This document summarizes a molecular dynamics simulation study of the HYD1 protein from Gibberella moniliformis. The study had four stages: 1) energy minimization to remove clashes, 2) equilibration involving NVT and NPT ensembles, 3) a 5 nanosecond production molecular dynamics simulation, and 4) analysis of the simulation results. Key results included the HYD1 protein remaining stable with a RMSD of around 0.2 nm, greater flexibility at the C-terminal tail, and validation that the simulation reached equilibrium and the correct density. The study provides insight into HYD1's dynamic behavior and stability to better understand its self-assembly mechanism.
Estimating the Biodegradation Kinetics by Mixed Culture Degrading Pyrene (Pyr)AZOJETE UNIMAID
This document discusses the biodegradation kinetics of pyrene (Pyr) degradation by a mixed culture. Experiments were conducted to determine the optimal temperature, pH, and Pyr concentrations for degradation. Kinetics experiments were then carried out at 30°C and pH 7 using initial Pyr concentrations ranging from 10-700 ppm. The results showed Pyr concentrations between 100-700 ppm inhibited the mixed culture. Concentrations between 10-100 ppm did not inhibit growth. A first-order rate constant model best described the degradation kinetics, with the highest rate (0.0487 mg/Lh) at 20 ppm Pyr. On average, the mixed culture could degrade over 0.0696 p
This document reports on a study investigating the influence of sodium carboxymethylcellulose (NaCMC) on the aggregation behavior of aqueous solutions of 1-hexadecyl-3-methylimidazolium chloride (C16MeImCl), a cationic surface active ionic liquid (SAIL). Electrical conductivity and surface tension measurements were used to study C16MeImCl aggregation in the presence of NaCMC. Two characteristic concentrations were identified before free C16MeImCl micelles form: the critical aggregation concentration and the polymer saturation concentration. The effects of temperature, NaCMC concentration, and NaCMC charge density on C16MeImCl self-aggregation were analyzed. Thermodynamic parameters of C16MeImCl mic
Polymeric composite membranes for temperature and pH-responsive delivery of d...Nanomedicine Journal (NMJ)
Abstract
Objective(s):
Nowadays hydrogels are one of the upcoming classes of polymer-based controlled-release drug delivery systems. Temperature and pH-responsive delivery systems have drawn much attention because some diseases reveal themselves by a change in temperature and/or pH. The objective of this work is to prepare and characterize composite membrane using responsive nanoparticles into a polymer matrix.
Materials and Methods:
These nanoparticles were made of the copolymer poly (N-isopropylacrylamide-co-methaçrylic acid) by an aqueous dispersion polymerization process and are responsible for dual sensitivity to temperature and pH. Morphology study with SEM, swelling behavior with Dynamic Light Scattering Technique, in vitro drug release behavior with side-by-side Diffusion Cells were also investigated in this paper. Doxorubicin hydrochloride was used as a model solute.
Results:
The study on the release of doxorubicin hydrochloride showed that the release rate was higher at pH 5 than pH 7.4, increased with the increase of temperature. Nevertheless, ionic strength only poses a minor direct effect at higher pH.
Conclusion:
Such system may be potentially used as a tumor-targeting doxorubicin hydrochloride delivery in the body.
This document describes a study investigating the cancer targeting potential of docetaxel (DTX) loaded onto multi-walled carbon nanotubes (MWCNTs) conjugated with folic acid (FA) and poly(ethylene glycol) (PEG). DTX was loaded onto both FA-PEG-conjugated MWCNTs (DTX/FA-PEG-MWCNTs) and plain MWCNTs (DTX/MWCNTs). In vitro studies showed the DTX/FA-PEG-MWCNTs had higher cytotoxicity against MCF-7 breast cancer cells and arrested cells in the G2 phase more than DTX/MWCNTs or free drug. Pharmacokinetic studies in mice
This document summarizes a study on the self-assembly and stability of stealth liposomes. Stealth liposomes were prepared using DPPC and DPPE-PEG 3000 and characterized using light scattering techniques. The incorporation of 10% PEGylated lipid led to smaller liposomes around 36 nm. Stealth liposomes were stable upon heating up to 50°C. Indomethacin-loaded stealth liposomes were also prepared and characterized, with drug incorporation efficiencies around 14%. The physicochemical properties of the stealth liposomes were stable for over two weeks.
The document describes research on developing doxorubicin-loaded, folic acid-conjugated multi-walled carbon nanotubes (DOX/FA-MWCNTs) for targeted cancer treatment. The nanotubes were engineered through purification, oxidation, and functionalization processes. Doxorubicin was loaded onto the nanotubes through pi-pi stacking interactions. In vitro studies found the DOX/FA-MWCNTs had high drug loading efficiency, controlled release, and preferential uptake by cancer cells. In vivo studies in tumor-bearing rats showed the DOX/FA-MWCNTs improved pharmacokinetics, biodistribution to tumors, and increased survival time compared to free doxorubicin
This document summarizes an article that appeared in a journal published by Elsevier. The attached copy is provided to the author for non-commercial research and education purposes, including instruction and sharing with colleagues. Other uses such as reproduction, distribution, selling, licensing or posting to third party websites are prohibited. Authors are allowed to post their version of the article to their personal or institutional websites or repositories, with some restrictions. The document provides a link to Elsevier's policies on author rights.
This document summarizes research on synthesizing polyiodopyrazoles that could have applications as agent defeat weapons. Thirteen polyiodopyrazoles were synthesized using an electrophilic iodination reaction. Calculations showed the compounds have low detonation velocities and pressures and would produce iodine and hydroiodic acid upon detonation, making them potential bioagent defeat agents. The synthesis method allows up to nine iodine atoms to be introduced in a single molecule. These stable, non-sublimating polyiodopyrazoles may not only serve as agent defeat weapons but also have uses in medicine, materials science, and organic chemistry.
Estimating the Biodegradation Kinetics by Mixed Culture Degrading Pyrene (Pyr)AZOJETE UNIMAID
This document discusses the biodegradation kinetics of pyrene (Pyr) degradation by a mixed culture. Experiments were conducted to determine the optimal temperature, pH, and Pyr concentrations for degradation. Kinetics experiments were then carried out at 30°C and pH 7 using initial Pyr concentrations ranging from 10-700 ppm. The results showed Pyr concentrations between 100-700 ppm inhibited the mixed culture. Concentrations between 10-100 ppm did not inhibit growth. A first-order rate constant model best described the degradation kinetics, with the highest rate (0.0487 mg/Lh) at 20 ppm Pyr. On average, the mixed culture could degrade over 0.0696 p
This document reports on a study investigating the influence of sodium carboxymethylcellulose (NaCMC) on the aggregation behavior of aqueous solutions of 1-hexadecyl-3-methylimidazolium chloride (C16MeImCl), a cationic surface active ionic liquid (SAIL). Electrical conductivity and surface tension measurements were used to study C16MeImCl aggregation in the presence of NaCMC. Two characteristic concentrations were identified before free C16MeImCl micelles form: the critical aggregation concentration and the polymer saturation concentration. The effects of temperature, NaCMC concentration, and NaCMC charge density on C16MeImCl self-aggregation were analyzed. Thermodynamic parameters of C16MeImCl mic
Polymeric composite membranes for temperature and pH-responsive delivery of d...Nanomedicine Journal (NMJ)
Abstract
Objective(s):
Nowadays hydrogels are one of the upcoming classes of polymer-based controlled-release drug delivery systems. Temperature and pH-responsive delivery systems have drawn much attention because some diseases reveal themselves by a change in temperature and/or pH. The objective of this work is to prepare and characterize composite membrane using responsive nanoparticles into a polymer matrix.
Materials and Methods:
These nanoparticles were made of the copolymer poly (N-isopropylacrylamide-co-methaçrylic acid) by an aqueous dispersion polymerization process and are responsible for dual sensitivity to temperature and pH. Morphology study with SEM, swelling behavior with Dynamic Light Scattering Technique, in vitro drug release behavior with side-by-side Diffusion Cells were also investigated in this paper. Doxorubicin hydrochloride was used as a model solute.
Results:
The study on the release of doxorubicin hydrochloride showed that the release rate was higher at pH 5 than pH 7.4, increased with the increase of temperature. Nevertheless, ionic strength only poses a minor direct effect at higher pH.
Conclusion:
Such system may be potentially used as a tumor-targeting doxorubicin hydrochloride delivery in the body.
This document describes a study investigating the cancer targeting potential of docetaxel (DTX) loaded onto multi-walled carbon nanotubes (MWCNTs) conjugated with folic acid (FA) and poly(ethylene glycol) (PEG). DTX was loaded onto both FA-PEG-conjugated MWCNTs (DTX/FA-PEG-MWCNTs) and plain MWCNTs (DTX/MWCNTs). In vitro studies showed the DTX/FA-PEG-MWCNTs had higher cytotoxicity against MCF-7 breast cancer cells and arrested cells in the G2 phase more than DTX/MWCNTs or free drug. Pharmacokinetic studies in mice
This document summarizes a study on the self-assembly and stability of stealth liposomes. Stealth liposomes were prepared using DPPC and DPPE-PEG 3000 and characterized using light scattering techniques. The incorporation of 10% PEGylated lipid led to smaller liposomes around 36 nm. Stealth liposomes were stable upon heating up to 50°C. Indomethacin-loaded stealth liposomes were also prepared and characterized, with drug incorporation efficiencies around 14%. The physicochemical properties of the stealth liposomes were stable for over two weeks.
