far-UV Circular Dichroism Research Articles

Exploration of the Stabilization Mechanism and Curcumin Bioaccessibility of Emulsions Stabilized by Whey Protein Hydrolysates after Succinylation and Glycation in Different Orders.

The combined effects of succinic anhydride (SA) succinylation and linear dextrin (LD) glycation on whey protein hydrolysates (WPH) and their stabilized emulsions were evaluated. Degree of succinylation (DS), degree of glycation (DG), and degree of browning of samples suggested that a competitive displacement of reactive groups existed when WPH reacted with SA and LD in different orders. Attenuated total reflection Fourier transform infrared (ATR-FTIR) and far-UV circular dichroism (CD) indicated that the order of modification methods had a significant effect on secondary structures of WPH. Succinylation combined with glycation effectively reduced the surface hydrophobicity and increased the molecular flexibility of WPH. Meanwhile, the total free -SH content decreased, and the exposed free -SH content increased. Results of storage stability and gastrointestinal fate of the curcumin-loaded emulsion revealed that the modified WPH with higher DS was more effective for improving the curcumin bioaccessibility, while that with higher DG was more effective for enhancing the stability of the emulsion.

Pomegranate seed oil stabilized with ovalbumin glycated by inulin: Physicochemical stability and oxidative stability

Pomegranate seed oil is rich of conjugated fatty acids which are highly appealing for a variety of applications in food industry. In this research, ovalbumin (OVA) and ovalbumin-inulin glycoconjugates with different Maillard reaction times were used to stabilize pomegranate seed oil emulsions and their impact on physicochemical stability and oxidative stability of the products was investigated. The OVA-inulin glycoconjugate produced on 10th day of Maillard reaction has exhibited significantly higher conjugation efficiency, lower surface hydrophobicity and lower surface tension than other glycoconjugates. The secondary conformation of OVA and conjugates determined by far-UV circular dichroism spectroscopy has remarkably changed. The reduction in intensity of Trp-fluorescence observed in glycated proteins with inulin indicated that the glycation affected partially the side chains of protein in tertiary structure through the Maillard reaction without great disruption of native structure. The emulsion stabilized by OVA-inulin glycoconjugate obtained by 10 days Maillard reaction has shown the best physicochemical stability. Compared with the OVA emulsion, the oxidative stability of the glycated OVA emulsion system was significantly improved (p < 0.05). Fatty acid profile results also confirmed that OVA-inulin glycoconjugates were able to prevent the pomegranate seed oil from oxidation. It is suggested that the inulin attached to OVA by glycation played a vital role in physicochemical stability and oxidative stability of pomegranate seed oil emulsions.

Dynamic elements and kinetics: Most favorable conformations of peptides in solution with measurements and simulations.

Small peptides in solution adopt a specific morphology as they function. It is of fundamental interest to examine the structural properties of these small biomolecules in solution and observe how they transition from one conformation to another and form functional structures. In this study, we have examined the structural properties of a simple dipeptide and a five-residue peptide with the application of far-UV circular dichroism (CD) spectroscopy as a function of temperature, fluorescence anisotropy, and all-atom molecular dynamics simulation. Analysis of the temperature dependent CD spectra shows that the simplest dipeptide N-acetyl-tryptophan-amide (NATA) adopts helical, beta sheet, and random coil conformations. At room temperature, NATA is found to have 5% alpha-helical, 37% beta sheet, and 58% random coil conformations. To our knowledge, this type of structural content in a simplest dipeptide has not been observed earlier. The pentapeptide (WK5) is found to have four major secondary structural elements with 8% 310 helix, 14% poly-L-proline II, 8% beta sheet, and 14% turns. A 56% unordered structural population is also present for WK5. The presence of a significant population of 310 helix in a simple pentapeptide is rarely observed. Fluorescence anisotropy decay (FAD) measurements yielded reorientation times of 45 ps for NATA and 120 ps for WK5. The fluorescence anisotropy decay measurements reveal the size differences between the two peptides, NATA and WK5, with possible contributions from differences in shape, interactions with the environment, and conformational dynamics. All-atom molecular dynamics simulations were used to model the structures and motions of these two systems in solution. The predicted structures sampled by both peptides qualitatively agree with the experimental findings. Kinetic modeling with optimal dimensionality reduction suggests that the slowest dynamic processes in the dipeptide involve sidechain transitions occurring on a 1 ns timescale. The kinetics in the pentapeptide monitors the formation of a distorted helical structure from an extended conformation on a timescale of 10 ns. Modeling of the fluorescence anisotropy decay is found to be in good agreement with the measured data and correlates with the main contributions of the measured reorientation times to individual conformers, which we define as dynamic elements. In NATA, the FAD can be well represented as a sum of contributions from representative conformers. This is not the case in WK5, where our analysis suggests the existence of coupling between conformational dynamics and global tumbling. The current study involving detailed experimental measurements and atomically detailed modeling reveals the existence of specific secondary structural elements and novel dynamical features even in the simplest peptide systems.

