA-paclitaxel complex was more stable than BSA-artemisinin complex. During the binding, the surroundings around Trp residue site was largely affected than Tyr site, especially Trp 214 to a more hydrophobic environment. In addition, the binding processes were mainly spontaneous through electrostatic force interaction. In summary, we concluded that the free drug of paclitaxel in blood was low and duration time of artemisinin was shorter.

Atomic-Resolution 1.3 Å Crystal Structure, Inhibition by Sulfate, and Molecular Dynamics of the Bacterial Enzyme DapE

We report the atomic-resolution (1.3 Å) X-ray crystal structure of an open conformation of the dapE-encoded N-succinyl-l,l-diaminopimelic acid desuccinylase (DapE, EC 3.5.1.18) from Neisseria meningitidis. This structure [Protein Data Bank (PDB) entry 5UEJ] contains two bound sulfate ions in the active site that mimic the binding of the terminal carboxylates of the N-succinyl-l,l-diaminopimelic acid (l,l-SDAP) substrate. We demonstrated inhibition of DapE by sulfate (IC50 = 13.8 ± 2.8 mM). Comparison with other DapE structures in the PDB demonstrates the flexibility of the interdomain connections of this protein. This high-resolution structure was then utilized as the starting point for targeted molecular dynamics experiments revealing the conformational change from the open form to the closed form that occurs when DapE binds l,l-SDAP and cleaves the amide bond. These simulations demonstrated closure from the open to the closed conformation, the change in RMS throughout the closure, and the independence in the movement of the two DapE subunits. This conformational change occurred in two phases with the catalytic domains moving toward the dimerization domains first, followed by a rotation of catalytic domains relative to the dimerization domains. Although there were no targeting forces, the substrate moved closer to the active site and bound more tightly during the closure event.

An experimental investigation on the influence of various buffer concentrations, osmolytes and gold nanoparticles on lysozyme: Spectroscopic and calorimetric study

Considering importance and several industrial applications of lysozyme, including natural antibiotic and preservative, identifier for the diagnosis of diseases, and extraction purposes, its reversibility and stability studies can be very important. In this paper, the role that buffer and osmolytes concentrations play on the thermodynamic stability of lysozyme denaturation process, that is a new simple and inexpensive method, was evaluated by Nano-DSC III, far- and near-UV CD and fluorescence techniques. In thermal denaturation study, RI and ΔG of protein increased from 25.62% to 58.82% and 48.87 to 63.63 kJ mol^-1 with the increment of buffer and osmolytes concentrations, respectively. These changes showed a significant increase of 129.59% in RI and 28.16% in ΔG. The effect of buffer and osmolytes concentrations on the secondary and tertiary structures of protein was also investigated. The results indicated that increment of buffer and osmolytes concentrations increase rigidity and thermodynamic stability of protein. Also, structure of protein may be changed by its interaction with GNPs. Hence, interaction of lysozyme with GNPs was studied at the buffer and osmolytes concentrations that gives the maximum RI and ΔG, respectively. The results showed that molten globule-like state was formed by lysozyme in the presence of GNPs.

Binding-Induced Unfolding of 1-Bromopropane in α-Cyclodextrin

Raman multivariate curve resolution vibrational spectroscopy and X-ray crystallography are used to quantify changes in the gauche-trans conformational equilibrium of 1-bromopropane (1-BP) upon binding to α-cyclodextrin (α-CD). Both conformers of 1-BP are found to bind to α-CD, although binding favors the unfolded trans conformation. Temperature-dependent measurements of the binding-induced change in the 1-BP conformation equilibrium constant indicate that the trans conformer is both enthalpically and entropically stabilized in the host cavity.

