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1.
Int J Mol Sci ; 25(17)2024 Aug 29.
Artículo en Inglés | MEDLINE | ID: mdl-39273310

RESUMEN

By performing differential scanning calorimetry(DSC) measurements on RNase A, we studied the stabilization provided by the addition of potassium aspartate(KAsp) or potassium glutamate (KGlu) and found that it leads to a significant increase in the denaturation temperature of the protein. The stabilization proves to be mainly entropic in origin. A counteraction of the stabilization provided by KAsp or KGlu is obtained by adding common denaturants such as urea, guanidinium chloride, or guanidinium thiocyanate. A rationalization of the experimental data is devised on the basis of a theoretical approach developed by one of the authors. The main contribution to the conformational stability of globular proteins comes from the gain in translational entropy of water and co-solute ions and/or molecules for the decrease in solvent-excluded volume associated with polypeptide folding (i.e., there is a large decrease in solvent-accessible surface area). The magnitude of this entropic contribution increases with the number density and volume packing density of the solution. The two destabilizing contributions come from the conformational entropy of the chain, which should not depend significantly on the presence of co-solutes, and from the direct energetic interactions between co-solutes and the protein surface in both the native and denatured states. It is the magnitude of the latter that discriminates between stabilizing and destabilizing agents.


Asunto(s)
Ácido Aspártico , Ácido Glutámico , Desnaturalización Proteica , Ácido Aspártico/química , Desnaturalización Proteica/efectos de los fármacos , Ácido Glutámico/química , Ribonucleasa Pancreática/química , Ribonucleasa Pancreática/metabolismo , Termodinámica , Rastreo Diferencial de Calorimetría , Entropía , Estabilidad Proteica , Guanidina/química , Guanidina/farmacología , Urea/química , Urea/farmacología , Conformación Proteica
2.
Protein Sci ; 33(9): e5146, 2024 Sep.
Artículo en Inglés | MEDLINE | ID: mdl-39150147

RESUMEN

D2 is a structural and cooperative domain of Thermotoga maritima Arginine Binding Protein, that possesses a remarkable conformational stability, with a denaturation temperature of 102.6°C, at pH 7.4. The addition of potassium thiocyanate causes a significant decrease in the D2 denaturation temperature. The interactions of thiocyanate ions with D2 have been studied by means of isothermal titration calorimetry measurements and molecular dynamics simulations. It emerged that: (a) 20-30 thiocyanate ions interact with the D2 surface and are present in its first solvation shell; (b) each of them makes several contacts with protein groups, both polar and nonpolar ones. The addition of guanidinium thiocyanate causes a marked destabilization of the D2 native state, because both the ions are denaturing agents. However, on adding to the solution containing D2 and guanidinium thiocyanate a stabilizing agent, such as TMAO, sucrose or sodium sulfate, a significant increase in denaturation temperature occurs. The present results confirm that counteraction is a general phenomenon for globular proteins.


Asunto(s)
Simulación de Dinámica Molecular , Estabilidad Proteica , Thermotoga maritima , Tiocianatos , Tiocianatos/química , Thermotoga maritima/química , Proteínas Bacterianas/química , Proteínas Bacterianas/metabolismo , Desnaturalización Proteica/efectos de los fármacos , Sulfatos/química , Metilaminas/química , Dominios Proteicos , Guanidinas/química
3.
Int J Biol Macromol ; 276(Pt 1): 133713, 2024 Sep.
Artículo en Inglés | MEDLINE | ID: mdl-38986993

RESUMEN

This article describes the molecular mechanism by which tetraalkylammonium chloride ([R4N]Cl: R- = methyl (Me), ethyl (Et), propyl (Pr),butyl (Bu)) modulates the stability, folding, and dynamics of cytochrome c (Cyt c). Analysis of [R4N]Cl effects on thermal/chemical denaturations, millisecond refolding/unfolding kinetics, and slow CO-association kinetics of Cyt c without and with denaturant providing some significant results: (i) [R4N]Cl decreasing the unfolding free energy estimated by thermodynamic and kinetic analysis of thermal/chemical denaturation curves and kinetic chevrons (Log kobs-[GdmCl]) of Cyt c, respectively (ii) hydrophobicity of R-group of [R4N]Cl, preferential inclusion of [R4N]Cl at the protein surface, and destabilizing enthalpic attractive interactions of [Me4N]Cl and steric entropic interactions of [Et4N]Cl,[Pr4N]Cl and [Bu4N]Cl with protein contribute to [R4N]Cl-induced decrease thermodynamic stability of Cyt c (iii) [R4N]Cl exhibits an additive effect with denaturant to decrease thermodynamic stability and refolding rates of Cyt c (iv) low concentrations of [R4N]Cl (≤ 0.5 M) constrain the motional dynamics while the higher concentrations (>0.75 M [R4N]Cl) enhance the structural-fluctuations that denture protein (v) hydrophobicity of R-group of [R4N]Cl alters the [denaturant]-dependent conformational stability, refolding-unfolding kinetics, and CO-association kinetics of Cyt c. Furthermore, the MD simulations depicted that the addition of 1.0 M of [R4N]Cl increased the conformational fluctuations in Cyt c leading to decreased structural stability in the order [Me4N]Cl < [Et4N]Cl < [Pr4N]Cl < [Bu4N]Cl consistent with the experimental results.


