11 research outputs found

    Graphite/Gold Nanoparticles Electrode for Direct Protein Attachment: Characterization and Gas Sensing Application

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    In this work, graphite/gold nanoparticles (G/AuNPs) were synthesized through a facile chemical method, and its potential application for direct protein attachment for electrochemical detection of carbon monoxide (CO) was investigated. The preparation of G/AuNPs electrodes was optimized by synthesizing the nanoparticles in different concentration of HAuCl4.3H2O at various temperatures. The G/AuNPs electrode was subsequently modified by four types of mercaptopropionic acid, including 1-mercaptopropionic, 3-mercaptopropionic, 6-mercaptopropionic, and 11-mercaptopropionic acid, to achieve the best structure for protein attachment. Visible absorption and electrochemical studies showed that 3-mercaptopropionic acid possesses the best performance regarding the electrical conductivity between electrode and protein redox center. The cyclic voltammetry results revealed that the modified electrode has an appropriate performance for CO detection at very low concentrations while keeping a linear response. The limit of detection for the modified electrode was calculated to be about 0.2 ppb. Finally, the interactions of cytochrome C and carbon monoxides were simulated using molecular dynamics (MD), and the effect of protein conformation changes on the electrochemical signal was thoroughly examined. The simulation results suggested that the proposed electrochemical sensor has an acceptable performance for the detection of CO due to less fluctuation of amino acids near the protein chain in the presence of CO molecules

    Molecular Dynamics and Intrinsic Disorder Analysis of the SARS-CoV-2 Nsp1 Structural Changes Caused by Substitution and Deletion Mutations

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    SARS-CoV-2 non-structural protein 1 (Nsp1) is a virulence factor that inhibits the translation of host mRNAs and interacts with viral RNA. To date, hundreds of mutations (base substitutions, deletions, and insertions) have been reported in SARS-CoV-2 Nsp1. Despite the relevance of Nsp1, a few studies have been conducted to understand the effect of those mutations on Nsp1 structure and function. In this study, the effects of the most frequent mutations were investigated using molecular dynamics simulations. We found that several mutations profoundly affect the local intrinsic disorder predisposition, with most deletions increasing disorder propensity and replacement mutations inducing variable effects. We found that deletions Δ80–90 and Δ156–158 destabilise the protein structure. For example, the Δ156–158 cause a higher root-mean-square deviation (RMSD) and Rg values than those of the wild-type of SARS-CoV-2 Nsp1. We also found that the SARS-CoV-2 Nsp1 is slightly more disordered than its counterpart from SARS-CoV. A better understanding of the complexity and dynamic nature of interactions between intrinsically disordered segments of Nsp1 and ribosome subunits might help develop novel therapeutic countermeasures against the SARS-CoV-2 variants

    Insights Into the Structural Peculiarities of The\u3cem\u3e N\u3c/em\u3e-terminal and Receptor Binding Domains of the Spike Protein from the SARS-CoV-2 Omicron Variant

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    Since the new variant of SARS-CoV-2, Omicron (BA.1) has raised serious concerns, it is important to investigate the effects of mutations in the NTD and RBD domains of the spike protein for the development of COVID-19 vaccines. In this study, computational analysis of the Wuhan and Omicron NTDs and RBDs in their unbound and bound states to mAb 4A8 and ACE2 were performed. In addition, the interaction of NTD with antibody and RBD with ACE2 were evaluated in the presence of long glycans. The results show that long glycans at the surface of NTDs can reduce the accessibility of protein epitopes, thereby reducing binding efficiency and neutralizing potency of specific antibodies. Also, our findings indicate that the existence of the long glycans result in increased stability and enhanced affinity of the RBD to ACE2 in the Wuhan and Omicron variant. Key residues that play an important role in increasing the structural stability of the protein were identified using RIN analysis and in the state of interaction with mAb 4A8 and ACE2 through per-residue decomposition analysis. Further, the results of the free energy binding calculation using MM/GBSA method show that the Omicron variant has a higher infectivity than the Wuhan. This study provides a better understanding of the structural changes in the spike protein and can be useful for the development of novel therapeutics

    Radioprotective Role of Vitamins C and E against the Gamma Ray-Induced Damage to the Chemical Structure of Bovine Serum Albumin

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    Radioprotective effects of vitamin C and vitamin E as a water-soluble and a lipid-soluble agent, respectively, were investigated at the molecular level during the imposition of gamma radiation-induced structural changes to bovine serum albumin (BSA) at the therapeutic dose of 3 Gy. Secondary and tertiary structural changes of control and irradiated BSA samples were investigated using circular dichroism and fluorescence spectroscopy. The preirradiation tests showed nonspecific and reversible binding of vitamins C and E to BSA. Secondary and tertiary structures of irradiated BSA considerably changed in the absence of the vitamins. Upon irradiation, α-helices of BSA transitioned to beta motifs and random coils, and the fluorescence emission intensity decreased relative to nonirradiated BSA. In the presence of the vitamins C or E, however, the irradiated BSA was protected from these structural changes caused by reactive oxygen species (ROS). The two vitamins exhibited different patterns of attachment to the protein surface, as inspected by blind docking, and their mechanisms of protection were different. The hydrophilicity of vitamin C resulted in the predominant scavenging of ROS in the solvent, whereas hydrophobic vitamin E localized on the nonpolar patches of the BSA surface, where it did not only form a barrier for diffusing ROS but also encountered them as an antioxidant and neutralized them thanks to the moderate BSA binding constant. Very low concentrations of vitamins C or E (0.005 mg/mL) appear to be sufficient to prevent the oxidative damage of BSA

    Structure and Stability Analysis of Cytotoxic Complex of Camel α-Lactalbumin and Unsaturated Fatty Acids Produced at High Temperature

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    Abstract α-Lactalbumin (α-La), together with oleic acid can be converted to a complex, which kills tumor cells selectively. Cytotoxic α-La -oleic acid and α-La -linoleic acid complexes were generated by adding fatty acid to camel holo α-La at 60°C (referred to as La-OA-60 and La-LA-60 state, respectively). Structural properties of these complexes were studied and compared to the camel α-La. The experimental results show that linoleic acid induces α-La partial unfolding but oleic acid does not change the protein structure significantly. Also the stability of La-OA-60 and La-LA-60 toward thermal denaturation was measured. The order of temperature at the transition midpoint is as follows: La-LA-60 < La-OA-60 < α-La. La-OA-60 complex inhibited tubulin polymerization in vitro. Although the structures of La-OA-60 and La-LA-60 were different, these two complexes had similar cytotoxic effect to DU145 human prostate cancer cells. Samples of La-OA-60 that have been renatured after denaturation lost the specific biological activity toward tumor cells

    An Overview of the Vaccine Platforms to Combat COVID-19 with a Focus on the Subunit Vaccines

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    Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is an emerging virus that has caused the recent coronavirus disease (COVID-19) global pandemic. The current approved COVID-19 vaccines have shown considerable efficiency against hospitalization and death. However, the continuation of the pandemic for more than two years and the likelihood of new strain emergence despite the global rollout of vaccination highlight the immediate need for the development and improvement of vaccines. mRNA, viral vector, and inactivated virus vaccine platforms were the first members of the worldwide approved vaccine list. Subunit vaccines. which are vaccines based on synthetic peptides or recombinant proteins, have been used in lower numbers and limited countries. The unavoidable advantages of this platform, including safety and precise immune targeting, make it a promising vaccine with wider global use in the near future. This review article summarizes the current knowledge on different vaccine platforms, focusing on the subunit vaccines and their clinical trial advancements against COVID-19
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