Spectroscopic, molecular docking and molecular dynamic simulation studies on the complexes of β-lactoglobulin, safranal and oleuropein

Herbal bioactive compounds have captured pronounced attention considering their health-promoting effects as well as their functional properties. In this study, the binding mechanism between milk protein bovine β-lactoglobulin (β-LG), oleuropein (OLE) and safranal (SAF) found in olive leaf extract and saffron, respectively via spectroscopic and in silico studies. Fluorescence quenching information exhibited that interactions with both ligands were spontaneous and hydrophobic interactions were dominant. Also, the CD spectroscopy results demonstrated the increase in β-sheet structure and decrease in the α-helix content for both ligands. Size of β-LG-OLE complex was higher than β-LG-SAF due to the conformation and larger molecular size. Molecular docking and simulation studies revealed that SAF and OLE bind in the central calyx of β-LG and the surface of β-LG next to hydrophobic residues. Lastly, OLE formed a more stabilized complex compared to SAF based on the molecular dynamic simulation results.

Comparative structural and mechanistic studies of 4-hydroxy-tetrahydrodipicolinate reductases from Mycobacterium tuberculosis and Vibrio vulnificus

BACKGROUND

The products of the lysine biosynthesis pathway, meso-diaminopimelate and lysine, are essential for bacterial survival. This paper focuses on the structural and mechanistic characterization of 4-hydroxy-tetrahydrodipicolinate reductase (DapB), which is one of the enzymes from the lysine biosynthesis pathway. DapB catalyzes the conversion of (2S, 4S)-4-hydroxy-2,3,4,5-tetrahydrodipicolinate (HTPA) to 2,3,4,5-tetrahydrodipicolinate in an NADH/NADPH dependent reaction. Genes coding for DapBs were identified as essential for many pathogenic bacteria, and therefore DapB is an interesting new target for the development of antibiotics.

METHODS

We have combined experimental and computational approaches to provide novel insights into mechanism of the DapB catalyzed reaction.

RESULTS

Structures of DapBs originating from Mycobacterium tuberculosis and Vibrio vulnificus in complexes with NAD⁺, NADP⁺, as well as with inhibitors, were determined and described. The structures determined by us, as well as currently available structures of DapBs from other bacterial species, were compared and used to elucidate a mechanism of reaction catalyzed by this group of enzymes. Several different computational methods were used to provide a detailed description of a plausible reaction mechanism.

CONCLUSIONS

This is the first report presenting the detailed mechanism of reaction catalyzed by DapB.

GENERAL SIGNIFICANCE

Structural data in combination with information on the reaction mechanism provide a background for development of DapB inhibitors, including transition-state analogues.

Unraveling the conformational dynamics of glycerol 3-phosphate dehydrogenase, a nicotinamide adenine dinucleotide-dependent enzyme of Leishmania mexicana

Allosteric changes modulate the enzymatic activity, leading to activation or inhibition of the molecular target. Understanding the induced fit accommodation mechanism of a ligand in its lowest-free energy state and the subsequent conformational changes induced in the protein are important questions for drug design. In the present study, molecular dynamics (MD) simulations, binding free energy calculations, and principal component analysis (PCA) were applied to analyze the glycerol-3-phosphate dehydrogenase of Leishmania mexicana (LmGPDH) conformational changes induced by its cofactor and substrate binding. GPDH is a nicotinamide adenine dinucleotide (NAD)-dependent enzyme, which has been reported as an interesting target for drug discovery and development against leishmaniasis. Despite its relevance for glycolysis and pentose phosphate pathways, the structural flexibility and conformational motions of LmGPDH in complex with NADH and dihydroxyacetone phosphate (DHAP) remain unexplored. Here, we analyzed the conformational dynamics of the enzyme-NADH complex (cofactor), and the enzyme-NADH-DHAP complex (adduct), mapped the hydrogen-bond interactions for the complexes and pointed some structural determinants of the enzyme that emerge from these contacts to NADH and DHAP. Finally, we proposed a consistent mechanism for the conformational changes on the first step of the reversible redox conversion of dihydroxyacetone phosphate to glycerol 3-phosphate, indicating key residues and interactions that could be further explored in drug discovery.

