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Vesicular glutamate transporters (VGLUTs) are essential components of synaptic transmission in the brain. Synaptic vesicles' luminal chloride and low pH regulate VGLUTs allosterically in a cooperative way. The luminal allosteric regulation of VGLUTs by chloride (Cl

In the present research, we performed a combination of detailed computational and spectroscopic methods to determine the effect of crystalline nanocellulose (CNC) on the structure and dynamics of human lysozyme (hLyz). Fluorescence spectroscopy revealed static quenching as the major mechanism in forming a stable CNC-hLyz complex, and the binding was energetically favorable. The obtained values of the thermodynamic parameters (∆G, ∆H, and ∆S) proposed that the complex formation between the enzyme and cellulose nanocrystals is driven by electrostatic interactions, which were also confirmed by molecular dynamics (MD) simulation. Additionally, the MD simulation analysis displays that the enzyme's structural elements and tertiary structure were primarily maintained, and only loops regions were affected in the presence of cellulose nanocrystals. At the same time, circular dichroism (CD) outcomes highlighted that higher cellulose nanocrystals concentration caused a reduction in the secondary structure of hLyz. Our observations proved that low cellulose nanocrystals concentrations have no considerable effect on the human lysozyme structure. The current research results provide a valuable opportunity to elucidate the molecular interactions between protein and nanocelluloses, guiding further investigations of CNC-based material for biomedical, pharmaceutical, and food industry applications.

Urea detection and elimination attracted great attention as a kind of representative toxin with the highest daily molar production for dialysis patients. Low molecular weight, high solubility, and low reactivity make it a challenge to absorb urea. Although there are different ways to for urea removal, there are some problems like causing side effects, being time-consuming, and wasting high amounts of absorbents. In the present research, urea adsorbents were prepared by synthesizing magnetic nanoparticles (Fe3O4 NPs) by co-precipitation method, functionalizing with SiO2 (Fe3O4@SiO2), and then modifying by surface imprinting poly (methyl methacrylate) with urea (MMIPs). The Fe3O4 and Fe3O4@SiO2 NPs were nearly spherical (5-20 nm in diameter) and in size. In 10 minutes, the MMIPs could absorb 50% of dialysate. The urea binding capacity of the system at the NP: Urea ratio of 0.5 and initial urea concentrations of 100 mg dL-1 were calculated at 1.06 mmol g-1. Under the control of a pseudo-first-order equation, the adsorption process was determined. The Freundlich isotherm model was fitted to the equilibrium adsorption data. These MMIPs are proposed as promising tools for urea removal in hemodialysis to reduce dialysis time and improve patient compliance with the therapy and also for dialysate regeneration.

Therapeutic proteins nowadays have increasingly been applied for their considerable potential in treating a wide variety of diseases. The effectiveness and potency of native therapeutic proteins are limited by various factors (e.g., stability, blood circulation time, specificity). Over the past years, a great deal of effort has been devoted to developing safe and efficient protein delivery systems. Entrapment of protein into polymeric and copolymeric matrices is common among the different types of protein-based drug formulation. However, despite the massive efforts toward developing therapeutic protein delivery in experimental studies and industrial applications, there is relatively little data on the influence of polymers and copolymers on therapeutic proteins at the atomic and molecular levels. Herein, molecular dynamics (MD) simulations are used to study the effects of biocompatible synthetic polymers including methoxy poly(ethylene glycol) (MPEG), poly(lactic acid) (PLA), and poly(lactic acid) copolymers (poly(lactic-co-glycolic acid)) PLGA and MPEG-PLA(PELA)) on the structure and dynamics of the human growth hormone (hGH), and the results are compared with previous experimental findings. Our results indicate that the hGH conformation remains stable both in pure water and in the presence of polymers, and these results are in good agreement with previous experimental data. It is shown that the MPEG chains are self-assembled and folded into a semicrystalline structure; therefore, only a small portion of the protein interacts with the polymer. The other three polymers, however, interact well with the protein and partially cover its surface. Our findings suggest that the use of these polymers for protein encapsulation has the advantage of reducing protein aggregation and thus increasing drug serum half-life. Eventually, we anticipate that the research results will expand the current knowledge about encapsulation mechanisms and the molecular interactions between hGH and the polymers.

Cucurbit[n]urils (CB[n], n = 5, 6, 7, 8, 10, 14) and their derivatives due to the hydrophobic cavities and polar carbonyl portals have been considerably explored for their potential uses as drug de...