Asunto(s)
Citocromos c , Desnaturalización Proteica , Pliegue de Proteína , Termodinámica , Citocromos c/química , Citocromos c/metabolismo , Caballos , Animales , Cinética , Pliegue de Proteína/efectos de los fármacos , Desnaturalización Proteica/efectos de los fármacos , Interacciones Hidrofóbicas e Hidrofílicas , Compuestos de Amonio Cuaternario/química , Compuestos de Amonio Cuaternario/farmacología
4.
Chem Biodivers ; 21(8): e202401038, 2024 Aug.
Artículo en Inglés | MEDLINE | ID: mdl-38849308

RESUMEN

The investigation into the behavior of ficin, bromelain, papain under thermal conditions holds both theoretical and practical significance. The production processes of medicines and cosmetics often involve exposure to high temperatures, particularly during the final product sterilization phase. Hence, it's crucial to identify the "critical" temperatures for each component within the mixture for effective technological regulation. In light of this, the objective of this study was to examine the thermal inactivation, aggregation, and denaturation processes of three papain-like proteases: ficin, bromelain, papain. To achieve this goal, the following experiments were conducted: (1) determination of the quantity of inactivated proteases using enzyme kinetics with BAPNA as a substrate; (2) differential scanning calorimetry (DSC); (3) assessment of protein aggregation using dynamic light scattering (DLS) and spectrophotometric analysis at 280 nm. Our findings suggest that the inactivation of ficin and papain exhibits single decay step which characterized by a rapid decline, then preservation of the same residual activity by enzyme stabilization. Only bromelain shows two steps with different kinetics. The molecular sizes of the active and inactive forms are similar across ficin, bromelain, and papain. Furthermore, the denaturation of these forms occurs at approximately the same rate and is accompanied by protein aggregation.


Asunto(s)
Bromelaínas , Ficaína , Papaína , Desnaturalización Proteica , Papaína/metabolismo , Papaína/química , Desnaturalización Proteica/efectos de los fármacos , Bromelaínas/química , Bromelaínas/metabolismo , Ficaína/química , Ficaína/metabolismo , Cinética , Temperatura , Agregado de Proteínas/efectos de los fármacos , Rastreo Diferencial de Calorimetría , Dispersión Dinámica de Luz
5.
Int J Biol Macromol ; 266(Pt 2): 131338, 2024 May.
Artículo en Inglés | MEDLINE | ID: mdl-38569987

RESUMEN

Development of nanoparticles (NPs) serving as contrast enhancing agents in MRI requires a combination of high contrasting effect with the biosafety and hemocompatibility. This work demonstrates that bovine serum albumin (BSA) molecules bound to paramagnetic Mn2+ ions are promising building blocks of such NPs. The desolvation-induced denaturation of BSA bound with Mn2+ ions followed by the glutaraldehyde-facilitated cross-linking provides the uniform in size 102.0 ± 0.7 nm BSA-based nanoparticles (BSA-NPs) loaded with Mn2+ ions, which are manifested in aqueous solutions as negatively charged spheres with high colloid stability. The optimal loading of Mn2+ ions into BSA-NPs provides maximum values of longitudinal and transverse relaxivity at 98.9 and 133.6 mM-1 s-1, respectively, which are among the best known from the literature. The spin trap EPR method indicates that Mn2+ ions bound to BSA-NPs exhibit poor catalytic activity in the Fenton-like reaction. On the contrary, the presence of BSA-NPs has an antioxidant effect by preventing the accumulation of hydroxyl radicals produced by H2O2. The NPs exhibit remarkably low hemolytic activity and hemagglutination can be avoided at concentrations lower than 110 µM. Thus, BSA-NPs bound with Mn2+ ions are promising candidates for combining high contrast effect with biosafety and hemocompatibility.


Asunto(s)
Manganeso , Albúmina Sérica Bovina , Agua , Albúmina Sérica Bovina/química , Manganeso/química , Agua/química , Animales , Protones , Bovinos , Reactivos de Enlaces Cruzados/química , Nanopartículas/química , Hemólisis/efectos de los fármacos , Desnaturalización Proteica/efectos de los fármacos , Imagen por Resonancia Magnética/métodos , Humanos
6.
Molecules ; 28(1)2022 Dec 21.
Artículo en Inglés | MEDLINE | ID: mdl-36615228

