Protein-protein interactions (PPIs) play a major role in many biological processes and they represent an important class of targets for therapeutic intervention. However, targeting PPIs is challenging because often no convenient natural substrates are available as starting point for small-molecule design. Here, we explored the characteristics of protein interfaces in five non-redundant datasets of 174 protein-protein (PP) complexes, and 161 protein-ligand (PL) complexes from the ABC database, 436 PP complexes, and 196 PL complexes from the PIBASE database and a dataset of 89 PL complexes from the Timbal database. In all cases, the small molecule ligands must bind at the respective PP interface. We observed similar amino acid frequencies in all three datasets. Remarkably, also the characteristics of PP contacts and overlapping PL contacts are highly similar.
IN connexion with a programme of studies of the relationships between biochemical and ethnological differentiations (some aspects of which have already been discussed1) proceeding in this Department, we wished to explore the possibility of improving existing procedures for the estimation of amino-acids separated on paper chromatograms2, before beginning an investigation of the patterns of urinary excretion of amino-acids by normal members of various ethnic groups living in Malaya.
Amino acids (AAs) are vital elements for growth, reproduction, and maintenance of organisms. Current technology uses genetically engineered microorganisms for AAs production, which has urged the search for a safer food-grade AA producer strain. The extracellular proteolytic activities of lactic acid bacteria (LAB) can be a vital tool to hydrolyze extracellular protein molecules into free AAs, thereby exhibiting great potential for functional AA production. In this study, eight LAB isolated from Malaysian foods were determined for their extracellular proteolytic activities and their capability of producing AAs. All studied LAB exhibited versatile extracellular proteolytic activities from acidic to alkaline pH conditions. In comparison, Pediococcus pentosaceus UP-2 exhibited the highest ability to produce 15 AAs extracellularly, including aspartate, lysine, methionine, threonine, isoleucine, glutamate, proline, alanine, valine, leucine, tryptophan, tyrosine, serine, glycine, and cystine, followed by Pediococcus pentosaceus UL-2, Pediococcus acidilactici UB-6, and Pediococcus acidilactici UP-1 with 11 to 12 different AAs production detected extracellularly. Pediococcus pentosaceus UL-6 demonstrated the highest increment of proline production at 24 h of incubation. However, Pediococcusacidilactici UL-3 and Lactobacillus plantarum I-UL4 exhibited the greatest requirement for AA. The results of this study showed that different LAB possess different extracellular proteolytic activities and potentials as extracellular AA producers.
Amino acids are known as anabolic factors that are essential for formation of muscle by stimulating protein synthesis while inhibiting proteolysis, and they are significant component for the synthesis of various nitrogenous compounds. There are 20 amino acids are essential to require in cell for formation of body protein of which about 10 amino acids, which cannot be synthesized by the birds are termed essential. Among the essential amino acid arginine one of the essential amino acids for chickens because, like other birds, they are unable to obtain Arginine from endogenous sources due to the absence of most of the enzymes involved in the urea cycle. This amino acid involved in synthesis of proline, hydroxyl proline and polyamines which are essential for connective tissue synthesis as well as increased growth of chicken. Moreover, L-arginine (L-Arg) is effective for reducing fat deposition in broiler. Moreover, it decrease heat stress increase meat quality and increase immune response of broiler. This re-view presents the recent advances in the relevance of the inclusion of excess L-Arginine in broiler ration to growth, fat deposition and immune response in broiler.
Ficus deltoidea (FD) is one of the native plants widely distributed in several countries in Southeast Asia. Previous studies have shown that FD leaf possess antinociceptive, wound healing and antioxidant properties. These beneficial effects have been attributed to the presence of primary and secondary metabolites such as polyphenols, amino acids and flavonoids.
