Displaying publications 1 - 20 of 30 in total

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  1. Ghani NSA, Emrizal R, Moffit SM, Hamdani HY, Ramlan EI, Firdaus-Raih M
    Nucleic Acids Res, 2022 Jul 05;50(W1):W375-W383.
    PMID: 35639505 DOI: 10.1093/nar/gkac402
    The GrAfSS (Graph theoretical Applications for Substructure Searching) webserver is a platform to search for three-dimensional substructures of: (i) amino acid side chains in protein structures; and (ii) base arrangements in RNA structures. The webserver interfaces the functions of five different graph theoretical algorithms - ASSAM, SPRITE, IMAAAGINE, NASSAM and COGNAC - into a single substructure searching suite. Users will be able to identify whether a three-dimensional (3D) arrangement of interest, such as a ligand binding site or 3D motif, observed in a protein or RNA structure can be found in other structures available in the Protein Data Bank (PDB). The webserver also allows users to determine whether a protein or RNA structure of interest contains substructural arrangements that are similar to known motifs or 3D arrangements. These capabilities allow for the functional annotation of new structures that were either experimentally determined or computationally generated (such as the coordinates generated by AlphaFold2) and can provide further insights into the diversity or conservation of functional mechanisms of structures in the PDB. The computed substructural superpositions are visualized using integrated NGL viewers. The GrAfSS server is available at http://mfrlab.org/grafss/.
    Matched MeSH terms: Amino Acids/chemistry
  2. Ezzat MA, Zare D, Karim R, Ghazali HM
    Food Chem, 2015 Apr 1;172:893-9.
    PMID: 25442635 DOI: 10.1016/j.foodchem.2014.09.158
    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.
    Matched MeSH terms: Amino Acids/chemistry*
  3. Nadzirin N, Willett P, Artymiuk PJ, Firdaus-Raih M
    Nucleic Acids Res, 2013 Jul;41(Web Server issue):W432-40.
    PMID: 23716645 DOI: 10.1093/nar/gkt431
    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/.
    Matched MeSH terms: Amino Acids/chemistry*
  4. Abdul Rahman MB, Jumbri K, Basri M, Abdulmalek E, Sirat K, Salleh AB
    Molecules, 2010 Apr 05;15(4):2388-97.
    PMID: 20428050 DOI: 10.3390/molecules15042388
    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.
    Matched MeSH terms: Amino Acids/chemistry*
  5. Lim YY, Liew LP
    J Colloid Interface Sci, 2002 Nov 15;255(2):425-7.
    PMID: 12505092
    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.
    Matched MeSH terms: Amino Acids/chemistry*
  6. Daniali G, Jinap S, Sanny M, Tan CP
    Food Chem, 2018 Apr 15;245:1-6.
    PMID: 29287315 DOI: 10.1016/j.foodchem.2017.10.070
    This work investigated the underlying formation of acrylamide from amino acids in frying oils during high temperatures and at different times via modeling systems. Eighteen amino acids were used in order to determine which one was more effective on acrylamide production. Significantly the highest amount of acrylamide was produced from asparagine (5987.5µg/kg) and the lowest from phenylalanine (9.25µg/kg). A constant amount of asparagine and glutamine in palm olein and soy bean oils was heated up in modelling system at different temperatures (160, 180 and 200°C) and times (1.5, 3, 4.5, 6, 7.5min). The highest amount of acrylamide was found at 200°C for 7.5min (9317 and 8511µg/kg) and lowest at 160°C for 1.5min (156 and 254µg/kg) in both frying oils and both amino acids. Direct correlations have been found between time (R2=0.884), temperature (R2=0.951) and amount of acrylamide formation, both at p<0.05.
    Matched MeSH terms: Amino Acids/chemistry*
  7. Ishak AA, Selamat J, Sulaiman R, Sukor R, Abdulmalek E, Jambari NN
    Molecules, 2019 Oct 24;24(21).
