far-UV Circular Dichroism Spectra Research Articles

An improved expression and purification protocol enables the structural characterization of Mnt1, an antifungal target from Candida albicans

BackgroundCandida albicans is one of the most prevalent fungi causing infections in the world. Mnt1 is a mannosyltransferase that participates in both the cell wall biogenesis and biofilm growth of C. albicans. While the cell wall performs crucial functions in pathogenesis, biofilm growth is correlated with sequestration of drugs by the extracellular matrix. Therefore, antifungals targeting CaMnt1 can compromise fungal development and potentially also render Candida susceptible to drug therapy. Despite its importance, CaMnt1 has not yet been purified to high standards and its biophysical properties are lacking.ResultsWe describe a new protocol to obtain high yield of recombinant CaMnt1 in Komagataella phaffii using methanol induction. The purified protein’s identity was confirmed by MALDI-TOF/TOF mass spectroscopy. The Far-UV circular dichroism (CD) spectra demonstrate that the secondary structure of CaMnt1 is compatible with a protein formed by α-helices and β-sheets at pH 7.0. The fluorescence spectroscopy results show that the tertiary structure of CaMnt1 is pH-dependent, with a greater intensity of fluorescence emission at pH 7.0. Using our molecular modeling protocol, we depict for the first time the ternary complex of CaMnt1 bound to its two substrates, which has enabled the identification of residues involved in substrate specificity and catalytic reaction. Our results corroborate the hypothesis that Tyr209 stabilizes the formation of an oxocarbenium ion-like intermediate during nucleophilic attack of the acceptor sugar, opposing the double displacement mechanism proposed by other reports.ConclusionsThe methodology presented here can substantially improve the yield of recombinant CaMnt1 expressed in flask-grown yeasts. In addition, the structural characterization of the fungal mannosyltransferase presents novelties that can be exploited for new antifungal drug’s development.

KCD: A prediction web server of knowledge-based circular dichroism.

We present a web server that predicts the far-UV circular dichroism (CD) spectra of proteins by utilizing their three-dimensional (3D) structures from the Protein Data Bank (PDB). The main algorithm is based on the classical theory of optical activity together with a set of atomic complex polarizabilities, which are obtained from the analysis of a series of synchrotron radiation CD spectra and their related 3D structures from the PDB. The results of our knowledge-based CD method (KCD) are in good agreement with measured spectra that could include the effect of D-amino acids. Our method also delivers some of the most accurate predictions, in comparison with the calculated spectra from well-established models. Specifically, using a metric of closeness based on normalized absolute deviations between experimental and calculated spectra, the mean values for a series of 57 test proteins give the following figures for such models: 0.26 KCD, 0.27 PDBMD2CD, 0.30 SESCA, and 0.47 DichroCalc. From another point of view, it is worth mentioning the remarkable capabilities of the recent approaches based on artificial intelligence, which can precisely predict the native structure of proteins. The structure of proteins, however, is flexible and can be modified by a diversity of environmental factors such as interactions with other molecules, mechanical stresses, variations of temperature, pH, or ionic strength. Experimental CD spectra together with reliable predictions can be utilized to assess eventual secondary structural changes. A similar kind of evaluation can be done for the case of an incomplete protein structure that has been reconstructed by using different approaches. The KCD method can be freely accessed from: https://kcd.cinvestav.mx/.

Spectroscopic insights with molecular docking and molecular dynamic simulation studies of anticancer drug 5-fluororouracil targeting human pyruvate kinase m2

This study was conducted to test the efficacy of 5-fluorouracil (5-FU) as an anticancer drug against the human pyruvate kinase isozyme M2 (PKM2) using spectroscopic, molecular docking and molecular dynamic simulation studies. PKM2 fluorescence quenching studies in the presence of 5-FU performed at three different temperatures indicates dynamic quenching processes with single-set of binding (n ≈ 1) profile. The biomolecular quenching constants (k q) and the effective binding constants (K b) obtained are shown to increase with temperature. The calculated enthalpy (ΔH) and entropy changes (ΔS) are estimated to be −118.06 kJ/mol and 146.14 kJ/mol/K respectively, which suggest the possible mode of interaction as electrostatic and hydrogen bonding. Further, these values were used to estimate the free energy changes (ΔG) and that increases with temperature. The negative ΔG values clearly indicates spontaneous binding process that stabilizes the complex formed between 5-FU and PKM2. Far-UV CD spectra of PKM2 in the presence of 5-FU shows decrease in α-helix contents which point towards the destabilization of secondary structure that weakens the biological activity of PKM2. The intrinsic fluorescence study and circular dichroism (CD) spectra showed minor conformational changes of PKM2 in the presence of 5-FU. Additionally, the results obtained from molecular docking and all-atom molecular dynamic simulation study supports the insight of the spectroscopic binding studies, and strengthens the dynamic stability of the complex between 5-FU and PKM2 through H-bonding. This study establishes a paradigm of 5-FU-PKM2 complexation and the efficacy of 5-FU that compromises the biological activity of the targeted PKM2. Communicated by Ramaswamy H. Sarma

