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. It was observed in some variants a point mutation caused extensive structural changes far from the mutation site, while an effect of some other mutations was limited to the site of the mutated residue. Also, the pattern of hydrogen bond networks and hydrophobic core arrangements were investigated. We figured out mutations that occurred at positions 128, 136, 150 and 153, affected two hydrophobic cores at the interface as well as mutations introduced at positions 129 and 154 interrupted two hydrogen bond networks of the interface, SPR data showed all of these mutations reduced binding affinity significantly. Overall, by scanning the SpA-Fc interface through the large numbers of introduced mutations, the new insights have been gained which would help to design high- affinity ligands of IgG.

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 N-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 via hydrophobic binding. Solvent effect theories also fail to propose a straightforward mechanism. To explore the role of water and the hydrophobic association, we disabled osmolyte-protein hydrophobic interactions by replacing water with hexane and using lipase enzyme as an anhydrous-stable protein. Biocatalysis experiments showed that under this non-aqueous condition, TMAO does not act as a stabilizer, but strongly deactivates the enzyme. Molecular dynamics (MD) simulations reveal that TMAO accumulates near the enzyme and makes many hydrogen bonds with it, like denaturing osmolytes. Some TMAO molecules even reach the active site and interact strongly with the catalystic traid. In aqueous solvent, the enzyme functions well: the extent of TMAO interactions is reduced and can be divided into both polar and non-polar terms. Structural analysis shows that in water, some TMAO molecules bind to the enzyme surface like a surfactant. We show that these interactions limit water-protein hydrogen bonds and unfavorable water-hydrophobic surface contacts. Moreover, a more hydrophobic environment is formed in the solvation layer, which reduces water dynamics and subsequently, rigidifies the backbone in aqueous solution. We show that osmolyte amphiphilicity and protein surface heterogeneity can address the weaknesses of exclusion and solvent effect theories about the TMAO mechanism.

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

Mercury (Hg2+) 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 Hg2+ and Ag+. This study introduces a low-cost paper-based aptasensor to monitor Hg2+ and Ag+, simultaneously. The strategy of the sensing array is according to the conformational changes of Hg2+- and Ag+-specific aptamers and their release from the GO surface after the injection of the target sample on the sensing platform. Through monitoring the fluorescence recovery changes against the concentrations of the ions, Hg2+ and Ag+ can be determined as low as 1.33 and 1.01 pM. The paper-based aptasensor can simultaneously detect the ions within about 10 min. The aptasensor is applied prosperously to monitor Hg2+ and Ag+ in human serum, water, and milk. The designed aptasensor with the main advantages of simplicity and feasibility holds the supreme potential to develop a cost-effective sensing method for environmental monitoring, food control, and human diagnostics.

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. OBJECTIVES: Firstly, determination of the optimum static conditions for safranal extraction through headspace solid-phase micro-extraction combined with gas chromatography (HS-SPME-GC) technique. Secondly, safranal measurement in different saffron flavoured products under the optimised static conditions. Thirdly, elucidation of the method efficiency for safranal measurement under non-equilibrium conditions for a saffron drink sample. METHODS: Different equilibrium times, pH and salt concentrations were applied on aqueous solutions of safranal. Accordingly, the optimised static conditions were determined for safranal extraction through HS-SPME-GC approach using polydimethylsiloxane (PDMS) fibre. RESULTS: Under static conditions, a linear response was obtained for standard curve within the safranal concentration range of 0.08-30 ppm, with R2 = 0.9999. The limits of detection and quantification were 0.04 and 0.08 ppm, respectively. Despite the fact that safranal peak area was an efficient parameter for quantifications under static conditions; its poor reproducibility was proved under dynamic conditions for the saffron drink sample. This observation necessitated application of kinetic studies on real food samples. CONCLUSIONS: Safranal extraction was successfully performed from aqueous matrices through HS-SPME-GC, under static conditions. Mathematical modelling resulted in kinetic parameters that improved the efficiency of safranal measurement under dynamic conditions, using PDMS fibre.