The document describes research on developing doxorubicin-loaded, folic acid-conjugated multi-walled carbon nanotubes (DOX/FA-MWCNTs) for targeted cancer treatment. The nanotubes were engineered through purification, oxidation, and functionalization processes. Doxorubicin was loaded onto the nanotubes through pi-pi stacking interactions. In vitro studies found the DOX/FA-MWCNTs had high drug loading efficiency, controlled release, and preferential uptake by cancer cells. In vivo studies in tumor-bearing rats showed the DOX/FA-MWCNTs improved pharmacokinetics, biodistribution to tumors, and increased survival time compared to free doxorubicin
This document summarizes an article that appeared in a journal published by Elsevier. The attached copy is provided to the author for non-commercial research and education purposes, including instruction and sharing with colleagues. Other uses such as reproduction, distribution, selling, licensing or posting to third party websites are prohibited. Authors are allowed to post their version of the article to their personal or institutional websites or repositories, with some restrictions. The document provides a link to Elsevier's policies on author rights.
This document summarizes research on synthesizing polyiodopyrazoles that could have applications as agent defeat weapons. Thirteen polyiodopyrazoles were synthesized using an electrophilic iodination reaction. Calculations showed the compounds have low detonation velocities and pressures and would produce iodine and hydroiodic acid upon detonation, making them potential bioagent defeat agents. The synthesis method allows up to nine iodine atoms to be introduced in a single molecule. These stable, non-sublimating polyiodopyrazoles may not only serve as agent defeat weapons but also have uses in medicine, materials science, and organic chemistry.
Physical and Structural Characterization of Biofield Treated Imidazole Deriva...albertdivis
The Aim of present study was to evaluate the impact of biofield treatment on two imidazole derivatives (i.e., imidazole and 2-methylimidazole) by various analytical methods.
COMPARISON FREE ENERGY BINDING SITES NEURAMINIDASEijabjournal
Neuraminidase (NA) is the essential surface glycoprotein of the influenza virus. High- affinity neuraminidase inhibitors have been designed that interact only with the conserved active site and binding site residues. The neuraminidase (NA) of influenza virus is the target of anti – flu drug.for treatment of this
disease a thorough knowledge of neuraminidase protein is essential in order to produce potent drugs to suppress this enzyme..Drug design is by QSAR and docking methods, so we need a complete knowledge of receptor ligand, target site and binding site. This paper, using bioinformatics, Molecular Dynamics, Monte carlo and studied binding site NA enzyme in 310K temperature and different dielectrics (1, 78.39 and
32.63) for the best drug designing. We measured the potential energy of amino acids binding to the drug.Molecular Mechanics, Molecular Dynamic and Nanobiological have done a great assistance in drug designing.
Structural characterization and cytotoxicity studies of ruthenium(ii)–dmso–ch...rkkoiri
This document describes the structural characterization and cytotoxicity studies of two new ruthenium(II) complexes containing chalcone and flavone ligands. Single crystal X-ray diffraction was used to determine the crystal structures of the two complexes, which were found to self-associate through non-covalent interactions into one-dimensional and two-dimensional supramolecular structures. The cytotoxicity of the complexes was evaluated using MTT assays on Dalton's Lymphoma cell lines, with the complexes exhibiting cytotoxic properties.
A Novel Polymeric Prodrugs Synthesized by Mechanochemical Solid-State Copolym...inventionjournals
:We developed the novel polymeric prodrugs synthesized by mechanochemical solid-state copolymerization of glucose-based polysaccharides (dextran orglycogen) and the methacryloyloxy derivative of 5-fluorouracil (5-FU). The copolymerization proceededreadily and each polymeric prodrug was quantitatively obtained within8 h reaction. The number average molecular weight (Mn) and polydispersity (H) of the polymeric prodrug synthesized from dextran was 24,000 g/mol and 5.10, respectively. The number average particle diameter of the polymeric prodrug derived from glycogen was 14.9 nm. The hydrolysis profiles of the polymeric prodrug synthesized from dextranapparently followed the first-order kinetics, and 100% drug release was observed under the experimental condition used. The polymeric prodrug derived from glycogen also continued to release 5-FU at the first-order rate up to 5 h, followed by its rate constant decreased gradually. These results suggest that lower accessibility of water molecules for the synthetic polymer chains inside the glycogen particle might cause the gradual decrease of drug release rate.
Stabilization or solidification of iron ore mine tailings using cementeSAT Journals
Abstract Current research emphasis is more on the utilization of materials that are considered as waste. Tailings and fly ash are major category of industrial wastes, whose disposal is problematic from environmental point of view. In this present research, Industrial byproducts, namely, lime (CaO) and class F type fly ash have been used as candidate materials along with the partial addition of ordinary Portland cement (OPC) in the Stabilization/solidification (S/S) of polymetallic iron ore mine tailings (TM). The effectiveness of S/S was assessed by comparing laboratory experimental values obtained from unconfined compressive strength (UCS), hydraulic conductivity and leaching propensity tests of S/S samples with regulatory standards for safe surface disposal of such wastes. Some S/S cured matrices were found unable to provide the required immobilization of pollutants. S/S and 28 days cured mine tailing specimens made with composite binders containing TM/10/0/0, TM/5/0/20, TM/10/0/40 and TM/0/10/40 significantly impaired the solubility of all contaminants investigated and proved successful in fixing metals within the matrix, in addition to achieving adequate UCS and hydraulic conductivity values, thus satisfying regulatory norms (U.S. EPA). Laboratory investigations revealed the TM blends (stabilized materials) were non-hazardous. The test results of this study are encouraging and it may be possible to undertake large-scale fill construction with stabilized tailing material that is sustainable and cost effective. Keywords: Tailing materials, Laboratory study, Compaction characteristics, unconfined compressive strength, Hydraulic conductivity, Heavy metal content.
J. Bukowczan - Various methods for one pot synthesis of triazoles from quinol...Jerzy_BN
This document describes various methods for synthesizing 1,2,3-triazoles from 4-amino-3-quinolinesulfonamides with a propargyl group. It discusses four reaction methods tried: (1) copper-catalyzed azide-alkyne cycloaddition, (2) phase transfer catalysis, (3) a two-step synthesis using an organic azide, and (4) a catalyst-free reaction in water. The copper-catalyzed and two-step methods produced the best yields of up to 99% and 82%, respectively. Thirteen new compounds were obtained and will be tested for potential anti-cancer activity, as the triazole, quin
A Semi-empirical based QSAR study of indole휷- Diketo acid, Diketo acid and Ca...iosrjce
In this study, a set of novel synthesized indole훽- diketo acid, diketo acid and carboxamide
derivativeswas investigated by quantitative structure–activity relationship (QSAR) analysis using semiempirical
(PM3) based descriptors. The best molecular descriptors identified were LogP, polar area
corresponding to absolute values of electrostatic potential greater than 75 (P-area(75)), Energy (E), Minimum
values of electrostatic potential (as mapped onto an electron density surface) (MinEIPot), Polar surface area
and Maximum values of electrostatic potential (as mapped onto an electron density surface) (MaxEIPot) that
contributed to the anti-HIV activity of the indole훽- diketo acid, diketo acid and carboxamide derivatives as
independent factors. The correlation of these descriptors with their anti-HIV activity increases indicating their
importance in studying biological activity. Quantitative structure activity relationship (QSAR) analysis was
applied to 37 of the above mentioned derivatives using physicochemical and structural molecular descriptors
obtained by the semi-empirical method by employing PM3 basis set. By using the multiple linear regression
(MLR) technique several QSAR models have been drown up with the help these calculated descriptors and the
anti-HIV activity of indole훽- diketo acid, diketo acid and carboxamide derivatives. The regression method was
used to derive the most significant models as a calibration model for predicting the LogIC50 of this class of
compounds. Among the obtained QSAR models presented in the study from the MLR method, statistically the
most significant one is the last model with the squared correlation coefficient 0.8932, Q = 3.1854 and F=
27.8644 that could be useful to predict the biological activity of indole훽- diketo acid, diketo acid and carboxamide derivatives as Potent HIV-1 Drugs.
This document summarizes an investigation into using lysine-functionalized dendrimers as potential detoxification agents for the organophosphate pesticide dichlorvos. Zeroth-, first-, and second-generation polyester dendrimers were synthesized with exactly 4, 8, and 16 lysine groups respectively on their periphery. The dendrimers were found to be water-soluble and showed low toxicity to cell lines. They were also able to efficiently capture dichlorvos, demonstrating their potential as antidotes to maintain acetylcholinesterase activity in cases of organophosphate poisoning.