Physicochemical Characterization of Altebrel™, a Proposed Etanercept Biosimilar.

Background: Etanercept is prescribed for the rapid and effective treatment of chronic immune-mediated inflammatory disorders. Due to the expiration of etanercept patents and worldwide demand for comparable and more affordable substitutes, several biosimilars of etanercept have been approved in different countries and new ones are in the process of approval. Objectives: In the present study, Altebrel™ as an etanercept proposed biosimilar was investigated in a side by side comparison using various orthogonal analytical methods. Materials and Methods: Three batches of the Altebrel™ and Enbrel® samples were used for the study. Several physicochemical properties of samples were compared according to international guidelines, incliding; sodium dodecyl sulfate polyacrylamide gel electrophoresis (SDS-PAGE), Capillary electrophoresis sodium dodecyl sulfate (CE-SDS), size exclusion high performance liquid chromatography (SE-HPLC), hydrophobic interaction chromatography high performance liquid chromatography (HIC-HPLC) and its biological activity was evaluated using surface plasmon resonance affinity analysis and tumor necrosis factor alpha (TNFα) neutralization biological assay. Amino acid analysis was applied to check the primary sequence and far-UV circular dichroism (CD) spectroscopy investigated the secondary structure. Results: The obtained results indicated a high degree of similarity between Altebrel™ and Enbrel®. Results of SDS-PAGE, CE-SDS, HIC-HPLC and SE-HPLC implied a comparable pattern of size variants for all samples. Based on the data achieved via in vitro bioactivity assays and SPR analysis, the functional property of Altebrel™ was proved comparable to that of the reference product. Moreover, amino acid analysis indicated similar primary structure and circular dichroism study implied a similar secondary structure for Altebrel™ and Enbrel®. Conclusion: Overall, our data provide analytical evidence for structural and in vitro functional similarity between Altebrel™ and Enbrel®.

Comparison of the structural dynamic and mitochondrial electron-transfer properties of the proapoptotic human cytochrome c variants, G41S, Y48H and A51V

Mitochondrial cytochrome c is associated with electron transfer in the respiratory chain and in apoptosis. Four cytochrome c variants have been identified in families that suffer from mild autosomal dominant thrombocytopenia, a platelet disorder associated with increased apoptosis. Three out of the four substitutions, G41S, Y48H and A51V are located on the 40–57 Ω-loop. The G41S and Y48H variants perturb key physicochemical and dynamic properties that result in enhanced functional features associated with apoptotic activity. Herein we characterise the ferric A51V variant. We show by chemical denaturation that this variant causes the native state to be destabilized. Through azide binding kinetics, the population of a pentacoordinate heme form, whereby the Met80 axial ligand is dissociated, is estimated to be of equal magnitude to that found in the Y48H variant. This pentacoordinate form gives rise to peroxidase activity, which despite the similar pentacoordinate population of the A51V variant to that of the Y48H variant, the peroxidase activity of the A51V variant is suppressed. Far-UV circular dichroism spectroscopy and pH jump studies, suggest that a combination of structural and dynamic features in addition to the population of the pentacoordinate form regulate peroxidase activity in these disease variants. Additionally, the steady-state ratio of ferric/ferrous cytochrome c when in turnover with cytochrome c oxidase has been investigated for all 40–57 Ω-loop variants. These studies show that the lower pKa of the alkaline transition for the disease causing variants increases the ferric to ferrous heme ratio, indicating a possible influence on respiration in vivo.