In the last three decades, nanoclay fillers have been increasingly used to improve the mechanical, thermal, barrier and biological properties of the polymers. Nevertheless, incorporation of clays into the hydrophobic polymer matrices leads to the formation of the microcomposites with the minimal improvement in properties. To overcome the intrinsic incompatibility between the clays and the hydrophobic polymers, clay particles are organophilized using organic modifiers. The organic modifier should be thermodynamically miscible with the polymer. In the case of the composites prepared at high temperatures, the organic modifier should also have a high thermal stability to withstand the processing temperature. Taking into account these requisites, this study proposes a novel procedure for screening the diverse sets of the ionic liquids to find the most appropriate organic modifiers for compatibilization of the clays and any given hydrophobic polymers. The proposed procedure has been used to find the appropriate organic modifier to compatibilize montmorillonite clay (MMT) and polyetheretherketone (PEEK). Composites of PEEK filled with MMT and the organically modified MMT (OMMT) were synthesized via melt compounding. Then, they were characterized by FTIR, XRD and TEM. The results showed that the selected organic modifier satisfied both the processing requirements and the thermodynamic considerations and improved the dispersion of MMT particles within the PEEK matrix. The XRD patterns and TEM micrographs confirmed the formation of the PEEK/OMMT nanocomposite with intercalated/exfoliated morphology. The findings of this study provide a practical means for compatibilization of immiscible clays and polymers.

Paclitaxel (PTX) is a natural terpenoid compound that has been broadly studied for its antitumor activities and widely used as a chemotherapy medication. The treatment efficacy of PTX is affected by its low aqueous solubility, thus causing a subject of extensive research. In recent years, synthetic molecular containers such as cucurbit[n]urils (CB[n]s) and their derivatives have been significantly developing because of their remarkable ability to bind hydrophobic and cationic drugs. Recent experimental studies have shown that acyclic CB[n]-type containers (aCB[n]s), as new derivatives of the family of CB[n]s, increase the solubility of insoluble pharmaceuticals. However, the nature by which the drug interacts with carriers remains largely unknown. In this study, molecular docking and molecular dynamics (MD) simulation were performed to understand how CB[7] and aCB[4] nanocontainers interact with PTX which affect its aqueous solubility. The results clarify how the flexibility of containers is influenced by their structure and how this affects their interactions with PTX. Our results reveal that although both CB[7] and aCB[4] are capable of binding to PTX, the affinity to aCB[4] is higher than that of CB[7]. It has also been shown that the binding to both CB[7] and aCB[4] is probably an entropy-driven process. This research supports the potential use of the cucurbit[n]urils and their acyclic derivatives as drug delivery systems.

Chitosan and its derivatives used in drug delivery investigations could contribute to improving peptide and protein drug delivery systems. Herein, the molecular dynamics (MD) simulation approach was applied to evaluate the important driving factors of the human insulin encapsulation into the chitosan and cholesterol-modified chitosan polymers. The MD results revealed that the native conformation of insulin was stabilized by the chitosan polymers. In the present study, the effect of cholesterol moieties of modified chitosan was also examined and the results indicated that the cholesterol components would decrease the tendency of chitosan polymers to human insulin. Further analyses showed that the intermolecular interactions between the tyrosine, phenylalanine, and acidic residues are important in the formation of the insulin-polymer complexes. Another interesting finding was that the van der Waals, electrostatic, and CH-π interactions play key roles in the encapsulation process. Generally, in the case of human insulin, the MD simulation results would seem to suggest that the chitosan nanoparticles could be the more suitable carrier than the cholesterol-grafted chitosan nanoparticles.

Vascular endothelial growth factors (VEGFs) and their receptors (VEGFRs) are pivotal regulators of angiogenesis. The VEGF–VEGFR system is therefore an important target of anti-angiogenesis therapy. Based on the X-ray structure of VEGF-B/VEGFR-1 D2, we designed a cyclic peptide (known as VGB1) reproducing the α1 helix and its adjacent region to interfere with signaling through VEGFR-1. Unexpectedly, VGB1 bound VEGFR-2 in addition to VEGFR-1, leading to inhibition of VEGF-stimulated proliferation of human umbilical vein endothelial cells and 4T1 murine mammary carcinoma cells, which express VGEFR-1 and VEGFR-2, and U87 glioblastoma cells that mostly express VEGFR-2. VGB1 inhibited different aspects of angiogenesis, including proliferation, migration and tube formation of endothelial cells stimulated by VEGF-A through suppression of extracellular signal-regulated kinase 1/2 and AKT (Protein Kinase B) phosphorylation. In a murine 4T1 mammary carcinoma model, VGB1 caused regression of tumors without causing weight loss in association with impaired cell proliferation (decreased Ki67 expression) and angiogenesis (decreased CD31 and CD34 expression), and apoptosis induction (increased TUNEL staining and p53 expression, and decreased Bcl-2 expression). According to far-UV circular dichroism (CD) and molecular dynamic simulation data, VGB1 can adopt a helical structure. These results, for the first time, demonstrate that α1 helix region of VEGF-B recognizes both VEGFR-1 and VEGFR-2.

