Molecular Dynamic Study on the Structure and Thermal Stability of Mutant Pediocin PA-1 Peptides Engineered with Cysteine Substitutions.

Pediocin and analogous bacteriocins, valued for thermal stability, serve as versatile antimicrobials in the food sector. Improving their resilience at high temperatures and deriving derivatives not only benefit food production but also offer broad-spectrum antimicrobial potential in pharmaceuticals, spanning treatments for peptic ulcers, women's health, and novel anticancer agents. The study aims to create mutant peptides capable of establishing a third disulfide bond or enhanced through cysteine substitutions. This involves introducing additional Cys residues into the inherent structure of pediocin PA-1 to facilitate disulfide bond formation. Five mutants (Mut 1-5) were systematically generated with double Cys substitutions and assessed for thermal stability through MD simulations across temperatures (298-394 K). The most robust mutants (Mut 1, Mut 4-5) underwent extended analysis via MD simulations, comparing their structural stability, secondary structure, and surface accessibility to the reference Pediocin PA-1 molecule. This comprehensive assessment aims to understand how Cys substitutions influence disulfide bonds and the overall thermal stability of the mutant peptides. In silico analysis indicated that Mut 1 and Mut 5, along with the reference structure, lose their helical structure and one natural disulfide bond at high temperatures, and may impacting antimicrobial activity. Conversely, Mut 4 retained its helical structure and exhibited thermal stability similar to Pediocin PA-1. Pending further experimental validation, this study implies Mut 4 may have high stability and exceptional resistance to high temperatures, potentially serving as an effective antimicrobial alternative.

Two-Dimensional (2D) materials in the detection of SARS-CoV-2.

The SARS-CoV-2 pandemic has resulted in a devastating effect on human health in the last three years. While tremendous effort has been devoted to the development of effective treatment and vaccines against SARS-CoV-2 and controlling the spread of it, collective health challenges have been encountered along with the concurrent serious economic impacts. Since the beginning of the pandemic, various detection methods like PCR-based methods, isothermal nucleic acid amplification-based (INAA) methods, serological methods or antibody tests, and evaluation of X-ray chest results have been exploited to diagnose SARS-CoV-2. PCR-based detection methods in these are considered gold standards in the current stage despite their drawbacks, including being high-cost and time-consuming procedures. Furthermore, the results obtained from the PCR tests are susceptible to sample collection methods and time. When the sample is not collected properly, obtaining a false result may be likely. The use of specialized lab equipment and the need for trained people for the experiments pose additional challenges in PCR-based testing methods. Also, similar problems are observed in other molecular and serological methods. Therefore, biosensor technologies are becoming advantageous with their quick response, high specificity and precision, and low-cost characteristics for SARS-CoV-2 detection. In this paper, we critically review the advances in the development of sensors for the detection of SARS-CoV-2 using two-dimensional (2D) materials. Since 2D materials including graphene and graphene-related materials, transition metal carbides, carbonitrides, and nitrides (MXenes), and transition metal dichalcogenides (TMDs) play key roles in the development of novel and high-performance electrochemical (bio)sensors, this review pushes the sensor technologies against SARS-CoV-2 detection forward and highlights the current trends. First, the basics of SARS-CoV-2 detection are described. Then the structure and the physicochemical properties of the 2D materials are explained, which is followed by the development of SARS-CoV-2 sensors by exploiting the exceptional properties of the 2D materials. This critical review covers most of the published papers in detail from the beginning of the outbreak.

Effect of Disulfide Bonds on the Thermal Stability of Pediocin: In-silico Screening Using Molecular Dynamics Simulation.