GFS Chemicals Organic Catalog - Building BlocksLiza Tallon
This document provides information about ordering from GFS Chemicals, including their contact information and methods for placing orders. It also summarizes some of their product offerings, including Grignard reagents, anhydrous cerous chloride, anhydrous lithium perchlorate, and expertise in liquid ammonia chemistries and acetylenic/olefinic specialties from acquiring the Farchan product line. Their goal is to be a full-service partner in developing reagents and catalysts to help customers leverage their chemical development and processing.
This document discusses a study on mixed-linker zeolitic imidazolate frameworks (ZIFs) containing two types of imidazole linkers. The researchers show that these mixed-linker ZIFs have tunable properties including pore size, hydrophilicity, and organophilicity. They synthesized a series of ZIF-8x-90100-x materials with different ratios of two linkers, resulting in a wide range of crystal sizes from 338 nm to 120 μm. Using various characterization and measurement techniques, they demonstrate that properties like hydrocarbon and alcohol diffusion can be continuously tuned over 2-3 orders of magnitude by varying the mixed-linker composition. This tunability allows mixed-linker ZIFs to
Enrichment of microorganisms by sugar cane molasses for polyehtylene degradationeSAT Publishing House
This document summarizes a study that enriched the growth of microorganisms using sugar cane molasses to degrade polyethylene films. Microorganisms were isolated from soil and grown in media containing different concentrations of molasses. Polyethylene strips were added and incubated for 6 months. Fourier transform infrared spectroscopy analysis showed new peaks and changes in peak intensities in treated films, indicating biodegradation. Higher molasses concentrations (above 2.5%) supported more efficient polyethylene degradation by microorganisms.
This document describes the synthesis, spectral characterization, and biological screening of transition metal complexes of the ligand 2-(5-mercapto-1,3,4-oxadiazol-2-yl)phenol. A series of complexes were prepared using Cu(II), Co(II), Ni(II), and Zn(II) and characterized using analytical data, magnetic susceptibility, IR, UV-Vis, 1H NMR, 13C NMR, EPR, and other techniques. Spectral data suggest an octahedral geometry around the metal ion. Biological screening showed the complexes have antibacterial, antifungal, and DNA cleavage activities.
Investigation of structural, kinetic and thermodynamic properties of proteins...Abesh Bhar
This is a presentation on protein interactions. Whenever the proteins interact with other chemicals it goes through some changes in it. As an example, we can say the thermodynamic, Kinetic stability of protein can be changed. The Protein can be denatured in a certain condition. These can be checked using Circular Dichroism Spectroscopy.
This document summarizes a study that developed a rapid and facile synthesis of 1-ferrocenylmethyl-3-alkyl and 1,3-di(ferrocenylmethyl)imidazolium salts. The synthesis involves reacting (ferrocenylmethyl)trimethylammonium iodide with various imidazole derivatives under reflux conditions. This approach produced the imidazolium salts in good to excellent yields, representing a significant improvement over previous synthesis methods. The synthesized compounds were characterized using analytical techniques such as NMR spectroscopy and elemental analysis.
Synthesis and Characterization of Cationic Surfactants Based (1)Nesreen A. Fatthallah
1) The document describes the synthesis and characterization of four cationic surfactants based on N-hexamethylenetetramine and alkyl chlorides.
2) The surfactants were tested for their antimicrobial activity against four bacterial strains. The maximum activity was observed for N-hexamethylenetetramine-N-ethyl silane ammonium trichloride (Ah) which showed 73% inhibition of Staphylococcus aureus.
3) Surface tension measurements were performed to determine properties like critical micelle concentration and thermodynamic parameters of adsorption and micellization. Fourier transform infrared spectroscopy and mass spectrometry were used to characterize the synthesized surfactants.
Four new cationic surfactants based on hexamethylenetetramine and alkyl chloride were synthesized and characterized. Their surface properties and antimicrobial activities were studied. Against gram-positive and gram-negative bacteria, the surfactant N-hexamethylenetetramine-N-ethyl silane ammonium trichloride showed the highest antimicrobial activity, with maximum inhibition of 73% against Staphylococcus aureus and minimum of 60% against Escherichia coli at a concentration of 5 mg/l, pH 7, and 37°C.
In vitro enzyme inhibition studies on new sulfonamide derivatives of 4-tosyl ...Jing Zang
Sulfonamides are considered to be pharmaceutically important class of compounds. In the present work, N-(2,4-dimethylphenyl)-4-toluenesulfonamide (3) was synthesized by the reaction of 2,4-dimethylaniline (1) and 4-tosyl chloride (2; 4-methylbenzenesulfonyl chloride) using 10% aqueous Na2CO3 solution as reaction medium. At the second step, the synthesized molecule 3 was made to react with different alkyl/aralkyl halides (4a-o) to yield the target compounds, 5a-o, using N,N-dimethylformamide (DMF) as reaction medium and lithium hydride as an activator. The synthesis of all the compounds was verified by spectral techniques using IR, 1H-NMR and EIMS; and further examined for their anti-enzymatic activities. The synthesized compound 5f represented a suitable inhibitory potential against α-glucosidase and lipoxygenase enzymes.
Adsorption kinetics of Copper, Lead and Zinc by Cow Dung, Poultry Manure and ...AJSERJournal
This study highlights the effect of cow dung, cocoa pod and poultry manure in the removal of heavy
metals from solution and their applicability to Langmuir and Freundlich models was studied in the Soil Science
Laboratory of Michael Okpara University of Agriculture, Umudike in Abia State, Ngeria. The amendments used in the
study were locally sourced, sundried, ground and sieved with 2mm sieve. The salts of the three heavy metals were
separately used to prepare heavy metal solutions of 100 mg/L. Batch study was carried out at room temperature on a
mechanical shaker using 120 ml plastic bottles at different time intervals of 15, 30 and 60minutes. After shaking, the
amendments and heavy metal solutions were separated using whatman No 1 filter paper, stored in the refrigerator and
analyzed for heavy metals concentration. The amount of heavy metals adsorbed was calculated. The results revealed
that high adsorption occur at low equilibrium concentrations in all the amendments with decreasing levels of
adsorption with increasing equilibrium with cow dung and cocoa pod having higher adsorption capacity than poultry
manure. Coefficient of determination (R2) showed that the experimental data fit in to both Langmuir and Freundlich
models. For reduced heavy metal uptake by plants and subsequent contamination of the food chain, cow dung, cocoa
pod and poultry manure should be used as amendments in heavy metal contaminated soils
This document summarizes metal-organic frameworks (MOFs), including their properties and applications. MOFs are highly porous materials formed by combining metal ions or metal clusters with organic ligands. They have extremely large surface areas, often exceeding 7,000 m2/g. Due to their tunable porous structures, MOFs show promise for applications such as gas storage, carbon capture, catalysis, and luminescence. While MOF research has advanced significantly in recent decades, further developing their potential applications and improving stability remains an active area of research.
THERMAL CONDUCTIVITY OF NANOFLUIDS PREPARED FROM BIOBASED NANOMATERIALS DISPE...IAEME Publication
In the present study, experimental investigation on thermal conductivity of green
nanofluids prepared from coconut fibre-based nanoparticles and suspended in 60:40
ethylene glycol (EG) water (W) mixture was carried out. The measurement of thermal
conductivity was conducted at 15 °C to 60 °C at mass fractions of 0.04 wt%, 0.08
wt%, 0.5 wt% and 1 wt%. The results show deterioration in thermal conductivity with
an increasing temperature. Also the deterioration increased as the mass fraction
increased.
Transcriptional profiling of Halobacterium sp. NRC-1 showed changes in gene expression in response to changes in salinity and temperature. Growth under high salt stress resulted in modulation of genes for ion transporters like potassium and phosphate transporters. Growth at cold temperatures altered expression of genes for lipid metabolism, gas vesicles, and cold shock proteins. Heat shock induced several chaperone genes. The study provides insights into Halobacterium's responses to environmental stresses at the gene expression level.
International Journal of Pharmaceutical Science Invention (IJPSI)inventionjournals
International Journal of Pharmaceutical Science Invention (IJPSI) is an international journal intended for professionals and researchers in all fields of Pahrmaceutical Science. IJPSI publishes research articles and reviews within the whole field Pharmacy and Pharmaceutical Science, new teaching methods, assessment, validation and the impact of new technologies and it will continue to provide information on the latest trends and developments in this ever-expanding subject. The publications of papers are selected through double peer reviewed to ensure originality, relevance, and readability. The articles published in our journal can be accessed online
Physical and Structural Characterization of Biofield Treated Imidazole Deriva...albertdivis
The Aim of present study was to evaluate the impact of biofield treatment on two imidazole derivatives (i.e., imidazole and 2-methylimidazole) by various analytical methods.