    PMID: 31652883 DOI: 10.3390/molecules24213828
    The formation of 2-amino-1-methyl-6-phenylimidazo[4,5-b]pyridine (PhIP) was investigated using a kinetic study approach as described by first-order, Arrhenius, and Eyring equations. Chemical model systems with different amino acid precursors (proline, phenylalanine, and glycine) were examined at different times (4, 8, 12, and 16 min) and temperatures (150, 180, 210, 240, and 270 °C). PhIP was detected using high-performance liquid chromatography equipped with fluorescence detector (HPLC-FLD). The good fit in first-order suggested that PhIP formation was influenced by the types of amino acids and PhIP concentration significantly increased with time and temperature (up to 240 °C). PhIP was detected in proline and phenylalanine model systems but not in the glycine model system. The phenylalanine model system demonstrated low activation energy (Ea) of 95.36 kJ/mol that resulted in a high rate of PhIP formation (great amount of PhIP formed). Based on the ∆S‡ values both proline and phenylalanine demonstrated bimolecular rate-limiting steps for PhIP formation. Altogether these kinetic results could provide valuable information in predicting the PhIP formation pathway.
    Matched MeSH terms: Amino Acids/chemistry*
  8. Camerino MA, Liu M, Moriya S, Kitahashi T, Mahgoub A, Mountford SJ, et al.
    J. Pept. Sci., 2016 Jun;22(6):406-14.
    PMID: 27282137 DOI: 10.1002/psc.2883
    Kisspeptin analogues with improved metabolic stability may represent important ligands in the study of the kisspeptin/KISS1R system and have therapeutic potential. In this paper we assess the activity of known and novel kisspeptin analogues utilising a dual luciferase reporter assay in KISS1R-transfected HEK293T cells. In general terms the results reflect the outcomes of other assay formats and a number of potent agonists were identified among the analogues, including β(2) -hTyr-modified and fluorescently labelled forms. We also showed, by assaying kisspeptin in the presence of protease inhibitors, that proteolysis of kisspeptin activity within the reporter assay itself may diminish the agonist outputs. Copyright © 2016 European Peptide Society and John Wiley & Sons, Ltd.
    Matched MeSH terms: Amino Acids/chemistry*
  9. Azilawati MI, Hashim DM, Jamilah B, Amin I
    J Chromatogr A, 2014 Aug 1;1353:49-56.
    PMID: 24797394 DOI: 10.1016/j.chroma.2014.04.050
    In-house method validation was conducted to determine amino acid composition in gelatin by a pre-column derivatization procedure with the 6-aminoquinolyl-N-hydroxysuccinimidyl carbamate reagent. The analytical parameters revealed that the validated method was capable of selectively performing a good chromatographic separation for 18 amino acids in less than 40 min; the overall detection and quantitation limit for amino acids fell into ranges of 5.68-12.48 and 36.0-39.0 pmol/μl, respectively; the matrix effect was not observed, and the linearity range was 37.5-1000 pmol/μl. The accuracy (precision and recovery) analyses of the method were conducted under repeatable conditions on different days in random order. Method precision revealed by HorRat values was significantly less than 2, except for histidine with a precision of 2.19, and the method recoveries had a range of 80-115% except for alanine which was recovered at 79.4%. The findings were reproducible and accurately defined, and the method was found to be suited to routine analysis of amino acid composition in gelatin-based ingredients.
    Matched MeSH terms: Amino Acids/chemistry
  10. Tan PY, Tan CP, Abas F, Ho CW, Mustapha WA
    Molecules, 2013 Jun 10;18(6):6792-803.
    PMID: 23752466 DOI: 10.3390/molecules18066792
    Palm sugar-like flavouring (PSLF) is a type of flavour product that is formed by heating amino acids and sugar under specific heating conditions. Unfortunately, PSLF has a salty taste and contains high amounts of acrylamide. Hence, the objective of this research was to reduce saltiness and acrylamide without negatively affecting the aroma properties of PSLF. A decrease in the sodium phosphate (NaHPO₄) buffer concentration from 0.20 to 0.02 M was found to reduce sodium to approximately 15% of the level found in original PSLF. A further decrease (~25%) in the sodium content was achieved by removing monobasic sodium phosphate (NaH₂PO₄) from the buffer system. Meanwhile, the addition of CaCl₂ at 20-40 mg/L reduced the acrylamide content in PSLF by as much as 58%. A CaCl₂ concentration of 20 mg/mL was most favourable as it most efficiently suppressed acrylamide formation while providing an acceptably high flavour yield in PSLF. In view of the high acrylamide content in PSLF, additional work is necessary to further reduce the amount of acrylamide by controlling the asparagine concentration in the precursor mixture.
    Matched MeSH terms: Amino Acids/chemistry
  11. Nadzirin N, Gardiner EJ, Willett P, Artymiuk PJ, Firdaus-Raih M
    Nucleic Acids Res, 2012 Jul;40(Web Server issue):W380-6.