Cycloplatinated(II) Derivatives of Mercaptopurine Capable of Binding Interactions with HSA/DNA.

In this study, two new bis-cyclometalated Pt(II) complexes, [Pt(C^N)(S^N)] [S^N = deprotonated 6-mercaptopurine (6-MP) and C^N = deprotonated 2-phenylpyridine (ppy), 2a; C^N = deprotonated benzo[h]quinoline (bhq), 2b], are synthesized by the reaction of [PtR(SMe2)(C^N)] (R = Me or p-MeC6H4) with 1 equiv of 6-mercaptopurine (6-HMP) at room temperature. The complexes are fully characterized using 1H and 13C NMR spectroscopies, electrospray ionization mass spectrometry, and elemental analysis. Biomolecular interaction of complex 2a with human serum albumin (HSA) is studied by fluorescence, UV-vis, and circular dichroism (CD) spectroscopies. The binding constants (Kb) and number of binding sites (n) are evaluated using the Stern-Volmer equation. The intrinsic fluorescence of protein is quenched by a static quenching mechanism, with a binding constant of Kb ∼ 105 reflecting a high affinity of complex 2a for HSA. The thermodynamic parameters (ΔH°, ΔG°, and ΔS°) indicate that the interaction is a spontaneous process and hydrophobic forces play a main role in the reaction. The displacement experiments demonstrate that the reactive binding sites of HSA to complex 2a are mainly located within its hydrophobic cavity in subdomain IIA (site I). Synchronous fluorescence spectra reveal that complex 2a affected the microenvironment of tryptophan-214 residues in subdomain IIA of HSA. In the case of interaction of complex 2b and HSA, because of overlapping of the emission spectra of complex 2b with HSA, chemometric approaches are applied. The results indicate significant interaction between the tryptophan residue of HSA and complex 2b. Moreover, the binding of Pt(II) complexes 2a and 2b causes a reduction of the α-helix content of HSA, as obtained by far-UV CD spectroscopy. The average binding distance (r) between Pt(II) complexes and HSA is obtained by Förster's resonance energy-transfer theory. Also, a molecular docking simulation reveals that π-π-stacking and hydrophobic interactions between these complexes and HSA are significant. Furthermore, the interactions of platinum complexes, 2, with calf-thymus DNA (CT-DNA) are investigated. The UV-vis results and ethidium bromide competitive studies support an intercalative interaction of both Pt(II) complexes with DNA. The new complexes 2 are also screened for anticancer activities. The results show that complexes 2 exhibit significant anticancer activity against the K562 (chronic myelogenous leukemia) cell line.

P5722Thermodynamic phenotypes guide the pathogenicity assessment of a variant of uncertain significance in cardiac myosin binding protein C

Abstract In the era of Next Generation Sequencing (NGS), genetic testing for inherited disorders identifies an ever-increasing number of variants, whose pathogenicity remains unclear. These variants of uncertain significant (VUS) limit the reach of genetic testing in clinical practice. The VUS for Hypertrophic Cardiomyopathy (HCM), the most common familial heart disease, constitute over 60% of entries for missense variants shown in ClinVar database. We have proposed a workflow to determine pathogenicity of VUS, which integrates bioinformatics evaluation and functional studies of RNA splicing and protein thermodynamic stability. This workflow was applied on a novel VUS in MYBPC3 gene, coding for cardiac myosin-binding protein C (cMyBP-C), which is the most mutated gene in HCM. The c.1809T&gt;G-p.I603M variant was identified during genetic screening of patient clinically affected by HCM and it was classified as VUS applying ACMG criteria. In silico prediction and mRNA analysis of c.1809T&gt;G-p.I603M variant indicated no alteration of RNA splicing (Figure 1). At protein level, the p.I603M mutation maps to the C4 domain of cMyBP-C. The homology modelling of domain C4 shows I603 to be buried in the protein structure, suggesting a potential destabilising role of this mutant. The Circular Dichroism (CD) confirms that the I603M variant does not perturb much the structure of domain, according to the far-UV and near-UV CD spectra. However, the thermodynamic stability of domain C4 is severely compromised, as shown by lower Tm and van't Hoff enthalpy (ΔHv) in thermal denaturation experiments by CD and Differential Scanning Calorimetry (DSC) (Figure 1). Furthermore, the Gibbs free energy change (ΔG) at 25°C of the unfolding process was also calculated from the DSC thermograms. The resulting ΔΔG of C4 I603M (4.5 kcal/mol) is comparable to other pathogenetic variants in other MYBPC3 domains. Taking into account our results, we propose reclassification of variant p.I603M as likely pathogenic. Figure 1. Workflow In conclusion, our strategy is useful to refine the assignment of pathogenicity in the absence of enough genetic support, improving the clinical management of HCM patients and their families. Acknowledgement/Funding MCNU: BIO2014-54768-P, BIO2017-83640-P (AEI/FEDER, UE), RYC-2014-16604, SEV-2015-0505- ISCIII: CB16/11/00425. Comunidad de Madrid: PEJ16/MED/TL-1593.

