Abstract: In order to find the particular interaction energy
between cylcloguanil and the amino acids surrounding the pocket of
wild type and quadruple mutant type PfDHFR enzymes, the MP2
method with basis set 6-31G(d,p) level of calculations was
performed. The obtained interaction energies found that Asp54 has
the strongest interaction energy to both wild type and mutant type of -
12.439 and -11.250 kcal/mol, respectively and three amino acids;
Asp54, Ile164 and Ile14 formed the H-bonding with cycloguanil
drug. Importantly, the mutation at Ser108Asn was the key important
of cycloguanil resistant with showing repulsive interaction energy.
Abstract: Pummelo is known to be the largest of all citrus fruits, with expected ratio of 2:1 (w/v) of producing juice, is an attractive opportunity for Malaysia to expand pummelo-s influence and marketability over the international market of juices. The purpose of this study is to identify and quantify the phenolic compounds in two Malaysian varieties of pummelo fruit juice: Ledang (PO55) and Tambun (PO52). Identifications of polyphenols composition were done using High Performance Liquid Chromatography Diode Array Detection (HPLC-DAD). The phenolic compounds that were found in both varieties were hydroxycinnamic acids and flavonones. This study proved that Tambun variety has the highest antioxidant and phenolic compounds in comparison to Ledang variety. However, considerations have to be made to suit consumer-s taste bud and the amount of enzyme needed to clarify the juice for its marketability.
Abstract: Oxidative stress is considered to be the cause for onset
and the progression of type 2 diabetes mellitus (T2DM) and
complications including neuropathy. It is a deleterious process that
can be an important mediator of damage to cell structures: protein,
lipids and DNA. Data suggest that in patients with diabetes and
diabetic neuropathy DNA repair is impaired, which prevents effective
removal of lesions. Objective: The aim of our study was to evaluate
the association of the hOGG1 (326 Ser/Cys) and XRCC1 (194
Arg/Trp, 399 Arg/Gln) gene polymorphisms whose protein is
involved in the BER pathway with DNA repair efficiency in patients
with diabetes type 2 and diabetic neuropathy compared to the healthy
subjects. Genotypes were determined by PCR-RFLP analysis in 385
subjects, including 117 with type 2 diabetes, 56 with diabetic
neuropathy and 212 with normal glucose metabolism. The
polymorphisms studied include codon 326 of hOGG1 and 194, 399
of XRCC1 in the base excision repair (BER) genes. Comet assay was
carried out using peripheral blood lymphocytes from the patients and
controls. This test enabled the evaluation of DNA damage in cells
exposed to hydrogen peroxide alone and in the combination with the
endonuclease III (Nth). The results of the analysis of polymorphism
were statistically examination by calculating the odds ratio (OR) and
their 95% confidence intervals (95% CI) using the ¤ç2-tests. Our data
indicate that patients with diabetes mellitus type 2 (including those
with neuropathy) had higher frequencies of the XRCC1 399Arg/Gln
polymorphism in homozygote (GG) (OR: 1.85 [95% CI: 1.07-3.22],
P=0.3) and also increased frequency of 399Gln (G) allele (OR: 1.38
[95% CI: 1.03-1.83], P=0.3). No relation to other polymorphisms
with increased risk of diabetes or diabetic neuropathy. In T2DM
patients complicated by neuropathy, there was less efficient repair of
oxidative DNA damage induced by hydrogen peroxide in both the
presence and absence of the Nth enzyme. The results of our study
suggest that the XRCC1 399 Arg/Gln polymorphism is a significant
risk factor of T2DM in Polish population. Obtained data suggest a
decreased efficiency of DNA repair in cells from patients with
diabetes and neuropathy may be associated with oxidative stress.
Additionally, patients with neuropathy are characterized by even
greater sensitivity to oxidative damage than patients with diabetes,
which suggests participation of free radicals in the pathogenesis of
neuropathy.