1. Two species of snakehead fish are available in Sabah, i.e. Channa striatus and Channa melanosoma, and are commonly known as haruan. Haruan is consumed by many Malaysians to induce healing after a clinical operations. However, there is no scientific evidence as yet to substantiate the claim, and so it was decided to analyse the biochemical composition in haruan to determine which compounds may have a possible role or potential in wound healing. 2. Samples (midline fillet) of both species were extracted separately in hexane for the qualitative analysis of fatty acids by a gas chromatography, Hewlett-Packard 5890A, using a 10 meter superox 11 column (Alltech) at temperature between 190 and 245 degrees C. Peak areas were calculated automatically using Hewlett-Packard 3393A computing integrator. Subsequently, the amino acid composition was analysed using a precolumn derivatization reverse phase HPLC waters PICO-TAG system. 3. Haruan is found to contain unusually high arachidonic acid (AA) but almost no eicosapentaenoic acid (EPA). AA which is a precursor of prostaglandin may initiate blood clotting and be responsible for growth. Haruan also contains all the essential amino acids for wound healing, particularly glycine which is the most important component of human skin collagen. Therefore, haruan contained all the basic biochemical requirements for wound healing.
Seaweed contains various nutrients that has the potential to be a source of nutritious food, but only a few studies done on
the red seaweeds in Malaysia. Therefore, this study was conducted to determine the macronutrients content, amino acid
profile and fatty acid component in Kappaphycus alvarezii and Kappaphycus striatum. The study found that the range
of moisture, fat, ash, protein, fiber and carbohydrates content for both red seaweeds were 6.9% - 7.3%, 0.5% - 2.6%,
29.4% - 30.9%, 2.5% - 5.7% , 5.3% - 5.5% and 50.1% - 53.3% respectively. A total of 16 amino acids were identified
in which the essential amino acid for K. alvarezii and K. striatum were 41.11% and 36.15% respectively. A total of 34
fatty acids were identified in which the content of saturated fatty acids (SFA) was the highest (42.7% - 72.8%), followed
by mono-unsaturated fatty acid (MUFA) (13.8% - 36.2%) and polyunsaturated fatty acids (PUFAs) was the lowest (13.5%
- 21.2%). In conclusion, this study suggest that K. alvarezii and K. striatum are potentially be used as raw materials or
food ingredients to improve the nutritional value of the human diet.
The aim of this paper was to describe the effects of treated sugar palm yarn fibre loading on the mechanical properties
of reinforced unsaturated polyester composites. Composites with varying fibre loads (10, 20, 30, 40 and 50 wt. %) were
prepared using a hand-layup process. The composites were tested for tensile, flexural and impact strength according to
ASTM D3930, ASTM D790 and ASTM D256 standards, respectively. The results showed that an increase in fibre loading
of up to 30 wt. % increased tensile strength (31.27 MPa), tensile modulus (4.83 GPa), flexural strength (58.14 MPa)
and modulus (4.48 GPa). Maximum loading can be attained at 40 wt. % of fibre loading for impact strength (38 kJ/
m2). The effectiveness of stress transfer mechanism through the fibre-matrix interaction, coupled with the optimization
of fibre loading in resisting fracture and failure, boosts the overall mechanical performance of sugar palm composite.
Ikan pekasam is a fermented fish product produced in Malaysia and is usually made from freshwater fish with ground roasted uncooked rice as the main source of carbohydrate. In this study, the amino acid, biogenic amine, and trans- and cis-urocanic acid (UCA) contents of fifteen commercial samples of Ikan pekasam made from Javanese carp and black tilapia, that had undergone either natural or acid-assisted fermentation, were quantified. The latter includes either tamarind (Tamarindus indica) pulp or dried slices of Garcinia atroviridis fruit in the fermentation process. Results showed that there are no significant differences in most of the biogenic amines including histamine, while there are significant differences in total UCA content, and trans- and cis-UCA contents between the two samples. Differences in the amino acid contents were largely fish-dependent.