Controlling Structure and Dimensions of a Disordered Protein via Mutations.

The dimensions of intrinsically disordered proteins (IDPs) are sensitive to small energetic-entropic differences between intramolecular and protein–solvent interactions. This is commonly observed on modulating solvent composition and temperature. However, the inherently heterogeneous conformational landscape of IDPs is also expected to be influenced by mutations that can (de)stabilize pockets of local and even global structure, native and non-native, and hence the average dimensions. Here, we show experimental evidence for the remarkably tunable landscape of IDPs by employing the DNA-binding domain of CytR, a high-sequence-complexity IDP, as a model system. CytR exhibits a range of structure and compactness upon introducing specific mutations that modulate microscopic terms, including main-chain entropy, hydrophobicity, and electrostatics. The degree of secondary structure, as monitored by far-UV circular dichroism (CD), is strongly correlated to average ensemble dimensions for 14 different mutants of CytR and is consistent with the Uversky–Fink relation. Our experiments highlight how average ensemble dimensions can be controlled via mutations even in the disordered regime, the prevalence of non-native interactions and provide testable controls for molecular simulations.

Functional Rescue of Cataract-Causing αA-G98R-Crystallin by Targeted Compensatory Suppressor Mutations in Human αA-Crystallin.

The G98R mutation in αA-crystallin is associated with the onset of presenile cataract and is characterized biochemically by an increased oligomeric mass, altered chaperone function, and loss of structural stability over time. Thus, far, it is not known whether the inherent instability caused by gain-of-charge mutation could be rescued by a compensatory loss of charge mutation elsewhere on the protein. To answer this question, we investigated whether αA-G98R-mediated instability could be rescued through suppressor mutations by introducing site-specific "compensatory" mutations in αA-G98R-crystallin, αA-R21Q/G98R, αA-G98R/R116C, and αA-R157Q/G98R. The recombinant proteins were expressed, purified, characterized, and evaluated by circular dichroism (CD), intrinsic fluorescence, and bis-ANS-binding studies. Chaperone-like activities of recombinant proteins were assessed using alcohol dehydrogenase (ADH) and insulin as unfolding substrates. Far-UV CD studies revealed an increased α-helical content in αA-G98R in comparison to αA-WT, αA-R21Q, R157Q, and the double mutants, αA-R21Q/G98R, and αA-R157Q/G98R. Compared to αA-WT, αA-R21Q, and αA-G98R, the double mutants showed an increased intrinsic tryptophan fluorescence, whereas the highest hydrophobicity (bis-ANS-binding) was shown by αA-G98R. Introduction of a second mutation in αA-G98R reduced its bis-ANS-binding activity. Both αA-R21Q/G98R and αA-R157Q/G98R showed greater chaperone-like activity against ADH aggregation than αA-G98R. However, among the three G98R mutants, only αA-R21Q/G98R protected ARPE-19 cells from H2O2-induced cytotoxicity. These results suggest that the lost chaperone-like activity of αA-G98R-crystallin can be rescued by another targeted mutation and that substitution of αA-R21Q-crystallin at the N-terminal region can rescue a deleterious mutation in the conserved α-crystallin domain of the protein.