Abstract: The overall objective of this research is a strain
improvement technology for efficient pectinase production. A novel
cells cultivation technology by immobilization of fungal cells has
been studied in long time continuous fermentations. Immobilization
was achieved by using of new material for absorption of stores of
immobilized cultures which was for the first time used for
immobilization of microorganisms. Effects of various conditions of
nitrogen and carbon nutrition on the biosynthesis of pectolytic
enzymes in Aspergillus awamori 1-8 strain were studied. Proposed
cultivation technology along with optimization of media components
for pectinase overproduction led to increased pectinase productivity
in Aspergillus awamori 1-8 from 7 to 8 times. Proposed technology
can be applied successfully for production of major industrial
enzymes such as α-amylase, protease, collagenase etc.
Abstract: This study proposes a basic molecular formula for all
proteins. A total of 10,739 proteins belonging to 9 different protein
groups classified on the basis of their functions were selected
randomly. They included enzymes, storage proteins, hormones,
signalling proteins, structural proteins, transport proteins,
immunoglobulins or antibodies, motor proteins and receptor proteins.
After obtaining the protein molecular formula using the ProtParam
tool, the H/C, N/C, O/C, and S/C ratios were determined for each
randomly selected sample. In this case, H, N, O, and S coefficients
were specified per carbon atom. Surprisingly, the results
demonstrated that H, N, O, and S coefficients for all 10,739 proteins
are similar and highly correlated. This study demonstrates that
despite differences in the structure and function, all known proteins
have a similar basic molecular formula CnH1.58 ± 0.015nN0.28 ± 0.005nO0.30
± 0.007nS0.01 ± 0.002n. The total correlation between all coefficients was
found to be 0.9999.
Abstract: Structured phospholipids from commercial soybean
lecithin with oil enriched omega-3 fatty acid form by product of tuna
canning is alternative procedure to provides the stability of omega-3
fatty acid structure and increase these bioactive function in
metabolism. Best treatment condition was obtain in 18 hours
acidolysis reaction with 30% enzyme concentration, which EPADHA
incorporation level was 127,47 mg/g and incorporation
percentage of EPA-DHA was 51,04% at phospholipids structure.
This structured phospolipids could reduce atherosclerosis risk in
male Sprague dawley rat. Provision of structured phospholipids has
significant effect (α = 0.05) on changes in lipid profile, intima-media
thickness of aorta rats (male Sprague dawley) fed atherogenic diet.
Structured phospholipids intake can lower total cholesterol 78.36
mg/dL, total triglycerides 94,57 mg/dL, LDL levels 87.08 mg/dL and
increased HDL level as much as 12,64 mg/dL in 10 weeks cares.
Structured phospholipids intake also can prevent the thickening of
the intima-media layer of the aorta.
Abstract: Formaldehyde is the illegal chemical substance used
for food preservation in fish and vegetable. It can promote
carcinogenesis. Superoxide dismutases are the important
antioxidative enzymes that catalyze the dismutation of superoxide
anion into oxygen and hydrogen peroxide. The resultant level of
oxidative stress in formaldehyde-treated lymphocytes was
investigated. The formaldehyde concentrations of 0, 20, 40, 60, 80
and 120μmol/L were treated in human lymphocytes for 12 hours.
After 12 treated hours, the superoxide dismutase activity change was
measured in formaldehyde-treated lymphocytes. The results showed
that the formaldehyde concentrations of 60, 80 and 120μmol/L
significantly decreased superoxide dismutase activities in
lymphocytes (P < 0.05). The change of superoxide dismutase
activity in formaldehyde-treated lymphocytes may be the biomarker
for detect cellular injury, such as damage to DNA, due to
formaldehyde exposure.
Abstract: The present study was conducted to investigate the
response of plants exposed to lignite-based thermal power plant
emission. For this purpose, five plant species were collected from 1.0
km distance (polluted site) and control plants were collected from
20.0 km distance (control site) to thermal power plant. The common
tree species Cassia siamea Lamk., Polyalthia longifolia. Sonn,
Acacia longifolia (Andrews) Wild., Azadirachta indica A.Juss, Ficus
religiosa L. were selected as test plants. Photosynthetic pigments
changes (chlorophyll a, chlorophyll b and carotenoids) and rubisco
enzyme modifications were studied. Reduction was observed in the
photosynthetic pigments of plants growing in polluted site and also
large sub unit of the rubisco enzyme was degraded in Azadirachta
indica A. Juss collected from polluted site.