Mitigation of the Deleterious Effect of Heavy Metals on the Conformational Stability of Ubiquitin through Osmoprotectants.

The Ubiquitin-Proteasome System (UPS) is important in protein homeostasis and is involved in many cell processes. UPS's wide range of regulatory activities is based on the unique and diverse signals transmitted through all-encompassing processes. Cells need a fully functional UPP to cope with oxidative stress, so cellular redox status modulates ubiquitin activity. However, these protein quality control systems are compromised under adverse conditions such as heavy metal stress, resulting in pathological conditions. Heavy metals disrupt the physiological action of sensitive proteins by forming complexes with side-chain functional groups or by dislocating critical metal ions in metalloproteins. In addition, perturbation in the structure of Ubiquitin may affect the ubiquitin-proteasome pathway. In this study, it has been investigated the effects of heavy metals likewise chromium (Cr), cadmium (Cd), and mercury chloride (HgCl2) on the conformational stability of Ubiquitin as well as overcome their hazardous effect, the interaction of osmo-protectants such as Sesamol, gallic acid, Glycine, and ascorbic acid have also been explored in the study. The near and far UV-circular dichroism measurements deduced the secondary and tertiary structural changes. The size of the Ubiquitin before and after exposure to heavy metals was measured by DLS (dynamic light scattering). Docking research was also used to investigate the interaction of Ubiquitin with various heavy metals. Near and far UV-circular dichroism (CD) measurements revealed that mercury, chromium, and cadmium disrupt Ubiquitin's secondary and tertiary structure. The effect of chromium, even at low concentrations, was significantly deleterious compared to cadmium and mercury chloride. Ubiquitin's far-UV circular dichroism spectra subjected to heavy metals were recorded in several osmo-protectants, such as ascorbic acid, Glycine, gallic acid, and Sesamol, which offset the adverse effects of heavy metals. DLS studies revealed a noteworthy change in the hydrodynamic radius of Ubiquitin in the presence of heavy metals. Docking analysis revealed a significant binding affinity of mercury and cadmium ions with Ubiquitin. This study can infer the heavy metals' disruption of Ubiquitin's secondary and tertiary structure. Osmo-protectants produced by animal cells are more effective against heavy metals than plant antioxidants.

A ShK-like Domain from Steinernema carpocapsae with Bioinsecticidal Potential.

Entomopathogenic nematodes are used as biological control agents against a broad range of insect pests. We ascribed the pathogenicity of these organisms to the excretory/secretory products (ESP) released by the infective nematode. Our group characterized different virulence factors produced by Steinernema carpocapsae that underlie its success as an insect pathogen. A novel ShK-like peptide (ScK1) from this nematode that presents high sequence similarity with the ShK peptide from a sea anemone was successfully produced recombinantly in Escherichia coli. The secondary structure of ScK1 appeared redox-sensitive, exhibiting a far-UV circular dichroism spectrum consistent with an alpha-helical secondary structure. Thermal denaturation of the ScK1 allowed estimating the melting temperature to 59.2 ± 0.1 °C. The results from toxicity assays using Drosophila melanogaster as a model show that injection of this peptide can kill insects in a dose-dependent manner with an LD50 of 16.9 µM per adult within 24 h. Oral administration of the fusion protein significantly reduced the locomotor activity of insects after 48 h (p < 0.05, Tukey's test). These data show that this nematode expresses insecticidal peptides with potential as next-generation insecticides.