Unfolding and partial refolding of a cellulase from the SDS-denatured state: From β-sheet to α-helix and back

Globular proteins are typically unfolded by SDS to form protein-decorated micelle-like structures. Several proteins have been shown subsequently to refold by addition of the nonionic surfactant octaethylene glycol monododecyl ether (C12E8). Thus SDS converts β-lactoglobulin, which has mainly β-sheet secondary structure, into a state rich in α-helicality, while addition of C12E8 leads to refolding and recovery of the original β-sheet structure. Here we extend these studies to the large β-sheet-rich cellulase Cel7b from Humicola insolens whose enzymatic activity provides a very sensitive refolding parameter. The enzymes widespread usage in the detergent industry makes it an obvious model system for protein-surfactant interactions. SDS-unfolding and subsequent refolding using C12E8 were investigated at pH 4.2 using near- and far-UV circular dichroism (CD), small-angle X-ray scattering (SAXS), isothermal titration calorimetry (ITC), size-exclusion chromatography (SEC) and activity measurements. The Cel7b:SDS complex can be described as a random configuration of 3–4 connected core-shell structures in which the protein is converted to a mainly α-helical secondary structure. Addition of C12E8 recovers almost all the secondary structure, part of the tertiary structure, about 50% of the activity and dissociates part of the protein population completely from detergent micelles. The lack of complete refolding may be due to charge neutralisation of Cel7b by SDS, kinetically trapping the enzyme into aggregated structures. In support of this, aggregates did not form when C12E8 was first mixed with Cel7b followed by addition of SDS. Formation of such aggregates may be a general phenomenon hampering quantitative refolding from the SDS-denatured state.

Design of β-lactoglobulin micro- and nanostructures by controlling gelation through physical variables

β-lactoglobulin (β-Lg) is the major protein fraction of bovine whey serum and its principal gelling agent. Its gelation capacity enables conformational changes associated with protein-protein interactions that allow the design of structures with different properties and morphologies. Thus, the aim of this work was to successfully use β-Lg, purified from a commercial whey protein isolate, to develop food-grade micro- (with diameters between 200 and 300 nm) and nano- (with diameters ≤ 100 nm) structures. For this purpose, the phenomena involved in β-Lg gelation were studied under combined effects of concentrations (from 5 to 15 mg mL−1), heating temperature (from 60 to 80 °C) and heating time (from 5 to 25 min) for pH values of 3, 4, 6 and 7. The effects of such conditions on β-Lg structures were evaluated and the protein was fully characterized in terms of size, polydispersity index (PDI) and surface charge (by dynamic light scattering – DLS), morphology (by transmission electron microscopy - TEM) and conformational structure (circular dichroism, intrinsic and extrinsic fluorescence). Results have shown that β-Lg nanostructures were formed at pH 3 (with diameters between 12.1 and 22.3 nm) and at 7 (with diameters between 8.9 and 35.3 nm). At pH 4 structures were obtained at macroscale (i.e., ≥ 6 μm) for all β-Lg concentrations when heated at 70 and 80 °C, independent of the time of heating. For pH 6, it was possible to obtain β-Lg structures either at micro- (245.0 – 266.4 nm) or nanoscale (≤ 100 nm) with the lowest polydispersity (PDI) values (≤ 0.25), in accordance with TEM analyses, for heating at 80 °C for 15 min. Intrinsic and extrinsic fluorescence data and far-UV circular dichroism spectra measurements revealed conformational changes on β-Lg structure that support these evidences. A strict control of the physical and environmental conditions is crucial for developing β-Lg structures with the desired characteristics, thus calling for the understanding of the mechanisms of protein aggregation and intermolecular interaction when designing β-Lg structures with novel functionalities.

Promotion Effect of Succinimide on Amyloid Fibrillation of Hen Egg-White Lysozyme.

