Unraveling the impact of ORF3a Q57H mutation on SARS-CoV-2: insights from molecular dynamics.

ORF3a is a conserved accessory protein of SARS-CoV-2, linked to viral infection and pathogenesis, with acquired mutations at various locations. Previous studies have shown that the occurrence of the Q57H mutation is higher in comparison to other positions in ORF3a. This mutation is known to induce conformational changes, yet the extent of structural alteration and its role in the viral adaptation process remain unknown. Here we performed molecular dynamics (MD) simulations of wt-ORF3a, Q57H, and Q57A mutants to analyze structural changes caused by mutations compared to the native protein. The MD analysis revealed that Q57H and Q57A mutants show significant structural changes in the dimer conformation than the wt-ORF3a. This dimer conformer narrows down the ion channel cavity, which reduces Na + or K + permeability leading to decrease the antigenic response that can help the virus to escape the host immune system. Non-bonding interaction analysis shows the Q57H mutant has more interacting residues, resulting in more stability within dimer conformation than the wt-ORF3a and Q57A. Moreover, both mutant dimers (Q57H and Q57A) form a novel salt-bridge interaction at the same position between A:Asp142 and B:Lys61, whereas such an interaction is absent in the wt-ORF3a dimer. We have also noticed that the TM3 domain's flexibility in Q57H is increased because of strong inter-domain interactions of TM1 and TM2 within the dimer conformation. These unusual interactions and flexibility of Q57H mutant can have significant impacts on the SARS-CoV-2 adaptations, virulence, transmission, and immune system evasion. Our findings are consistent with the previous experimental data and provided details information on the structural perturbation in ORF3a caused by mutations, which can help better understand the structural change at the molecular level as well as the reason for the high virulence properties of this variant.Communicated by Ramaswamy H. Sarma.

Antioxidant assessment of agricultural produce using fluorescence techniques: a review.

The study of bioactive compounds like food antioxidants is getting huge attention and curiosity by researchers and other relevant stakeholders (e.g., food and pharmaceutical industries) due to their health benefits. However, the currently available protocols to estimate the antioxidant activity of foods are time-consuming, destructive, require complex procedures for sample preparation, need technical persons, and not possible for real-time application, which are very important for large-scale or industrial applications. On the other hand, fluorescence spectroscopy and imaging techniques are relatively new, fast, mostly nondestructive, and possible to apply real-time to detect the antioxidants of foods. However, there is no review article on fluorescence techniques for estimating antioxidants in agricultural produces. Therefore, the present review comprehensively summarizes the overview of fluorescence phenomena, techniques (i.e., spectroscopy and computer vision), and their potential to monitor antioxidants in fruits and vegetables. Finally, opportunities and challenges of fluorescence techniques are described toward developing next-generation protocols for antioxidants measurement. Fluorescence techniques (both spectroscopy and imaging) are simpler and faster than available traditional methods of antioxidants measurement. Moreover, the fluorescence imaging technique has the potential to apply in real-time antioxidant identification in agricultural produce such as fruits and vegetables. Therefore, this technique might be used as a next-generation protocol for qualitative and quantitative antioxidants measurement after improvements like new material technologies for sensor (detector) and light sources for higher sensitivity and reduce the cost of implementing real-world applications.

Predicting protein function and orientation on a gold nanoparticle surface using a residue-based affinity scale.

The orientation adopted by proteins on nanoparticle surfaces determines the nanoparticle's bioactivity and its interactions with living systems. Here, we present a residue-based affinity scale for predicting protein orientation on citrate-gold nanoparticles (AuNPs). Competitive binding between protein variants accounts for thermodynamic and kinetic aspects of adsorption in this scale. For hydrophobic residues, the steric considerations dominate, whereas electrostatic interactions are critical for hydrophilic residues. The scale rationalizes the well-defined binding orientation of the small GB3 protein, and it subsequently predicts the orientation and active site accessibility of two enzymes on AuNPs. Additionally, our approach accounts for the AuNP-bound activity of five out of six additional enzymes from the literature. The model developed here enables high-throughput predictions of protein behavior on nanoparticles, and it enhances our understanding of protein orientation in the biomolecular corona, which should greatly enhance the performance and safety of nanomedicines used in vivo.

Quantitative Measurement of Multiprotein Nanoparticle Interactions Using NMR Spectroscopy.

An effective intensity-based reference is a cornerstone for quantitative nuclear magnetic resonance (NMR) studies, as the molecular concentration is encoded in its signal. In theory, NMR is well suited for the measurement of competitive protein adsorption onto nanoparticle (NP) surfaces, but current referencing systems are not optimized for multidimensional experiments. Presented herein is a simple and novel referencing system using 15N tryptophan (Trp) as an external reference for 1H-15N 2D NMR experiments. The referencing system is validated by the determination of the binding capacity of a single protein onto gold NPs. Then, the Trp reference is applied to protein mixtures, and signals from each protein are accurately quantified. All results are consistent with previous studies, but with substantially higher precision, indicating that the Trp reference can accurately calibrate the residue peak intensities and reduce systematic errors. Finally, the proposed Trp reference is used to kinetically monitor in situ and in real time the competitive adsorption of different proteins. As a challenging test case, we successfully apply our approach to a mixture of protein variants differing by only a single residue. Our results show that the binding of one protein will affect the binding of the other, leading to an altered NP corona composition. This work therefore highlights the importance of studying protein-NP interactions in protein mixtures in situ, and the referencing system developed here enables the quantification of binding kinetics and thermodynamics of multiple proteins using various 1H-15N 2D NMR techniques.