Structural Insights Into the Impact of the Glycine-Rich Loop Mutation in Noonan Syndrome on the ATP Binding Pocket of CRAF Kinase.

The pathogenic G361A variant of CRAF, associated with increased intrinsic kinase activity in Noonan syndrome (NS), remains poorly understood in terms of its molecular and structural impact on kinase activity. To elucidate the mechanistic implications of the glycine to alanine substitution at residue 361 in CRAF, we employed molecular dynamics simulations. Our findings reveal that this mutation predominantly affects the ATP binding pocket and critical intermolecular interactions within the active cleft that favors the phosphate transfer reaction.

Personalized biocorona as disease biomarker: The challenges and opportunities.

It is well known that when nanoparticles interact with biological fluids, a layer of proteins and biological components forms on them. This layer may alter the biological fate and efficiency of the nanomaterial. Recent studies have shown that illness states have a major impact on the structure of the biocorona, sometimes referred to as the "personalized protein corona.

Impact of surface-active ionic solutions on the structure and function of laccase from trametes versicolor: Insights from molecular dynamics simulations.

Many protein-ionic liquid investigations have examined laccase interactions. Laccases are a class of poly-copper oxidoreductases that retain significant biotechnological relevance owing to their notable oxidative capabilities and their application in the elimination of synthetic dyes, phenolic compounds, insecticides, and various other substances. This study investigates the impact of surface active ionic liquids (SAILs), namely, decyltrimethylammonium bromide [N][Br] and 1-decyl-3-methylimidazolium chloride [C][Cl] as cationic surfactant ionic liquids and cholinium decanoate [Chl][Dec], an anionic surfactant ionic liquid, on the structure and function of laccase from the fungus Trametes versicolor (TvL) by the molecular dynamics (MD) simulation method.

Nucleotide sequence characterization, amino acid variations and 3D structural analysis of HN protein of the NDV VIId genotype.

Background: Haemagglutinin-neuraminidase (HN) is one of the membrane proteins of Newcastle disease virus (NDV) that plays a significant role during host viral infection. Therefore, antibodies against HN are vital for the host's ability to protect itself against NDV infection due to their critical functions in viral infection. As a result, HN has been a candidate protein in vaccine development against the Newcastle disease virus.

Designing and prototyping a novel biosensor based on a volumetric bar-chart chip for urea detection.

A volumetric bar-chart chip (V-chip) is a microfluidic device based on distance-based quantitative measurement that visualizes analyte concentration without the need for apparatus or data processing. This typically utilizes special receptors and catalysis parts that generate oxygen, so ink can be moved inside the channels, and enables instant visual quantitation of the analyte. However, the low stability of some macromolecules, the use of expensive catalysts, and difficulty in controlling the process cause inaccurate readings, and therefore, limit further development and the use of these systems.

Designing a bioadjuvant candidate vaccine targeting infectious bursal disease virus (IBDV) using viral VP2 fusion and chicken IL-2 antigenic epitope: A bioinformatics approach.

Infectious Bursal Disease (IBD) is a common and contagious viral infection that significantly affects the poultry industry. This severely suppresses the immune system in chickens, thereby threating their health and well-being. Vaccination is the most effective strategy for preventing and controlling this infectious agent.

Molecular analyses of the C-terminal CRAF variants associated with cardiomyopathy reveal their opposing impacts on the active conformation of the kinase domain.

The germline mutations in the C-terminus of CRAF kinase, particularly L603, and S612T/L613V, are associated with congenital heart disorders, for example, dilated cardiomyopathy (DCM) and hypertrophic cardiomyopathy (HCM). The experimental data suggest that genetic alternation at position 603 impairs, while those at positions 612/613 enhance the CRAF kinase activity. However, the underlying mechanistic details by which these mutations increase or decrease kinase activity remain elusive.

New insights into the effect of mutations on affibody-Fc interaction, a molecular dynamics simulation approach.

Staphylococcal protein A (SpA) domain B (the basis of affibody) has been widely used in affinity chromatography and found therapeutic applications against inflammatory diseases through targeting the Fc part of immunoglobulin G (IgG). We have performed extensive molecular dynamics simulation of 41 SpA mutants and compared their dynamics and conformations to wild type. The simulations revealed the molecular details of structural and dynamics changes that occurred due to introducing point mutations and helped to explain the SPR results.