Amyloid fibrillation is closely associated with a series of neurodegenerative diseases. According to that, the intermediate soluble oligomers and protofibrils are more toxic; reducing their concentrations in protein solutions by accelerating fibrillation is believed as a feasible strategy for treatment or remission of the diseases. Using hen egg-white lysozyme (HEWL) as a model protein, the promotion effect of succinimide was revealed by a series of experiments, e.g., atomic force microscopy (AFM), thioflavin T (ThT) fluorescence assay, Far-UV circular dichroism (CD) and Raman spectroscopy, and modeling the effect of succinimide-like derivative intermediates of intramolecular deamidation of the backbone during amyloid fibrillation. The AFM measurement confirmed that succinimide effectively accelerated the morphological changes of HEWL, while at the molecular level, the accelerative transformation of protein secondary structures was also clarified by ThT fluorescence assay and Far-UV CD spectroscopy. The incubation time-dependent Raman spectroscopy further revealed that the direct transformation from α-helices to organized β-sheets occurred upon skipping the intermediate random coils under the action of succinimide. This "bridge" effect of succinimide was attributed to its special influence on disulfide bonds. In the presence of succinimide in protein solutions, the native disulfide bonds of lysozyme could be broken more efficiently and quickly within hydrolysis, resulting in exposure of the buried hydrophobic residues and accelerating the formation of cross β-sheet structures. The present investigation provides very useful information for understanding the effect of intramolecular deamidation on the whole amyloid fibrillation.

Expression and characterization of an extremely thermophilic 1,4-α-glucan branching enzyme from Rhodothermus obamensis STB05

A gene encoding 1,4-α-glucan branching enzyme (GBE, EC 2.4.1.18) from the extremely thermophilic bacterium Rhodothermus obamensis STB05 was successfully cloned and expressed in Escherichia coli. Extracellular expression of the recombinant enzyme (R.o-GBE) was achieved with a yield of 1080 mg/L. Then it was purified and further characterized biochemically. R.o-GBE was optimally active at pH 7.0 and 65 °C. It remained stable at temperatures up to 80 °C and had a half-life at 85 °C of approximately 31 min. Far-UV circular dichroism and intrinsic fluorescence analyses revealed that high temperatures reduced its activity by changing the secondary and tertiary structure of R.o-GBE. The enzyme had broad pH stability between pH 3.0 and 11.0 at 4 °C, and preferred weakly acidic conditions at high temperatures. None of the metal ions enhanced the activity of R.o-GBE, but Ca2+ may be required for its activity. Its specific activity with amylopectin was 6651 U/mg, which is much higher than that reported for other GBEs. Its excellent thermostability, broad pH stability, and high specific activity make R.o-GBE highly suitable for industrial applications.

Perturbation of tubulin structure by stellate gold nanoparticles retards MDA-MB-231 breast cancer cell viability.

Gold nanoparticles (GNPs) of different sizes and shapes have been investigated extensively for their therapeuticpotentialagainst several diseases including cancer. However, the mechanisms with which they affect the cells are yet to be fully comprehended. In this study, we report the strong antiproliferative potential of novel, star-shaped ("stellate") GNPs that target tubulin-the building-block protein of the cytoskeletal filaments called microtubules-and disrupt microtubule network integrity. The stellate GNPs ("sGNPs") were synthesized from tryptone-stabilized GNPs ("tGNPs") and characterized by various spectroscopy methods combined with high-resolution transmission electron microscopy. Among a panel of cancer cell lines tested, they showed strong antiproliferative and anti-clonogenic efficacy against MDA-MB-231 cells. The antiproliferative mechanism of the sGNPs involves perturbation of the secondary and tertiary conformation of tubulin as evidenced by far-UV circular dichroism and anilinonaphthalene sulphate-binding assays. The structural perturbation of tubulin retarded its assembly competence as evidenced by polymer mass analysis and electron microscopy imaging of tubulin assembled in vitro and by immunofluorescence visualization of the cellular microtubules. The treated cells also induced cell cycle arrest at G1 phase. Taken together, our data suggest that sGNPs are potent, tubulin-targeted antiproliferative particles that can be evaluated further for their anticancer potential.