Investigation of structural changes in human serum albumin after binding with elaidic acid

Elaidic acid (EA) is an unsaturated trans-fatty acid and one of the most important fatty acids obtained from solidifying vegetable oils. The increase in the consumption of EA is associated with rise and decline of LDL-cholesterol and HDL-cholesterol levels, respectively. It activates pro-inflammatory markers in the body and increases heart stroke and cardiovascular diseases. In this study, to understand the impact of EA in humans, we investigated the molecular interaction between EA and human serum albumin (HSA) and its binding affinity using spectroscopic, molecular dynamics (MD), and molecular docking techniques. According to fluorescence quenching experiments, EA could quench the inherent fluorescence of HSA via a static quenching mechanism. The thermodynamic characteristics of EA binding on HSA demonstrated hydrogen bonds and Van der Waals forces within the interaction, which matched molecular docking results. Further, the negative amount of ΔG° indicated the spontaneous binding of HSA to EA. Based on Förster's resonance energy transfer, the spatial distance between EA and HSA was 3.493 nm. The far-UV circular dichroism spectrum showed the decrease in the contents of the β-sheet and α-helix in the HSA structure. According to the RMSF data, the HSA structure's flexibility was diminished. The molecular dynamic simulation and spectroscopic studies also indicated that the binding interactions altered the milieu of the Trp chromophore and HSA structures. All experimental data could be matched with molecular dynamics simulation.

Insight into the Conformational Transitions of Serine Acetyl Transferase Isoforms in E. histolytica: Implications for Structural and Functional Balance

Serine acetyl transferase (SAT) is one of the crucial enzymes in the cysteine biosynthetic pathway and an essential enzyme for the survival of Entamoeba histolytica, the causative agent of amoebiasis. E. histolytica expresses three isoforms of SAT, where SAT1 and SAT2 are inhibited by the final product cysteine, while SAT3 is not inhibited. SAT3 has a slightly elongated C-terminus compared to SAT1. To understand the stability and conformational transition between two secondary structures of proteins, we measured the effect of urea, a chemical denaturant, on two isoforms of SAT (SAT1 and SAT3) of E. histolytica. The effect of urea on the structure and stability of SAT1 and SAT3 was determined by measuring changes in their far-UV circular dichroism (CD), Trp fluorescence, and near-UV absorption spectra. The urea-induced normal transition curves suggested that the structural transition is reversible and follows a two-state process. Analysis of the urea-induced transition of all optical properties for the stability parameters ΔGD° (Gibbs free energy change (ΔGD) in the absence of urea), m (dependence of ΔGD on urea concentration), and Cm (midpoint of urea transition) suggested that SAT1 is more stable than SAT3. Characterization of the end product of the urea-induced transition of both proteins by the far-UV CD and Trp-fluorescence and near-UV absorbance suggested that urea causes α-helix to β-sheet transition and burial of Trp residues, respectively. To support the in vitro findings, 100 ns molecular dynamics simulations (in silico study) were performed. Both the spectroscopic and molecular dynamics approaches clearly indicated that SAT1 is more stable than SAT3. SAT3 has evolved to escape the feedback inhibition to keep producing cysteine, but in the process, it compromises its structural stability relative to SAT1.

Circular Dichroism Spectra of α-Chymotrypsin-SDS Solutions Depend on the Procedure of Their Preparation.

We recorded the far- and near-UV circular dichroism (CD) spectra of solutions of α-chymotrypsin and sodium dodecyl sulfate (SDS) with the final surfactant concentration significantly above the critical micellization concentration. Solutions were prepared using three different procedures. The reference procedure was to mix the chymotrypsin solution with the SDS solution once, immediately achieving the final SDS concentration. In alternative procedures, the protein solutions initially contained some SDS and were mixed with pure SDS solutions at a concentration to provide the same final surfactant as the reference mixing. We demonstrate that the supplementation to the selected final concentration of SDS of the pure chymotrypsin solution leads to different CD spectra than the supplementation to this final concentration of SDS in the chymotrypsin solution containing a small concentration of a few millimolar SDS. These differences disappear when the initial concentration of SDS in the protein solution, which we then supplement to the indicated final concentration, is higher. This suggests the irreversibility of the processes caused by the addition of SDS to chymotrypsin and the influence of the initial amount of this surfactant on the processes occurring with its further addition to the solution. For quantitative analysis of far-UV CD spectra in terms of populations of protein secondary structure elements, we used four well-established software packages. All programs consistently indicate that the observed differences in the far-UV CD spectra can be explained by the differences in the increase in the population of helical forms in chymotrypsin under the influence of SDS.

