Displaying publications 21 - 40 of 69 in total

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  1. Fulltext Antioxidant and antibacterial activity of Rhoeo spathacea (Swartz) Stearn leaves
    Tan JB, Lim YY, Lee SM
    J Food Sci Technol, 2015 Apr;52(4):2394-400.
    PMID: 25829624 DOI: 10.1007/s13197-013-1236-z
    The decoction and infusion of Rhoeo spathacea (Swartz) Stearn leaves have been recognized as a functional food particularly in South America, but has not yet gained international popularity as a beverage. The primary aim of this study was to establish the viability of R. spathacea aqueous leaf extracts as a beverage, in terms of its antioxidant activity and antibacterial activity. The antioxidant contents of aqueous and methanol leaf extracts were evaluated by the total phenolic content (TPC) and total flavonoid content (TFC) assays. The antioxidant activities measured were DPPH radical scavenging activity (FRS), ferric reducing power (FRP) and ferrous ion chelating (FIC) activity. The aqueous leaf extracts in the forms of decoction and infusion, were found to have comparable TPC and antioxidant activity with other herbal teas previously reported by our research group. Both decoction and infusion also exhibited antibacterial activity against six species of Gram positive and four species of Gram negative bacteria, notably methicillin-resistant Staphylococcus aureus and Neisseria gonorrhoeae. A total of four different known phenolic compounds were identified by HPLC and MS, three of which have not been previously reported to be found in this plant. Both the decoction and infusion of the leaves R. spathacea have potential to be popularized into a common beverage.
  2. Fulltext Antioxidant Content, Antioxidant Activity, and Antibacterial Activity of Five Plants from the Commelinaceae Family
    Tan JB, Yap WJ, Tan SY, Lim YY, Lee SM
    Antioxidants (Basel), 2014 Nov 17;3(4):758-69.
    PMID: 26785239 DOI: 10.3390/antiox3040758
    Commelinaceae is a family of herbaceous flowering plants with many species used in ethnobotany, particularly in South America. However, thus far reports of their bioactivity are few and far between. The primary aim of this study was to quantify the antioxidant and antibacterial activity of five Commelinaceae methanolic leaf extracts. The antioxidant content was evaluated by the total phenolic content (TPC), total tannin content (TTC), and total flavonoid content (TFC) assays. The antioxidant activities measured were DPPH free radical scavenging (FRS), ferric reducing power (FRP), and ferrous ion chelating (FIC); of the five plants, the methanolic leaf extract of Tradescantia zebrina showed the highest antioxidant content and activity, and exhibited antibacterial activity against six species of Gram-positive and two species of Gram-negative bacteria in a range of 5-10 mg/mL based on the broth microdilution method.
  3. Electrospun cellulose acetate butyrate/polyethylene glycol (CAB/PEG) composite nanofibers: A potential scaffold for tissue engineering
    Tan HL, Kai D, Pasbakhsh P, Teow SY, Lim YY, Pushpamalar J
    Colloids Surf B Biointerfaces, 2020 Apr;188:110713.
    PMID: 31884080 DOI: 10.1016/j.colsurfb.2019.110713
    Electrospinning is a common method to prepare nanofiber scaffolds for tissue engineering. One of the common cellulose esters, cellulose acetate butyrate (CAB), has been electrospun into nanofibers and studied. However, the intrinsic hydrophobicity of CAB limits its application in tissue engineering as it retards cell adhesion. In this study, the properties of CAB nanofibers were improved by fabricating the composite nanofibers made of CAB and hydrophilic polyethylene glycol (PEG). Different ratios of CAB to PEG were tested and only the ratio of 2:1 resulted in smooth and bead-free nanofibers. The tensile test results show that CAB/PEG composite nanofibers have 2-fold higher tensile strength than pure CAB nanofibers. The hydrophobicity of the composite nanofibers was also reduced based on the water contact angle analysis. As the hydrophilicity increases, the swelling ability of the composite nanofiber increases by 2-fold with more rapid biodegradation. The biocompatibility of the nanofibers was tested with normal human dermal fibroblasts (NHDF). The cell viability assay results revealed that the nanofibers are non-toxic. In addition to that, CAB/PEG nanofibers have better cell attachment compared to pure CAB nanofibers. Based on this study, CAB/PEG composite nanofibers could potentially be used as a nanofiber scaffold for applications in tissue engineering.
  4. Effects of Aminocarboxylate Ligands of Surface Active Copper(II) Complexes on the Hydrolysis of p-Nitrophenyldiphenylphosphate
    Ship CP, Zainudin A, Lim YY
    J Colloid Interface Sci, 1999 Sep 1;217(1):211-213.
    PMID: 10441432
    The rate of hydrolysis of p-nitrophenyldiphenylphosphate in the presence of micellized [Cu(C(12)tmed)(L)](+) where C(12)tmed is N,N,N'-trimethyl-N'-dodecylethylenediamine and L is the anion part of the amino acid has been investigated. It was found that the observed maximum rate obtained under the excess surfactant over the substrate condition depends very much on the ability of the amino acid ligand to form a mixed-chelate complex with the [Cu(C(12)tmed)](2+) moiety. In general, a chelating ligand with better coordination ability gives a slower rate because of the reduction in the supply of Cu-OH nucleophile in the micelle. Copyright 1999 Academic Press.
  5. Enzymatic synthesis of quercetin oleate esters using Candida antarctica lipase B
    Saik AY, Lim YY, Stanslas J, Choo WS
    Biotechnol Lett, 2017 Feb;39(2):297-304.
    PMID: 27812823 DOI: 10.1007/s10529-016-2246-5
    OBJECTIVES: To investigate the lipase-catalyzed acylation of quercetin with oleic acid using Candida antarctica lipase B.