    PMID: 22573174 DOI: 10.1093/nar/gks401
    Similarities in the 3D patterns of amino acid side chains can provide insights into their function despite the absence of any detectable sequence or fold similarities. Search for protein sites (SPRITE) and amino acid pattern search for substructures and motifs (ASSAM) are graph theoretical programs that can search for 3D amino side chain matches in protein structures, by representing the amino acid side chains as pseudo-atoms. The geometric relationship of the pseudo-atoms to each other as a pattern can be represented as a labeled graph where the pseudo-atoms are the graph's nodes while the edges are the inter-pseudo-atomic distances. Both programs require the input file to be in the PDB format. The objective of using SPRITE is to identify matches of side chains in a query structure to patterns with characterized function. In contrast, a 3D pattern of interest can be searched for existing occurrences in available PDB structures using ASSAM. Both programs are freely accessible without any login requirement. SPRITE is available at http://mfrlab.org/grafss/sprite/ while ASSAM can be accessed at http://mfrlab.org/grafss/assam/.
    Matched MeSH terms: Amino Acids/chemistry
  12. Muhammad N, Man Z, Bustam MA, Mutalib MI, Wilfred CD, Rafiq S
    Appl Biochem Biotechnol, 2011 Oct;165(3-4):998-1009.
    PMID: 21720837 DOI: 10.1007/s12010-011-9315-y
    In the present work, the dissolution of bamboo biomass was tested using a number of ionic liquids synthesized in laboratory. It was observed that one of the synthesized amino acid-based ionic liquids, namely 1-ethyl-3-methylimidazolium glycinate, was capable of dissolving the biomass completely. The dissolved biomass was then regenerated using a reconstitute solvent (acetone/water) and was characterized using Fourier transform infrared spectroscopy, X-ray diffraction, and scanning electron microscopy. The results were compared to preconditioned bamboo biomass. The regenerated biomass was found to have a more homogenous macrostructure, which indicates that the crystalline form and structure of its cellulose has changed from type Ι to type ΙΙ during the dissolution and regeneration process.
    Matched MeSH terms: Amino Acids/chemistry
  13. Raih MF, Ahmad S, Zheng R, Mohamed R
    Biophys Chem, 2005 Apr 1;114(1):63-9.
    PMID: 15792862
    A non-redundant database of 4536 structural domains, comprising more than 790,000 residues, has been used for the calculation of their solvent accessibility in the native protein environment and then in the isolated domain environment. Nearly 140,000 (18%) residues showed a change in accessible surface area in the above two conditions. General features of this change under these two circumstances have been pointed out. Propensities of these interfacing amino acid residues have been calculated and their variation for different secondary structure types has been analyzed. Actual amount of surface area lost by different secondary structures is higher in the case of helix and strands compared to coil and other conformations. Overall change in surface area in hydrophobic and uncharged residues is higher than that in charged residues. An attempt has been made to know the predictability of interface residues from sequence environments. This analysis and prediction results have significant implications towards determining interacting residues in proteins and for the prediction of protein-protein, protein-ligand, protein-DNA and similar interactions.
    Matched MeSH terms: Amino Acids/chemistry*
  14. Ali NM, Yeap SK, Yusof HM, Beh BK, Ho WY, Koh SP, et al.
    J Sci Food Agric, 2016 Mar 30;96(5):1648-58.
    PMID: 26009985 DOI: 10.1002/jsfa.7267
    BACKGROUND: Mung bean and soybean have been individually reported previously to have antioxidant, cytotoxic and immunomodulatory effects, while fermentation is a well-known process to enhance the bioactive compounds that contribute to higher antioxidant, cytotoxic and immunomodulation effects. In this study, the free amino acids profile, soluble phenolic acids content, antioxidants, cytotoxic and immunomodulatory effects of fermented and non-fermented mung bean and soybean were compared.

    RESULTS: Fermented mung bean was recorded to have the highest level of free amino acids, soluble phenolic acids (especially protocatechuic acid) and antioxidant activities among all the tested products. Both fermented mung bean and soybean possessed cytotoxicity activities against breast cancer MCF-7 cells by arresting the G0/G1 phase followed by apoptosis. Moreover, fermented mung bean and soybean also induced splenocyte proliferation and enhanced the levels of serum interleukin-2 and interferon-γ.

    CONCLUSION: Augmented amounts of free amino acids and phenolic acids content after fermentation enhanced the antioxidants, cytotoxicity and immunomodulation effects of mung bean and soybean. More specifically, fermented mung bean showed the best effects among all the tested products. This study revealed the potential of fermented mung bean and soybean as functional foods for maintenance of good health.