Making bovine trypsin more stable and active by Erythritol: A multispectroscopic analysis, docking and computational simulation methods

The present study was conducted to investigate the interaction between erythritol as a ligand and bovine trypsin. The interaction of trypsin with ligand was investigated by UV–vis, fluorescence quenching, circular dichroism (CD), activity, molecular docking, and molecular simulation methods. Intrinsic fluorescence intensity of trypsin was slowly quenched by erythritol. The binding constants were taken from the fluorescence quenching analysis. The results displayed the static mode of quenching in the interaction of trypsin with erythritol. Binding constant Ka ≈ 5.72 reflected the relatively moderate affinity of erythritol for trypsin. The negative ΔG° value represented the spontaneous process of the trypsin-erythritol interaction. According to the thermodynamic analysis, effective forces in the formation of the trypsin-erythritol complex were van der Waals interactions and hydrogen bonds. Activity assay also showed that erythritol acted as an activator for trypsin. Far-UV circular dichroism also revealed that erythritol could change the trypsin secondary structure via a slight increase in the α-helix content (from 5.04 to 6.69) and a slight decrease in the β-sheet content (from 40.8 to 38.0). Furthermore, molecular docking and simulation results confirmed the fluorescence results. Generally, erythritol could serve as a stabilizer and an activator for trypsin.

Biomolecular interaction of a platelet aggregation inhibitor, 3,4-methylenedioxy-β-nitrostyrene with human serum albumin: multi-spectral and computational characterization

Molecular interaction of the 3,4-methylenedioxy-β-nitrostyrene (MNS), an inhibitor of platelet aggregation with the main transport protein, albumin from human serum (HSA) was explored using absorption, fluorescence and circular dichroism (CD) spectroscopy in combination with in silico analyses. The MNS–HSA complexation was corroborated from the fluorescence and absorption spectral results. Implication of static quenching mechanism for MNS–HSA system was predicted from the Stern–Volmer constant, KSV-temperature relationship as well as the bimolecular quenching rate constant, kq values. Stabilization of the complex was affirmed by the value of the binding constant (Ka = 0.56-1.48 × 104 M−1). Thermodynamic data revealed that the MNS–HSA association was spontaneously driven mainly through hydrophobic interactions along with van der Waal’s interaction and H-bonds. These results were well supported by in silico interpretations. Far-UV and near-UV CD spectral results manifested small variations in the protein’s secondary and tertiary structures, respectively, while three-dimensional fluorescence spectra displayed microenvironmental fluctuations around protein’s fluorophores, upon MNS binding. Significant improvement in the protein’s thermostability was evident from the temperature-stability results of MNS-bound HSA. Binding locus of MNS, as identified by competitive drug displacement findings as well as in silico analysis, was found to be located in subdomain IIA (Sudlow’s site I) of the protein.Communicated by Ramaswamy H. Sarma

Conformational changes in Chikungunya virus E2 protein upon heparan sulfate receptor binding explain mechanism of E2-E1 dissociation during viral entry.

Receptor binding is the first step in viral cell entry. In enveloped virus cell entry, viral and host membrane fusion follows receptor binding. Viral surface receptor-binding protein associates with membrane fusion protein and masks its structure, to prevent pre-mature fusion activity. Dissociation of receptor-binding protein from fusion protein is an essential step before membrane fusion. Mechanism of receptor binding leading to dissociation of receptor binding and fusion protein is poorly understood in alphaviruses. Chikungunya virus (CHIKV), an alphavirus, re-emerged as a global pathogen in recent past. CHIKV surface envelope proteins, E2 and E1, function as receptor binding and fusion protein, respectively. Site of heparan sulfate (HS) receptor binding on E2–E1 heterodimer and its effect on E2–E1 heterodimer conformation is not known. Using molecular docking, we mapped HS binding to a positively charged pocket on E2 that is structurally conserved in alphaviruses. Based on our results from docking and sequence analysis, we identified a novel HS-binding sequence motif in E2. Purified E2 binds to heparin and HS specifically through charge interactions. Binding affinity of E2 to HS is comparable with other known HS–protein interactions (K d ∼ 1.8 μM). Mutation of charged residues in the predicted HS-binding motif of E2 to alanine resulted in reduction of HS binding. Molecular dynamics (MD) simulations on E2, after docking HS, predicted allosteric domain movements. Fluorescence spectroscopy, far-UV circular dichroism spectroscopy, fluorescence resonance energy transfer experiments on HS-bound E2 corroborate our findings from MD simulations. We propose a mechanism where receptor-binding results in allosteric domain movements in E2, explaining E2–E1 dissociation.

Evaluating the predictions of the protein stability change upon single amino acid substitutions for the FXN CAGI5 challenge.