    RESULTS: Three acylated analogues were produced: quercetin 4'-oleate (C33H42O8), quercetin 3',4'-dioleate (C51H74O9) and quercetin 7,3',4'-trioleate (C69H106O10). Their identities were confirmed with UPLC-ESI-MS and (1)H NMR analyses. The effects of temperature, duration and molar ratio of substrates on the bioconversion yields varied across conditions. The regioselectivity of the acylated quercetin analogues was affected by the molar ratio of substrates. TLC showed the acylated analogues had higher lipophilicity (152% increase) compared to quercetin. Partition coefficient (log P) of quercetin 4'-oleate was higher than those of quercetin and oleic acid. Quercetin 4'-oleate was also stable over 28 days of storage.

    CONCLUSIONS: Quercetin oleate esters with enhanced lipophilicity can be produced via lipase-catalyzed reaction using C. antarctica lipase B to be used in topical applications.

  6. Fulltext Broad specificity of immune helminth scFv library to identify monoclonal antibodies targeting Strongyloides
    Rahumatullah A, Balachandra D, Noordin R, Baharudeen Z, Lim YY, Choong YS, et al.
    Sci Rep, 2021 01 28;11(1):2502.
    PMID: 33510342 DOI: 10.1038/s41598-021-82125-3
    Antibodies have different chemical properties capable of targeting a diverse nature of antigens. Traditionally, immune antibody libraries are perceived to be disease-specific with a skewed repertoire. The complexity during the generation of a combinatorial antibody library allows for a skewed but diverse repertoire to be generated. Strongyloides stercoralis is a parasite that causes strongyloidiasis, a potentially life-threatening disease with a complex diagnosis that impedes effective control and treatment of the disease. This study describes the isolation of monoclonal antibodies against S. stercoralis NIE recombinant protein using an immune antibody phage display library derived from lymphatic filaria-infected individuals. The isolated antibody clones showed both lambda and kappa light chains gene usage, with diverse amino acid distributions. Structural analysis showed that electropositivity and the interface area could determine the binding affinity of the clones with NIE. The successful identification of S. stercoralis antibodies from the filarial immune library highlights the breadth of antibody gene diversification in an immune antibody library that can be applied for closely related infections.
  7. Fulltext Anti-dengue virus serotype 2 activity of tannins from porcupine dates
    Pong LY, Yew PN, Lee WL, Lim YY, Sharifah SH
    Chin Med, 2020;15:49.
    PMID: 32467721 DOI: 10.1186/s13020-020-00329-7
    Background: Dengue fever is currently endemic in tropical and subtropical countries worldwide and effective drug against DENV infection is still unavailable. Porcupine dates, which are traditionally used to treat dengue fever, might contain potential anti-dengue compounds. Two porcupine dates, black date (BD) and powdery date (PD) from Himalayan porcupine (Hystrix brachyura), were investigated for their antiviral activities against DENV-2 in vitro.