    Matched MeSH terms: Amino Acids/chemistry*
  15. Kavousi P, Mirhosseini H, Ghazali H, Ariffin AA
    Food Chem, 2015 Sep 1;182:164-70.
    PMID: 25842323 DOI: 10.1016/j.foodchem.2015.02.135
    5-Hydroxymethylfurfural (HMF) is formed during heat treatment of carbohydrate-containing foods, especially in a deep-fat frying process. This study aimed to investigate the effect of amino acids on the formation and reduction of HMF from glucose, fructose and sucrose at frying temperature in model systems containing binary mixtures of an amino acid and a sugar in equal concentrations (0.3M). The results revealed that the formation of HMF from sugars accelerated in the presence of acidic amino acids (i.e. glutamic and aspartic acids). Conversely, the presence of basic amino acids (i.e. lysine, arginine and histidine) led to reduced concentrations of HMF to non-detectable levels in model systems. The results showed that both pH and heating time significantly affected the formation of HMF from fructose in the presence of glutamic acid. In this regard, a higher amount of HMF was formed at lower pH.
    Matched MeSH terms: Amino Acids/chemistry
  16. Tan NH, Saifuddin MN
    Int. J. Biochem., 1991;23(3):323-7.
    PMID: 2044840
    1. Substrate specificity of purified king cobra (Ophiophagus hannah) venom L-amino acid oxidase was investigated. 2. The enzyme was highly specific for the L-enantiomer of amino acid. Effective oxidation of L-amino acid by the enzyme requires the presence of a free primary alpha-amino group but the alpha-carboxylate group is not as critical for the catalysis. 3. The enzyme was very active against L-Lys, L-Phe, L-Leu, L-Tyr, L-Tryp, L-Arg, L-Met, L-ornithine, L-norleucine and L-norvaline and moderately active against L-His, L-cystine and L-Ileu. Other L-amino acids were oxidized slowly or not oxidized. 4. The data suggest the presence of a side chain binding site in the enzyme, and that the binding site comprises at least five 'subsites': the hydrophobic subsites a, b and c; and the two 'amino' binding subsites d and e. Subsite b appears to be able to accommodate two methylene/methyl carbons.
    Matched MeSH terms: Amino Acids/chemistry
  17. Juneta-Nor AS, Noordin NM, Azra MN, Ma HY, Husin NM, Ikhwanuddin M
    J Zhejiang Univ Sci B, 2020 10 13;21(10):823-834.
    PMID: 33043647 DOI: 10.1631/jzus.B2000126
    Ecdysis is a common phenomenon that happens throughout the life phase of the giant freshwater prawn Macrobrachium rosenbergii. It is vital to better understand the correlation between cannibalism and biochemical compound that exists during the moulting process. The objective of the present study was to determine the amino acid profile released by M. rosenbergii during the ecdysis process that promotes cannibalism. To accomplish this, changes in amino acid levels (total amino acid (TAA) and free amino acid (FAA)) of tissue muscle, exoskeleton, and sample water of culture medium from the moulting (E-stage) and non-moulting (C-stage) prawns were analysed using high-performance liquid chromatography (HPLC). Comparison study revealed that among the TAA compounds, proline and sarcosine of tissues from moulting prawn were found at the highest levels. The level of FAA from water that contains moulting prawns (E-stage) was dominated by tryptophan and proline. Significant values obtained in the present study suggested that these amino acid compounds act as a chemical cue to promote cannibalism in M. rosenbergii during ecdysis. The knowledge of compositions and compounds that were released during the moulting process should be helpful for better understanding of the mechanism and chemical cues that play roles on triggering cannibalism, and also for future dietary manipulation to improve feeding efficiencies and feeding management, which indirectly impacts productivity and profitability.
    Matched MeSH terms: Amino Acids/chemistry*
  18. Wsoo MA, Shahir S, Mohd Bohari SP, Nayan NHM, Razak SIA
    Carbohydr Res, 2020 May;491:107978.