The major regulator of systemic iron homeostasis is controlled by human Hepcidin, which is a 25 amino acid cysteine-rich cationic antimicrobial peptide (HAMP) hormone, that was first identified in ...

The rusticyanin protein, a blue monomeric copper protein type-1, is one of the main components in the iron-electron transfer chain of the

Different bioinformatic methods apply various approaches to predict how much the effect of a SNP could be deleterious and therefore their results may differ significantly. However, variation studies often need to consider an integrated prediction result to analyze the effect of SNPs. To address this problem, we used an algorithm to map ordinal predictions to a numeral space and averaging them, and based on it we developed the ISNPranker web-tool ( http://isnpranker.semilab.ir/ ). It takes heterogonous outputs of different predictors and generates integrated numerical predictions and ranks SNPs based on them. Afterward, we used ISNPranker to identify the most deleterious coding SNPs (cSNPs) of the human aryl hydrocarbon receptor (AHR) gene. AHR is a ligand-activated transcription factor that governs many molecular and cellular mechanisms and cSNPs may affect its structure, interactions, and function. Forty validated cSNPs of AHR were initially analyzed using 16 publicly available SNP analyzers and the results were introduced to the ISNPranker and integrated predictions were obtained. The cSNPs were ranked in 34 levels of danger and rs200257782 in the ARNT dimerization domain (ADD121-289) of AHR was identified as the most deleterious cSNP. The rs148360742, which affect ADD40-79 and Hsp90 binding domain (HBD27-79) was in the second rank and the third and fourth ranks were occupied by ADD121-289-located variations rs571123681 and rs141667112 respectively. In conclusion, we introduced ISNPranker, which is a web-tool for integrative ranking of SNPs, and we showed that AHR structure and function may be highly sensitive to the cSNPs in the ARNT dimerization domain.

The rusticyanin protein, a blue monomeric copper protein type-1, is one of the main components in the iron-electron transfer chain of the Acidithiobacillus ferrooxidans, and is the product of the rus gene expression. Herein, first the bacterial DNA of Acidithiobacillus sp. FJ2 was extracted. Then, the rus gene sequence and the sequence amino acid rusticyanin protein were determined. The Met148Leu mutation increased the oxidase activity of the rusticyanin protein, thereby enhancing the efficiency of the bioleaching process by bacteria Acidithiobacillus ferroxidans. Met148Leu mutation was created in the rusticyanin protein, then molecular dynamics (MD) simulations and structural analysis were performed. The MD analysis of the wild-type and mutant protein demonstrated a slight instability in the mutant protein and significant instability in the active site of the mutant protein. The usefulness of this study is the genetic manipulation of the native Acidithiobacillus sp. FJ2 bacterium, which can boost the bioleaching efficiency of the bacterium to some extent, and investigating its effects on the structure of a mutant protein using computational methods. Communicated by Ramaswamy H. Sarma

Encapsulation of peptide and protein-based drugs in polymeric nanoparticles is one of the fundamental fields in controlled-release drug delivery systems. The molecular mechanisms of absorption of peptides to the polymeric nanoparticles are still unknown, and there is no precise molecular data on the encapsulation process of peptide and protein-based drugs. Herein, the self-assembly of different polymers and block copolymers with combinations of the various molecular weight of blocks and the effects of resultant polymer and copolymer nanomicelles on the stability of magainin2, an α-helical antimicrobial peptide, were investigated by means of all-atom molecular dynamics (MD) simulation. The micelle forming, morphology of micellar aggregations and changes in the first hydration shell of the micelles during micelles formation were explored as well. The results showed that the peptide binds to the polymer and copolymer micelles and never detaches during the MD simulation time. In general, all polymers and copolymers simultaneously encapsulated the peptide during micelles formation and had the ability to maintain the helical structure of the peptide, whereas the first hydration shell of the peptide remained unchanged. Among the micelles, the polyethylene glycol (PEG) micelles completely encapsulated magainin2 and, surprisingly, the NMR structure of the peptide was perfectly kept during the encapsulation process. The MD results also indicated that the aromatic and basic residues of the peptide strongly interact with polymers/copolymers and play important roles in the encapsulation mechanism. This research will provide a good opportunity in the design of polymer surfaces for drug delivery applications such as controlled-release peptide delivery systems.

The mycobacterial enzyme pyrazinamidase (PZase) is the target of key tuberculosis drug, pyrazinamide. Mutations in PZase cause drug resistance. Herein, three point mutations, W68G, L85P, and V155G, were investigated through over 8 µs of molecular dynamics simulations coupled with essential dynamics and binding pocket analysis at neutral (pH = 7) and acidic (pH = 4) ambient conditions. The 51-71 flap region exhibited drastic displacement leading to enlargement of binding cavity, especially at the lower pH. Accessibility of solvent to the active site of the mutant enzymes was also reduced. The protonation of key surface residues at low pH results in more contribution of these residues to structural stability and integrity of the enzyme and reduced interactions with solvent molecules, which acts as a cage, keeping the enzyme together. The observed results suggest a pattern of structural alterations due to point mutations in PZase, which is consistent with other experimental and theoretical investigations and, can be harnessed for drug design purposes.