Abstract: 17α-ethinylestradiol (EE2) is a recalcitrant micropollutant which is found in small amounts in municipal wastewater. But these small amounts still adversely affect for the reproductive function of aquatic organisms. Evidence in the past suggested that full-scale WWTPs equipped with nitrification process enhanced the removal of EE2 in the municipal wastewater. EE2 has been proven to be able to be transformed by ammonia oxidizing bacteria (AOB) via co-metabolism. This research aims to clarify the EE2 degradation pattern by different consortium of ammonia oxidizing microorganism (AOM) including AOA (ammonia oxidizing archaea) and investigate contribution between the existing ammonia monooxygenase (AMO) and new synthesized AOM. The result showed that AOA or AOB of N. oligotropha cluster in enriched nitrifying activated sludge (NAS) from 2mM and 5mM, commonly found in municipal WWTPs, could degrade EE2 in wastewater via co-metabolism. Moreover, the investigation of the contribution between the existing ammonia monooxygenase (AMO) and new synthesized AOM demonstrated that the new synthesized AMO enzyme may perform ammonia oxidation rather than the existing AMO enzyme or the existing AMO enzyme may has a small amount to oxidize ammonia.
Abstract: A new strategy for oriented immobilization of proteins was proposed. The strategy contains two steps. The first step is to search for a docking site away from the active site on the protein surface. The second step is trying to find a ligand that is able to grasp the targeted site of the protein. To avoid ligand binding to the active site of protein, the targeted docking site is selected to own opposite charges to those near the active site. To enhance the ligand-protein binding, both hydrophobic and electrostatic interactions need to be included. The targeted docking site should therefore contain hydrophobic amino acids. The ligand is then selected through the help of molecular docking simulations. The enzyme α-amylase derived from Aspergillus oryzae (TAKA) was taken as an example for oriented immobilization. The active site of TAKA is surrounded by negatively charged amino acids. All the possible hydrophobic sites on the surface of TAKA were evaluated by the free energy estimation through benzene docking. A hydrophobic site on the opposite side of TAKA-s active site was found to be positive in net charges. A possible ligand, 3,3-,4,4- – Biphenyltetra- carboxylic acid (BPTA), was found to catch TAKA by the designated docking site. Then, the BPTA molecules were grafted onto silica gels and measured the affinity of TAKA adsorption and the specific activity of thereby immobilized enzymes. It was found that TAKA had a dissociation constant as low as 7.0×10-6 M toward the ligand BPTA on silica gel. The increase in ionic strength has little effect on the adsorption of TAKA, which indicated the existence of hydrophobic interaction between ligands and proteins. The specific activity of the immobilized TAKA was compared with the randomly adsorbed TAKA on primary amine containing silica gel. It was found that the orderly immobilized TAKA owns a specific activity twice as high as the one randomly adsorbed by ionic interaction.
Abstract: The effect of phosphorus supplementation of ammoniated rice straw was studied. The in vitro experiment was carried out following the first stage of Tilley and Terry method. The treatments consisting of four diets were A = 50% ammoniated rice straw + 50% concentrate (control), B = A + 0.2% Phosphor (P) supplement, C = A + 0.4% Phosphor (P) supplement, and D = A + 0.6% Phosphor (P) supplement of dry matter. Completely randomized design was used as the experimental design with differences among treatment means were examined using Duncan multiple range test. Variables measured were total bacterial and cellulolytic bacterial population, cellulolytic enzyme activity, ammonia (NH3) and volatile fatty acid (VFA) concentrations, as fermentability indicators and synthesized microbial protein, as well as degradability indicators including dry matter (DM), organic matter (OM), neutral detergent fibre (NDF), acid detergent fibre (ADF) and cellulose. The results indicated that fermentability and degradability of diets consisting ammoniated rice straw with P supplementation were significantly higher than the control diet (P< 0.05). It is concluded that P supplementation is important to improve fermentability and degradability of rations containing ammoniated RS and concentrate. In terms of the most effective level of P supplementation occurred at a supplementation rate of 0.4% of dry matter.