COMPARISON FREE ENERGY BINDING SITES NEURAMINIDASEijabjournal
Neuraminidase (NA) is the essential surface glycoprotein of the influenza virus. High- affinity neuraminidase inhibitors have been designed that interact only with the conserved active site and binding site residues. The neuraminidase (NA) of influenza virus is the target of anti – flu drug.for treatment of this
disease a thorough knowledge of neuraminidase protein is essential in order to produce potent drugs to suppress this enzyme..Drug design is by QSAR and docking methods, so we need a complete knowledge of receptor ligand, target site and binding site. This paper, using bioinformatics, Molecular Dynamics, Monte carlo and studied binding site NA enzyme in 310K temperature and different dielectrics (1, 78.39 and
32.63) for the best drug designing. We measured the potential energy of amino acids binding to the drug.Molecular Mechanics, Molecular Dynamic and Nanobiological have done a great assistance in drug designing.
Structural characterization and cytotoxicity studies of ruthenium(ii)–dmso–ch...rkkoiri
This document describes the structural characterization and cytotoxicity studies of two new ruthenium(II) complexes containing chalcone and flavone ligands. Single crystal X-ray diffraction was used to determine the crystal structures of the two complexes, which were found to self-associate through non-covalent interactions into one-dimensional and two-dimensional supramolecular structures. The cytotoxicity of the complexes was evaluated using MTT assays on Dalton's Lymphoma cell lines, with the complexes exhibiting cytotoxic properties.
A Novel Polymeric Prodrugs Synthesized by Mechanochemical Solid-State Copolym...inventionjournals
:We developed the novel polymeric prodrugs synthesized by mechanochemical solid-state copolymerization of glucose-based polysaccharides (dextran orglycogen) and the methacryloyloxy derivative of 5-fluorouracil (5-FU). The copolymerization proceededreadily and each polymeric prodrug was quantitatively obtained within8 h reaction. The number average molecular weight (Mn) and polydispersity (H) of the polymeric prodrug synthesized from dextran was 24,000 g/mol and 5.10, respectively. The number average particle diameter of the polymeric prodrug derived from glycogen was 14.9 nm. The hydrolysis profiles of the polymeric prodrug synthesized from dextranapparently followed the first-order kinetics, and 100% drug release was observed under the experimental condition used. The polymeric prodrug derived from glycogen also continued to release 5-FU at the first-order rate up to 5 h, followed by its rate constant decreased gradually. These results suggest that lower accessibility of water molecules for the synthetic polymer chains inside the glycogen particle might cause the gradual decrease of drug release rate.
Stabilization or solidification of iron ore mine tailings using cementeSAT Journals
Abstract Current research emphasis is more on the utilization of materials that are considered as waste. Tailings and fly ash are major category of industrial wastes, whose disposal is problematic from environmental point of view. In this present research, Industrial byproducts, namely, lime (CaO) and class F type fly ash have been used as candidate materials along with the partial addition of ordinary Portland cement (OPC) in the Stabilization/solidification (S/S) of polymetallic iron ore mine tailings (TM). The effectiveness of S/S was assessed by comparing laboratory experimental values obtained from unconfined compressive strength (UCS), hydraulic conductivity and leaching propensity tests of S/S samples with regulatory standards for safe surface disposal of such wastes. Some S/S cured matrices were found unable to provide the required immobilization of pollutants. S/S and 28 days cured mine tailing specimens made with composite binders containing TM/10/0/0, TM/5/0/20, TM/10/0/40 and TM/0/10/40 significantly impaired the solubility of all contaminants investigated and proved successful in fixing metals within the matrix, in addition to achieving adequate UCS and hydraulic conductivity values, thus satisfying regulatory norms (U.S. EPA). Laboratory investigations revealed the TM blends (stabilized materials) were non-hazardous. The test results of this study are encouraging and it may be possible to undertake large-scale fill construction with stabilized tailing material that is sustainable and cost effective. Keywords: Tailing materials, Laboratory study, Compaction characteristics, unconfined compressive strength, Hydraulic conductivity, Heavy metal content.
J. Bukowczan - Various methods for one pot synthesis of triazoles from quinol...Jerzy_BN
This document describes various methods for synthesizing 1,2,3-triazoles from 4-amino-3-quinolinesulfonamides with a propargyl group. It discusses four reaction methods tried: (1) copper-catalyzed azide-alkyne cycloaddition, (2) phase transfer catalysis, (3) a two-step synthesis using an organic azide, and (4) a catalyst-free reaction in water. The copper-catalyzed and two-step methods produced the best yields of up to 99% and 82%, respectively. Thirteen new compounds were obtained and will be tested for potential anti-cancer activity, as the triazole, quin
A Semi-empirical based QSAR study of indole휷- Diketo acid, Diketo acid and Ca...iosrjce
In this study, a set of novel synthesized indole훽- diketo acid, diketo acid and carboxamide
derivativeswas investigated by quantitative structure–activity relationship (QSAR) analysis using semiempirical
(PM3) based descriptors. The best molecular descriptors identified were LogP, polar area
corresponding to absolute values of electrostatic potential greater than 75 (P-area(75)), Energy (E), Minimum
values of electrostatic potential (as mapped onto an electron density surface) (MinEIPot), Polar surface area
and Maximum values of electrostatic potential (as mapped onto an electron density surface) (MaxEIPot) that
contributed to the anti-HIV activity of the indole훽- diketo acid, diketo acid and carboxamide derivatives as
independent factors. The correlation of these descriptors with their anti-HIV activity increases indicating their
importance in studying biological activity. Quantitative structure activity relationship (QSAR) analysis was
applied to 37 of the above mentioned derivatives using physicochemical and structural molecular descriptors
obtained by the semi-empirical method by employing PM3 basis set. By using the multiple linear regression
(MLR) technique several QSAR models have been drown up with the help these calculated descriptors and the
anti-HIV activity of indole훽- diketo acid, diketo acid and carboxamide derivatives. The regression method was
used to derive the most significant models as a calibration model for predicting the LogIC50 of this class of
compounds. Among the obtained QSAR models presented in the study from the MLR method, statistically the
most significant one is the last model with the squared correlation coefficient 0.8932, Q = 3.1854 and F=
27.8644 that could be useful to predict the biological activity of indole훽- diketo acid, diketo acid and carboxamide derivatives as Potent HIV-1 Drugs.
This document summarizes an investigation into using lysine-functionalized dendrimers as potential detoxification agents for the organophosphate pesticide dichlorvos. Zeroth-, first-, and second-generation polyester dendrimers were synthesized with exactly 4, 8, and 16 lysine groups respectively on their periphery. The dendrimers were found to be water-soluble and showed low toxicity to cell lines. They were also able to efficiently capture dichlorvos, demonstrating their potential as antidotes to maintain acetylcholinesterase activity in cases of organophosphate poisoning.
GFS Chemicals Organic Catalog - Building BlocksLiza Tallon
This document provides information about ordering from GFS Chemicals, including their contact information and methods for placing orders. It also summarizes some of their product offerings, including Grignard reagents, anhydrous cerous chloride, anhydrous lithium perchlorate, and expertise in liquid ammonia chemistries and acetylenic/olefinic specialties from acquiring the Farchan product line. Their goal is to be a full-service partner in developing reagents and catalysts to help customers leverage their chemical development and processing.
This document discusses a study on mixed-linker zeolitic imidazolate frameworks (ZIFs) containing two types of imidazole linkers. The researchers show that these mixed-linker ZIFs have tunable properties including pore size, hydrophilicity, and organophilicity. They synthesized a series of ZIF-8x-90100-x materials with different ratios of two linkers, resulting in a wide range of crystal sizes from 338 nm to 120 μm. Using various characterization and measurement techniques, they demonstrate that properties like hydrocarbon and alcohol diffusion can be continuously tuned over 2-3 orders of magnitude by varying the mixed-linker composition. This tunability allows mixed-linker ZIFs to
Enrichment of microorganisms by sugar cane molasses for polyehtylene degradationeSAT Publishing House
This document summarizes a study that enriched the growth of microorganisms using sugar cane molasses to degrade polyethylene films. Microorganisms were isolated from soil and grown in media containing different concentrations of molasses. Polyethylene strips were added and incubated for 6 months. Fourier transform infrared spectroscopy analysis showed new peaks and changes in peak intensities in treated films, indicating biodegradation. Higher molasses concentrations (above 2.5%) supported more efficient polyethylene degradation by microorganisms.
This document describes the synthesis, spectral characterization, and biological screening of transition metal complexes of the ligand 2-(5-mercapto-1,3,4-oxadiazol-2-yl)phenol. A series of complexes were prepared using Cu(II), Co(II), Ni(II), and Zn(II) and characterized using analytical data, magnetic susceptibility, IR, UV-Vis, 1H NMR, 13C NMR, EPR, and other techniques. Spectral data suggest an octahedral geometry around the metal ion. Biological screening showed the complexes have antibacterial, antifungal, and DNA cleavage activities.