The cationic antimicrobial peptide GF-17, a 17-mer-derived peptide from human cathelicidin LL-37, has a significant strength in the killing of the methicillin-resistant Staphylococcus aureus and Escherichia coli strains. Herein, we conducted a series of all-atom molecular dynamics simulations to investigate the ability of GF-17 in perturbing the model membranes of the gram-positive, S. aureus, and gram-negative, E. coli, bacteria. We also explored the contributions of the specific residues in the peptide activity. The molecular dynamics results indicated that the peptide is stabilized on the membrane surface and rapidly binds to the phosphate headgroups of the model membranes through the electrostatic interactions and hydrogen bonds. Furthermore, both polar and nonpolar interactions are energetically favored for the binding with the membrane surface. The research also revealed the important roles of the phenylalanine residues in the early insertion of the peptide into the bacterial model membranes. In addition, the results demonstrated that the central residues Arg23 and Lys25 played a critical role in the binding of GF-17 to both gram-negative and gram-positive model membranes, in excellent agreement with experimental studies. This study emphasizes on the pivotal role of basic residues in prompt association of the peptide on the model membrane surface and on the significance of residues Phe17, Ile24, Phe27, and Val32 in hydrophobic interactions. Therefore, our observations provide insights into the membrane-GF-17 interactions at atomic details that are useful to develop potent antimicrobial peptides targeting multidrug-resistant bacteria.

Endoglucanase Cel9A from Alicyclobacillus acidocaldarius (AaCel9A) has an Ig-like domain and the enzyme stability is dependent to calcium. In this study the effect of calcium on the structure and stability of the wild-type enzyme and the truncated form (the wild-type enzyme without Ig-like domain, AaCel9AΔN) was investigated. Fluorescence quenching results indicated that calcium increased and decreased the rigidity of the wild-type and truncated enzymes, respectively. RMSF results indicated that AaCel9A has two flexible regions (regions A and B) and deleting the Ig-like domain increased the truncated enzyme stability by decreasing the flexibility of region B probably through increasing the hydrogen bonds. Calcium contact map analysis showed that deleting the Ig-like domain decreased the calcium contacting residues and their calcium binding affinities, especially, in region B which has a role in calcium binding site in AaCel9A. Metal depletion and activity recovering as well as stability results showed that the structure and stability of the wild-type and truncated enzymes are completely dependent on and independent of calcium, respectively. Finally, one can conclude that the deletion of Ig-like domain makes AaCel9AΔN independent of calcium via decreasing the flexibility of region B through increasing the hydrogen bonds. This suggests a new role for the Ig-like domain which makes AaCel9A structure dependent on calcium.

Inside the cells, proteins are surrounded by mixtures of different osmolytes. However, our current understanding of the combinatorial effects of such mixtures on the stability of proteins remains elusive. In the present study, the stability and structure of recombinant pyrazinamidase (PZase) from Mycobacterium tuberculosis were analyzed in the presence of stabilizing osmolytes (sorbitol, sucrose and glycerol) and alcohols (methanol, ethanol, isopropanol and n-propanol). The far-UV and near-UV circular dichroism (CD), intrinsic fluorescence and thermostability results indicated that methanol, unexpectedly, has stronger effect on destabilization of the enzyme compared to ethanol which has larger log P. Interestingly, the relative half-life of PZase was longer in mixtures methanol with the osmolytes, sorbitol or sucrose (expectedly), or glycerol (unexpectedly), compared to other alcohols. Molecular dynamics simulation results showed that methanol increases the flexibility of region 5-40 and loop 51-71 in the PZase, which are potentially crucial for the stability and activity of the enzyme, respectively. Our results indicated that methanol can interact with PZase via hydrophobic interactions and hydrogen bonds, and therefore resulting in destabilization of the structure of the enzyme. In addition, glycerol probably increases the stability of the enzyme in methanol by disrupting the unfavorable hydrophobic interactions and hydrogen bonds.