Computational Kinetic Modeling of the Catalytic Cycle of Glutathione Peroxidase Nanomimic: Effect of Nucleophilicity of Thiols on the Catalytic Activity.

The catalytic cycle of a new derivative of ebselen, 1, was elucidated via three steps by the density functional theory and solvent-assisted proton exchange procedure involving indirect proton exchange through a hydrogen-bonded transfer network. Different behaviors of the aromatic and aliphatic thiols were investigated in the reduction of selenoxide (step 2 → 3) and selenurane (step 3 → 1) based on their nucleophilicity. The reduction of selenoxide in the presence of thiophenol (ΔG‡ = 15.9 kcal·mol-1) is faster than that of methanethiol (ΔG‡ = 29.3 kcal·mol-1), and methanethiol makes the reduction of selenoxide unspontaneous and kinetically unfavorable (ΔG = 2.8 kcal·mol-1). The nucleophilic attack may be enhanced by using the thiophenol backbone at the selenium center to lower the energy barrier of the selenoxide reduction (ΔG‡ = 15.9 kcal·mol-1). On the basis of the turnover frequency calculations, during the catalytic cycle, the rate of the reaction was analyzed and discussed. Low values of the electron density and Laplacian at the transition states are the evidence of the covalent O-H and O-O bonds rupture in the presence of methanethiol and thiophenol. The nature of the critical bond points was characterized, using the quantum theory of atoms in molecules, based on the electron location function and localized orbital locator values. Finally, the charge transfer process at the rate-determining step was investigated based on the natural bond orbital analysis.

A Computational Exploration of H2S and CO2 Capture by Ionic Liquids Based on α-Amino Acid Anion and N7,N9-Dimethyladeninium Cation.

Hydrogen sulfide (H2S) and carbon dioxide (CO2) adsorption on a series of the aliphatic amino acid ionic liquids (AAILs) composed of N7,N9- dimethyladeninium cation with amino acid anions (AA = Gly, Ala, Val, Leu, and Ile) as the functionalized ILs with dual groups of amine have been investigated. On the basis of the obtained data, the possible sites of H2S adsorption are twice those of CO2 on the ionic liquids, and also the average adsorption energy of H2S (ΔE = -51.5 kJ mol-1) in the most stable region of adsorption is twice greater than that of CO2 (ΔE = -25.5 kJ mol-1). An increase in the length of the side chain of the amino acids increases the interaction energy of the H2S and CO2 capture (on the amine group of the [AA]- anions). Quantum theory of atoms in molecules analysis confirmed the noncovalent nature of the N···C bond formed between CO2 and N atom in both of the amine groups and S-H···O and S-H···N bond critical points of H2S on [dMA][AA]. Natural bond orbital analysis indicates that charge transfer in H2S adsorption is more important than CO2 capture. Finally, a correlation between the adsorption energy and the sum of stability energies (∑E(2)) in the most stable region has been obtained and discussed.

Sensing Ability of Hybrid Cyclic Nanopeptides Based on Thiourea Cryptands for Different Ions, A Joint DFT-D3/MD Study.

Theoretical studies, including quantum chemistry (QM) calculations and 25 ns molecular dynamic (MD) simulations, were performed on two types of hybrid cyclic nanopeptides (HCNPs) that are constructed of tren-capped cryptand (HCNP1) and 1,3,5-triethylbenzene-capped cryptand (HCNP2) for selective complex formation with OAC-, NO3-, HSO4-, F-, Br-, and Cl- ions in the gas phase and DMSO. Obtained data by M05-2X, M05-2X-D3, B3LYP, and B3LYP-D3 functionals indicated that HCNPs form a stable complex with F- in comparison to other ions. DFT-D3 results and quantum theory of atoms in molecules (QTAIM) analysis indicated that dispersion and electrostatic interactions are the most important driving forces in HCNP-ion complex formation, respectively. Moreover, HOMO-LUMO analysis reveals that the reactivity of HCNP2, due to a lower band gap, is more than HCNP1. High sensing ability of the studied HCNPs for different ions was confirmed by Fermi level shifting of HNCPs to higher values during the complex formation. Finally, MD simulation results in DMSO are in good agreement with QM calculations and indicate that F- forms the most stable complexes with HCNPs because of stronger electrostatic interactions.