Investigation of structural, kinetic and thermodynamic properties of proteins...Abesh Bhar
This is a presentation on protein interactions. Whenever the proteins interact with other chemicals it goes through some changes in it. As an example, we can say the thermodynamic, Kinetic stability of protein can be changed. The Protein can be denatured in a certain condition. These can be checked using Circular Dichroism Spectroscopy.
This document summarizes a study that developed a rapid and facile synthesis of 1-ferrocenylmethyl-3-alkyl and 1,3-di(ferrocenylmethyl)imidazolium salts. The synthesis involves reacting (ferrocenylmethyl)trimethylammonium iodide with various imidazole derivatives under reflux conditions. This approach produced the imidazolium salts in good to excellent yields, representing a significant improvement over previous synthesis methods. The synthesized compounds were characterized using analytical techniques such as NMR spectroscopy and elemental analysis.
Synthesis and Characterization of Cationic Surfactants Based (1)Nesreen A. Fatthallah
1) The document describes the synthesis and characterization of four cationic surfactants based on N-hexamethylenetetramine and alkyl chlorides.
2) The surfactants were tested for their antimicrobial activity against four bacterial strains. The maximum activity was observed for N-hexamethylenetetramine-N-ethyl silane ammonium trichloride (Ah) which showed 73% inhibition of Staphylococcus aureus.
3) Surface tension measurements were performed to determine properties like critical micelle concentration and thermodynamic parameters of adsorption and micellization. Fourier transform infrared spectroscopy and mass spectrometry were used to characterize the synthesized surfactants.
Four new cationic surfactants based on hexamethylenetetramine and alkyl chloride were synthesized and characterized. Their surface properties and antimicrobial activities were studied. Against gram-positive and gram-negative bacteria, the surfactant N-hexamethylenetetramine-N-ethyl silane ammonium trichloride showed the highest antimicrobial activity, with maximum inhibition of 73% against Staphylococcus aureus and minimum of 60% against Escherichia coli at a concentration of 5 mg/l, pH 7, and 37°C.
In vitro enzyme inhibition studies on new sulfonamide derivatives of 4-tosyl ...Jing Zang
Sulfonamides are considered to be pharmaceutically important class of compounds. In the present work, N-(2,4-dimethylphenyl)-4-toluenesulfonamide (3) was synthesized by the reaction of 2,4-dimethylaniline (1) and 4-tosyl chloride (2; 4-methylbenzenesulfonyl chloride) using 10% aqueous Na2CO3 solution as reaction medium. At the second step, the synthesized molecule 3 was made to react with different alkyl/aralkyl halides (4a-o) to yield the target compounds, 5a-o, using N,N-dimethylformamide (DMF) as reaction medium and lithium hydride as an activator. The synthesis of all the compounds was verified by spectral techniques using IR, 1H-NMR and EIMS; and further examined for their anti-enzymatic activities. The synthesized compound 5f represented a suitable inhibitory potential against α-glucosidase and lipoxygenase enzymes.
Adsorption kinetics of Copper, Lead and Zinc by Cow Dung, Poultry Manure and ...AJSERJournal
This study highlights the effect of cow dung, cocoa pod and poultry manure in the removal of heavy
metals from solution and their applicability to Langmuir and Freundlich models was studied in the Soil Science
Laboratory of Michael Okpara University of Agriculture, Umudike in Abia State, Ngeria. The amendments used in the
study were locally sourced, sundried, ground and sieved with 2mm sieve. The salts of the three heavy metals were
separately used to prepare heavy metal solutions of 100 mg/L. Batch study was carried out at room temperature on a
mechanical shaker using 120 ml plastic bottles at different time intervals of 15, 30 and 60minutes. After shaking, the
amendments and heavy metal solutions were separated using whatman No 1 filter paper, stored in the refrigerator and
analyzed for heavy metals concentration. The amount of heavy metals adsorbed was calculated. The results revealed
that high adsorption occur at low equilibrium concentrations in all the amendments with decreasing levels of
adsorption with increasing equilibrium with cow dung and cocoa pod having higher adsorption capacity than poultry
manure. Coefficient of determination (R2) showed that the experimental data fit in to both Langmuir and Freundlich
models. For reduced heavy metal uptake by plants and subsequent contamination of the food chain, cow dung, cocoa
pod and poultry manure should be used as amendments in heavy metal contaminated soils
This document summarizes metal-organic frameworks (MOFs), including their properties and applications. MOFs are highly porous materials formed by combining metal ions or metal clusters with organic ligands. They have extremely large surface areas, often exceeding 7,000 m2/g. Due to their tunable porous structures, MOFs show promise for applications such as gas storage, carbon capture, catalysis, and luminescence. While MOF research has advanced significantly in recent decades, further developing their potential applications and improving stability remains an active area of research.
THERMAL CONDUCTIVITY OF NANOFLUIDS PREPARED FROM BIOBASED NANOMATERIALS DISPE...IAEME Publication
In the present study, experimental investigation on thermal conductivity of green
nanofluids prepared from coconut fibre-based nanoparticles and suspended in 60:40
ethylene glycol (EG) water (W) mixture was carried out. The measurement of thermal
conductivity was conducted at 15 °C to 60 °C at mass fractions of 0.04 wt%, 0.08
wt%, 0.5 wt% and 1 wt%. The results show deterioration in thermal conductivity with
an increasing temperature. Also the deterioration increased as the mass fraction
increased.
Transcriptional profiling of Halobacterium sp. NRC-1 showed changes in gene expression in response to changes in salinity and temperature. Growth under high salt stress resulted in modulation of genes for ion transporters like potassium and phosphate transporters. Growth at cold temperatures altered expression of genes for lipid metabolism, gas vesicles, and cold shock proteins. Heat shock induced several chaperone genes. The study provides insights into Halobacterium's responses to environmental stresses at the gene expression level.
International Journal of Pharmaceutical Science Invention (IJPSI)inventionjournals
International Journal of Pharmaceutical Science Invention (IJPSI) is an international journal intended for professionals and researchers in all fields of Pahrmaceutical Science. IJPSI publishes research articles and reviews within the whole field Pharmacy and Pharmaceutical Science, new teaching methods, assessment, validation and the impact of new technologies and it will continue to provide information on the latest trends and developments in this ever-expanding subject. The publications of papers are selected through double peer reviewed to ensure originality, relevance, and readability. The articles published in our journal can be accessed online
A STUDY TO EVALUATE THE IN VITRO ANTIMICROBIAL ACTIVITY AND ANTIANDROGENIC E...Dr. Pradeep mitharwal
The present paper deals with synthesis and characterization
of some new chromium (III) Schiff base complexes using microwave irradiation
technique as well as conventional heating. The S∩N donor benzothiazolines, 1-
(2-furanyl) ethanone benzothiazoline (Bzt1N
∩
SH), 1-(2-thienyl) ethanone
benzothiazoline (Bzt2N
∩
SH) and 1-(2-pyridyl) ethanone benzothiazoline
(Bzt3N
∩
SH) were prepared by the condensation of ortho-aminothiophenol with
respective ketones in ethanol.
This document summarizes research characterizing the intact 14-subunit respiratory membrane bound [NiFe]-hydrogenase complex (MBH) from the hyperthermophilic archaeon Pyrococcus furiosus. The researchers expressed a His-tagged version of MBH in P. furiosus and purified the intact detergent-solubilized complex using affinity chromatography. The purified MBH complex contained all 14 subunits and exhibited catalytic hydrogen production with physiological electron donors, similar to the membrane-bound form. Small angle X-ray scattering was used to generate a structural model of the purified MBH complex, providing insights into its Z-shaped structure and relationship to other respiratory complexes like Complex I.
Crosslinked Microgels as Platform for Hydrolytic Catalysts Article pubs.acs.o...aaaa zzzz
This document describes the development of a new protocol for synthesizing crosslinked microgels via UV-initiated free radical polymerization of miniemulsions at ambient temperature or below. The microgels are formed from butyl acrylate, ethylene glycol dimethacrylate, and a catalyst-precursor ligand. The catalytic activity of the microgels is demonstrated through the hydrolysis of 4-methylumbelliferyl β-D-galactopyranoside. A correlation is observed between the crosslinking content of the microgels and their catalytic proficiency, with peak performance at 40 mol% crosslinking.
This document summarizes the engineering and characterization of a soluble cytoplasmic subcomplex (C-MBH) of the membrane-bound respiratory hydrogenase (MBH) from the hyperthermophilic archaeon Pyrococcus furiosus. The researchers engineered a P. furiosus strain that differentially expresses the 14-gene MBH operon, producing a 4-subunit C-MBH complex containing an affinity tag. They purified the C-MBH using affinity chromatography without detergent. The purified C-MBH had catalytic activity and generated hydrogen from the physiological electron donor reduced ferredoxin, optimally at 60°C. This is the first report of engineering and characterizing a soluble
Plasma is the fourth state of matter created when a gas is heated to high temperatures, ionizing its atoms. Cold plasma is generated at near room temperatures and does not cause thermal damage to foods. It inactivates microbes through chemical reactions with cell membranes from reactive species, UV damage to DNA and membranes, and breaks DNA strands. Applications include surface decontamination of meats, produce, and packaging. It improves properties of cereals and dairy. Limitations include potential oxidation and effects on color and firmness of some foods.