Abstract: Agricultural residue such as oil palm fronds (OPF) is
cheap, widespread and available throughout the year. Hemicelluloses
extracted from OPF can be hydrolyzed to their monomers and used in
production of xylooligosaccharides (XOs). The objective of the
present study was to optimize the enzymatic hydrolysis process of
OPF hemicellulose by varying pH, temperature, enzyme and substrate
concentration for production of XOs. Hemicelluloses was extracted
from OPF by using 3 M potassium hydroxide (KOH) at temperature of
40°C for 4 hrs and stirred at 400 rpm. The hemicellulose was then
hydrolyzed using Trichoderma longibrachiatum xylanase at different
pH, temperature, enzyme and substrate concentration. XOs were
characterized based on reducing sugar determination. The optimum
conditions to produced XOs from OPF hemicellulose was obtained at
pH 4.6, temperature of 40°C , enzyme concentration of 2 U/mL and
2% substrate concentration. The results established the suitability of
oil palm fronds as raw material for production of XOs.
Abstract: The halophilic proteinase showed a maximal activity
at 50°C and pH 9~10, in 20% NaCl and was highly stabilized by
NaCl. It was able to hydrolyse natural actomyosin (NAM), collagen
and anchovy protein. For NAM hydrolysis, the myosin heavy chain
was completely digested by halophilic proteinase as evidenced by the
lowest band intensity remaining, but partially hydrolysed actin. The
SR5-3 proteinase was also capable hydrolyzing two major
components of collagen, β- and α-compounds, effectively. The
degree of hydrolysis (DH) of the halophilic proteinase and
commercial proteinases (Novozyme, Neutrase, chymotrypsin and
Flavourzyme) on the anchovy protein, were compared, and it was
found that the proteinase showed a greater degree of hydrolysis
towards anchovy protein than that from commercial proteinases. DH
of halophilic proteinase was sharply enhanced according to the
increase in the concentration of enzyme from 0.035 U to 0.105 U.
The results warranting that the acceleration of the production of fish
sauce with higher quality, may be achieved by adding of the
halophilic proteinase from this bacterium.
Abstract: Nowadays, butyl acetate, a pineapple flavor has been applied widely in food, beverage, cosmetic and pharmaceutical industries. In this study, Butyl acetate, a flavor ester was successfully synthesized via green synthesis of enzymatic reaction route. Commercial immobilized lipase from Rhizomucor miehei (Lipozyme RMIM) was used as biocatalyst in the esterification reaction between acetic acid and butanol. Various reaction parameters such as reaction time (RT), temperature (T) and amount of enzyme (E) were chosen to optimize the reaction synthesis in solvent-free system. The optimum condition to produce butyl acetate was at reaction time (RT), 18 hours; temperature (T), 37°C and amount of enzyme, 25 % (w/w of total substrate). Analysis of yield showed that at optimum condition, >78 % of butyl acetate was produced. The product was confirmed as butyl acetate from FTIR analysis whereby the presence of an ester group was observed at wavenumber of 1742 cm-1.
Abstract: Tandem mass spectrometry (MS/MS) is the engine
driving high-throughput protein identification. Protein mixtures possibly
representing thousands of proteins from multiple species are
treated with proteolytic enzymes, cutting the proteins into smaller
peptides that are then analyzed generating MS/MS spectra. The
task of determining the identity of the peptide from its spectrum
is currently the weak point in the process. Current approaches to de
novo sequencing are able to compute candidate peptides efficiently.
The problem lies in the limitations of current scoring functions. In this
paper we introduce the concept of proteome signature. By examining
proteins and compiling proteome signatures (amino acid usage) it is
possible to characterize likely combinations of amino acids and better
distinguish between candidate peptides. Our results strongly support
the hypothesis that a scoring function that considers amino acid usage
patterns is better able to distinguish between candidate peptides. This
in turn leads to higher accuracy in peptide prediction.