RESUMEN

Ornamental plants often gain relevance not only for their decorative use, but also as a source of phytochemicals with interesting healing properties. Herein, spontaneous Centranthus ruber (L.) DC. and Tropaeolum majus L., mainly used as ornamental species but also traditionally consumed and used in popular medicine, were investigated. The aerial parts were extracted with methanol trough maceration, and resultant crude extracts were partitioned using solvents with increasing polarity. As previous studies mostly dealt with the phenolic content of these species, the phytochemical investigation mainly focused on nonpolar constituents, detected with GC-MS. The total phenolic and flavonoid content was also verified, and HPTLC analyses were performed. In order to explore the potential antiarthritic and anti-obesity properties, extracts and their fractions were evaluated for their anti-denaturation effects, with the use of the BSA assay, and for their ability to inhibit pancreatic lipase. The antioxidant properties and the inhibitory activity on the NO production were verified, as well. Almost all the extracts and fractions demonstrated good inhibitory effects on NO production. The n-hexane and dichloromethane fractions from T. majus, as well as the n-hexane fraction from C. ruber, were effective in protecting the protein from heat-induced denaturation (IC50 = 154.0 ± 1.9, 270.8 ± 2.3 and 450.1 ± 15.5 µg/mL, respectively). The dichloromethane fractions from both raw extracts were also effective in inhibiting pancreatic lipase, with IC50 values equal to 2.23 ± 0.02 mg/mL (for C. ruber sample), and 2.05 ± 0.02 mg/mL (T. majus). Obtained results support the traditional use of these species for their beneficial health properties and suggest that investigated plant species could be potential sources of novel antiarthritic and anti-obesity agents.


Asunto(s)
Fármacos Antiobesidad , Antioxidantes , Pancrelipasa , Fitoquímicos , Extractos Vegetales , Tropaeolum , Valerianaceae , Antioxidantes/química , Antioxidantes/aislamiento & purificación , Antioxidantes/farmacología , Cloruro de Metileno , Fitoquímicos/química , Fitoquímicos/aislamiento & purificación , Fitoquímicos/farmacología , Extractos Vegetales/farmacología , Extractos Vegetales/química , Tropaeolum/química , Valerianaceae/química , Pancrelipasa/antagonistas & inhibidores , Pancrelipasa/química , Desnaturalización Proteica/efectos de los fármacos , Fármacos Antiobesidad/química , Fármacos Antiobesidad/aislamiento & purificación , Fármacos Antiobesidad/farmacología
7.
Molecules ; 26(23)2021 Dec 06.
Artículo en Inglés | MEDLINE | ID: mdl-34885979

RESUMEN

The global burden of disease caused by a respiratory syncytial virus (RSV) is becoming more widely recognized in young children and adults. Heparan sulfate helps in attaching the virion through G protein with the host cell membrane. In this study, we examined the structural changes of ectodomain G protein (edG) in a wide pH range. The absorbance results revealed that protein maintains its tertiary structure at physiological and highly acidic and alkaline pH. However, visible aggregation of protein was observed in mild acidic pH. The intrinsic fluorescence study shows no significant change in the λmax except at pH 12.0. The ANS fluorescence of edG at pH 2.0 and 3.0 forms an acid-induced molten globule-like state. The denaturation transition curve monitored by fluorescence spectroscopy revealed that urea and GdmCl induced denaturation native (N) ↔ denatured (D) state follows a two-state process. The fluorescence quenching, molecular docking, and 50 ns simulation measurements suggested that heparan sulfate showed excellent binding affinity to edG. Our binding study provides a preliminary insight into the interaction of edG to the host cell membrane via heparan sulfate. This binding can be inhibited using experimental approaches at the molecular level leading to the prevention of effective host-pathogen interaction.


Asunto(s)
Dominio Catalítico , Heparitina Sulfato/metabolismo , Interacciones Huésped-Patógeno , Simulación del Acoplamiento Molecular/métodos , Virus Sincitial Respiratorio Humano/metabolismo , Proteínas del Envoltorio Viral/química , Proteínas del Envoltorio Viral/metabolismo , Membrana Celular/metabolismo , Humanos , Enlace de Hidrógeno , Concentración de Iones de Hidrógeno , Agregado de Proteínas , Agregación Patológica de Proteínas/metabolismo , Desnaturalización Proteica/efectos de los fármacos , Estructura Terciaria de Proteína , Espectrometría de Fluorescencia/métodos , Urea/farmacología
8.
Curr Top Med Chem ; 21(31): 2839-2850, 2021.
Artículo en Inglés | MEDLINE | ID: mdl-34749611

RESUMEN

BACKGROUND: Sphingosine kinase 1 (SPhK1) is a crucial signaling enzyme involved in cell proliferation, cellular survival, stimulation of angiogenesis, and apoptosis prevention. Recently, we have reported the unfolding kinetics of SPhK1 using molecular dynamics (MD) simulation, circular dichroism, and fluorescence spectroscopy. We found that SPhK1 showed a biphasic unfolding with an intermediate state (~ 4.0 M urea). OBJECTIVE: We aim to understand the impact of MD simulation duration on the structure, function, and dynamics of proteins. In order to get deeper insights into the folding mechanism, an extended MD simulation is required. METHODS: Here, we extended the MD simulations time scale from 100 to 300 ns on SPhK1 at increasing urea concentration to explore structural changes in the SPhK1. RESULTS: The results suggested a constant form of the unfolding of SPhK1 upon extending the simulation time scale at different urea concentrations. Furthermore, we showed step by step unfolding and percentage of secondary structure contents in SPhK1 under the influence of urea at each concentration. CONCLUSION: The results from the current work revealed a uniform pattern of the SPhK1 unfolding at different urea concentrations. This study provides deeper mechanistic insights into the urea-induced denaturation of SPhK1.