Frataxin (FXN) is a highly conserved protein found in prokaryotes and eukaryotes that is required for efficient regulation of cellular iron homeostasis. Experimental evidence associates amino acid substitutions of the FXN to Friedreich Ataxia, a neurodegenerative disorder. Recently, new thermodynamic experiments have been performed to study the impact of somatic variations identified in cancer tissues on protein stability. The Critical Assessment of Genome Interpretation (CAGI) data provider at the University of Rome measured the unfolding free energy of a set of variants (FXN challenge data set) with far-UV circular dichroism and intrinsic fluorescence spectra. These values have been used to calculate the change in unfolding free energy between the variant and wild-type proteins at zero concentration of denaturant . The FXN challenge data set, composed of eight amino acid substitutions, was used to evaluate the performance of the current computational methods for predicting the value associated with the variants and to classify them as destabilizing and not destabilizing. For the fifth edition of CAGI, six independent research groups from Asia, Australia, Europe, and North America submitted 12 sets of predictions from different approaches. In this paper, we report the results of our assessment and discuss the limitations of the tested algorithms.

Alpha-cyclodextrin turns SDS-induced amyloid fibril into native-like structure

Amyloid fibril formation causes multiple neurodegenerative diseases and its possible therapy is still not available. The aim of this study was to determine the solubilizing and refolding potential of α‑cyclodextrin (α-CD) on SDS-induced amyloid fibril formation of lysozyme at pH 7.4 using turbidity, intrinsic fluorescence, dynamic light scattering (DLS), ThT binding assay, far-UV circular dichroism, and molecular docking. Spectroscopic data showed that lysozyme forms amyloid-like aggregates in the presence of 0.3 mM SDS at pH 7.4. SDS-induced lysozyme fibrils were solubilized by α-CD in a dose-dependent manner. At concentrations lower than 1.0 mM, α-CD was unable to solubilize SDS-induced lysozyme fibrils, while higher concentrations of α-CD produced complete solubilization. Far-UV CD and intrinsic fluorescence data suggest that the secondary and tertiary structures of lysozyme were restored at higher α-CD concentrations. The hydrodynamic radius was found to increase in the presence of SDS and radius is restored in the presence α-CD. Molecular docking data suggest that α-CD binds the same site on lysozyme as that occupied by SDS, albeit with higher affinity. Moreover, molecular docking between SDS and α-CD shows a direct contact via hydrogen bonding between O-atom of SDS and –OH group of α-CD. We hypothesize that the higher affinity of α-CD towards the binding site on lysozyme along with its direct interaction with SDS allows it to act as a chemical chaperone displacing SDS. The mechanisms underlying this action of α-CD may provide a foundation for the identification of drugs for the suppression of fibrillogenesis.

A molecular investigation into the interaction of SiO2 nanoparticles with elastase by multispectroscopic techniques and kinetic studies

The increasing use of nanoparticles in various industries has triggered the need to study their interconnection with biological macromolecules. The goal of this study was to survey the SiO2-nanoparticles efficacy on the thermal denaturation, conformation and activity of elastase at three temperatures of 303, 313 and 323K in the Tris buffer at pH of 8.5. In this work, distinct techniques such as UV–vis Spectrophotometry, Spectrofluorometry, and circular dichroism were employed. The fluorescence studies showed that SiO2 nanoparticles extremely reduced the intensity of elastase with the static mechanism. Thermodynamic parameter analysis also indicated that the process of binding of SiO2-nanoparticles to elastase was spontaneous, thereby suggesting that van der Waals forces or hydrogen bonding interactions played a key role in determining the complex stability. Far-UV circular dichroism studies further revealed that SiO2 nanoparticles could cause 9.79% reduction in the content of the α-helix and 3.24% increase in the content of the β-sheet.Furthermore, kinetic parameters (Vmax and Kcat/Km) indicated that SiO2 nanoparticles had an activation effect on the elastase activity. Melting temperature studies at the selected concentration of SiO2 nanoparticles also showed that by adding SiO2 nanoparticles, elastase thermal stability was slightly increased. Overall, these nanoparticles modified the structure of the elastase, ultimately changing the activity and stability of this enzyme.