Displaying publications 21 - 40 of 61 in total

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  1. Heterologous Expression of PA8FAD9 and Functional Characterization of a Δ9-Fatty Acid Desaturase from a Cold-Tolerant Pseudomonas sp. A8
    Garba L, Ali MS, Oslan SN, Rahman RN
    Mol Biotechnol, 2016 Nov;58(11):718-728.
    PMID: 27629791
    Fatty acid desaturase enzymes are capable of inserting double bonds between carbon atoms of saturated fatty acyl-chains to produce unsaturated fatty acids. A gene coding for a putative Δ9-fatty acid desaturase-like protein was isolated from a cold-tolerant Pseudomonas sp. A8, cloned and heterologously expressed in Escherichia coli. The gene named as PA8FAD9 has an open reading frame of 1185 bp and codes for 394 amino acids with a predicted molecular weight of 45 kDa. The enzyme showed high Δ9-fatty acid desaturase-like protein activity and increased overall levels of cellular unsaturated fatty acids in the recombinant E. coli cells upon expression at different temperatures. The results showed that the ratio of palmitoleic to palmitic acid in the recombinant E. coli cells increased by more than twice the amount observed in the control cells at 20 °C using 0.4 mM IPTG. GCMS analysis confirmed the ability of this enzyme to convert exogenous stearic acid to oleic acid incorporated into the recombinant E. coli membrane phospholipids. It may be concluded that the PA8FAD9 gene from Pseudomonas sp. A8 codes for a putative Δ9-fatty acid desaturase protein actively expressed in E. coli under the influence of temperature and an inducer.
  2. Fulltext Expression and characterization of thermotolerant lipase with broad pH profiles isolated from an Antarctic Pseudomonas sp strain AMS3
    Latip W, Raja Abd Rahman RNZ, Chor Leow AT, Mohd Shariff F, Mohamad Ali MS
    PeerJ, 2016;4:e2420.
    PMID: 27781152 DOI: 10.7717/peerj.2420
    A gene encoding a thermotolerant lipase with broad pH was isolated from an Antarctic Pseudomonas strain AMS3. The recombinant lipase AMS3 was purified by single-step purification using affinity chromatography, yielding a purification fold of approximately 1.52 and a recovery of 50%. The molecular weight was approximately ∼60 kDa including the strep and affinity tags. Interestingly, the purified Antarctic AMS3 lipase exhibited broad temperature profile from 10-70 °C and stable over a broad pH range from 5.0 to pH 10.0. Various mono and divalent metal ions increased the activity of the AMS3 lipase, but Ni(2+) decreased its activity. The purified lipase exhibited the highest activity in the presence of sunflower oil. In addition, the enzyme activity in 25% v/v solvents at 50 °C particularly to n-hexane, DMSO and methanol could be useful for catalysis reaction in organic solvent and at broad temperature.
  3. Fulltext Enhancement of a protocol purifying T1 lipase through molecular approach
    Che Hussian CHA, Raja Abd Rahman RNZ, Thean Chor AL, Salleh AB, Mohamad Ali MS
    PeerJ, 2018;6:e5833.
    PMID: 30479887 DOI: 10.7717/peerj.5833
    T1 Lipase is a thermostable secretary protein of Geobacillus zalihae strain previously expressed in a prokaryotic system and purified using three-step purification: affinity 1, affinity 2, and ion exchange chromatography (IEX). This approach is time consuming and offers low purity and recovery yield. In order to enhance the purification strategy of T1 lipase, affinity 2 was removed so that after affinity 1, the cleaved Glutathione S-transferase (GST) and matured T1 lipase could be directly separated through IEX. Therefore, a rational design of GST isoelectric point (pI) was implemented by prediction using ExPASy software in order to enhance the differences of pI values between GST and matured T1 lipase. Site-directed mutagenesis at two locations flanking the downstream region of GST sequences (H215R and G213R) was successfully performed. Double point mutations changed the charge on GST from 6.10 to 6.53. The purified lipase from the new construct GST tag mutant-T1 was successfully purified using two steps of purification with 6,849 U/mg of lipase specific activity, 33% yield, and a 44-fold increase in purification. Hence, the increment of the pI values in the GST tag fusion T1 lipase resulted in a successful direct separation through IEX and lead to successful purification.
  4. Fulltext Optimized artificial neural network to improve the accuracy of estimated fault impedances and distances for underground distribution system
    Naidu K, Ali MS, Abu Bakar AH, Tan CK, Arof H, Mokhlis H
    PLoS One, 2020;15(1):e0227494.
    PMID: 31999711 DOI: 10.1371/journal.pone.0227494
    This paper proposes an approach to accurately estimate the impedance value of a high impedance fault (HIF) and the distance from its fault location for a distribution system. Based on the three-phase voltage and current waveforms which are monitored through a single measurement in the network, several features are extracted using discrete wavelet transform (DWT). The extracted features are then fed into the optimized artificial neural network (ANN) to estimate the HIF impedance and its distance. The particle swarm optimization (PSO) technique is employed to optimize the parameters of the ANN to enhance the performance of fault impedance and distance estimations. Based on the simulation results, the proposed method records encouraging results compared to other methods of similar complexity for both HIF impedance values and estimated distances.
  5. Opportunistic yeast pathogen Candida spp.: Secreted and membrane-bound virulence factors
    Lim SJ, Mohamad Ali MS, Sabri S, Muhd Noor ND, Salleh AB, Oslan SN
    Med Mycol, 2021 Dec 03;59(12):1127-1144.
    PMID: 34506621 DOI: 10.1093/mmy/myab053
    Candidiasis is a fungal infection caused by Candida spp. especially Candida albicans, C. glabrata, C. parapsilosis and C. tropicalis. Although the medicinal therapeutic strategies have rapidly improved, the mortality rate as candidiasis has continuously increased. The secreted and membrane-bound virulence factors (VFs) are responsible for fungal invasion, damage and translocation through the host enterocytes besides the evasion from host immune system. VFs such as agglutinin-like sequences (Als), heat shock protein 70, phospholipases, secreted aspartyl proteinases (Sap), lipases, enolases and phytases are mostly hydrolases which degrade or interact with the enterocyte membrane components. Candidalysin, however, acts as a peptide toxin to induce necrotic cell lysis. To date, structural studies of the VFs remain underexplored, hindering their functional analyses. Among the VFs, only Sap and Als have their structures deposited in Protein Data Bank (PDB). Therefore, this review scrutinizes the mechanisms of these VFs by discussing the VF-deficient studies of several Candida spp. and their abilities to produce these VFs. Nonetheless, their latest reported sequential and structural analyses are discussed to impart a wider perception of the host-pathogen interactions and potential vaccine or antifungal drug targets. This review signifies that more VFs structural investigations and mining in the emerging Candida spp. are required to decipher their pathogenicity and virulence mechanisms compared to the prominent C. albicans.