A new robust, simple and economic high performance thin layer chromatographic method was developed for simultaneous estimation of L-glutamic acid and γ-amino butyric acid in brain homogenate. The high performance thin layer chromatographic separation of these amino acid was achieved using n-butanol:glacial acetic acid:water (22:3:5 v/v/v) as mobile phase and ninhydrin as a derivatising agent. Quantitation of the method was achieved by densitometric method at 550 nm over the concentration range of 10-100 ng/spot. This method showed good separation of amino acids in the brain homogenate with Rf value of L-glutamic acid and γ-amino butyric acid as 21.67±0.58 and 33.67±0.58, respectively. The limit of detection and limit of quantification for L-glutamic acid was found to be 10 and 20 ng and for γ-amino butyric acid it was 4 and 10 ng, respectively. The method was also validated in terms of accuracy, precision and repeatability. The developed method was found to be precise and accurate with good reproducibility and shows promising applicability for studying pathological status of disease and therapeutic significance of drug treatment.
The purpose of this study was to investigate the relationship of biochemical (enzymes) and nutritional components in the selected honey samples from Malaysia. The relationship is important to estimate the quality of honey based on the concentration of these nutritious components. Such a study is limited for honey samples from tropical countries with heavy rainfall throughout the year.
Optimisation of protein extraction yield from pinto bean was investigated using response surface methodology. The maximum protein yield of 54.8 mg/g was obtained with the optimal conditions of: temperature=25 °C, time=1 h and buffer-to-sample ratio=20 ml/g. PBPI was found to obtain high amount of essential amino acids such as leucine, lysine, and phenylalanine compared to SPI. The predominant proteins of PBPI were vicilin and phytohemagglutinins whereas the predominant proteins of SPI were glycinin and conglycinins. Significantly higher emulsifying capacity was found in PBPI (84.8%) compared to SPI (61.9%). Different isoelectric points were found in both PBPI (4.0-5.5) and SPI (4.0-5.0). Also, it was found that PBPI obtained a much higher denaturation temperature of 110.2 °C compared to SPI (92.5 °C). Other properties such as structural information, gelling capacity, water- and oil-holding capacities, emulsion stability as well as digestibility were also reported.
We describe a server that allows the interrogation of the Protein Data Bank for hypothetical 3D side chain patterns that are not limited to known patterns from existing 3D structures. A minimal side chain description allows a variety of side chain orientations to exist within the pattern, and generic side chain types such as acid, base and hydroxyl-containing can be additionally deployed in the search query. Moreover, only a subset of distances between the side chains need be specified. We illustrate these capabilities in case studies involving arginine stacks, serine-acid group arrangements and multiple catalytic triad-like configurations. The IMAAAGINE server can be accessed at http://mfrlab.org/grafss/imaaagine/.
Soy sauce taste has become a focus of umami taste research. Umami taste is a 5th basic taste, which is associated to a palatable and pleasurable taste of food. Soy sauce has been used as an umami seasoning since the ancient time in Asia. The complex fermentation process occurred to soy beans, as the raw material in the soy sauce production, gives a distinct delicious taste. The recent investigation on Japanese and Indonesian soy sauces revealed that this taste is primarily due to umami components which have molecular weights lower than 500 Da. Free amino acids are the low molecular compounds that have an important role to the taste, in the presence of sodium salt. The intense umami taste found in the soy sauces may also be a result from the interaction between umami components and other tastants. Small peptides are also present, but have very low, almost undetected umami taste intensities investigated in their fractions.
This paper reports the synthesis of a series of new tetraethylammonium-based amino acid chiral ionic liquids (CILs). Their physico-chemical properties, including melting point, thermal stability, viscosity and ionic conductivity, have been comprehensively studied. The obtained results indicated that the decomposition for these salts proceeds in one step and the temperature of decomposition (T(onset)) is in the range of 168-210 degrees C. Several new CILs prepared in this work showed high ionic conductivity compared to the amino acid ionic liquids (AAILs) found in the literature.