This document describes the development of an in vitro model to study the foreign body response by modulating biomaterial surface properties. The model uses polymeric rods with tailored surface topography, roughness, wettability and chemistry achieved through surface modification techniques. Results showed that surface microstructuring increased cell adhesion, proliferation, and balanced cytokine secretion to optimize collagen and elastin synthesis for tissue regeneration. By linking surface parameters to cell activity, the fate of regenerated tissue could be determined to create successful soft tissue replacements.
Batch adsorption experiments were carried out for
the adsorption of cationic dye from aqueous solution onto
composite activated carbon. The composite activated carbon was
prepared from brewer’s spent grain and sea bean shell at a ratio
of 1:1. The equilibrium studies were done at different
concentrations and temperatures. The equilibrium data were
fitted to Langmuir, Freundlich, Dubinin-Radushkevich, and
Temkin isotherm models. The results showed that both Lagmuir
and Freundlich isotherm model fitted the data reasonably well
but Freundlich isotherm fitted better in the temperature range
studied. This confirmed that the adsorption is heterogeneous,
non-specific and non-uniform in nature. Kinetic studies were also
undertaken in terms of first order, second order, pseudo first
order, pseudo second order, Elovich, Boyd, and intra-particle
diffusion models. The results indicated that the data followed
pseudo second order model with surface adsorption and intraparticle
diffusion concurrently operating during the adsorbateadsorbent
interaction. The values of the thermodynamic
parameters computed from Van’t Hoff plot confirmed the
process to be endothermic and spontaneous in nature.
This document discusses a study on the synthesis, molecular structure, and quantum chemical computational interpretations of (E)-N'-(3,4-Dimethoxybenzylidene)-nicotinohydrazide monohydrate. Density functional theory calculations were performed using B3LYP and M06-2X levels of theory to optimize the geometry and study vibrational modes, natural bond orbital analysis, HOMO-LUMO analysis, molecular electrostatic potential, and thermodynamic properties. FT-IR, FT-Raman, and UV-Vis spectroscopy experiments were also carried out. The results from quantum chemical calculations showed good agreement with experimental data and provided insights into the structural stability and charge transfer interactions
This document summarizes a paper presented at the Second International Conference on New Research in Chemistry and Chemical Engineering. The paper presents an artificial neural network model developed to estimate the solubility of carbon dioxide in brine. The neural network takes temperature, pressure and salinity as inputs and outputs the estimated CO2 solubility. It is compared to the Duan and Sun (2003) model and Henry's correlation, showing improved performance over existing methods for a wide range of temperature, pressure and salinity conditions.
Two-Phase Improves Performance of Anaerobic MembraneBioreact.docxjuliennehar
Two-Phase Improves Performance of Anaerobic Membrane
Bioreactor Treatment of Food Waste at High Organic Loading Rates
Yamrot M. Amha,† Michael Corbett,‡ and Adam L. Smith*,†
†Astani Department of Civil and Environmental Engineering, University of Southern California, 3620 South Vermont Avenue, Los
Angeles, California 90089, United States
‡Divert, Inc., 23 Bradford Street, 3rd Floor, Concord, Massachusetts 01742, United States
*S Supporting Information
ABSTRACT: Anaerobic membrane bioreactors (AnMBRs)
are in use at the full-scale for energy recovery from food waste
(FW). In this study, the potential for two-phase (acid/gas)
AnMBR treatment of FW was investigated as a strategy to
increase microbial diversity, thereby improving performance.
Two bench-scale AnMBRs were operated in single-phase (SP)
and two-phase (TP) mode across incremental increases in
organic loading rate (OLR) from 2.5 to 15 g total chemical
oxygen demand (COD) L·d−1. The TP acid-phase (TP-AP)
enriched total VFAs by 3-fold compared to influent FW and
harbored a distinct microbial community enriched in
fermenters that thrived in the low pH environment. The TP methane phase (TP-MP) showed increased methane production
and resilience relative to SP as OLR increased from 3.5 to 10 g COD L·d−1. SP showed signs of inhibition (i.e., rapid decrease in
methane production per OLR) at 10 g COD L·d−1, whereas both systems were inhibited at 15 g COD L·d−1. At 10 g COD L·
d−1, where the highest difference in performance was observed (20.3% increase in methane production), activity of syntrophic
bacteria in TP-MP was double that of SP. Our results indicate that AnMBRs in TP mode could effectively treat FW at OLRs up
to 10 g COD·L day−1 by improving hydrolysis rates, microbial diversity, and syntroph activity, and enriching resistant
communities to high OLRs relative to AnMBRs in SP mode.
1. INTRODUCTION
As landfills rapidly reach capacity in the US and elsewhere,
diversion of organic wastes is expected to become the norm.
Anaerobic membrane bioreactors (AnMBRs), which combine
anaerobic treatment with membrane separation, have emerged
as a sustainable food waste (FW) management strategy with
reduced environmental footprint relative to landfilling and
composting, while also providing energy recovery via biogas
production.1 Compared to conventional anaerobic digesters
(ADs), membrane separation in AnMBRs decouples solid
retention time (SRT) and hydraulic retention time (HRT),
enabling operation at longer SRTs. This can be advantageous
for FW management due to the high organic content and
temporal heterogeneity in waste characteristics. The long SRT
and membrane separation drastically improves effluent quality
relative to conventional AD, an important feature in
decentralized FW management where effluent discharge to
local publicly owned treatment works is necessary. AnMBRs
may also permit operation at higher OLR than ADs, a critical
parameter that dictates system capacity and reactor dimen- ...
We present a micro fluidic device that allows rapid and defined delivery of discrete and homogeneous reagents or samples to allow kinetic studies of surface-tethered biomolecules. We developed an Electro Osmotic Flow (EOF) based device consisting of an asymmetric Y-junction with an incorporated fast, pressure driven valve, two embedded measurement electrodes and reservoirs. The EOF is used to circumvent kinetic limitations on reagent transport to the surface of these tethered biomolecules due to the slow diffusion across parabolic concentration gradients in conventional pressure-driven flow devices. Using Fluorescein isothiocyanate (FITC) as the pH sensitive surface-immobilized biomolecules, we show that the reagent solution can be repeatedly exchanged within milliseconds, and that by using a synchronized triggering scheme we can monitor the reaction of our sensor biomolecules to the change of the environment on a time scale of 10ms.
- The document describes a new method for creating molecularly imprinted polymer-based core-shell structures on pencil graphite electrodes for electrochemical sensing of anti-HIV drugs lamivudine and zidovudine.
- Solid and hollow core-shell structures were created by imprinting polymers on vinylated silica nanospheres. Hollow structures allowed better diffusion of analyte and probe molecules through inner and outer surfaces compared to solid structures.
- The hollow core-shell molecularly imprinted polymer sensors showed high sensitivity and selectivity for lamivudine and zidovudine, with detection limits in the low ng/mL range in various real samples like water, blood serum, and pharmaceuticals.
This document describes a study that characterized the major and minor groove environments of DNA using fluorescent probes. Specifically:
- Fluorescent oligonucleotides were created by incorporating a dansyl fluorophore into the major groove at specific sites.
- The fluorescence properties of these probes were used to estimate that the dielectric constant of the major groove is around 55D, compared to 20D for the minor groove.
- Binding of the minor groove ligand netropsin could be quantitatively monitored by changes in fluorescence of the dansyl group in the major groove, suggesting an information network between the two grooves.
This document summarizes research on engineering a subcomplex of the hydrogenase enzyme from Pyrococcus furiosus that is capable of producing hydrogen. Key points:
- Researchers successfully produced a heterodimeric form of the cytoplasmic hydrogenase I from P. furiosus (SHI) containing only two of the four subunits in the native enzyme.
- The engineered heterodimer is highly active in producing hydrogen using an artificial electron donor and is thermostable.
- Unlike the native enzyme, the heterodimer directly utilizes reducing power from pyruvate ferredoxin oxidoreductase without needing an intermediate electron carrier.