An analogue of a kinase inhibitor exhibits subjective characteristics that contribute to its inhibitory activities as a potential anti-cancer candidate: insights through computational biomolecular modelling of UM-164 binding with lyn protein

The recent emergence of lyn kinase as a driver of aggressive behaviour in triple-negative breast cancer (TNBC) remains a major concern posing a burden for people living with breast cancer and drug development. The binding of UM-164 to lyn protein has been noted to impact the conformational dynamics required for drug fitness. Herein, we provide the first account of the molecular impact of an experimental drug, UM-164 binding on lyn protein using various computational approaches including molecular docking and molecular dynamics simulation. These computational modelling methods enabled us to analyse parameters, for example principal component analysis (PCA), dynamics cross-correlation matrices (DCCM) analysis, hydrogen bond occupancy, thermodynamics calculation and ligand–residue interaction. Findings from these analyses revealed that UM-164 exhibited a higher binding affinity of −9.9 kcal mol⁻¹ with lyn protein than Dasatinib, with a binding affinity of −8.3 kcal mol⁻¹ on docking. It was observed that the binding of UM-164 to lyn protein decreases the capacity of its loop to fluctuate, influences the ligand optimum orientation on the conformational space of lyn protein, and increases the hydrogen bond formation in the lyn-UM-164 system. Also, an increase in drug binding energy of UM-164 was recorded with increasing residue correlation in the lyn-UM-164 system. It is quite informative to note that Met85 was a key stabilising factor in the binding of UM-164 to lyn protein. These findings can provide important insights that will potentially serve as a baseline in the design of novel lyn inhibitors. It could also stimulate further research into multidimensional approaches required to curb the influence of lyn protein in TNBC.

This study provides the first account of the molecular impact of UM-164 binding on lyn protein using various computational approaches.

Different effects of Forsythia suspensa metabolites on bovine serum albumin (BSA)

Forsythia suspensa metabolites have many bioactivities, such as selective immuno suppression, antioxidation, anti-hepatic injury, etc. In the present study, the interactions of the three metabolites with BSA have been investigated in a buffer (pH 7.40) using multi-spectroscopic techniques in combination with molecular docking methods. Two isoformers, forsythoside A and forsythoside I can statically quench BSA intrinsic fluorescence by forming the complexes with BSA at stoichiometric ratio of 1:1 that is again proved by UV-visible absorption. During the binding, the proportion of α-helix in BSA increases, the microenvironment around Tryptophan 213 changes and FRET is one of the major factors to quench fluorescence. Forsythoside E forms BSA-forsythoside E complex (1:1) and thus enhances the intrinsic fluorescence of BSA. During the process, forsythoside E affects not only Tryptophan residues but also Tyrosine residues so that the conformation of BSA is consequently changed. All above binding processes are spontaneous mainly through hydrogen bonding and the hydrophobic force interaction, which is supported by docking analysis and thermodynamic parameters. In addition, three compounds do not induce BSA aggregation. These findings are beneficial to understand the detailed information of the interactions of Forsythia suspensa metabolites with BSA.

The impact of Thr91 mutation on c-Src resistance to UM-164: molecular dynamics study revealed a new opportunity for drug design

The emergence of a drug resistant non-receptor tyrosine kinase (c-Src) in triple-negative breast cancer (TNBC) remains a prime concern in relation to the burden of TNBC among people living with breast cancer and drug development. Thr91 mutation was found to induce a complete loss of protein conformation required for drug fitness. Herein, we provide the first account of the molecular impact of the Thr91 mutation on c-Src resistance to experimental drug UM-164 using various computational approaches, namely molecular dynamics simulation, principal component analysis (PCA), dynamic cross-correlation matrices (DCCM) analysis, hydrogen bond occupancy, thermodynamics calculation, ligand-residue interaction and residue interaction networks (RINs). Findings from this study revealed that Thr91 mutation leads to a steric conflict between UM-164 and the side chain of methionine (Met91); this mutation distorts the UM-164 optimum orientation on the conformational space of mutant c-Src compared to the wild-type; decreases hydrogen bond formation between the residues in the mutant protein structure; decreases the UM-164 binding energy in the mutant by -13.416 kcal mol^-1; reduces the residue correlation in the mutant protein structure; induces a change in the overall protein structure conformation from an inactive to active conformation; and distorts the ligand atomic interaction network and the residue interaction network. This report provides important insights that will assist in the further design of novel dual kinase inhibitors to minimise the chances of drug resistance in triple negative breast cancer.