High environmental temperature has detrimental effects on the gastrointestinal tract of poultry. An experiment was conducted to determine the effect of acute heat stress on endogenous amino acid (EAA) flow in broiler chickens. A total of 90, day-old broiler chicks were housed in battery cages in an environmentally controlled chamber. Chicks were fed a nitrogen-free diet on day 42 following either no heat exposure (no-heat) or 2 weeks exposure to 35 ± 1 °C for 3 h from days 28 to 42 (2-week heat) or 1 week exposure to 35 ± 1 °C for 3 h from days 35 to 42 (1 week heat). The most abundant amino acid in the ileal flow was glutamic acid, followed by aspartic acid, serine and threonine in non-heat stressed group. The EAA flow in 1-week heat and 2-week heat birds were significantly (p < 0.05) higher than those under no heat exposure (14682, 11161 and 9597 mg/kg of dry matter intake respectively). Moreover, the EAA flow of 2-week heat group was less than 1-week heat group by approximately 36%. These observations suggest that the effect of heat stress on EAA flow is mostly quantitative; however, heat stress may also alter the content of EAA flow qualitatively.
The effect of preparation methods (raw, half-boiled and hard-boiled) on protein and amino acid contents, as well as the protein quality (amino acid score) of regular, kampung and nutrient enriched Malaysian eggs was investigated.
The protein content was determined using a semi-micro Kjeldahl method whereas the amino acid composition was determined using HPLC.
The protein content of raw regular, kampung and nutrient enriched eggs were 49.9 ±0.2%, 55.8 ±0.2% and 56.5 ±0.5%, respectively. The protein content of hard-boiled eggs of regular, kampung and nutrient enriched eggs was 56.8 ±0.1%, 54.7 ±0.1%, and 53.7 ±0.5%, while that for half-boiled eggs of regular, kampung and nutrient enriched eggs was 54.7 ±0.6%, 53.4 ±0.4%, and 55.1 ±0.7%, respectively. There were significant differences (p < 0.05) in protein and amino acid contents of half-boiled, hard-boiled as compared with raw samples, and valine was found as the limiting amino acid. It was found that there were significant differences (p < 0.05) of total amino score in regular, kampung and nutrient enriched eggs after heat treatments.Furthermore, hard-boiling (100°C) for 10 minutes and half-boiling (100°C) for 5 minutes affects the total amino score, which in turn alter the protein quality of the egg.
The rate of autooxidation of 3,5-di-tert-butylcatechol (3,5-DTBC) in the presence of micelles formed from mixing equal concentrations of [Cu(C(12)-tmed)Br(2)] (where C(12)-tmed is N,N,N'-trimethyl-N'-dodecylethylenediamine) and several amino acids has been investigated. It was found that the rate in air-saturated solution is very much dependent on pH, which affects the availability of copper(II) coordination site for the catechol and the degree of micellization. At a given pH, the rates in [Cu(C(12)-tmed)Br(2)] micellar media are greatly enhanced in the presence sodium halide.
Quantitative structure-retention relationship(QSRR) method was used to model reversed-phase high-performance liquid chromatography (RP-HPLC) separation of 18 selected amino acids. Retention data for phenylthiocarbamyl (PTC) amino acids derivatives were obtained using gradient elution on ODS column with mobile phase of varying acetonitrile, acetate buffer and containing 0.5 ml/l of triethylamine (TEA). Molecular structure of each amino acid was encoded with 36 calculated molecular descriptors. The correlation between the molecular descriptors and the retention time of the compounds in the calibration set was established using the genetic neural network method. A genetic algorithm (GA) was used to select important molecular descriptors and supervised artificial neural network (ANN) was used to correlate mobile phase composition and selected descriptors with the experimentally derived retention times. Retention time values were used as the network's output and calculated molecular descriptors and mobile phase composition as the inputs. The best model with five input descriptors was chosen, and the significance of the selected descriptors for amino acid separation was examined. Results confirmed the dominant role of the organic modifier in such chromatographic systems in addition to lipophilicity (log P) and molecular size and shape (topological indices) of investigated solutes.