Synthesis, Characterization and Fluorescence Properties of Zn(II) and Cu(II) Complexes: DNA Binding Study of Zn(II) Complex.

Zinc(II) and copper(II) complexes containing Schiff base, 2- methoxy-6((E)-(phenylimino) methyl) phenol ligand (HL) were synthesized and characterized by elemental analysis, IR, NMR, and single crystal X-ray diffraction technique. The fluorescence properties and quantum yield of zinc complex were studied. Our data showed that Zn complex could bind to DNA grooves with Kb = 10(4) M(-1). Moreover, Zn complex could successfully be used in staining of DNA following agarose gel electrophoresis. MTT assay showed that Zn complex was not cytotoxic in MCF-7 cell line. Here, we introduce a newly synthesized fluorescence probe that can be used for single and double stranded DNA detection in both solution and agarose gels.

Biophysical probing of the binding properties of a Cu(II) complex with G-quadruplex DNA: an experimental and computational study.

Telomerase inhibition through G-quadruplex stabilization by small molecules is of great interest as a novel anticancer therapeutic strategy. Here, we show that newly synthesized Cu-complex binds to G-quadruplex DNA and induces changes in its stability. This biophysical interaction was investigated in vitro using spectroscopic, voltammetric and computational techniques. The binding constant for this complex to G-quadruplex using spectroscopic and electrochemical methods is in the order of 10(5) . The binding stoichiometry was investigated using spectroscopic techniques and corresponded to a ratio of 1: 1. Fluorescence titration results reveal that Cu-complex is quenched in the presence of G-quadruplex DNA. Analysis of the fluorescence emission at different temperatures shows that ΔH° > 0, ΔS° > 0 and ΔG° < 0, and indicates that hydrophobic interactions played a major role in the binding processes. MD simulation results suggested that this ligand could stabilize the G-quadruplex structure. An optimized docked model of the G-quadruplex-ligand mixture confirmed the experimental results. Based on the results, we conclude that Cu-complex as an anticancer candidate can bind and stabilize the G-quadruplex DNA structure.

A combined molecular dynamic and quantum mechanic study of the solvent and guest molecule effect on the stability and length of heterocyclic peptide nanotubes.

Molecular dynamic simulations were performed to investigate the stability of heterocyclic peptide nanotubes composed of 1,4-disubstituted-1,2,3-triazol ε-amino acid. 45 ns MD simulations were conducted on the cyclic peptide nanotube (CPNT) and cyclic peptide dimer in methanol, chloroform, and water and revealed that these structures are more stable in nonpolar solvents. MM-PBSA and MM-GBSA calculations were employed to analyze the solvent effect on the stability and length of the CPNT. These calculations showed that CPNT in chloroform was more stable and longer as compared to other solvents. In addition, the effect of the guest molecule (ethanol) inside the dimer and CPNT was investigated. The obtained results confirmed that guest molecule(s) stabilized the dimer and CPNT in all solvents. Quantum chemistry calculations on the cyclic peptide dimer were performed at the M06-2X/6-31G(d) level in the gas phase and three solvents. The obtained results from the quantum chemistry study were in good agreement with the MD simulation results. DFT calculations showed that the guest molecule stabilized the dimer structure and electrostatically interacted with the cyclic peptide dimer. Finally, for investigation of the solvent effects on the hydrogen bonds of the cyclic peptide dimer, NBO and AIM analysis were performed.