Helicobacter pylori purine nucleoside phosphorylase shows new distribution patterns of open and closed active site conformations and unusual biochemical features

Even with decades of research, purine nucleoside phosphorylases (PNPs) are enzymes whose mechanism is yet to be fully understood. This is especially true in the case of hexameric PNPs, and is probably, in part, due to their complex oligomeric nature and a whole spectrum of active site conformations related to interactions with different ligands. Here we report an extensive structural characterization of the apo forms of hexameric PNP from Helicobacter pylori (HpPNP), as well as its complexes with phosphate (P_i ) and an inhibitor, formycin A (FA), together with kinetic, binding, docking and molecular dynamics studies. X-ray structures show previously unseen distributions of open and closed active sites. Microscale thermophoresis results indicate that a two-site model describes P_i binding, while a three-site model is needed to characterize FA binding, irrespective of P_i presence. The latter may be related to the newly found nonstandard mode of FA binding. The ternary complex of the enzyme with P_i and FA shows, however, that P_i binding stabilizes the standard mode of FA binding. Surprisingly, HpPNP has low affinity towards the natural substrate adenosine. Molecular dynamics simulations show that P_i moves out of most active sites, in accordance with its weak binding. Conformational changes between nonstandard and standard binding modes of nucleoside are observed during the simulations. Altogether, these findings show some unique features of HpPNP and provide new insights into the functioning of the active sites, with implications for understanding the complex mechanism of catalysis of this enzyme.

DATABASES

The atomic coordinates and structure factors have been deposited in the Protein Data Bank: with accession codes 6F52 (HpPNPapo_1), 6F5A (HpPNPapo_2), 6F5I (HpPNPapo_3), 5LU0 (HpPNP_PO4), 6F4W (HpPNP_FA) and 6F4X (HpPNP_PO4_FA).

ENZYMES

Purine nucleoside orthophosphate ribosyl transferase, EC2.4.2.1, UniProtID: P56463.

Re-emergence of an orphan therapeutic target for the treatment of resistant prostate cancer - a thorough conformational and binding analysis for ROR-γ protein

Recent studies have linked a deadly form of prostate cancer known as metastatic castration-resistant prostate cancer to retinoic acid-related orphan-receptor gamma (ROR-γ). Most of these studies continued to place ROR-γ as orphan because of unidentifiable inhibitor. Recently identified inhibitors of ROR-γ and their therapeutic potential were evaluated, among which inhibitor XY018 was the potent. However, molecular understanding of the conformational features of XY018-ROR-γ complex is still elusive. Herein, molecular dynamics simulations were conducted on HC9-ROR-γ and XY018-ROR-γ complexes to understand their conformational features at molecular level and the influence of XY018 binding on the dynamics of ROR-γ with the aid of post-dynamic analytical tools. These include; principal component analysis, radius of gyration, binding free energy calculation (MM/GBSA), per-residue fluctuation and hydrogen bond occupancy. Findings from this study revealed that (1) hydrophobic packing contributes significantly to binding free energy, (2) Ile136 and Leu60 exhibited high hydrogen-bond occupancy in XY018-ROR-γ and HC9-ROR-γ, respectively, (3) XY018-ROR-γ displayed a relatively high loop region residue fluctuation compared to HC9-ROR-γ, (4) electrostatic interactions are a potential binding force in XY018-ROR-γ complex compared to HC9-ROR-γ, (5) XY018-ROR-γ assumes a rigid conformation which is highlighted by a decrease in residual fluctuation, (6) XY018 could potentially induce pseudoporphyria, nephritis and interstitial nephritis but potentially safe in renal failure. This study could serve as a base line for the design of new potential ROR-γ inhibitors.