Asunto(s)
Simulación de Dinámica Molecular , Fosfotransferasas (Aceptor de Grupo Alcohol)/química , Desnaturalización Proteica , Desplegamiento Proteico , Urea , Dicroismo Circular , Humanos , Fosfotransferasas (Aceptor de Grupo Alcohol)/metabolismo , Conformación Proteica , Desnaturalización Proteica/efectos de los fármacos , Pliegue de Proteína , Desplegamiento Proteico/efectos de los fármacos , Espectrometría de Fluorescencia , Urea/farmacología
9.
Biochemistry ; 60(41): 3071-3085, 2021 10 19.
Artículo en Inglés | MEDLINE | ID: mdl-34606713

RESUMEN

Rhodopseudomonas palustris cytochrome c', a four-helix bundle, and the second ubiquitin-associated domain, UBA(2), a three-helix bundle from the human homologue of yeast Rad23, HHR23A, deviate from random coil behavior under denaturing conditions in a fold-specific manner. The random coil deviations in each of these folds occur near interhelical turns and loops in their tertiary structures. Here, we examine an additional three-helix bundle with an identical fold to UBA(2), but a highly divergent sequence, the first ubiquitin-associated domain, UBA(1), of HHR23A. We use histidine-heme loop formation methods, employing eight single histidine variants, to probe for denatured state conformational bias of a UBA(1) domain fused to the N-terminus of iso-1-cytochrome c (iso-1-Cytc). Guanidine hydrochloride (GuHCl) denaturation shows that the iso-1-Cytc domain unfolds first, followed by the UBA(1) domain. Denatured state (4 and 6 M GuHCl) histidine-heme loop formation studies show that as the size of the histidine-heme loop increases, loop stability decreases, as expected for the Jacobson-Stockmayer relationship. However, loops formed with His35, His31, and His15, of UBA(1), are 0.6-1.1 kcal/mol more stable than expected from the Jacobson-Stockmayer relationship, confirming the importance of deviations of the denatured state from random coil behavior near interhelical turns of helical domains for facilitating folding to the correct topology. For UBA(1) and UBA(2), hydrophobic clusters on either side of the turns partially explain deviations from random coil behavior; however, helix capping also appears to be important.


Asunto(s)
Citocromos c/química , Proteínas de Saccharomyces cerevisiae/química , Citocromos c/genética , Guanidina/química , Cinética , Mutagénesis Sitio-Dirigida , Mutación , Conformación Proteica , Desnaturalización Proteica/efectos de los fármacos , Saccharomyces cerevisiae/química , Proteínas de Saccharomyces cerevisiae/genética , Termodinámica
10.
Int J Biol Macromol ; 189: 194-205, 2021 Oct 31.
Artículo en Inglés | MEDLINE | ID: mdl-34428485

RESUMEN

In the current study, a novel derivative of sulfamethoxazole (a sulfonamide containing anti-biotic) named ZM-093 (IUPAC name: (E)-4-((4-(bis(2-hydroxyethyl)amino)phenyl)diazenyl)-N-(5-methylisoxazole-3-yl)benzenesulfonamide) was synthesized via common diazotization-coupling reactions from sulfamethoxazole and subsequently characterized through NMR/FT-IR spectroscopy. After evaluation, the compound was geometrically optimized at the DFT level of theory with BL3YP method and 6/31++G (d,p) basis set and from the optimized structure, several molecular descriptors important in the biological reactivity of the compound, such as global reactivity parameters, molecular electrostatic potential, average local ionization energy, and drug-likeness features of the compound were computationally analyzed. The experimental in vitro investigations of the interaction between ZM-093 and heat shock protein 70 (HSP70), a protein that is highly expressed in several types of cancers, exhibited a significant inhibitory effect against the chaperone activity of HSP70 for the titled compound (P-value < 0.01) and the comparison between the experimental studies with the mentioned computational analysis, as well as molecular docking, illustrated that ZM-093 may inhibit HSP70 through binding to its substrate-binding domain. Finally, by taking all the previous results into account, a new method for assessing the inhibitory activity of ligand to HSP70 is introduced based on protonography, a recently developed method that is dependent on the catalytic activity of carbonic anhydrase on polyacrylamide gel electrophoresis.