- This represents a two-enzyme system
Similar to molecular dynamics simulation of HYD1.compressed (20)
2. International Journal of Science and Research (IJSR)
ISSN (Online): 2319-7064
Impact Factor (2012): 3.358
Volume 3 Issue 8, August 2014
www.ijsr.net
Licensed Under Creative Commons Attribution CC BY
Molecular Dynamics Simulation Studies of HYD1
Cephas Mawere1
, Suresh Kumar G2
1, 2
Department of Bioinformatics, School of IT, Jawaharlal Nehru Technological University Hyderabad, India
Abstract: The unique features of HYD1 protein and its primary involvement in fungal pathogenesis of Gibberella moniliformis have
drawn attention to insilico study of potential inhibitors. This destructive mold is also on the rise of causing cancer related diseases in
both humans and animals upon ingestion of the infected maize and/or rice grains. To date, currently used fungicides are ineffective
against G. moniliformis as the fungus can grow and adapt to any environment. It has been realized that such behavior is attributed to
class I hydrophobins where HYD1 belongs. These bio-surfactant macromolecules spontaneously self assemble at hydrophobic:
hydrophilic interfaces into thin nanometric rodlet biofilms. For this reason, this paper focuses on refining a predicted HYD1 protein and
studying its conformational and thermodynamic properties. Molecular dynamics simulation studies thus prove the protein to be
thermally stable, compact, and results in a better quality model. This will help in understanding the self assembly mechanism of HYD1
and future docking studies.
Keywords: HYD1, Gibberella moniliformis, Hydrophobins, Bio-surfactant, Self-assemble, Molecular dynamics simulation
1.Introduction
Hydrophobins are a group of small surface active protein
uniquely found in filamentous fungi [1] like G. moniliformis.
They constitute ten percent of the fungal cell wall as
structural components and when secreted they are localized
on the surface of aerial mycelia [3]. At hydrophilic:
hydrophobic interfaces these proteins spontaneously self-
assemble into different types of supramolecules. Based on
this unique property, solubility and the pattern of Cys
residues in their primary sequence, hydrophobins are divided
into two groups- class I and class II [2]. Class I
hydrophobins, where HYD1 belongs, can spontaneously self-
assemble into a 10 nm wide amphipathic rodlet film in the
presence of a hydrophilic: hydrophobic interface [5]. This
biofilm lowers the surface tension of the medium or
substratum in/on which G. moniliformis will grow [6]. Of
interest, class I hydrophobins exists in three states; as
monomers they are soluble in water, but self- assemble into
the beta state at water-air interface. However, at the interface
between water and a hydrophobic solid like Teflon, HYD1
attains an alpha helical structure [7]. Such a self assembly
property of HYD1 causes it to be thermally resistant to heat
treatments below 90o
C. The protein also tends to be insoluble
in aqueous solvents only to be dissociated by harsh treatment
with strong acids such as concentrated TFA [9]. It has
therefore been suggested by Wosten et al [1] that the eight
conserved cysteine residues that form four disulphide bridges
prevent self- assembly of the hydrophobin in the absence of a
hydrophilic: hydrophobic interface, while the N-terminal part
of hydrophobin, at least partly, determines wettability of the
hydrophobic side of the assemblage. Experimental evidence
of related class I hydrophobins also indicate that the alpha
helical state is an intermediate while the end form of
assembly is the beta state [8]. These two assembled forms
have an amphipathic nature which confers water repellent
properties to many conidia, hyphae and multicellular
structures. The rodlet layer is covered by a mucilaginous
extracellular matrix that helps the fungal conidia to bind to
the substrate [6]. This makes class I hydrophobins, which
includes HYD1, to be essential for the G. moniliformis to
complete its biological life cycle. As such, class I
hydrophobins are actively involved in formation of
hydrophobic aerial structures like spores and fruiting bodies,
in fungal development, environmental adaptation and
pathogenic interactions. During pathogenesis, for instance,
class I hydrophobins mediate attachment of hyphae to each
other [3] and to the hydrophobic surface of the host plant
before penetration and infection commence [4]. For this
cause G. moniliformis has been a destructive pathogen to
more than 11,000 plant species including maize and rice [9].
This study therefore seeks to characterize the dynamic
behaviour of HYD1 in water, prior to docking simulations in
a quest to find a potential class I hydrophobin inhibitor for
the aforementioned fungus.
2.Materials and Methods
A predicted HYD1 protein model from the M4T_HYD1
server [10] validated by PROCHECK and Verify3D was
used for MD simulation studies. GROMACS 4.5.4 package
[11] was thus chosen to explore the dynamic behavior of
M4T_HYD1 protein with the empirical force-field
GROMOS96 43a1 being used. The study on protein
conformation, stability, compactness and refinement was
therefore done in a four staged simulation process as
indicated in Fig. 1 below.
Figure 1: The four staged molecular dynamics simulation
Paper ID: 02015360 678
3. International Journal of Science and Research (IJSR)
ISSN (Online): 2319-7064
Impact Factor (2012): 3.358
Volume 3 Issue 8, August 2014
www.ijsr.net
Licensed Under Creative Commons Attribution CC BY
2.1 Energy Minimization
In order to understand the atomic scale mechanisms of
HYD1, a topology file (.top), a GROMACS-compatible
coordinate file (.gro) and a position restraints file (.itp) were
created using the ‘pdb2gmx’ command. The .gro file of
HYD1 was then used to prepare the system simulation cell.
The resulting cubic box was defined by a 1.0 Ao
edge length.
This was followed by centering the protein in the box. An
SPC (a single three-point water model coordinate) file
(spc216.gro) was then used to fill up the box, hence solvating
the system. The system net charge was then neutralized by
replacing six solvent molecules (SOL) in the .top file with
Three Na+
and three Cl-
ions. In order to relax the molecular
geometry of the system by getting rid of atomic clashes or
any existing irregularities certain parameters were
considered. These include a maximum force (emtol) was set
at 100kJ/mol/nm, periodic boundary conditions in the
directions x, y, z, 0.8 nm cut-offs for short range VDW and
electrostatic interactions as well as a particle-mesh Ewald
long range electrostatics. Once these factors were set, the
system was minimized for 50,000 steps using the steepest
descent algorithm.
2.2 Equilibration
System equilibration was characterized by two ensemble
based simulations- NVT and NPT. Once minimization was
complete the system was first simulated at 25,000 steps with
a 2fs time step (a total of 50ps) to bring it to equilibrium.
Thus, an NVT ensemble was used to create trajectories at a
Langevin temperature of 298 K and a constant volume of 158
nm3
using Berendsen coupling algorithm. Position restraints
were applied on the protein backbone to avoid any wild
fluctuations. Also, all velocities were evenly distributed
across all molecule types by coupling protein atoms and non-
proteins in separate baths to keep the M4T_HYD1 rigid.
Finally, the linear constraint solver (LINCS) algorithm was
employed to constrain all bonds.
After this calibration step to a target temperature, the system
was relaxed with an NPT ensemble. This allows the system
to find the correct density. This time, the simulation was
extended to 500ps with position restraints still being applied
to the backbone of M4T_HYD1. A Nose-Hoover thermostat
was then used in place of the Berendsen method to keep the
kinetic energy of the system from fluctuating wildly. Lastly,
pressure was isotropically (the same in all directions) coupled
to a value of one bar.
2.3 Production MD
As soon as the system reached equilibrium and the correct
density was found, a classical molecular dynamics simulation
step was introduced. Here, the position restraints on the
backbone of M4T_HYD1 were lifted. As such, all other
parameters applied in the NPT equilibration were used for
2,500,000 MD steps with a 2fs timestep, totaling 5,000 ps (or
5ns) of sampling.
2.4 Analysis
A ‘trjconv’ command was used to convert trajectory files to
.xtc and .pdb format for further analysis. A ‘g_energy’ was
also used to output total energy, volume, potential energy,
kinetic energy and pressure data results for the equilibration
stage and energy minimization stage. ‘g_rms’, ‘g_rmsf’,
‘g_sas’, and ‘g_gyrate’ commands were respectively
employed to calculate the RMSD, RMSF, Solvent Accessible
Area, and Radius of gyration of the simulated protein.
Likewise ‘g_mindist’ and ‘g_dist’ were used to measure the
distance between atomic residues. The resulting files (.xvg)
were analyzed using xmgrace tool [12]. Moreover, the
‘g_confirms’ command was used to generate a pdb file of the
original M4T_HYD1 protein superimposed to the simulated
structure. RasMol [13] and PYMOL Viewer [14] programs
were used to visualize and interpret the trajectories, the
generated protein simulate, and the generated rmsf.pdb file.
Finally, the secondary structure content of the simulated
M4T_HYD1 as a function of time was analyzed against that
of the original protein using the DSSP (Dictionary of
Secondary Structure of Proteins) tool [15].
3.Results and Discussion
3.1 Energy minimization (EM)
EM of M4T_HYD1 foresaw steepest descent algorithm
converging to Fmax (maximum force) in less than 100 in
6,153 steps (approx. 6ns). This resulted in the system
potential energy being reduced from -1.8e+05 kJ/mol to
global minimum value of -2.7129166e+05 kJ/mol (Fig. 2).
Thus, energy minimization has ensured that we have a
reasonable starting structure, in terms of geometry, solvent
orientation and without sterical clashes.
Figure 2: Potential energy graph for minimized M4T_HYD1
3.2 Equilibration
a) NVT Simulation
Equilibration using the NVT ensemble was validated as
successful based on results obtained for energy attributes like
temperature, potential energy, kinetic energy, and total
energy. From Table 1.0 and temperature and total energy
plots (Fig. 3 and Fig. 4) it is apparent that the system is well
equilibrated around the target temperature (298 K) and total
system energy in the first 50ps.