    Methods: The methanol crude extracts (MBD and MPD) were prepared from the raw material of porcupine dates. The tannin-rich fractions (BDTF and PDTF) were isolated from their methanol crude extracts using column chromatography. The presence of tannins in BDTF and PDTF extracts was determined by fourier-transform infrared spectroscopy (FTIR) and nuclear magnetic resonance (NMR) analyses. The cytotoxicity and anti-DENV-2 activities including virus yield inhibition, virucidal, virus attachment and pre-treatment assays of the extracts were examined in Vero cells.

    Results: Our findings revealed that all the extracts of porcupine dates exhibited antiviral activity against DENV-2 in Vero cells. The IC50 of BDTF and PDTF were 25 µg/mL and 11 µg/mL respectively, while their methanol crude extracts demonstrated lower antiviral efficacy (IC50 ≈ 101-107 µg/mL). BDTF and PDTF also exerted a similar higher virucidal effect (IC50 of 11 µg/mL) than methanol crude extracts (IC50 ≈ 52-66 µg/mL). Furthermore, all the extracts inhibited the attachment of DENV-2 by at least 80%. Pre-treatments of cells with BDTF and PDTF markedly prevented DENV-2 infection when compared to methanol crude extracts.

    Conclusion: This study suggests that porcupine dates possess antiviral properties against DENV-2, which is attributed to its tannin compounds.