The protein-stabilizing effects of TMAO in aqueous and non-aqueous conditions.

We present a new water-dependent molecular mechanism for the widely-used protein stabilizing osmolyte, trimethylamine -oxide (TMAO), whose mode of action has remained controversial. Classical interpretations, such as osmolyte exclusion from the vicinity of protein, cannot adequately explain the behavior of this osmolyte and were challenged by recent data showing the direct interactions of TMAO with proteins, mainly hydrophobic binding. Solvent effect theories also fail to propose a straightforward mechanism.

A novel nanocomposite (g-CN/FeO@PWV) with dual function in organic dyes degradation and cysteine sensing.

Among the important needs of human societies is the elimination of environmental pollution and also the construction of high-performance and inexpensive biosensors. In this regard, the construction of multi-functional composites has been considered. A novel magnetic graphite carbon nitride decorated by tri-vanadium substituted Dawson-type heteropolytungstate nanocomposite (CN/FeO@PWV) effectively synthesized and characterized by prevalent functional analysis.

An overview of progress from empirical to rational design in modern vaccine development, with an emphasis on computational tools and immunoinformatics approaches.

Vaccination remains the most effective strategy for preventing and controlling infectious diseases. Numerous conventional vaccines, especially live attenuated, inactivated (killed) microorganisms and subunit vaccines, lead to an effective induction of protective immune responses, mainly antibody-mediated responses against pathogens. However, it has become known that a wide range of highly dangerous pathogens are uncontrollable via conventional vaccination strategies.

Investigation of static magnetic field effect on horseradish peroxidase enzyme activity and stability in enzymatic oxidation process.

The activity of Horseradish Peroxidase (HRP) Enzyme exposed to a static magnetic field (SMF) during the oxidation reaction of pyrogallol (PGL) and the epigallocatechin gallate (EPCG) flavonoid was recorded at different times. As the data showed, the enzyme activity increased by 77.17% with increasing incubation time up to 30 min.

Recent advances in computational methods for biosensor design.

Biosensors are analytical tools with a great application in healthcare, food quality control, and environmental monitoring. They are of considerable interest to be designed by using cost-effective and efficient approaches. Designing biosensors with improved functionality or application in new target detection has been converted to a fast-growing field of biomedicine and biotechnology branches.

The effect of anion on aggregation of amino acid ionic liquid: Atomistic simulation.

Aggregation behavior of dodecyl betaine chloride [DB][Cl], as an amino acid ionic liquid, and dodecyl betaine N-acetyl glycinate [DB][AG], as a bio ionic liquid, in aqueous media was studied through molecular dynamics simulation. The aggregating was investigated by radial distribution function, coordination numbers, and hydrogen bond numbers. The results demonstrated the hydrogen bond between [DB] and [AG] that leads to aggregation.

The effect of magnetized water on the oxidation reaction of phenol derivatives and aromatic amines by horseradish peroxidase enzyme.

The present study aimed to investigate, for the first time, the rate of the oxidation reaction of some derivatives of phenol and aromatic amines, that is, pyrogallol, catechol, resorcinol, ortho-aminophenol, meta-aminophenol, para-aminophenol, ortho-phenylenediamine, and para-phenylenediamine, in the presence of hydrogen peroxide in pure and magnetized solvents using horseradish peroxidase enzyme. The reaction was studied in the absence and presence of a magnetized solvent under completely identical conditions. The results showed that magnetized solvent could change the structure of the enzyme and reduce its activity.

A DFT study on the metal ion selectivity of deferiprone complexes.

In this work, systematic density functional theory (DFT) calculations were performed to study the interactions of various metal ions (Al, Fe, Co, Ni, Cu, and Zn) and the clinically useful chelating agent called deferiprone (DFP) at the M05-2X/6-31G(d) level of theory. The thermodynamic parameters of metal-deferiprone complexes were determined in water. Based on the obtained data, the theoretical binding energy trend is as follows: Al > Fe > Cu > Ni > Co > Zn, confirming that [Al(DFP)] has the most interaction energy.

Computer-Aided aptamer design for sulfadimethoxine antibiotic: step by step mutation based on MD simulation approach.