Exploration of ligand-induced protein conformational alteration, aggregate formation, and its inhibition: A biophysical insight

The association of protein aggregates with plentiful human diseases has fascinated studies regarding the biophysical characterization of protein misfolding and ultimately their aggregate formation mechanism. Protein-ligand interaction, their mechanism, conformational changes by ligands, and protein aggregate formation have been studied upon exploiting experimental techniques and computational methodologies. Such studies for the exploration of ligand-induced conformational changes in protein, misfolding and aggregation, has confirmed drastic progresses in the study of aggregate formation pathways. This review comprises of an inclusive description of contemporary experimental techniques as well as theoretical improvements in the interpretation of the conformational properties of protein. We have also discussed various factors responsible for the microenvironment change around protein that sequentially causes amyloidoses. Biophysical techniques and cell-based assays to gain comprehensive understandings of protein-ligand interaction, protein folding, and aggregation pathways have also been described. The promising therapeutic methods used to inhibit the protein fibrillogenesis have also been discussed.

PXR: More Than Just a Master Xenobiotic Receptor

Pregnane X receptor (PXR) is a nuclear receptor considered to be a master xenobiotic receptor that coordinately regulates the expression of genes encoding drug-metabolizing enzymes and drug transporters to essentially detoxify and eliminate xenobiotics and endotoxins from the body. In the past several years, the function of PXR in the regulation of xenobiotic metabolism has been extensively studied, and the role of PXR as a xenobiotic sensor has been well established. It is now clear, however, that PXR plays many other roles in addition to its xenobiotic-sensing function. For instance, recent studies have discovered previously unidentified roles of PXR in inflammatory response, cell proliferation, and cell migration. PXR also contributes to the dysregulation of these processes in diseases states. These recent discoveries of the role of PXR in the physiologic and pathophysiologic conditions of other cellular processes provides the possibility of novel targets for drug discovery. This review highlights areas of PXR regulation that require further clarification and summarizes the recent progress in our understanding of the nonxenobiotic functions of PXR that can be explored for relevant therapeutic applications.

Biophysical insight into the interaction mechanism of plant derived polyphenolic compound tannic acid with homologous mammalian serum albumins

Numerous phenolic compounds have been reported in the last decade that have a good antioxidant property and interaction affinity towards mammalian serum albumins. In the present study, we have utilized mammalian serum albumins as a model protein to examine their comparative interaction property with polyphenolic compound tannic acid (TA) by using various spectroscopic and calorimetric methods We have also monitored the esterase and antioxidant activity of mammalian serum albumins in the absence and presence of TA. The obtain results recommended that the TA have a good binding affinity (∼10⁴ to 10⁶M^-1) towards mammalian serum albumins and shows double sequential binding sites, which depends on the concentration of TA that induced the conformational alteration which responsible for the thermal stability of proteins. Binding affinity, structural transition and thermodynamic parameters were calculated from spectroscopic and calorimetric method reveals that non-covalent interaction causes partial conformational alteration in the secondary structure of protein ie.; increase in α-helical content with decrease in β-sheet, random coil and other structure. Meanwhile, we have found that esterase activities of serum albumins were also stabilized against hydrolysis and shows higher antioxidant activity in the presence of TA because albumins its self have an immense antioxidant activity beside TA.

Molecular mechanism of tobramycin with human serum albumin for probing binding interactions: multi-spectroscopic and computational approaches

Highlighting novelty: comprehensive in vitro and in silico insights for understanding the novel binding site of TOB with HSA.