Asunto(s)
Simulación por Computador , Proteínas HSP70 de Choque Térmico/antagonistas & inhibidores , Sulfametoxazol/farmacología , Adenosina Trifosfatasas/metabolismo , Anhidrasas Carbónicas/metabolismo , Colorimetría , Proteínas HSP70 de Choque Térmico/química , Proteínas HSP70 de Choque Térmico/metabolismo , Espectroscopía de Resonancia Magnética , Conformación Molecular , Simulación del Acoplamiento Molecular , Preparaciones Farmacéuticas/química , Desnaturalización Proteica/efectos de los fármacos , Replegamiento Proteico/efectos de los fármacos , Protones , Sulfametoxazol/química
11.
Sci Rep ; 11(1): 15579, 2021 08 02.
Artículo en Inglés | MEDLINE | ID: mdl-34341408

RESUMEN

Human acidic fibroblast growth factor (hFGF1) is an all beta-sheet protein that is involved in the regulation of key cellular processes including cell proliferation and wound healing. hFGF1 is known to aggregate when subjected to thermal unfolding. In this study, we investigate the equilibrium unfolding of hFGF1 using a wide array of biophysical and biochemical techniques. Systematic analyses of the thermal and chemical denaturation data on hFGF1 variants (Q54P, K126N, R136E, K126N/R136E, Q54P/K126N, Q54P/R136E, and Q54P/K126N/R136E) indicate that nullification of charges in the heparin-binding pocket can significantly increase the stability of wtFGF1. Triple variant (Q54P/K126N/R136E) was found to be the most stable of all the hFGF1 variants studied. With the exception of triple variant, thermal unfolding of wtFGF1 and the other variants is irreversible. Thermally unfolded triple variant refolds completely to its biologically native conformation. Microsecond-level molecular dynamic simulations reveal that a network of hydrogen bonds and salt bridges linked to Q54P, K126N, and R136E mutations, are responsible for the high stability and reversibility of thermal unfolding of the triple variant. In our opinion, the findings of the study provide valuable clues for the rational design of a stable hFGF1 variant that exhibits potent wound healing properties.


Asunto(s)
Factor 1 de Crecimiento de Fibroblastos/química , Factor 1 de Crecimiento de Fibroblastos/metabolismo , Desplegamiento Proteico , Temperatura , Secuencia de Aminoácidos , Animales , Sitios de Unión , Proliferación Celular/efectos de los fármacos , Guanidina/farmacología , Heparina/metabolismo , Humanos , Ratones , Proteínas Mutantes/química , Mutación/genética , Células 3T3 NIH , Conformación Proteica , Desnaturalización Proteica/efectos de los fármacos , Estabilidad Proteica , Electricidad Estática , Urea/farmacología
12.
Biochim Biophys Acta Gen Subj ; 1865(10): 129970, 2021 10.
Artículo en Inglés | MEDLINE | ID: mdl-34339807

RESUMEN

BACKGROUND: Human fibrinogen, which plays a key role in plasma haemostasis, is a highly vulnerable target for oxidants. Fibrinogen undergoes posttranslational modifications that can potentially disrupt protein structure and function. METHODS: For the first time, by differential scanning calorimetry, dynamic and elastic light scattering and confocal laser scanning microscopy, the consequences of HOCl/-OCl-induced oxidation of fibrinogen on its thermal denaturation, molecular size distribution and fibrin clot network have been explored. RESULTS: Within a wide range of HOCl/-OCl concentrations (50-300 µM), the molecular size distribution remained unimodal; however, the average size of the hydrated molecules decreased. HOCl/-OCl-induced oxidation of fibrinogen resulted in the diminished thermal stability of regions D and E. As evidenced by elastic light scattering and confocal laser scanning microscopy, HOCl/-OCl caused the formation of abnormal fibrin with a decreased diameter of individual fibres. CONCLUSIONS: The current results along with data from previous studies enable one to conclude that the effect of HOCl/-OCl-mediated oxidation on the thermal stability of region D is influenced directly by oxidative damage to the D region structure. Since the E region is not subjected to oxidative modification, its structural damage is likely to be mediated by the oxidation of other protein structures, in particular α-helical coiled-coils. GENERAL SIGNIFICANCE: The experimental findings acquired in the current study could help to elucidate the consequences of oxidative stress in vivo on damage to the structure of fibrinogen/fibrin under the action of different ROS species.