    PMID: 32163784 DOI: 10.1016/j.carres.2020.107978
    Cellulose acetate (CA) is a remarkable biomaterial most extensively used in biomedical applications due to their properties. This review highlighted the synthesis and chemical structure of CA polymer as well as focused on the mechanical, chemical, thermal, biocompatible, and biodegradable properties of electrospun CA nanofibers. These properties are essential in the evaluation of the CA nanofibers and provide information as a reference for the further utilization and improvement of CA nanofibers. Moreover, we have summarized the use of electrospun CA nanofibers in the drug delivery system as a carrier for drugs and classify them according to the drug class, including anti-inflammatory, anticancer, antioxidant, antimicrobial agents, vitamins and amino acids. Our review has been concluded that CA nanofibers cannot wholly be biodegraded within the human body due to the absence of cellulase enzyme but degraded by microorganisms. Hence, the biodegradation of CA nanofibers in vivo has addressed as a critical challenge.
    Matched MeSH terms: Amino Acids/chemistry
  19. Hun Lee T, Hau Lee C, Alia Azmi N, Kavita S, Wong S, Znati M, et al.
    Chem Biodivers, 2020 Jan;17(1):e1900419.
    PMID: 31721431 DOI: 10.1002/cbdv.201900419
    This work investigated the polar (PC: protein, amino acid and metabolite) and non-polar (NPC: fatty acid) compounds and bioactivity characteristics of the EBN harvested from the state of Johor in Malaysia. The electrophoretic gels exhibited 15 protein bands (16-173 kD) with unique protein profile. Amino acids analysis by AccQ⋅Tag method revealed 18 types of amino acids in EBN. Metabolite profiling was performed using High-Performance Liquid Chromatography coupled with Quadrupole Time-of-Flight Mass Spectrometer (HPLC-QTOF/MS) technique and a total of 54 compounds belonging to different groups were detected and identified. These findings help to uncover the relation of therapeutic activity of EBN. The EBN was further extracted with AcOEt and BuOH. The AcOEt extract was fractionated into three fractions (F1 -F3 ), and the high triglyceride content in F2 was verified by gC-FID. The three groups of fatty acids discovered in EBN are 48.43 % of poly-unsaturated (PUFA), 25.35 % of saturated fatty acids (SFA) and 24.74 % of mono-unsaturated fat (MUFA). This is the first time to report results ofEBN, BuOH, and AcOEt extracts and of fraction F2 (TEBN) on their analysis for their antioxidant activities by DPPH, ABTS and catalase assay and for their paraoxonase and anti-tyrosinase activities. The results showed that TEBN exhibited the significant bioactivity in all assays. These findings suggest that TEBN is a good source for natural bioactive compounds in promoting body vigor. Current work widened the content of EBN especially on the triglyceride and also marked the content of specific location (Johor, Malaysia) of EBN origin.
    Matched MeSH terms: Amino Acids/chemistry
  20. Adamu A, Wahab RA, Shamsir MS, Aliyu F, Huyop F
    Comput Biol Chem, 2017 Oct;70:125-132.
    PMID: 28873365 DOI: 10.1016/j.compbiolchem.2017.08.007
    The l-2-haloacid dehalogenases (EC 3.8.1.2) specifically cleave carbon-halogen bonds in the L-isomers of halogenated organic acids. These enzymes have potential applications for the bioremediation and synthesis of various industrial products. One such enzyme is DehL, the l-2-haloacid dehalogenase from Rhizobium sp. RC1, which converts the L-isomers of 2-halocarboxylic acids into the corresponding D-hydroxycarboxylic acids. However, its catalytic mechanism has not been delineated, and to enhance its efficiency and utility for environmental and industrial applications, knowledge of its catalytic mechanism, which includes identification of its catalytic residues, is required. Using ab initio fragment molecular orbital calculations, molecular mechanics Poisson-Boltzmann surface area calculations, and classical molecular dynamic simulation of a three-dimensional model of DehL-l-2-chloropropionic acid complex, we predicted the catalytic residues of DehL and propose its catalytic mechanism. We found that when Asp13, Thr17, Met48, Arg51, and His184 were individually replaced with an alanine in silico, a significant decrease in the free energy of binding for the DehL-l-2-chloropropionic acid model complex was seen, indicating the involvement of these residues in catalysis and/or structural integrity of the active site. Furthermore, strong inter-fragment interaction energies calculated for Asp13 and L-2-chloropropionic acid, and for a water molecule and His184, and maintenance of the distances between atoms in the aforementioned pairs during the molecular dynamics run suggest that Asp13 acts as the nucleophile and His184 activates the water involved in DehL catalysis. The results of this study should be important for the rational design of a DehL mutant with improved catalytic efficiency.
    Matched MeSH terms: Amino Acids/chemistry
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