Biophysical insights into the interaction of hen egg white lysozyme with therapeutic dye clofazimine: modulation of activity and SDS induced aggregation of model protein

The present study details the binding process of clofazimine to hen egg white lysozyme (HEWL) using spectroscopy, dynamic light scattering, transmission electron microscopy (TEM), and molecular docking techniques. Clofazimine binds to the protein with binding constant (K_b) in the order of 1.57 × 10⁴ at 298 K. Binding process is spontaneous and exothermic. Molecular docking results suggested the involvement of hydrogen bonding and hydrophobic interactions in the binding process. Bacterial cell lytic activity in the presence of clofazimine increased to more than 40% of the value obtained with HEWL only. Interaction of the drug with HEWL induced ordered secondary structure in the protein and molecular compaction. Clofazimine also effectively inhibited the sodium dodecyl sulfate (SDS) induced amyloid formation in HEWL and caused disaggregation of preformed fibrils, reinforcing the notion that there is involvement of hydrophobic interactions and hydrogen bonding in the binding process of clofazimine with HEWL and clofazimine destabilizes the mature fibrils. Further, TEM images confirmed that fibrillar species were absent in the samples where amyloid induction was performed in the presence of clofazimine. As clofazimine is a drug less explored for the inhibition of fibril formation of the proteins, this study reports the inhibition of SDS-induced amyloid formation of HEWL by clofazimine, which will help in the development of clofazimine-related molecules for the treatment of amyloidosis.

Studies on the interaction between promethazine and human serum albumin in the presence of flavonoids by spectroscopic and molecular modeling techniques

Fluorescence, absorption, time-correlated single photon counting (TCSPC), and circular dichroism (CD) spectroscopic techniques as well as molecular modeling methods were used to study the binding characterization of promethazine (PMT) to human serum albumin (HSA) and the influence of flavonoids, rutin and baicalin, on their affinity. The results indicated that the fluorescence quenching mechanism of HSA by PMT is a static quenching due to the formation of complex. The reaction was spontaneous and mainly mediated by hydrogen bonds and hydrophobic interactions. The binding distance between the tryptophan residue of HSA and PMT is less than 8nm, which indicated that the energy transfer from the tryptophan residue of HSA to PMT occurred. The binding site of PMT on HSA was located in sites I and the presence of PMT can cause the conformational changes of HSA. There was the competitive binding to HSA between PMT and flavonoids because of the overlap of binding sites in HSA. The flavonoids could decrease the association constant and increase the binding distance. In addition, their synergistic effect can further change the conformation of HSA. The decrease in the affinities of PMT binding to HSA in the presence of flavonoids may lead to the increase of free drug in blood, which would affect the transportation or disposition of drug and evoke an adverse or toxic effect. Hence, rationalising dosage and diet regimens should be taken into account in clinical application of PMT.

Biophysical and molecular docking insight into interaction mechanism and thermal stability of human serum albumin isoforms with a semi-synthetic water-soluble camptothecin analog irinotecan hydrochloride

In the present work, we have examined the binding parameters, thermodynamics, and stability of human serum albumin (HSA) isoforms at pH 7.4 and 9.0, using spectroscopic, calorimetric, and molecular docking methods in the presence of water-soluble camptothecin analog irinotecan hydrochloride (CPT-11). We observed that CPT-11 binds to HSA through a static quenching procedure of ground-state complex formation with N-isoform and B-isoform. Hydrogen bond and hydrophobic interactions are the major governing forces that participating in the formation of protein-drug complex. To determine the binding site of CPT-11 within HSA molecules, we also have performed molecular docking experiments. We explored the CPT-11-mediated stability and modulation of HSA by performing dynamic light scattering (DLS) and differential scanning calorimetry (DSC) experiments. DLS and DSC techniques are used to determine the size and the melting point (Tm) of HSA, which was decreased in the presence of CPT-11. Therefore, CPT-11 plays an important role in HSA stability and protein-ligand interactions. The present study provides valuable information in the field of pharmacokinetics, pharmaco-dynamics, and drug discovery.