Asunto(s)
Fibrina/antagonistas & inhibidores , Fibrinógeno/antagonistas & inhibidores , Ácido Hipocloroso/farmacología , Temperatura , Adulto , Fibrina/química , Fibrina/metabolismo , Fibrinógeno/química , Fibrinógeno/metabolismo , Humanos , Oxidación-Reducción , Estrés Oxidativo/efectos de los fármacos , Desnaturalización Proteica/efectos de los fármacos
13.
Int J Mol Sci ; 22(12)2021 Jun 17.
Artículo en Inglés | MEDLINE | ID: mdl-34204483

RESUMEN

Oxidative stress, photo-oxidation, and photosensitizers are activated by UV irradiation and are affecting the photo-stability of proteins. Understanding the mechanisms that govern protein photo-stability is essential for its control enabling enhancement or reduction. Currently, two major mechanisms for protein denaturation induced by UV irradiation are available: one generated by the local heating of water molecules bound to the proteins and the other by the formation of reactive free radicals. To discriminate which is the likely or dominant mechanism we have studied the effects of thermal and UV denaturation of aqueous protein solutions with and without DHR-123 as fluorogenic probe using circular dichroism (CD), synchrotron radiation circular dichroism (SRCD), and fluorescence spectroscopies. The results indicated that the mechanism of protein denaturation induced by VUV and far-UV irradiation were mediated by the formation of reactive free radicals (FR) and reactive oxygen species (ROS). The development at Diamond B23 beamline for SRCD of a novel protein UV photo-stability assay based on consecutive repeated CD measurements in the far-UV (180-250 nm) region has been successfully used to assess and characterize the photo-stability of protein formulations and ligand binding interactions, in particular for ligand molecules devoid of significant UV absorption.


Asunto(s)
Radicales Libres/química , Desnaturalización Proteica , Proteínas/química , Especies Reactivas de Oxígeno/química , Rayos Ultravioleta , Dicroismo Circular , Calefacción , Desnaturalización Proteica/efectos de los fármacos , Desnaturalización Proteica/efectos de la radiación , Especies Reactivas de Oxígeno/metabolismo , Análisis Espectral , Agua/química
14.
Int J Mol Sci ; 22(12)2021 Jun 18.
Artículo en Inglés | MEDLINE | ID: mdl-34207146

RESUMEN

Human phenylalanine hydroxylase (PAH) is a metabolic enzyme involved in the catabolism of L-Phe in liver. Loss of conformational stability and decreased enzymatic activity in PAH variants result in the autosomal recessive disorder phenylketonuria (PKU), characterized by developmental and psychological problems if not treated early. One current therapeutic approach to treat PKU is based on pharmacological chaperones (PCs), small molecules that can displace the folding equilibrium of unstable PAH variants toward the native state, thereby rescuing the physiological function of the enzyme. Understanding the PAH folding equilibrium is essential to develop new PCs for different forms of the disease. We investigate here the urea and the thermal-induced denaturation of full-length PAH and of a truncated form lacking the regulatory and the tetramerization domains. For either protein construction, two distinct transitions are seen in chemical denaturation followed by fluorescence emission, indicating the accumulation of equilibrium unfolding intermediates where the catalytic domains are partly unfolded and dissociated from each other. According to analytical centrifugation, the chemical denaturation intermediates of either construction are not well-defined species but highly polydisperse ensembles of protein aggregates. On the other hand, each protein construction similarly shows two transitions in thermal denaturation measured by fluorescence or differential scanning calorimetry, also indicating the accumulation of equilibrium unfolding intermediates. The similar temperatures of mid denaturation of the two constructions, together with their apparent lack of response to protein concentration, indicate the catalytic domains are unfolded in the full-length PAH thermal intermediate, where they remain associated. That the catalytic domain unfolds in the first thermal transition is relevant for the choice of PCs identified in high throughput screening of chemical libraries using differential scanning fluorimetry.


Asunto(s)
Fenilalanina Hidroxilasa/química , Desnaturalización Proteica , Pliegue de Proteína , Sitios de Unión , Rastreo Diferencial de Calorimetría , Dominio Catalítico , Humanos , Simulación del Acoplamiento Molecular , Simulación de Dinámica Molecular , Fenilalanina Hidroxilasa/aislamiento & purificación , Fenilcetonurias , Conformación Proteica , Desnaturalización Proteica/efectos de los fármacos , Pliegue de Proteína/efectos de los fármacos , Estabilidad Proteica , Temperatura , Termodinámica , Urea/química
15.
Molecules ; 26(9)2021 May 10.
Artículo en Inglés | MEDLINE | ID: mdl-34068693

RESUMEN

The intracellular environment is overcrowded with a range of molecules (small and large), all of which influence protein conformation. As a result, understanding how proteins fold and stay functional in such crowded conditions is essential. Several in vitro experiments have looked into the effects of macromolecular crowding on different proteins. However, there are hardly any reports regarding small molecular crowders used alone and in mixtures to observe their effects on the structure and stability of the proteins, which mimics of the cellular conditions. Here we investigate the effect of different mixtures of crowders, ethylene glycol (EG) and its polymer polyethylene glycol (PEG 400 Da) on the structural and thermal stability of myoglobin (Mb). Our results show that monomer (EG) has no significant effect on the structure of Mb, while the polymer disrupts its structure and decreases its stability. Conversely, the additive effect of crowders showed structural refolding of the protein to some extent. Moreover, the calorimetric binding studies of the protein showed very weak interactions with the mixture of crowders. Usually, we can assume that soft interactions induce structural perturbations while exclusion volume effects stabilize the protein structure; therefore, we hypothesize that under in vivo crowded conditions, both phenomena occur and maintain the stability and function of proteins.