Despite efforts to achieve a long-acting formulation for human growth hormone (hGH), daily injections are still prescribed for children with growth hormone deficiency. To grapple with the issue, acquiring a deep knowledge of the protein and understanding its interaction mechanism with the carrier can be beneficial. Herein, we designed and synthesized a novel chitosan-based copolymer and investigated its interaction with hGH using a combination of experimental and computational strategies. To construct the amphiphilic triblock copolymers (CDP), we grafted deoxycholic acid (DCA) and polyacrylic acid (PAA) onto the chitosan chains, and Fourier-transform infrared (FTIR) analysis confirmed the proper formation of CDP. Circular dichroism (CD) demonstrated the preservation of the secondary structure of hGH interacting with CDP, and, further, fluorescence spectroscopy proved the stability of the tertiary structure of the protein. Applying molecular dynamics simulation (MD), we examined the dynamics and integrity of hGH in the presence of the copolymer and compared its behavior with the protein in aquatic environments. Additionally, energy and contact analysis illustrated that the residues involved in the interaction were located predominantly in the connecting loops, and van der Waals (vdW) and electrostatic interactions were the main driving forces of the polymer-protein complex formation. This research's main aim was to trace the protein-polymer interaction's mechanism. We anticipate that the utility of the copolymer can address the challenges of fabricating a new sustained-release delivery platform for therapeutic proteins.

Laccase is a blue enzyme with a remarkable ability to eliminate environmental pollutants. The use of the eco-friendly enzyme for removing ecological contaminants is extensive. In addition, there are some restrictions like its deactivation in various environmental conditions. Researchers have applied many strategies to improve the Laccase stability in different conditions, but those ways are expensive or demanding. Herein, we used betaine, a co-solvent, to increase the enzyme stability in various temperatures and pHs as an appropriate alternative strategy to improve the Laccase stability. The experimental results showed that the enzyme's stability would increase in the presence of betaine at high temperatures. Although no significant changes were detected for the enzyme secondary structure contents, betaine at high temperatures exhibited a protective effect on the enzyme's alpha-helical contents. The simulation results indicated that betaine and ion molecules could be excluded from the enzyme surface and help Laccase maintain its stability and activity. Increasing the betaine concentration up to 0.5 M increased the Tm value of laccase. The molecular dynamics (MD) simulation results also demonstrated that the enzyme's polar amino acids play essential roles in making hydrogen bonds with betaine molecules. Lys377 was also recognized as the most critical residue for electrostatic interactions with the osmolyte at low and high temperatures. At the same time, the higher temperatures could not considerably affect the electrostatic interactions between the carboxyl group of betaine and the basic residues. The results indicated that the negatively charged amino acids could strengthen electrostatic interactions with betaine at high temperatures. The computational analyses also demonstrated that the hydrated state of betaine would not change even at high temperatures. This study's outcomes could be valuable to researchers who seek to use a more affordable approach to increase Laccase activity in severe environmental conditions.

Herein, ethanol's effect on the structure and dynamics of bovine serum albumin (BSA) and the nanoparticle formation was studied using united-atom and coarse-grained molecular dynamics (CG-MD) simulations. The results indicated that the BSA conformation remains stable both in pure water and ethanol/water environment. Molecular docking showed that ethanol-induced conformation changes do not reduce the drug loading. In the experimental approach, the prednisolone-loaded bovine serum albumin nanoparticles (PD-BSA NPs) were prepared using a desolvation technique. The nanoparticles were evaluated for nanocarrier production yield, particle size, shape, and surface morphology. The prepared BSA-NPs were then analyzed for their PD loading capacity, the adsorption profile, and in vitro release behavior. Our results showed the formation of spherical BSA-NPs of 200 nm average diameter and negative surface charge with a yield of 98%. The equilibrium isotherms of PD to BSA fitted to various models showed the best fit for the Langmuir model (R2 = 0.999). The kinetic data for prednisolone release from the BSA-NPs was slow (about 68% of the drug was released within 30 h) and followed the Gallagher-Corrigan equation (with R2 = 0.9957), which demonstrated the mechanism of Fickian diffusion and BSA-NPs matrix bulk erosion.

Non-viral vectors have attracted great interest, as they are simple to prepare, easy to modify and relatively safe, compared to viral vectors. Kidney-targeted gene delivery systems depict a promising technology to improve drug efficacy in renal diseases treatments. In order to develop a novel kidney-targeted gene delivery system, we synthesized polyamine-PEI conjugates using polymyxin B as ligand and investigated their potential targeting efficiency. After grafting either PEI25 kDa or PEI10 kDa with polymyxin B through amidation reaction, the modified-polymyxin-PEI/DNA-nanoplexes were produced via electrostatic attraction between the cationic polymers and EGFP plasmid. The properties of modified polymers including size, surface charge density, DNA condensation ability, buffering capacity and cytotoxicity were evaluated. Results revealed that the average size of -modified-polymyxin- PEI25kDa was about 143-180nm and modified-polymyxin-PEI10kDa 115-194nm. The zeta potentials were in the range of 16.4±1.87 to 23.43±1.25mV and 11.3±1.4 to 19.3±2.1mV for conjugates based on PEI25 and PEI10 respectively. The AFM images revealed that the complexes were spherical and nano-sized at C/P=4. The buffering capacity of both PEI 10 and 25kDa increased as the percentage of polymyxin B grafting increased. In vitro study demonstrated that modified-polymyxin-PEI conjugates could remarkably improve the gene transfection efficiency to kidney cells. The transfection efficiency of the polyplexes was dependent on the weight ratio of ligand in the formulation (~12 and 8 fold increase for PEI25 and PEI10kDa, respectively) and was significantly higher than that of unmodified PEIs/DNA nanoparticles. These results suggest that modified-polymyxin-PEI /DNA nanoparticles can effectively target megalin-expressing kidney cells and show improved transfection efficiency and low cytotoxicity in In vitro and In vivo studies. Animal studies confirmed the in vivo study. Thus, these conjugates can be considered as a safe and efficient non-viral therapeutic therapy vector for kidney diseases.