Rosin Surfactant QRMAE Can Be Utilized as an Amorphous Aggregate Inducer: A Case Study of Mammalian Serum Albumin

Quaternary amine of diethylaminoethyl rosin ester (QRMAE), chemically synthesized biocompatible rosin based cationic surfactant, has various biological applications including its use as a food product additive. In this study, we examined the amorphous aggregation behavior of mammalian serum albumins at pH 7.5, i.e., two units above their isoelectric points (pI ~5.5), and the roles played by positive charge and hydrophobicity of exogenously added rosin surfactant QRMAE. The study was carried out on five mammalian serum albumins, using various spectroscopic methods, dye binding assay, circular dichroism and electron microscopy. The thermodynamics of the binding of mammalian serum albumins to cationic rosin modified surfactant were established using isothermal titration calorimetry (ITC). It was observed that a suitable molar ratio of protein to QRMAE surfactant enthusiastically induces amorphous aggregate formation at a pH above two units of pI. Rosin surfactant QRMAE-albumins interactions revealed a unique interplay between the initial electrostatic and the subsequent hydrophobic interactions that play an important role towards the formation of hydrophobic interactions-driven amorphous aggregate. Amorphous aggregation of proteins is associated with varying diseases, from the formation of protein wine haze to the expansion of the eye lenses in cataract, during the expression and purification of recombinant proteins. This study can be used for the design of novel biomolecules or drugs with the ability to neutralize factor(s) responsible for the aggregate formation, in addition to various other industrial applications.

Gelsolin Amyloidogenesis Is Effectively Modulated by Curcumin and Emetine Conjugated PLGA Nanoparticles

Small molecule based therapeutic intervention of amyloids has been limited by their low solubility and poor pharmacokinetic characteristics. We report here, the use of water soluble poly lactic-co-glycolic acid (PLGA)-encapsulated curcumin and emetine nanoparticles (Cm-NPs and Em-NPs, respectively), as potential modulators of gelsolin amyloidogenesis. Using the amyloid-specific dye Thioflavin T (ThT) as an indicator along with electron microscopic imaging we show that the presence of Cm-NPs augmented amyloid formation in gelsolin by skipping the pre-fibrillar assemblies, while Em-NPs induced non-fibrillar aggregates. These two types of aggregates differed in their morphologies, surface hydrophobicity and secondary structural signatures, confirming that they followed distinct pathways. In spite of differences, both these aggregates displayed reduced toxicity against SH-SY5Y human neuroblastoma cells as compared to control gelsolin amyloids. We conclude that the cytotoxicity of gelsolin amyloids can be reduced by either stalling or accelerating its fibrillation process. In addition, Cm-NPs increased the fibrillar bulk while Em-NPs defibrillated the pre-formed gelsolin amyloids. Moreover, amyloid modulation happened at a much lower concentration and at a faster rate by the PLGA encapsulated compounds as compared to their free forms. Thus, besides improving pharmacokinetic and biocompatible properties of curcumin and emetine, PLGA conjugation elevates the therapeutic potential of both small molecules against amyloid fibrillation and toxicity.

Effects of 2-amino-8-hydroxyquinoline interaction on the conformation of physiological isomers of human serum albumin