Asunto(s)
Sustancias Macromoleculares/química , Mioglobina/química , Replegamiento Proteico , Temperatura , Animales , Dispersión Dinámica de Luz , Glicol de Etileno/química , Fluorescencia , Guanidina/farmacología , Caballos , Hidrodinámica , Simulación del Acoplamiento Molecular , Polietilenglicoles/química , Conformación Proteica , Desnaturalización Proteica/efectos de los fármacos , Replegamiento Proteico/efectos de los fármacos , Estabilidad Proteica/efectos de los fármacos
16.
Int J Biol Macromol ; 181: 552-560, 2021 Jun 30.
Artículo en Inglés | MEDLINE | ID: mdl-33744250

RESUMEN

Macromolecular crowding can have significant consequences on the structure and dynamics of a protein. The size and shape of a co-solute molecule and the nature of protein contribute significantly in macromolecular crowding, which results in different outcomes in similar conditions. The structure of apo-myoglobin (apo-Mb) both in the absence and presence of denaturants (GdmCl and urea) was investigated in crowded conditions at pH 7.0, with a comparable size of crowders (~70 kDa) but of different shapes (ficoll and dextran) at various concentrations using spectroscopic techniques like absorption and circular dichroism to monitor changes in secondary and tertiary structure, respectively. The crowders in the absence of denaturants showed structural stabilization of the tertiary structure while no significant change in the secondary structure was observed. The effect of crowders on the stability of the protein was also investigated using probes such as Δε291 and θ222 using chemical denaturants. The analysis of chemical-induced denaturation curves showed that both the crowders stabilize apo-Mb by increasing the values of the midpoint of transition (Cm) and change in free energy in the absence of denaturant (∆GD°), and it was observed that dextran 70 shows more stabilization than ficoll 70 under similar conditions. In this study apo-Mb showed stabilization under crowded conditions, which is a deviation from earlier work from our group where holo form of the same protein was destabilized. This study emphasizes that volume exclusion is a dominant force in a simple protein while soft interactions may play important role in the proteins that are possessing prosthetic group. Hence, the effect of crowders is protein-dependent, and excluded volume plays a great role in the stabilization of apo-Mb, which does not interact with the crowders.


Asunto(s)
Apoproteínas/química , Guanidina/farmacología , Hemo/química , Sustancias Macromoleculares/química , Mioglobina/química , Desnaturalización Proteica , Urea/farmacología , Animales , Dextranos/química , Ficoll/química , Caballos , Conformación Proteica , Desnaturalización Proteica/efectos de los fármacos , Estabilidad Proteica/efectos de los fármacos , Espectrofotometría Ultravioleta , Termodinámica
17.
Braz J Microbiol ; 52(2): 531-539, 2021 Jun.
Artículo en Inglés | MEDLINE | ID: mdl-33788178

RESUMEN

Accurate testing to detect SARS-CoV-2 RNA is key to counteract the virus spread. Nonetheless, the number of diagnostic laboratories able to perform qPCR tests is limited, particularly in developing countries. We describe the use of a virus-inactivating, denaturing solution (DS) to decrease virus infectivity in clinical specimens without affecting RNA integrity. Swab samples were collected from infected patients and from laboratory personnel using a commercially available viral transport solution and the in-house DS. Samples were tested by RT-qPCR, and exposure to infective viruses was also accessed by ELISA. The DS used did not interfere with viral genome detection and was able to maintain RNA integrity for up to 16 days at room temperature. Furthermore, virus loaded onto DS were inactivated, as attested by attempts to grow SARS-CoV-2 in cell monolayers after DS desalt filtration to remove toxic residues. The DS described here provides a strategy to maintain diagnostic accuracy and protects diagnostic laboratory personnel from accidental infection, as it has helped to protect our lab crew.


Asunto(s)
Prueba de COVID-19/métodos , COVID-19/diagnóstico , Estabilidad del ARN/efectos de los fármacos , ARN Viral/análisis , SARS-CoV-2/genética , Manejo de Especímenes/métodos , Pruebas Diagnósticas de Rutina , Genoma Viral/genética , Humanos , Desnaturalización Proteica/efectos de los fármacos , ARN Viral/genética , Reacción en Cadena en Tiempo Real de la Polimerasa , SARS-CoV-2/efectos de los fármacos
18.
J Enzyme Inhib Med Chem ; 36(1): 605-617, 2021 Dec.
Artículo en Inglés | MEDLINE | ID: mdl-33557644

RESUMEN

The aim of this study was to prepare and characterise inclusion complexes of a low water-soluble drug, mefenamic acid (MA), with ß-cyclodextrin (ß-CD). First, the phase solubility diagram of MA in ß-CD was drawn from 0 to 21 × 10-3 M of ß-CD concentration. A job's plot experiment was used to determine the stoichiometry of the MA:ß-CD complex (2:1). The stability of this complex was confirmed by molecular modelling simulation. Three methods, namely solvent co-evaporation (CE), kneading (KN), and physical mixture (PM), were used to prepare the (2:1) MA:ß-CD complexes. All complexes were fully characterised. The drug dissolution tests were established in simulated liquid gastric and the MA water solubility at pH 1.2 from complexes was significantly improved. The mechanism of MA released from the ß-CD complexes was illustrated through a mathematical treatment. Finally, two in vitro experiments confirmed the interest to use a (2:1) MA:ß-CD complex.