  8. Enhancing the Bandwidth and Energy Production of Piezoelectric Energy Harvester Using Novel Multimode Bent Branched Beam Design for Human Motion Application
    Piyarathna IE, Lim YY, Edla M, Thabet AM, Ucgul M, Lemckert C
    Sensors (Basel), 2023 Jan 26;23(3).
    PMID: 36772411 DOI: 10.3390/s23031372
    In recent years, harvesting energy from ubiquitous ultralow-frequency vibration sources, such as biomechanical motions using piezoelectric materials to power wearable devices and wireless sensors (e.g., personalized assistive tools for monitoring human locomotion and physiological signals), has drawn considerable interest from the renewable energy research community. Conventional linear piezoelectric energy harvesters (PEHs) generally consist of a cantilever beam with a piezoelectric patch and a proof mass, and they are often inefficient in such practical applications due to their narrow operating bandwidth and low voltage generation. Multimodal harvesters with multiple resonances appear to be a viable solution, but most of the previously proposed designs are unsuitable for ultralow-frequency vibration. This study investigated a novel multimode design, which included a bent branched beam harvester (BBBH) to enhance PEHs' bandwidth output voltage and output power for ultralow-frequency applications. The study was conducted using finite element method (FEM) analysis to optimize the geometrical design of the BBBH on the basis of the targeted frequency spectrum of human motion. The selected design was then experimentally studied using a mechanical shaker and human motion as excitation sources. The performance was also compared to the previously proposed V-shaped bent beam harvester (VBH) and conventional cantilever beam harvester (CBH) designs. The results prove that the proposed BBBH could harness considerably higher output voltages and power with lower idle time. Its operating bandwidth was also remarkably widened as it achieved three close resonances in the ultralow-frequency range. It was concluded that the proposed BBBH outperformed the conventional counterparts when used to harvest energy from ultralow-frequency sources, such as human motion.
  9. Fulltext Linear Segmented Arc-Shaped Piezoelectric Branch Beam Energy Harvester for Ultra-Low Frequency Vibrations
    Piyarathna IE, Thabet AM, Ucgul M, Lemckert C, Lim YY, Tang ZS
    Sensors (Basel), 2023 Jun 01;23(11).
    PMID: 37299984 DOI: 10.3390/s23115257
    Piezoelectric energy harvesting systems have been drawing the attention of the research community over recent years due to their potential for recharging/replacing batteries embedded in low-power-consuming smart electronic devices and wireless sensor networks. However, conventional linear piezoelectric energy harvesters (PEH) are often not a viable solution in such advanced practices, as they suffer from a narrow operating bandwidth, having a single resonance peak present in the frequency spectrum and very low voltage generation, which limits their ability to function as a standalone energy harvester. Generally, the most common PEH is the conventional cantilever beam harvester (CBH) attached with a piezoelectric patch and a proof mass. This study investigated a novel multimode harvester design named the arc-shaped branch beam harvester (ASBBH), which combined the concepts of the curved beam and branch beam to improve the energy-harvesting capability of PEH in ultra-low-frequency applications, in particular, human motion. The key objectives of the study were to broaden the operating bandwidth and enhance the harvester's effectiveness in terms of voltage and power generation. The ASBBH was first studied using the finite element method (FEM) to understand the operating bandwidth of the harvester. Then, the ASBBH was experimentally assessed using a mechanical shaker and real-life human motion as excitation sources. It was found that ASBBH achieved six natural frequencies within the ultra-low frequency range (<10 Hz), in comparison with only one natural frequency achieved by CBH within the same frequency range. The proposed design significantly broadened the operating bandwidth, favouring ultra-low-frequency-based human motion applications. In addition, the proposed harvester achieved an average output power of 427 μW at its first resonance frequency under 0.5 g acceleration. The overall results of the study demonstrated that the ASBBH design can achieve a broader operating bandwidth and significantly higher effectiveness, in comparison with CBH.
  10. Fulltext Factors associated with poor academic achievement among urban primary school children in Malaysia
    Ong LC, Chandran V, Lim YY, Chen AH, Poh BK
    Singapore Med J, 2010 Mar;51(3):247-52.
    PMID: 20428748
    The aim of this study was to identify factors associated with poor academic achievement during the early school years.
  11. Current anti-biofilm strategies and potential of antioxidants in biofilm control
    Ong KS, Mawang CI, Daniel-Jambun D, Lim YY, Lee SM
    Expert Rev Anti Infect Ther, 2018 11;16(11):855-864.
    PMID: 30308132 DOI: 10.1080/14787210.2018.1535898