Herein, we investigated the effect of the chitosan nanoparticles (CsNP) on the structure, dynamics, and activity of trypsin. The enzyme activity in complex with the nanoparticles slightly increased, which represents the interactions between the nanoparticles and the enzyme. The kinetic parameters of the enzyme, Km and kcat, increased after adding the nanoparticles, resulting in a slight increase in the catalytic efficiency (kcat/Km). However, the effect of the nanoparticles on the kinetic stability of trypsin has not exhibited significant variations. Fluorescence spectroscopy did not show remarkable changes in the trypsin conformation in the presence of the nanoparticles. The circular dichroism (CD) spectroscopy results also revealed the secondary structure of trypsin attached to the nanoparticles slightly changed. Furthermore, we used molecular dynamics (MD) simulation to find more information about the interaction mechanisms between the nanoparticles and trypsin. The root mean square deviation (RMSD) of Cα atoms results have shown that in the presence of the nanoparticles, trypsin was stable. The simulation and the calculation of the binding free energy demonstrate that the nonpolar interactions are the most important forces for the formation of stable nanoparticle-trypsin complex. This study has explicitly elucidated that the nanoparticles have not considerable effect on the trypsin.

Aryl hydrocarbon receptor (AHR) is responsible for crucial events in male reproductive biology. Here, the association of the AHR transitions c.-742C>T and c.1661G>A with idiopathic male infertility was investigated in a case-control study, which is followed by a meta-analysis and a bioinformatic investigation. Blood and semen samples were obtained from a total of 135 idiopathic infertile men and 130 healthy controls. Participants were genotyped for the transitions using a PCR-RFLP method. A meta-analysis of five sets of data evaluated the association of c.1661G>A with male infertility, and using an in silico analysis, the possible molecular effects of the transitions predicted. Genotypes and alleles of AHR-c.-742C>T and c.1661G>A polymorphisms were not associated with the risk of male infertility significantly. However, the frequency of C/A haplotype was significantly associated with the increased risk of male infertility, and T/A haplotype was higher among controls significantly. Also, the frequencies of combined genotypes CT/GG, CT/GA and TT/GG were significantly associated with decreased risk of infertility. And, the meta-analysis showed that the AA versus GA/GG recessive model is associated with decreased risk of male infertility among the Iranian population. In silico analysis predicted that c.-742C>T does not alter the binding sites of the proposed transcription factors, but c.1661G>A poses a tolerable structural disturbance in AHR protein. In conclusion, these results showed that AHR c.-742C>T and c.1661G>A transitions separately could not be nominated as a risk or protective factor for male infertility. However, some combined models could affect infertility risk, especially among Iranian men.

Interactions of carbon nanotubes (CNTs) and blood proteins are of interest for nanotoxicology and nanomedicine. It is believed that the interactions of blood proteins and glycoproteins with CNTs may have important biological effects. In spite of many experimental studies of single-walled carbon nanotubes (SWCNT) and glycoproteins with different methods, little is known about the atomistic details of their association process or of structural alterations occurring in adsorbed glycoproteins. In this study, we have applied molecular dynamics simulation to investigate the interaction of follicle stimulating hormone (hFSH) with SWCNT. The aim of this work is to investigate possible mechanisms of nanotoxicity at a molecular level. We present details of the molecular dynamics, structure, and free energy of binding of hFSH on the surface of SWCNT. We find that hFSH in aqueous solution strongly adsorbs onto SWCNT via their concave surface as evidenced by high binding free energies for residues in both protein subunits. It was found that hydrophobic, π-cation, and π-π stacking interactions are the main driving forces for the adsorption of the protein at the nanotube surface.