Theoretical design of the cyclic lipopeptide nanotube as a molecular channel in the lipid bilayer, molecular dynamics and quantum mechanics approach.

In this article, cyclic peptides (CP) with lipid substituents were theoretically designed. The dynamical behavior of the CP dimers and the cyclic peptide nanotube (CPNT) without lipid substituents in the solution (water and chloroform) during the 50 ns molecular dynamic (MD) simulations has been investigated. As a result, the CP dimers and CPNT in a non-polar solvent are more stable than in a polar solvent and CPNT is a good container for non-polar small molecules such as chloroform. The effect of the lipid substituents on the CP dimers and CPNT has been investigated in the next stage of our studies. Accordingly, these substituents increase the stability of the CP dimers and CPNT, significantly, in polar solvents. MM-PBSA and MM-GBSA calculations confirm that substitution has an important effect on the stability of the CP dimers and CPNT. Finally, the dynamical behavior of CPNT with lipid substituents in a fully hydrated DMPC bilayer shows the high ability of this structure for molecule transmission across the lipid membrane. This structure is stable enough to be used as a molecular channel. DFT calculations on the CP dimers in the gas phase, water and chloroform, indicate that H-bond formation is the driving force for dimerization. CP dimers are more stable in the gas phase in comparison to in solution. HOMO-LUMO orbital analysis indicates that the interaction of the CP units in the dimer structures is due to the molecular orbital interactions between the NH and CO groups.

Spectroscopic and molecular modeling based approaches to study on the binding behavior of DNA with a copper (II) complex.

Blocking the division of tumor cells by small-molecules is currently of great interest for the design of new antitumor drugs. The interaction of a new metal complex with DNA was investigated through several techniques. Absorption spectroscopy and gel electrophoresis studies on the interaction of the Cu-complex of (2a-4mpyH)2 [Cu(pyzdc)2 (H2O)2].6 H2O with DNA have shown that this complex can bind to CT-DNA with binding constant 3.99 × 10(5) M(-1). The cyclic voltammetry (CV) responses of the metal complex in the presence of CT-DNA have shown that the metal complex can bind to CT-DNA through partial intercalation mode and this is consistent with molecular docking analysis, quenching process and thermal denaturation experiments. The cytotoxicity of this complex has been evaluated by MTT assay. The results of cell viability assay on DU145 cell line revealed that the metal complex had cytotoxic effects.

How a protein can remain stable in a solvent with high content of urea: insights from molecular dynamics simulation of Candida antarctica lipase B in urea : choline chloride deep eutectic solvent.

Deep eutectic solvents (DESs) are utilized as green and inexpensive alternatives to classical ionic liquids. It has been known that some of DESs can be used as solvent in the enzymatic reactions to obtain very green chemical processes. DESs are quite poorly understood at the molecular level. Moreover, we do not know much about the enzyme microstructure in such systems. For example, how some hydrolase can remain active and stable in a deep eutectic solvent including 9 M of urea? In this study, the molecular dynamics of DESs as a liquid was simulated at the molecular level. Urea : choline chloride as a well-known eutectic mixture was chosen as a model DES. The behavior of the lipase as a biocatalyst was studied in this system. For comparison, the enzyme structure was also simulated in 8M urea. The thermal stability of the enzyme was also evaluated in DESs, water, and 8M urea. The enzyme showed very good conformational stability in the urea : choline chloride mixture with about 66% urea (9 M) even at high temperatures. The results are in good agreement with recent experimental observations. In contrast, complete enzyme denaturation occurred in 8M urea with only 12% urea in water. It was found that urea molecules denature the enzyme by interrupting the intra-chain hydrogen bonds in a "direct denaturation mechanism". However, in a urea : choline chloride deep eutectic solvent, as a result of hydrogen bonding with choline and chloride ions, urea molecules have a low diffusion coefficient and cannot reach the protein domains. Interestingly, urea, choline, and chloride ions form hydrogen bonds with the surface residues of the enzyme which, instead of lipase denaturation, leads to greater enzyme stability. To the best of our knowledge, this is the first study in which the microstructural properties of a macromolecule are examined in a deep eutectic solvent.