The thermal stability properties of pediocin at 310, 313, 323, 333, 343, and 348 K (37, 40, 50, 60, 70, and 75°C, respectively) are reported in this study. A theoretical approach, such as the molecular dynamics method, was used to analyze the structure. Molecular dynamics simulation confirms the stability of molecules with Cys. Furthermore, this study reveals that Cys residues play an essential role in structure stability at high temperatures. To understand the structural basis for the stability of pediocin, a detailed in-silico analysis using molecular dynamics simulations to explore the thermal stability profiles of the compounds was conducted. This study shows that thermal effects fundamentally alter the functionally crucial secondary structure of pediocin. However, as previously reported, pediocin's activity was strictly conserved due to the disulfide bond between Cys residues. These findings reveal, for the first time, the dominant factor behind the thermodynamic stability of pediocin.

Electrochemical detection of lactate produced by foodborne presumptive lactic acid bacteria.

The detection of lactate is an important indicator of the freshness, stability, and storage stability of products as well as the degree of fermentation in the food industry. In addition, it can be used as a diagnostic tool in patients' healthcare since it is known that the lactate level in blood increases in some pathological conditions. Thus, the determination of lactate level plays an important role in not only the food industry but also in health fields. As a result, biosensor technologies, which are quick, cheap, and easy to use, have become important for lactate detection. In the current study, amperometric lactate biosensors based on lactate oxidase immobilization (with Nafion 5% wt) were designed and the limit of detection, linear range, and sensitivity values were determined to be 31 µM, 50-350 µM, and 0.04 µA µM-1 cm-2, respectively. Then, it was used for the measurement of lactic acid that produced by six different and morphologically identified presumptive lactic acid bacteria (LAB) which are isolated from different naturally fermented cheese samples. The biosensors were then used to successfully perform lactate measurements within 3 min for each sample, even though a few of them were out of the limit of detection. Thus, electrochemical biosensors should be used as an alternative and quick solutions for the measurement of lactate metabolites rather than the traditional methods which require long working hours. This is the first study to use a biosensor to measure lactate produced by foodborne LAB in a real sample.

SARS-CoV-2 Mutations and their Viral Variants.

Mutations in the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) occur spontaneously during replication. Thousands of mutations have accumulated and continue to since the emergence of the virus. As novel mutations continue appearing at the scene, naturally, new variants are increasingly observed. Since the first occurrence of the SARS-CoV-2 infection, a wide variety of drug compounds affecting the binding sites of the virus have begun to be studied. As the drug and vaccine trials are continuing, it is of utmost importance to take into consideration the SARS-CoV-2 mutations and their respective frequencies since these data could lead the way to multi-drug combinations. The lack of effective therapeutic and preventive strategies against human coronaviruses (hCoVs) necessitates research that is of interest to the clinical applications. The reason why the mutations in glycoprotein S lead to vaccine escape is related to the location of the mutation and the affinity of the protein. At the same time, it can be said that variations should occur in areas such as the receptor-binding domain (RBD), and vaccines and antiviral drugs should be formulated by targeting more than one viral protein. In this review, a literature survey in the scope of the increasing SARS-CoV-2 mutations and the viral variations is conducted. In the light of current knowledge, the various disguises of the mutant SARS-CoV-2 forms and their apparent differences from the original strain are examined as they could possibly aid in finding the most appropriate therapeutic approaches.

Host variations in SARS-CoV-2 infection.

The novel severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the zoonotic pathogen that causes the "Coronavirus Disease of 2019 (COVID-19)", and COVID-19 itself is yet to be thoroughly understood. Both the disease as well as the mechanisms by which the host interacts with the SARS-CoV-2 have not been fully enlightened. The epidemiological factors -e.g. age, sex, race-, the polymorphisms of the host proteins, the blood types and individual differences have all been in discussions about affecting the progression and the course of COVID-19 both individually and collectively, as their effects are mostly interwoven. We focused mainly on the effect of polymorphic variants of the host proteins that have been shown to take part in and/or affect the pathogenesis of COVID-19. Additionally, how the procedures of diagnosing and treating COVID-19 are affected by these variants and what possible changes can be implemented are the other questions, which are sought to be answered.