Asunto(s)
Ácido Mefenámico/química , beta-Ciclodextrinas/química , Animales , Bovinos , Eritrocitos/efectos de los fármacos , Humanos , Ácido Mefenámico/farmacología , Modelos Moleculares , Estructura Molecular , Desnaturalización Proteica/efectos de los fármacos , Albúmina Sérica Bovina/química , Solubilidad , beta-Ciclodextrinas/farmacología
19.
Artículo en Inglés | MEDLINE | ID: mdl-32961276

RESUMEN

We studied the mechanism of HDL denaturation with concomitant apoA-I dissociation with HDL preparations from 48 patients with a wide range of plasma HDL-C and evaluated the contribution of lipid-free apoA-I into cholesterol efflux from macrophage, in particular, mediated by cholesterol transporter ABCA1. We prepared HDL by precipitation of apoB-containing lipoproteins by polyethylene glycol and used the chaotropic agent urea to denature HDL preparations. Apo-I dissociation from urea-treated HDL was assessed by the increase of preß-band fraction with agarose gel electrophoresis followed by electro transfer and immunodetection and by the increase of ABCA1-mediated efflux of fluorescent analogue BODIPY-Cholesterol from RAW 264.7 macrophages. The HDL denaturation is governed by a single transition to fully dissociated apoA-I and the transition cooperativity decreases with increasing HDL-C. The apoA-I release depends on phospholipid concentration of HDL preparation and HDL compositional and structural heterogeneity and is well described by apolipoprotein partition between aqueous and lipid phases. Dissociated apoA-I determines the increase of ABCA1-mediated efflux of BODIPY-Cholesterol from RAW 264.7 macrophages to patient HDL. The increase in apoA-I dissociation is associated with the increase of ABCA1 gene transcript in peripheral blood mononuclear cells from patients. The low level of plasma HDL particles may be compensated by their increased potency for apoA-I release, thus suggesting apoA-I dissociation as a new HDL functional property.


Asunto(s)
Transportador 1 de Casete de Unión a ATP/metabolismo , Apolipoproteína A-I/metabolismo , HDL-Colesterol/sangre , Dislipidemias/sangre , Urea/química , Transportador 1 de Casete de Unión a ATP/genética , Adulto , Animales , Apolipoproteína A-I/genética , Transporte Biológico , Índice de Masa Corporal , Compuestos de Boro/química , LDL-Colesterol/sangre , Estudios de Cohortes , Dislipidemias/genética , Dislipidemias/patología , Colorantes Fluorescentes/química , Expresión Génica , Humanos , Masculino , Ratones , Persona de Mediana Edad , Polietilenglicoles/química , Desnaturalización Proteica/efectos de los fármacos , Células RAW 264.7 , Coloración y Etiquetado/métodos , Triglicéridos/sangre , Urea/farmacología
20.
Food Chem ; 335: 127647, 2021 Jan 15.
Artículo en Inglés | MEDLINE | ID: mdl-32739816

RESUMEN

The inhibition mechanism of the texture deterioration of tilapia fillets after treatment with polyphenols during partial freezing for 49 days was studied. Carnosic acid (CA), procyanidin (PA), quercetin (QE), and resveratrol (RSV) treatments had significantly higher hardness values (over 230 g) than the control group (183 g) on day 49 (P < 0.05). Polyphenol treatments were effective in delaying the protein degradation, lipid oxidation and spoilage microbe growth. Moreover, the kinetic model showed that the predicted shelf life of tilapia fillets treated with PA (102 d) was extended by 25 d compared to the control group (77 d). It was the proposed possible mechanism that polyphenols comprehensively maintained the protein conformation (increased hydrogen bonds and decreased disulfide bonds) and retarded protein denaturation and degradation, protecting the texture of the fillets. Therefore, polyphenols can be used to maintain texture and extend the shelf life of tilapia fillets during partial freezing.


Asunto(s)
Conservación de Alimentos/métodos , Conservantes de Alimentos/farmacología , Carne/análisis , Polifenoles/análisis , Polifenoles/farmacología , Animales , Biflavonoides/química , Catequina/química , Proteínas de Peces/química , Conservación de Alimentos/instrumentación , Congelación , Oxidación-Reducción/efectos de los fármacos , Proantocianidinas/química , Desnaturalización Proteica/efectos de los fármacos , Tilapia
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