This study introduces a computational method to design a new aptamer with higher binding affinity to a special target in comparison with the experimentally available aptamers. The method is called step by step mutation based on MD simulation, which includes some steps. First, MD simulation is performed for the SELEX-introduced (native) aptamer in the presence of the target.

A low-cost paper-based aptasensor for simultaneous trace-level monitoring of mercury (II) and silver (I) ions.

Mercury (Hg) and silver (Ag) ions possess the harmful effects on public health and environment that makes it essential to develop the sensing techniques with great sensitivity for the ions. Metal ions commonly coexist in the different biological and environmental systems. Hence, it is an urgent demand to design a simple method for the simultaneous detection of metal ions, peculiarly in the case of coexisting Hg and Ag.

Effects of the deglycosylation on the structure and activity of chloroperoxidase: Molecular dynamics simulation approach.

Chloroperoxidase (CPO) is a versatile fungal heme-thiolate protein that catalyzes a variety of one electron and two-electron oxidations. Chloroperoxidase is a versatile fungal heme-thiolate protein that catalyzes a variety of oxidations. CPO enzyme contains thirteen sugars, including five N-acetyl D-glucosamines (NAG) and eight mannoses (MAN), which are attached to the protein via the glycosidic bonds.

Innovative method for analysis of safranal under static and dynamic conditions through combination of HS-SPME-GC technique with mathematical modelling.

Introduction: Saffron (Crocus sativus L.) is a well-known spice which is used as the colourant and flavouring agent in food products. Safranal could act as an indicator for saffron grading, authentication and adulteration, as well as for quality evaluation of saffron flavoured products; since it is the main odourant and the most aroma-active compound of saffron.

The investigation of the G-quadruplex aptamer selectivity to Pb ion: a joint molecular dynamics simulation and density functional theory study.

The aptamers with the ability to form a G-quadruplex structure can be stable in the presence of some ions. Hence, study of the interactions between such aptamers and ions can be beneficial to determine the highest selective aptamer toward an ion. In this article, molecular dynamics (MD) simulations and quantum mechanics (QM) calculations have been applied to investigate the selectivity of the T30695 aptamer toward Pb in comparison with some ions.

Self-Assembly of a Structurally Defined Chiro-Optical Peptide-Oligothiophene Hybrid Material.

Conducting polymers are routinely used in optoelectronic biomaterials, but large polymer polydispersity and poor aqueous compatibility complicate integration with biomolecular templates and development of discrete and defined supramolecular complexes. Herein, we report on a chiro-optical hybrid material generated by the self-assembly of an anionic peptide and a chemically defined cationic pentameric thiophene in aqueous environment. The peptide acts as a stereochemical template for the thiophene and adopts an α-helical conformation upon association, inducing optical activity in the thiophene π-π* transition region.

Multifunctional CuO nanoparticles with cytotoxic effects on KYSE30 esophageal cancer cells, antimicrobial and heavy metal sensing activities.

In this work, fluorescent copper oxide nanoparticles (CuO NPs) were green synthesized using viable cells, cell lysate supernatant (CLS) and protein extracts of luminescent Vibrio sp. VLC. Biogenic CuO NPs were then characterized by XRD, FTIR, UV/Vis spectroscopy, TEM, DLS, and PL spectroscopy.

A simple paper-based aptasensor for ultrasensitive detection of lead (II) ion.

In this study, a simple paper-based aptasensor has been developed for the ultrasensitive detection of lead (Pb) ion within about 10 min. The aptasensor has been successfully designed by taking advantages of the Förster Resonance Energy Transfer (FRET) process and the super fluorescence quenching property of graphene oxide (GO) sheet. The sensing mechanism of the aptasensor is based on the conformational switch of the Pb-specific aptamer from a random coil to a G-quadruplex structure.

Role of in the biosynthesis of AgNPs and their antibacterial properties.

Silver nanoparticles (AgNPs) have been biosynthesised through the extracts of fruits, which served as the reducing agents and capping agents. Biosynthesised AgNPs have been found to be ultraviolet-visible (UV-vis) absorption spectra since they have displayed one surface plasmon resonance peak at 438 nm, attesting the formation of spherical NPs. These particles have been characterised by UV-vis, field-emission scanning electron microscopy, energy-dispersive X-ray spectroscopy, X-ray diffraction, Fourier transform infrared spectroscopy, and transmission electron microscopy analysis.