Pleurocidin, a 25-residue cationic peptide, has antimicrobial activity against bacteria and fungi but exhibits very low hemolytic activity against human red blood cells (RBC). The peptide inserts into the bacterial membrane and causes the membrane to become permeable by either toroidal or carpet mechanism. Herein, to investigate the molecular basis for membrane selectivity of Pleurocidin, the interaction of the peptide with the different membrane models including the RBC, DOPC, DOPC/DOPG (3:1), POPE/POPG (3:1), and POPE/POPG (1:3) bilayers were studied by performing all-atom molecular dynamics (MD) simulation. The MD results indicated that the peptide interacted weakly with the neutral phospholipid bilayers (DOPC), whereas it made strong interactions with the negatively charged phospholipids. Pleurocidin maintained its α-helical structure during interactions with the anionic model membranes, but the peptide lost its secondary structure adjacent to the neutral model membranes. The results also revealed that the Trp-2, Phe-5, and Phe-6 residues, located in the N-terminal region of the peptide, played major roles in the insertion of the peptide into the model membranes. In addition, the peptide deeply inserted into the DOPC/DOPG membrane. The order analysis showed that Pleurocidin affected the order of anionic phospholipids more than zwitterionic phospholipids. The cholesterol molecules help the RBC membrane conserve integrity in response to Pleurocidin. This research has provided data on the Pleurocidin-membrane interactions and the reasons of resistance of eukaryotic membrane to the Pleurocidin at atomic details that are useful to develop potent AMPs targeting multidrug-resistant bacteria.

Among different nanomaterials, dendrimers stand out because of their inherent broad range of activity against viruses, bacteria, and cancer cells. Herein, a total of 15 molecular systems have been simulated to characterize the structural features and geometry of low generation polyamidoamine (PAMAM) dendrimers (G0-G2) after they attached to various membranes (1,2-dipalmitoyl-sn-glycero-3-phosphocholine (DPPC) and 1,2-dipalmitoyl-sn-glycero-3-phosphocholine (DPPC)/1,2-dipalmitoyl-sn-glycero-3-phosphorylglycerol (DPPG) with a different ratio of cholesterol (CHL) to explain their membrane activity in cancer cells. The results indicated that the local membrane order parameters were increased in membranes containing 20 and 40 mol% cholesterol molecules. Furthermore, the PAMAM dendrimers were able to make a substantial number of holes in the membranes containing cholesterol. The results also showed that hydrogen bonds, and electrostatic interactions, govern the interactions between the PAMAM dendrimers and the membranes. Neutral bilayers could drive back the PAMAM dendrimers from the bilayer surface, whereas phosphatidylcholine (PC) bilayers mixed with phosphatidylglycerol (PG) phospholipids (as mimics of negatively charged cancer cell membranes) bond firmly to the hyperbranched polymers. Moreover, the negatively charged phospholipids crowded in regions where dendrimers interacted with membranes. This investigation provided an explanation and mechanistic insight for the activity of PAMAM dendrimers against the negatively charged cancer cells.

Structural modification of curcumin represents a strategy to improve its stability, water solubility, pharmaceutical properties and bioactivity. In this context, numerous structural analogues of curcumin, including curcuminoids, have been developed. In this paper, the precise density functional theory computations were used for investigating the electronic and geometrical structure of curcumin and some of its derivatives. The chemical activity of the considered molecules was investigated with the help of the global softness and hardness concepts. Among the studied molecules, bisdemethoxycurcumin had the most chemical activity and hexahydrocurcumin had the most stable structure. Among two isomers of the curcumin, the enol isomer was found to be active.

Aryl hydrocarbon receptor (AhR) acts as an enhancer binding ligand-activated intracellular receptor. Chromatin remodeling components and general transcription factors such as TATA-binding protein (TBP) are evoked on AhR-target genes by interaction with its flexible transactivation domain (TAD). AhR-G1661A single nucleotide polymorphism (SNP: rs2066853) causes an arginine to lysine substitution in the acidic sub-domain of TAD at position 554 (R554K). Although, numerous studies associate the SNP with some abnormalities such as cancer, other reliable investigations refuse the associations. Consequently, the interpretation of the phenotypic results of G1661A-transition has been controversial. In this study, an in silico analysis were performed to investigate the possible effects of the transition on AhR-mRNA, protein structure, interaction properties and modifications. The analysis revealed that the R554K substitution affects secondary structure and solvent accessibility of adjacent residues. Also, it causes to decreasing of the AhR stability; altering the hydropathy features of the local sequence and changing the pattern of the residues at the binding site of the TAD-acidic sub-domain. Generating of new sites for ubiquitination and acetylation for AhR-K554 variant respectively at positions 544 and 560 was predicted. Our findings intensify the idea that the AhR-G1661A transition may affects AhR-TAD interactions, especially with the TBP, which influence AhR-target genes expression. However, the previously reported flexibility of the modular TAD could act as an intervening factor, moderate the SNP effects and causes distinct outcomes in different individuals and tissues.