    INTRODUCTION: Biofilm formation is a strategy for microorganisms to adapt and survive in hostile environments. Microorganisms that are able to produce biofilms are currently recognized as a threat to human health. Areas covered: Many strategies have been employed to eradicate biofilms, but several drawbacks from these methods had subsequently raised concerns on the need for alternative approaches to effectively prevent biofilm formation. One of the main mechanisms that drives a microorganism to transit from a planktonic to a biofilm-sessile state, is oxidative stress. Chemical agents that could target oxidative stress regulators, for instance antioxidants, could therefore be used to treat biofilm-associated infections. Expert commentary: The focus of this review is to summarize the function and limitation of the current anti-biofilm strategies and will propose the use of antioxidants as an alternative method to treat, prevent and eradicate biofilms. Studies have shown that water-soluble and lipid-soluble antioxidants can reduce and prevent biofilm formation, by influencing the expression of genes associated with oxidative stress. Further in vivo work should be conducted to ensure the efficacy of these antioxidants in a biological environment. Nevertheless, antioxidants are promising anti-biofilm agents, and thus is a potential solution for biofilm-associated infections in the future.
  12. Approach to preserve phenolics in Thunbergia laurifolia leaves by different drying treatments
    Oh HKF, Siow LF, Lim YY
    J Food Biochem, 2019 07;43(7):e12856.
    PMID: 31353691 DOI: 10.1111/jfbc.12856
    Different drying methods and blanching were investigated as to their effects on antioxidant and oxidase activities of Thunbergia laurifolia leaves. Results showed that oven-drying had the highest degradation of total phenolic content (TPC) and antioxidant activity at >85%, while freeze-drying had the lowest at <20%. However, inactivation of oxidase enzymes by blanching at 100°C resulted in a lesser decrease in TPC for oven-drying at 50 and 100°C (51% and 65%, respectively), indicating the importance of inactivating the oxidase enzymes for lower degradation of phenolics on drying. The high-performance liquid chromatography analysis showed that its major antioxidant, rosmarinic acid, degraded tremendously in the presence of oxidase enzymes, but only degraded slightly upon inactivation of oxidase enzymes. Hence, this work showed that by controlling the enzymatic activity, the preservation of phenolics with specific bioactivity in herbal tea leaves can be achieved. PRACTICAL APPLICATIONS: Thunbergia laurifolia leaves have been frequently consumed in the form of a tea or pill due to its medicinal properties. Processing of fresh herbal plant leaves by drying is required to preserve antioxidant phenolic compounds and quality of the plant leaves. Although the drying effects on the antioxidant properties have been studied, the factors that cause the change in properties have not been investigated in-depth. Controlling the factors that affect the phenolic content can help to preserve the beneficial antioxidants when processing the leaves by drying. The result of this study will be of relevance and beneficial to the herbal tea industry.
  13. Fulltext Inducible RasGEF1B circular RNA is a positive regulator of ICAM-1 in the TLR4/LPS pathway
    Ng WL, Marinov GK, Liau ES, Lam YL, Lim YY, Ea CK
    RNA Biol, 2016 09;13(9):861-71.
    PMID: 27362560 DOI: 10.1080/15476286.2016.1207036
    Circular RNAs (circRNAs) constitute a large class of RNA species formed by the back-splicing of co-linear exons, often within protein-coding transcripts. Despite much progress in the field, it remains elusive whether the majority of circRNAs are merely aberrant splicing by-products with unknown functions, or their production is spatially and temporally regulated to carry out specific biological functions. To date, the majority of circRNAs have been cataloged in resting cells. Here, we identify an LPS-inducible circRNA: mcircRasGEF1B, which is predominantly localized in cytoplasm, shows cell-type specific expression, and has a human homolog with similar properties, hcircRasGEF1B. We show that knockdown of the expression of mcircRasGEF1B reduces LPS-induced ICAM-1 expression. Additionally, we demonstrate that mcircRasGEF1B regulates the stability of mature ICAM-1 mRNAs. These findings expand the inventory of functionally characterized circRNAs with a novel RNA species that may play a critical role in fine-tuning immune responses and protecting cells against microbial infection.
  14. Fulltext Transcriptomic analysis of the role of RasGEF1B circular RNA in the TLR4/LPS pathway
    Ng WL, Marinov GK, Chin YM, Lim YY, Ea CK
    Sci Rep, 2017 09 25;7(1):12227.
    PMID: 28947785 DOI: 10.1038/s41598-017-12550-w
    Circular RNAs (circRNAs) have recently emerged as a large class of novel non-coding RNA species. However, the detailed functional significance of the vast majority of them remains to be elucidated. Most functional characterization studies targeting circRNAs have been limited to resting cells, leaving their role in dynamic cellular responses to stimuli largely unexplored. In this study, we focus on the LPS-induced cytoplasmic circRNA, mcircRasGEF1B, and combine targeted mcircRasGEF1B depletion with high-throughput transcriptomic analysis to gain insight into its function during the cellular response to LPS stimulation. We show that knockdown of mcircRasGEF1B results in altered expression of a wide array of genes. Pathway analysis revealed an overall enrichment of genes involved in cell cycle progression, mitotic division, active metabolism, and of particular interest, NF-κB, LPS signaling pathways, and macrophage activation. These findings expand the set of functionally characterized circRNAs and support the regulatory role of mcircRasGEF1B in immune response during macrophage activation and protection against microbial infections.
  15. Identification of α-tocopherol as a bioactive component of Dicranopteris linearis with disrupting property against preformed biofilm of Staphylococcus aureus
    Mawang CI, Lim YY, Ong KS, Muhamad A, Lee SM
    J Appl Microbiol, 2017 Nov;123(5):1148-1159.
    PMID: 28869803 DOI: 10.1111/jam.13578
    AIMS: The potential of Dicranopteris linearis leaves' extract and its bioactive components were investigated for the first time for its disrupting ability against Staphylococcus aureus biofilms.