Multifunctions of α‐Synuclein Explained by Its Dynamic Heterogeneous Conformations with a Hierarchy of Transition Times

α‐Synuclein plays essential roles in synaptic vesicle homeostasis and neurotransmitter release through the interaction with membrane, while α‐synuclein aggregates have been associated with several neurodegenerative diseases, especially Parkinson’s disease. The different roles of α‐synuclein could be attributed to the heterogenous conformations adopted by this intrinsically disordered protein. To demystify the physiological functions of α‐synuclein and understand its pathogenic mechanism of Parkinson’s disease, characterizing the monomeric structural ensemble and identifying the aggregation‐prone and non‐aggregation‐prone structures are of particular importance. Here, we use inter‐residue distance distributions derived from time‐resolved FRET experiments as constraints to guide discrete molecular dynamics simulations of α‐synuclein monomer. We explore the conformational space of α‐synuclein and verify the generated conformational ensemble by additional experiments including far‐UV circular dichroism spectrum and cross‐linking mass spectrometry. We find that some conformational states of α‐synuclein are surprisingly stable displaying dynamic transitions less than milliseconds. A comprehensive analysis of the conformational ensemble uncovers important structural features and potential conformations that are critical to stabilize the monomeric state or induce different oligomerization pathways.

A Trade-off Between Thermostability and Binding Affinity of Anti-(4-hydroxy-3-nitrophenyl)Acetyl Antibodies During the Course of Affinity Maturation.

Somatic hypermutation (SHM) is one of the driving forces that increases antibody (Ab) affinity. We studied the effects of SHM on thermostability and affinity using three single-chain Fv fragments (scFvs) of anti-(4-hydroxy-3-nitrophenyl)acetyl Abs, namely 9TG, 9T7, and E11. 9TG has a germline structure that lacks SHM and is an ancestor of 9T7 with 11 mutations. E11, which has 21 mutations, is a mature Ab and has its own ancestor. The thermostabilities and antigen-Ab interactions were analyzed by circular dichroism (CD), differential scanning calorimetry (DSC), and isothermal titration calorimetry (ITC). Far-UV CD spectra showed that all scFvs were folded into a structure referred to as immunoglobulin-fold and were unfolded by heating at different melting temperatures. Comparison of thermodynamic parameters obtained from DSC and ITC revealed that the magnitude of stabilization free energy at 37°C was in the order, 9TG > 9T7 > E11, while that of the free energy of interaction with antigen was 9TG < 9T7 < E11, suggesting that Abs make a trade-off between stability and affinity during affinity maturation.

Circular dichroism spectroscopic assessment of structural changes upon protein thermal unfolding at contrasting pH: Comparison with molecular dynamics simulations

In most instances, the usual fastness of protein unfolding events hinders determining changes in secondary structures associated with this process because these determinations rely on the recording of high-resolution circular dichroism (CD) spectra. In this work, far-UV CD spectra, recorded at ten-minute intervals, were used to evaluate the time course followed by four classes of secondary structures in the slow temperature-induced unfolding of yeast triosephosphate isomerase (yTIM) under distinct pH conditions. CONTIN-LL and SELCON3 algorithms were used for the deconvolution of spectra. Both algorithms furnished helix and unordered structure contents that changed according to first-order kinetics, agreeing with the behavior shown by CD data at specific wavelengths. Analyses of unfolded yTIM spectra, using a dataset that includes spectra of unfolded proteins and either one of the two algorithms, clearly showed a more unordered protein structure at high pH; this finding was corroborated with analysis of the difference spectra. Molecular dynamics (MD) simulations performed with AMBER and OPLS force fields resulted in more extensive loss of helices and gain in coils at high pH, in agreement with spectroscopic results. However, structural differences between low- and high-pH unfolded yTIM were relatively small. Comparison of results from CD and MD thus point to the need of fine-tuning of MD procedures.

The Structure of the Potato Virus A Particles Elucidated by Small Angle X-Ray Scattering and Complementary Techniques