Herein, we performed meticulous experimental and computational studies to explore the stability, activity, and dynamics of laccase in the presence of various organic and inorganic solvents. It is well known that laccases are eco-friendly enzymes, which can quickly eliminate recalcitrant chemicals from contaminated media. We determined the Asp96 (COO−)---Arg43 (N-H2), Asp131 (COO−)---Arg197(N-H1), Asp138(COO−)---Arg195 (N-H2), Asp140(COO−)---Arg199(N-H2), Asp214(COO−)---Arg260(N-H2), Asp224(COO−)---Arg423(N-H2), Asp424(COO−)---Arg243(N-H1), Asp424(COO−)---Arg243(N-H2), Glu288(COO−)---Arg176(N-H1) and Glu288(COO−)---Arg176(N-H2) salt bridges as the crucial ones in maintaining the structural integrity of laccase. Furthermore, the fluorescence, circular dichroism (CD) spectroscopies, and molecular dynamics simulation outcomes highlighted that the secondary structure elements and tertiary structure of the enzyme did not change significantly in the presence of both selected organic (ethanol and hexane) and inorganic (1-Butyl-3-methylimidazolium hexafluorophosphate ([BMIM][PF6]) co-solvents. The obtained experimental results demonstrated that the enzyme was more stable in the hexane and aqueous ionic liquid solutions than in the ethanol solution. Additionally, laccase exhibited more activity in the presence of the hexane and aqueous ionic liquid solutions. Probably due to more accessibility of the substrate to the active site of laccase. Interestingly, the activity of laccase in the presence of the co-solvents was in decreasing order of hexane

To investigate the molecular interactions of sodium dodecyl sulfate (SDS) with human ubiquitin and its unfolding mechanisms, a comparative study was conducted on the interactions of the protein in the presence and absence of SDS at different temperatures using six independent 500 ns atomistic molecular dynamics (MD) simulations. Moreover, the effects of partial atomic charges on SDS aggregation and micellar structures were investigated at high SDS concentrations. The results demonstrated that human ubiquitin retains its native-like structure in the presence of SDS and pure water at 300 K, while the conformation adopts an unfolded state at a high temperature. In addition, it was found that both SDS self-assembly and the conformation of the resulting protein may have a significant effect of reducing the partial atomic charges. The simulations at 370 K provided evidence that the SDS molecules disrupted the first hydration shell and expanded the hydrophobic core of ubiquitin, resulting in complete protein unfolding. According to these results, SDS and temperature are both required to induce a completely unfolded state under ambient conditions. We believe that these findings could be useful in protein folding/unfolding studies and structural biology.

With regard to high reactivity and chemoselectivity of HYNIC towards carbonyl of acyclic form of 18FDG and its stable complexes with 99mTc, in this study, LIKKPF as the model peptide was conjugated with HYNIC and labelled with 99mTc (RCP >90 %) and 18FDG for the first time. The RCP of >70 % was achieved for labelling with 18FDG, in the presence of glucose (50–250 μg/mL). Our results showed the high potential of HYNIC conjugated peptides for labelling with 99mTc and 18FDG as 18F-fluorinated prosthetic group, to be clinically accepted for the radiolabelling of peptides.

The effect of glycerol and sorbitol on the stability of porcine pancreas trypsin was investigated in this work. Molecular dynamics simulation and thermostability results showed that trypsin has two flexible regions, and polyols (sorbitol and glycerol) stabilize the enzyme by decreasing the flexibility of these regions. Radial distribution function results exhibited that sorbitol and glycerol were excluded from the first water layer of the enzyme, therefore decrease the flexibility of the regions by preferential exclusion. Also, results showed that the stabilization effect of sorbitol is more than glycerol. This observation could be because of the larger decrease in the fluctuations of trypsin in the presence of sorbitol. We also examined the role of solvent's hydrophobicity in enzyme stabilization by sorbitol and glycerol. To do so, the thermostability of trypsin was evaluated in the presence of solvents with different hydrophobicity (methanol, ethanol, isopropanol and n-propanol) in addition to the polyols. Our results depicted that glycerol is a better stabilizer than sorbitol in the presence of hydrophobic solvents (n-propanol), whereas sorbitol is a better stabilizer than glycerol in the presence of hydrophilic solvents (methanol).

Chitosan (CHS) and chitin (CHT) biopolymers have found many applications in the field of controlled-release drug delivery systems. Herein, molecular dynamics (MD) simulation and binding free energy calculations were used to investigate the potentials of CHS and CHT polymers for the controlled release of follicle-stimulating hormone (FSH). The results indicated that FSH conformation did not change in the presence of CHS and CHT. In addition, FSH-polymer interactions caused stability of the 310-helix structure of the alpha subunits of FSH (FSHα). Both the biopolymers interacted with the protein mainly through the hydrophobic forces. CHS has more affinity for FSH when compared with CHT. Furthermore, in both systems, the affinity of polymers for FSHα was more than that for beta subunits of FSH (FSHβ). The results suggested that the polysaccharides might improve the controlled-release FSH delivery.