    METHODS AND RESULTS: The leaves of D. linearis were subjected to sonication-assisted extraction using hexane (HEX), dichloromethane, ethyl acetate and methanol (MeOH). It was found that only the MeOH fraction exhibited antimicrobial activity using broth microdilution assay; while all four fractions do not exhibit biofilm inhibition activity against S. aureusATCC 6538P, S. aureusATCC 43300, S. aureusATCC 33591 and S. aureusATCC 29213 using crystal violet assay. Among the four fractions tested, only the HEX fraction showed biofilm disrupting ability, with 60-90% disruption activity at 5 mg ml-1against all four S. aureus strains tested. Bioassay-guided purification of the active fraction has led to the isolation of α-tocopherol. α-Tocopherol does not affect the cells within the biofilms but instead affects the biofilm matrix in order to disrupt S. aureus biofilms.

    CONCLUSIONS: α-Tocopherol was identified to be the bioactive component of D. linearis with disruption activity against S. aureus biofilm matrix.

    SIGNIFICANCE AND IMPACT OF THE STUDY: The use of α-tocopherol as a biofilm disruptive agent might potentially be useful to treat biofilm-associated infections in the future.

  16. Fulltext Inhibition of euchromatic histone methyltransferase 1 and 2 sensitizes chronic myeloid leukemia cells to interferon treatment
    Loh SW, Ng WL, Yeo KS, Lim YY, Ea CK
    PLoS One, 2014;9(7):e103915.
    PMID: 25079219 DOI: 10.1371/journal.pone.0103915
    H3K9 methylation is one of the essential histone post-translational modifications for heterochromatin formation and transcriptional repression. Recently, several studies have demonstrated that H3K9 methylation negatively regulates the type I interferon response.
  17. A method for cross-cultural adaptation of a verbal memory assessment
    Lim YY, Prang KH, Cysique L, Pietrzak RH, Snyder PJ, Maruff P
    Behav Res Methods, 2009 Nov;41(4):1190-200.
    PMID: 19897828 DOI: 10.3758/BRM.41.4.1190
    Verbal memory tests-although important to the neuropsychological assessment of memory-are biased to many cultures. In the present article, we highlighted the limitations associated with the direct translation of tests and word matching, as well as the lack of ecological validity and cultural appropriateness when tests developed in one culture are used in another. To overcome these limitations, a verbal memory paradigm was developed that framed the memory assessment with a shopping-list format, but that developed culturally specific stimuli for the different language groups. The aim of the present study was to determine the equivalence of this shopping list memory test in different cultural and language groups. Eighty-three adults from English-, French-, Malay-, and Chinese-speaking cultures participated in four experiments. The results of all the experiments indicated that performance of verbal list learning is equivalent, irrespective of the language used. These results support the use of this methodology for minimizing cross-cultural test bias, and have important implications for testing culturally and linguistically diverse individuals.
  18. Effects of aminoacids on the autooxidation of 3,5-di-tert-butylcatechol in the presence of surface-active copper(II) complexes
    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.
  19. Interaction of Aqueous Solutions of a Surface Active Copper(II) Complex with Several Common Surfactants
    Lim YY, Lim KH
    J Colloid Interface Sci, 1997 Dec 01;196(1):116-9.
    PMID: 9441659
    Micellar properties of binary mixed surfactants of a surface active mixed copper(II) chelate, [Cu(C12-tmed)(acac)Cl] (where C12-tmed is N,N,N'-trimethyl-N'-dodecylethylenediamine) with three common surfactants, viz. sodium dodecyl sulfate (SDS), cetyltrimethylammonium bromide (CTAB), and octaethylene glycol monododecyl ether (C12E8), were investigated by surface tensiometry, ESR, and UV-visible absorption techniques. The surface tension data were treated with Rubingh's method for mixed micelle formation and Rosen's method for mixed monolayer formation at the aqueous solution/air interface. It was found that in the mixed micelle there is strong attractive interaction between cationic copper surfactant and anonic dodecyl sulfate while there is almost ideal mixing between copper surfactant and CTAB and C12E8. From the ESR and UV-visible studies, a mixed block-type arrangement of head groups is proposed. Copyright 1997 Academic Press. Copyright 1997Academic Press
  20. Structural approaches for the DNA binding motifs prediction in Bacillus thuringiensis sigma-E transcription factor (σETF)
    Lim YY, Lim TS, Choong YS
    J Mol Model, 2019 Sep 05;25(10):301.
    PMID: 31486892 DOI: 10.1007/s00894-019-4192-3
    The sigma-E transcription factor (σETF) can be found in most of the bacteria cells including Bacillus thuringiensis. However, the cellular regulatory mechanisms of these transcription factors in the mass production of δ-endotoxins during sporulation stage are yet to be revealed. In addition, the recognition of DNA towards σETF DNA binding motifs that led to the transcription activities is also being poorly studied. Therefore, this work studied the possible DNA binding motifs of σETF by utilising in silico approaches. The structure of σETF was first built via three different computational methods. A cognate DNA sequence was then docked to the predicted σETF DNA-binding motifs. The binding free energy calculated using molecular mechanics/Poisson-Boltzmann surface area (MM-PBSA) for triplicate 50 ns simulation of σETF-DNA complex revealed favourable binding energy of DNA to σETF (average ∆Gbind = -34.57 kcal/mol) mainly driven by non-polar interactions. This study revealed that σETF LYS131, ARG133, PHE138, TRP146, ARG222, LYS225 and ARG226 are most likely the key residues upon the binding and recognition of DNA prior to transcription actives. Since determination of genome-regulating protein which recognises specific DNA sequence is important to discriminate between the proteins preferences for different genes, this study might provide some understanding on the possible σETF-DNA recognition prior to transcription initiated for the δ-endotoxins production.
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