Potato virus A (PVA) protein coat contains on its surface partially unstructured N-terminal domain of the viral coat protein (CP), whose structural and functional characteristics are important for understanding the mechanism of plant infection with this virus. In this work, we investigated the properties and the structure of intact PVA and partially trypsinized PVAΔ32 virions using small-angle X-ray scattering (SAXS) and complimentary methods. It was shown that after the removal of 32 N-terminal amino acids of the CP, the virion did not disintegrate and remained compact, but the helical pitch of the CP packing changed. To determine the nature of these changes, we performed ab initio modeling, including the multiphase procedure, with the geometric bodies (helices) and restoration of the PVA structure in solution using available high-resolution structures of the homologous CP from the PVY potyvirus, based on the SAXS data. As a result, for the first time, a low-resolution structure of the filamentous PVA virus, both intact and partially degraded, was elucidated under conditions close to natural. The far-UV circular dichroism spectra of the PVA and PVAΔ32 samples differed significantly in the amplitude and position of the main negative maximum. The extent of thermal denaturation of these samples in the temperature range of 20-55°C was also different. The data of transmission electron microscopy showed that the PVAΔ32 virions were mostly rod-shaped, in contrast to the flexible filamentous particles typical of the intact virus, which correlated well with the SAXS results. In general, structural analysis indicates an importance of the CP N-terminal domain for the vital functions of PVA, which can be used to develop a strategy for combating this plant pathogen.

Higher-Order Structure Comparison of a Proposed Biosimilar and the Innovator Biotherapeutic Trastuzumab using Circular Dichroism Coupled with Statistical Analysis

We employ a novel circular dichroism (CD) technology coupled with statistical analysis to assess the higher-order structure (HOS) similarity of commercially available trastuzumab and a proposed biosimilar. This technology shows good potential for enabling the comparison of similarities and differences in secondary and tertiary structures of proteins. Multiple CD spectra in far- and near-UV are obtained reproducibly from a CD spectrometer with fully integrated autosampler and flow cell to eliminate the errors typically associated with sample handling on manual CD spectrometers. The significance of similarities or differences was quantified statistically using three analytical methods (weighted spectral difference, correlation coefficient, and area of overlap). HOS comparison of the secondary structure (far-UV CD spectra) suggested similarity between the innovator drug, trastuzumab (Herceptin®), and biosimilar products. However, the tertiary structure (near-UV CD spectra) suggested statistically significant differences. These differences may be due to changes in tertiary structure or to modifications and degradations during the process of production or storage. The results show that the automated circular dichroism technology coupled with statistical analysis is a robust tool for enabling the comparison of similarities and differences in secondary and tertiary structures of protein products.

Probing coupled motions of peptides in solution with fluorescence anisotropy and molecular dynamics simulation

Abstract Here we present an atomically detailed study of local and global motions in two peptide systems, N-acetyl-tryptophanamide (NATA) and a pentapeptide WA3K (WK5) combining detailed spectroscopic measurements and comprehensive computer simulations. We have measured fluorescence lifetimes, fluorescence anisotropy decay (FAD), far-UV circular dichroism (CD) spectra as a function of temperature, and carried out molecular dynamics (MD) simulation with an improved water model (TIP4P/EW). Fluorescence lifetime analysis showed the presence of a heterogeneous population of conformations in both peptides and a quenched fluorescence in WK5. Far-UV CD measurements quantified structural populations in both peptides specifying alpha-helix and sheet for NATA and 310 helix and polyproline II for WK5 and their variation with temperature. FAD showed a bi-exponentiality in the reorientation dynamics, indicating the presence coupled motions in solution. The faster time constants, 6 ps for NATA, and 26 ps for WK5 are nearly temperature-independent and the slower components, 60 ps for NATA and 246 ps for WK5 at room temperature, vary with temperature. These faster and slower time constants are likely associated with the initiation and propagation steps of the reorientation dynamics. Results from MD simulation are in good agreement with the measured reorientation time and structural conformations. MD analysis showed that the measured faster time constants may be ascribed to delocalized molecular vibrations. Kinetic analysis found motions in the 1 ns in NATA and 10 ns in WK5. Both peptides exhibited markedly slower internal fluctuations compared to freely moving systems in the absence of overall translations and rotations, indicating a significant coupling between local and global dynamics. This study, focusing on simple model systems, has generated new insights into the dynamic behavior of peptides in solution.

Structural Studies on an Anti-Angiogenic Peptide Using Molecular Modeling.