Abstract: The enzyme alkaline protease production was determined under
solid state fermentation using the soil bacteria Serratia marcescens
sp7. The maximum production was obtained from wheat bran
medium than ground nut shell and chemically defined medium. The
physiological fermentation factors such as pH of the medium (pH 8),
Temperature (40oC) and incubation time (48 hrs) played a vital role
in alkaline protease production in all the above. 100Mm NaCl has
given better resolution during elution of the enzymes. The enzyme
production was found to be associated with growth of the bacterial
culture.
Abstract: Carbonic anhydrases (CAs) has been focused as
biological catalysis for CO2 sequestration process because it can
catalyze the conversion of CO2 to bicarbonate. Here, codon-optimized
sequence of α type-CA cloned from Duneliala species. (DsCAopt) was
constructed, expressed, and characterized. The expression level in E.
coli BL21(DE3) was better for codon-optimized DsCAopt than intact
sequence of DsCAopt. DsCAopt enzyme shows high-stability at pH
7.6/10.0. In final, we demonstrated that in the Ca2+ solution, DsCAopt
enzyme can catalyze well the conversion of CO2 to CaCO3, as the
calcite form.
Abstract: Malting is usually carried out on intact barley seed,
while hull is still attached to it. In this study, oat grain with and
without hull was subjected to controlled germination to optimize its
enzymes activity, in such a way that lipase has the lowest and α-
amylase and proteinase the highest activities. Since pH has a great
impact on the activity of the enzymes, the pH of germination media
was set up to 3 to 8. In dehulled oats, lipase and α-amylase had the
lowest and highest activities in pHs 3 and 6, respectively whereas the
highest proteinase activity was evidenced at pH 7 and 4 in the oats
with and without hull respectively. While measurements indicated
that the effect of hull on the enzyme activities particularly in lipase
and amylase at each level of the pH are significantly different, the
best results were obtained in those samples in which their hull had
been removed. However, since the similar lipase activity in
germinated dehulled oat were recorded at the pHs 4 and 5, therefore
it was concluded that pH 5 in dehulled oat seed may provide the
optimum enzyme activity for all the enzymes.
Abstract: Lignocellulosic materials are new targeted source to
produce second generation biofuels like biobutanol. However, this
process is significantly resisted by the native structure of biomass.
Therefore, pretreatment process is always essential to remove
hemicelluloses and lignin prior to the enzymatic hydrolysis.
The goals of pretreatment are removing hemicelluloses and
lignin, increasing biomass porosity, and increasing the enzyme
accessibility. The main goal of this research is to study the important
variables such as pretreatment temperature and time, which can give
the highest total sugar yield in pretreatment step by using dilute
phosphoric acid. After pretreatment, the highest total sugar yield of
13.61 g/L was obtained under an optimal condition at 140°C for 10
min of pretreatment time by using 1.75% (w/w) H3PO4 and at 15:1
liquid to solid ratio. The total sugar yield of two-stage process
(pretreatment+enzymatic hydrolysis) of 27.38 g/L was obtained.
Abstract: 3-hydroxy-3-methylglutaryl coenzyme A reductase (HMGR) catalyzes the conversion of HMG-CoA to mevalonate using NADPH and the enzyme is involved in rate-controlling step of mevalonate. Inhibition of HMGR is considered as effective way to lower cholesterol levels so it is drug target to treat hypercholesterolemia, major risk factor of cardiovascular disease. To discover novel HMGR inhibitor, we performed structure-based pharmacophore modeling combined with molecular dynamics (MD) simulation. Four HMGR inhibitors were used for MD simulation and representative structure of each simulation were selected by clustering analysis. Four structure-based pharmacophore models were generated using the representative structure. The generated models were validated used in virtual screening to find novel scaffolds for inhibiting HMGR. The screened compounds were filtered by applying drug-like properties and used in molecular docking. Finally, four hit compounds were obtained and these complexes were refined using energy minimization. These compounds might be potential leads to design novel HMGR inhibitor.