The methods of synthetic chemistry create small molecules rapidly for screening, and ligand-protein interaction studies provide information on how a potential drug interacts with target or carrier proteins such as serum albumin. In this work, we investigate the interaction of amino derivative of 8-hydroxyquinoline, 2-amino-8-hydroxyquinoline (A8HQ), and the effects of its binding on the conformation of different isomers of human serum albumin (HSA) using multispectroscopic techniques and molecular modeling. We found that B isomer, which exists at pH 9, bound A8HQ (K a = 1.92 ± 0.07 × 10(5) M(-1) at 298 K) more strongly as compared with N isomer (K a = 1.19 ± 0.04 × 10(5) M(-1) at 298 K) of HSA, which is known to exist around pH 6. The binding constant at physiological pH (7.4) was also determined, and the value (K a = 1.38 ± 0.05 × 10(5) M(-1) at 298 K) was found to fall between those for N and B isomers, suggesting that both the N and B isomers exist in an equilibrium in plasma. We also determined the thermodynamic parameters such as changes in enthalpy, entropy , and free energy of binding by measuring the binding at four different temperatures. Based on molecular modeling and thermodynamic studies, we propound that the A8HQ-HSA binding involves mainly hydrophobic interactions and hydrogen bonding. Site-specific marker displacement experiments and molecular modeling showed that the molecule preferably binds in subdomain IIA close to Trp214. A8HQ binding to HSA isomers was found to cause both secondary and tertiary structural alterations in the protein.

Identification and characterization of a novel phosphodiesterase from the metagenome of an Indian coalbed

Phosphoesterases are involved in the degradation of organophosphorus compounds. Although phosphomonoesterases and phosphotriesterases have been studied in detail, studies on phosphodiesterases are rather limited. In our search to find novel phosphodiesterases using metagenomic approach, we cloned a gene encoding a putative phosphodiesterase (PdeM) from the metagenome of the formation water collected from an Indian coal bed. Bioinformatic analysis showed that PdeM sequence possessed the characteristic signature motifs of the class III phosphodiesterases and phylogenetic study of PdeM enabled us to identify three distinct subclasses (A, B, and C) within class III phosphodiesterases, PdeM clustering in new subclass IIIB. Bioinformatic, biochemical and biophysical characterization of PdeM further revealed some of the characteristic features of the phosphodiesterases belonging to newly described subclass IIIB. PdeM is a monomer of 29.3 kDa, which exhibits optimum activity at 25°C and pH 8.5, but low affinity for bis(pNPP) as well as pNPPP. The recombinant PdeM possessed phosphodiesterase, phosphonate-ester hydrolase and nuclease activity. It lacked phosphomonoesterase, phosphotriesterase, and RNAse activities. Overexpression of PdeM in E.coli neither affected catabolite respression nor did the recombinant protein hydrolyzed cAMP in vitro, indicating its inability to hydrolyze cAMP. Although Mn²⁺ was required for the activity of PdeM, but addition of metals (Mn²⁺ or Fe³⁺) did not induce oligomerization. Further increase in concentration of Mn²⁺ upto 3 mM, increased α-helical content as well as the phosphodiesterase activity. Structural comparison of PdeM with its homologs showed that it lacked critical residues required for dimerization, cAMP hydrolysis, and for the high affinity binding of bis(pNPP). PdeM, thus, is a novel representative of new subclass of class III phosphodiesterases.

Probing the binding of an endocrine disrupting compound-Bisphenol F to human serum albumin: insights into the interactions of harmful chemicals with functional biomacromolecules

Bisphenol F (BPF) as an endocrine disrupting compounds (EDCs) pollutant in the environment poses a great threat to human health. To evaluate the toxicity of BPF at the protein level, the effects of BPF on human serum albumin (HSA) were investigated at three temperatures 283, 298, and 308 K by multiple spectroscopic techniques. The experimental results showed that BPF effectively quenched the intrinsic fluorescence of HSA via static quenching. The number of binding sites, the binding constant, the thermodynamic parameters and the binding subdomain were measured, and indicated that BPF could spontaneously bind with HSA on subdomain IIA through H-bond and van der Waals interactions. Furthermore, the conformation of HSA was demonstrably changed in the presence of BPF. The work provides accurate and full basic data for clarifying the binding mechanisms of BPF with HSA in vivo and is helpful for understanding its effect on protein function during its transportation and distribution in blood.