Background: Development of VEGF antagonists, which inhibit its interaction with the receptors, is a widely used strategy for the inhibition of angiogenesis and tumor growth.Objectives: In the present study, a VEGFR-1 antagonistic peptide was designed and its potential for binding to VEGFR-1 and VEGFR-2 was evaluated by theoretical studies.Materials and Methods: Based on the X-ray structure of VEGF-B/VEGFR-1 D2 (PDB ID: 2XAC), an antagonistic peptide (known as VGB1) was designed, and its model structure was constructed using homology modeling in the MODELLER, version 9.16. The validity of the modeled structures was estimated employing several web tools. Finally, one model was chosen and molecular dynamics (MD) simulation was applied using the GROMACS package, version 5.1.4, to allow conformational relaxation of the structure. Next, docking process of the peptide with VEGFR-1 and VEGFR-2 was performed by HADDOCK web server and the docking structures were optimized by MD simulation for 20 ns. The far-UV circular dichroism (CD) spectrum of VGB1 was recorded to evaluate the overall structure of the peptide. Results: The far-UV CD spectrum indicated that VGB1 contains α helix structure. The results from docking studies suggested that Van der Waals and nonpolar interactions play the most important role in the peptide binding to VEGFR-1. In addition, our results implicated the relevance of both Van der Waals and electrostatic interactions in the formation of complex between VGB1 and VEGFR-2. In addition to the common binding residues in the corresponding region of VEGF-A and VEGF-B, additional binding residues also were predicted for the interaction of VGB1 with VEGFR-1 and VEGFR-2.Conclusions: The results of MD and molecular docking simulations predicted that VGB1 recognizes both VEGFR-1 and VEGFR-2, which may lead to the prevention of the downstream signaling triggered by these receptors.

Sunset yellow degradation product, as an efficient water-soluble inducer, accelerates 1N4R Tau amyloid oligomerization: In vitro preliminary evidence against the food colorant safety in terms of “Triggered Amyloid Aggregation”

Today, Alzheimer’s disease (AD) as the most prevalent type of dementia turns into one of the most severe health problems. Neurofibrillary tangle (NFT), mostly comprised of fibrils formed by Tau, is a hallmark of a class of neurodegenerative diseases. Tau protein promotes assembly and makes stable microtubules that play a role in the appropriate function of neurons. Polyanionic cofactors such as heparin, and azo dyes, can induce aggregation of tau protein in vitro. Sunset Yellow is a food colorant used widely in food industries. In the current work, we introduced degradation product (DP) of Sunset Yellow as an effective inducer of Tau aggregation. Two Tau aggregation inducers were produced, and then the aggregation kinetics and the structure of 1N4R Tau amyloid fibrils were characterized using ThT fluorescence spectroscopy, X-Ray Diffraction (XRD), circular dichroism (CD) and atomic force microscopy (AFM). Also, the toxic effects of the induced aggregates on RBCs and SH-SY5Y cells were demonstrated by hemolysis and LDH assays, respectively. Both inducers efficiently accelerated the formation of the amyloid fibril. Along with the confirmation of the β-sheets structure in Tau aggregates by Far-UV CD spectra, X-ray diffractions revealed the typical cross-β diffraction pattern. The oligomer formation in the presence of DPs was also confirmed by AFM. The possible in vivo effect of artificial azo dyes on Tau aggregation should be considered seriously as a newly opened dimension in food safety and human health.

Bluetongue virus viral protein 7 stability in the presence of glycerol and sodium chloride

PurposeThe Orbivirus Bluetongue virus (BTV) is an economically significant disease that affects mainly wild and domestic ruminants. BTV is most often seen symptomatically in sheep, but is easily carried by goats, cattle, and wild ruminants. To date there are several problems with the vaccines currently available for BTV, and one of the most promising candidates to increase vaccine efficacy is a protein-based vaccine, for which viral protein 7 (VP7) is a great candidate to be included in it. In order to further these studies, the stability of BTV VP7 in common vaccine additives needs to be investigated.Materials and MethodsRecombinant BTV VP7 was expressed in a bacterial cell system and purified before being analysed using spectroscopic techniques including far-ultraviolet (UV) circular dichroism and intrinsic tryptophan fluorescence. BTV was analysed in a number of different buffer conditions.ResultsWe report here that BTV VP7 maintains its native secondary structure until at least 52℃ and native-like tertiary structure to at least 80℃. Far-UV circular dichroism and intrinsic tryptophan fluorescence emission spectra indicate significant secondary and tertiary structure remaining even at 90℃, respectively. Six M guanidinium chloride is able to unfold BTV VP7 while 8 M urea could not.ConclusionTwenty percent glycerol and 300 mM sodium chloride appear to have a protective effect on BTV VP7's structure, as significantly more structure is seen at 90℃ when compared to BTV VP7 without the addition of these chemicals. Both glycerol and sodium chloride are common vaccine additives.

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.

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.

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.