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. In this article, we introduced a novel approach that eliminates the use of catalysts in V-chips and provides an efficient and simple path in the design of biosensors. The product of the enzymatic reaction of urease with urea is bicarbonate, which turns into CO2 gas in an acidic environment. Therefore, the amount of gas produced is proportional to the amount of urea in the sample, and it can be quantitatively measured by visual detection from the amount of ink movement caused by CO2 gas pressure. This biosensor has a linear response range of 0 to 1000 µg ml-1 and a detection limit of 3.6 µg ml-1 in raw milk. The recovery of urea in raw milk at 100 and 400 µg ml-1 concentrations was 96.5% and 98.9%, respectively. This volumetric chip shows potential for determining urea levels in real samples without requiring additional equipment. The combination of the sensitivity and specificity of enzymatic reactions, inherent gas-generating reactions, and the processability of microchips discussed in this paper can be the basis for the comprehensive development of volumetric chips, which can create a new path for the development of efficient and cheap biosensors.

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. METHODS: This report used the full-length sequence of the HN protein of NDV isolated in Iran (VIId subgenotype). We characterize and identify amino acid substitutions in comparison to other more prevalent NDV genotypes, VII subgenotypes and vaccine strains. Furthermore, bioinformatics tools were applied to determine the three-dimensional structure, molecular dynamics simulation and prediction of B-cell antigenic epitopes. RESULTS: The results showed that the antigenic regions of our isolate are quite comparable to the other VII subgenotypes of NDV isolated from different geographical places. Moreover, by employing the final 3D structure of our HN protein, the amino acid residues are proposed as a B-cell epitope by epitope prediction servers, which leads to the introduction of linear and conformational antigenic sites. CONCLUSIONS: Immunoinformatic vaccine design principles currently exhibit tremendous potential for developing a new generation of candidate vaccines quickly and economically to eradicate infectious viruses, including the NDV. In order to accomplish this, focus is directed on residues that might be considered antigenic.

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 [N10111][Br] and 1-decyl-3-methylimidazolium chloride [C10mim][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. In summary, this study showed that laccase solvent-accessible surface area increased in the ionic liquid [Chl][Dec] while it decreased in the other two ionic liquids. Interestingly, [Chl][Dec] ionic liquid components formed hydrogen bonds with laccase, while [N10111][Br] and [C10mim][Cl] components were unable to form hydrogen bonds with laccase. The quantity of hydrogen bonds formed between water molecules and the enzyme was also diminished in the presence of [Chl][Dec] in comparison to the other two ionic liquids. especially at a concentration of 250 mM. In 250 mM concentrations of [N10111][Br] and [C10mim][Cl], clusters of long-chain cations are likely to form near the copper T1 site. However, even at low [Chl][Dec] concentrations, long [Dec]- chains were observed to penetrate the enzyme near the copper T1 site, and at 250 mM [Chl][Dec], a large cluster of anions occupied the opening of the active site. The results of the analysis also show that the interaction between the [Dec]- anion and the enzyme is stronger than the interaction between [N10111]+ and [C10mim]+ with laccase; in addition, the [Dec]- anion, compared to [Br]- and [Cl]- has a much greater tendency to bind with the enzyme residues.

Quantum chemistry aspects of the solvent effects on 3,4-dimethyl-2,5-dihydrothiophen-1,1-dioxide pyrolysis reaction.