Paper ID: 02015360 679
4. International Journal of Science and Research (IJSR)
ISSN (Online): 2319-7064
Impact Factor (2012): 3.358
Volume 3 Issue 8, August 2014
www.ijsr.net
Licensed Under Creative Commons Attribution CC BY
Figure 3: System temperature as a function of time during
NVT equilibration
Figure 4: Total Energy of system under equilibration
Table 1: Attributes used to validate the equilibration stage
Attribute
Average
Score
Err.
Est
RMSD
Total
drift
S.I
Unit
Temperatur 296.69 1.6 13.3317 8.8066 K
Pot. Energy -207614 270 2455.01 1462.4 kJ/mol
Kin. Energy 37238 200 1673.29 1105.3 kJ/mol
Tot. Energy -170093 44 1395.11 206.91 kJ/mol
Pressure 2.67034 2.3 186.631 -12.82 Bar
Volume 157.371 0.031 0.18585
7
-0.125 nm3
Density 994.646 0.2 1.17671 0.7904 Kg/m3
b) NPT Simulation
However, a correct density among other factors like pressure
and volume (Table 1) are required to authenticate a
successful position restraint based simulation.
Figure 5: System density as a function of time during NVT
equilibration
Accordingly, the density of the system appears to have
quickly reached equilibrium quite near to a physiological
value as shown by the density plot (Fig. 5).
3.3 Analysis
3.3.1 RMSD, RMSF and Radius of Gyration
The root means square deviation (RMSD) is a measure of
how much the structure of a protein changes over the course
of the simulation. For small, globular proteins like HYD1,
changes on the order of 1-3 Angstroms are acceptable and
expected [16]. Beyond this range the protein might be
misbehaving. In this study, the backbone option was chosen
for the least fit and for the RMSD measurement, and the
output ‘rmsd.xvg’ file was visualized in Grace (xmgrace):
Figure 6: M4T_HYD1 backbone RMSD during a 5ns
simulation
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The black line in Fig. 6 thus represents the RMSD of the
protein backbone during the simulation, which lies in the
acceptable range. Despite this being a 5ns simulation,
M4T_HYD1 is reasonably stable around 0.2 nm. Now, while
RMSD measures the global backbone deviation, the local
changes are measured using the root mean square fluctuation
(RMSF). In this study much interest was in the entire residue
fluctuation (Fig. 7) as well as the residues of the protein
backbone (Fig. 9). Thus the ‘g_rmsf’ command resulted in
two important output files; a data file of RMSF values plotted
by residue number that can be viewed with Grace and a
structure file (.pdb) that contains beta-factors equal to RMSF
values.
Figure 7: RMS fluctuations of protein residues during
simulation
On this plot, peaks indicate areas of the protein that
fluctuated the most during the simulation. The C-terminal tail
here fluctuated much more than any other part of the HYD1
protein.
Figure 8: RMSF protein residues as viewed in RasMol
When the rmsf.pdb for the above plot was loaded in RasMol
and visualized using the temperature colour scheme, the
above structure was produced. Here, blue value indicates the
most fluctuation which decreases in the colour order : red-
orange- yellow- yellowgreen- green. Information from
RasMol also reveals that HYD1 has 6 strands, 12 turns and I
helix. It therefore appears that the beta sheet is the most
stable part of the protein. However, for rms fluctuation of
backbone residues each residue is coded according to the
anisotropic temperature (beta) value stored in the pdb file
[13]. Typically, this gives the measure of the mobility of a
given residue’s position. The beta value thus increases in
order from blue-cyan- green- yellow- orange then to red as
shown in Fig. 10.
Figure 9: RMS fluctuations of backbone residues during
simulation
Also, in plot for backbone residues, three residues that form
two beta strands fluctuated the most as indicated by the red
colour in Fig. 10.
Figure 10: RMSF backbone residues as viewed in RasMol
These include Valine-47, Glycine-46 and Leucine-45.
Fluctuations were also noticed with Alanine-26 and
Glytamine-97 residues as they transition to form a fully
solvated and dynamic HYD1 protein.
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Figure 11: Radius of gyration of protein residues over 5ns
Upon compact assessment with g_gyrate which measures the
radius of gyration, the structure of M4T_HYD1 seemed to
collapse from 1.08 nm to 1.04 nm. Unusual peaks were
observed at 1ns and 3ns as the protein tried to resolve into its
original shape, before it finally attained a constant stable
structure at 1.05nm towards the 5ns mark (Fig. 11). The
collapse of the HYD1 protein was probably accompanied by
changes to its secondary structure, as revealed by backbone
fluctuations in the rmsf plot (Fig. 8, 10) and DSSP Table 2.
3.3.2Trajectory Analysis
Trajectory data generated from the classical MD simulation
step and converted to pdb format was viewed using PYMOL
tool. The protein file thus contained 2,500 frames which
caused the protein to rotate around all three axes. Six frames
were thus selected at time intervals shown in Fig. 12 below.
Figure 12: Snapshots of protein conformations in cartoon
representation during the classical MD step
The circled area is a region of beta strands and turns where
most fluctuations where observed (Fig. 7-10). Consistent to
RMSD and Rg plots significant residue/ atomic fluctuations
were observed at 1ns, and 3ns before HYD1 conformed to a
stable dynamic structure between 4ns and 5ns.
Of interest, the simulated protein seem to have slowly
exposed and partly exposed its binding cavity in the
hydrophobic region of strands resulting in an increase in the
surface accessible area for inhibitors to bind to the exposed
pocket. Fig. 13 reveals a gradual reduction of the
hydrophobic area with a sudden drop being observed towards
1ns (which is 1000ps) from 27 nm2
to 21.6 nm2
. However,
from 2ns till the end of the simulation M4T_HYD1 keeps an
average hydrophobic area of 24 nm2
.
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Figure 13: Hydrophobicity measurement as a function of
time during simulation of M4T_HYD1
3.3.3 Overall Conformation Analysis
When the solvated protein now in dynamic form is analyzed
against the original M4T_HYD1 protein, the conformation
shows an RMSD value score of 0.291738 nm. Again the
deviation lies in the acceptable range and can be credited to
the secondary structure changes observed by DSSP (Table
2).
Figuer 14: Superimposed backbone structures of original
and simulated HYD1 protein
Comparison of these two structurally aligned proteins with
DSSP reveals that as HYD1 conformed to a less compact
structure, there were significant loss of beta sheets, and less
of the helix to other secondary structure elements like bends,
hydrogen bond turns and amino acids not in atom records:
Table 2: DSSP three state composition of HYD1
DSSP value (%)
Method M4T_HYD1 Simulated HYD1
Helix 15.3 13.9
Sheet 37.5 23.6
Others 47.2 62.5
However, the total content of sheet against that of helix in the
secondary structure of the simulated protein still remains
greater by approximately double that of helix. This can prove
the theoretical fact that class hydrophobins attain a beta state
in a water solvent.
4.Conclusion and Future Scope
MD simulations were used to compute atomic trajectories by
solving equations of motion numerically using the
GROMOS96 43a1 empirical force field. From a dynamic
point of view the HYD1 protein proved to be thermally
stable in the presence of an explicit water environment at
298K and constant pressure conditions. The protein also
attained a compact structure which was credited to the low
energy fluctuating beta strands. These findings are in
agreement with previous theoretical and experimental
evidence on dynamics of class I hydrophobins in related
filamentous fungi. The authors therefore look forward to use
the simulated M4T_HYD1 structure for docking studies in
pursuit of a potential inhibitor molecule against G.
moniliformis.
Acknowledgements
The authors would like to thank Dr. A. Govardhan, Director,
School of Information Technology (SIT), Jawaharlal Nehru
Technological University Hyderabad (JNTUH) for his
support and encouragement in this research.
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Paper ID: 02015360 683
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ISSN (Online): 2319-7064
Impact Factor (2012): 3.358
Volume 3 Issue 8, August 2014
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Author Profile
Cephas Mawere is an M.Tech Student in the
field of Bioinformatics currently underway at the
SIT, JNTUH, India. He attained his B. Tech.
Degree in Biotechnology from CUT, Zimbabwe
in 2010. He is a Harare Institute of Technology staff
development research fellow. His research interests are in the
area of Microbiology, Molecular Dynamics Simulation,
Computer- Aided Drug Design, High Performance
Computing and Proteomics.
Suresh Kumar G is a Lecturer in Bioinformatics
at School of Information Technology (SIT),
Jawaharlal Nehru Technological University
Hyderabad (JNTUH), Hyderabad, India. He has
received Masters Degree (M.Tech) in Bioinformatics from
University of Hyderabad, Hyderabad, India. His research
interests include Computer- Aided Drug Design Molecular
Modeling, Docking, 3D-QSAR studies, Genomics and
Proteomics, Computational Systems Biology.
Paper ID: 02015360 684