A theoretical density functional theory (DFT) study was employed to investigate solvent effects on a retro-cheletropic ene reaction. The use of a nonpolar solvent in this retro-ene reaction is desirable to improve the reaction rate. Interactions between 14 different solvents and the reaction mixtures (reactant and transition state) were considered using DFT solvation calculations. These results were used to determine the role of solvents on the rate constants. Theoretical calculations at the B3LYP/6-311++G(d,p) level revealed that in the presence of solvents with low polarity the reaction becomes faster, which is in accordance with experimental data. Transition state-solvent interactions were analyzed by the quantum theory of atoms in molecules (QTAIM) and natural bond orbital (NBO) analysis. Finally, several correlations between electron densities in bond critical points of the C-S bond and interaction energy as well as vibrational frequencies at the transition state have been investigated.

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. The development of VP2-based DNA vaccines combined with biological adjuvants has recently received considerable attention due to their effectiveness in eliciting both humoral and cellular immune responses. In this study, we applied bioinformatics tools to design a fused bioadjuvant candidate vaccine from the full-length sequence of the VP2 protein of IBDV isolated in Iran using the antigenic epitope of chicken IL-2 (chiIL-2). Furthermore, to improve the antigenic epitope presentation and to maintain the three-dimensional structure of the chimeric gene construct, the P2A linker (L) was used to fuse the two fragments. Our in-silico analysis for the design of a candidate vaccine indicates that a continuous sequence of amino acid residues ranging from 105 to 129 in chiIL-2 is proposed as a B cell epitope by epitope prediction servers. The final 3D structure of the VP2-L-chiIL-2105-129 was subjected to physicochemical property determination, molecular dynamic simulation, and antigenic site determination. The results of these analyses led to the development of a stable candidate vaccine that is non-allergenic and has the potential for antigenic surface display potential and adjuvant activity. Finally, it is necessary to investigate the immune response induced by our proposed vaccine in avian hosts. Notably, increasing the immunogenicity of DNA vaccines can be achieved by combining antigenic proteins with molecular adjuvants using the principle of rational vaccine design.

A novel nanocomposite (g-C3N4/Fe3O4@P2W15V3) 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 (C3N4/Fe3O4@P2W15V3) effectively synthesized and characterized by prevalent functional analysis. The prepared nano-catalyst presents bi-functional usage involving photocatalytic removal of dyes (methylene blue, congo red and phenyl red) (around 98%) under visible light radiation and greatly sensitive colorimetric sensing of cysteine in an aqueous media. Moreover, synthesized nano-catalyst successfully recovered five times without any considerable deficiency on its photocatalytic ability. Further, Moreover, we propose a novel method for cysteine detection based on the C3N4/Fe3O4@P2W15V3 nanocomposite. This nanocomposite displayed a privileged catalytic feature for cysteine oxidation to extend a clock reaction of methylene blue as an indicator in the presence of NaBH4 in acidic solution. More importantly, this colorimetric sensing method of cysteine presents an easy, low-cost, selective, and rapid colorimetric assay with a detection limit value of 7.2 µM in the acceptable linear range of 5-600 µM.

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. Afterwards, conformational factor (Pi) is calculated for the simulated system, which obtains the affinity of the aptamer residues to the target. A nucleotide exchange is done for the residue with the least Pi parameter to the nucleotide with the highest Pi value that results in a mutant aptamer. MD simulation is performed for the target-mutant complex, and Pi values are calculated again. The nucleotide exchange is performed similarly, and the designing process is proceeded repeatedly that results in a mutant with the improved specificity to the target. The aptamer affinity to the target is also determined in each step through calculating the binding Gibbs energy (ΔGBind) as a reliable parameter. The introduced strategy is utilized efficiently to design a mutant aptamer with improved specificity toward sulfadimethoxine (SDM) antibiotic as a case study. The great difference in the ΔGBind values about 579.856 kJ mol-1 highlights that the M5 mutant possesses the improved specificity toward SDM in comparison with the native aptamer. Besides, the selectivity of the M5 aptamer toward SDM is examined among some conventional interfering compounds by using MD simulation that confirms the applicability of the designed aptamer for further experimental studies.