    LAY SUMMARY: Candida virulence factors (VFs) including mainly enzymes and proteins play vital roles in breaching the human intestinal barrier and causing deadly invasive candidiasis. Limited VFs' structural studies hinder deeper comprehension of their mechanisms and thus the design of vaccines and antifungal drugs against fungal infections.

  6. Fulltext Directed Evolution of Recombinant C-Terminal Truncated Staphylococcus epidermidis Lipase AT2 for the Enhancement of Thermostability
    Veno J, Ahmad Kamarudin NH, Mohamad Ali MS, Masomian M, Raja Abd Rahman RNZ
    Int J Mol Sci, 2017 Nov 04;18(11).
    PMID: 29113034 DOI: 10.3390/ijms18112202
    In the industrial processes, lipases are expected to operate at temperatures above 45 °C and could retain activity in organic solvents. Hence, a C-terminal truncated lipase from Staphylococcus epidermis AT2 (rT-M386) was engineered by directed evolution. A mutant with glycine-to-cysteine substitution (G210C) demonstrated a remarkable improvement of thermostability, whereby the mutation enhanced the activity five-fold when compared to the rT-M386 at 50 °C. The rT-M386 and G210C lipases were purified concurrently using GST-affinity chromatography. The biochemical and biophysical properties of both enzymes were investigated. The G210C lipase showed a higher optimum temperature (45 °C) and displayed a more prolonged half-life in the range of 40-60 °C as compared to rT-M386. Both lipases exhibited optimal activity and stability at pH 8. The G210C showed the highest stability in the presence of polar organic solvents at 50 °C compared to the rT-M386. Denatured protein analysis presented a significant change in the molecular ellipticity value above 60 °C, which verified the experimental result on the temperature and thermostability profile of G210C.
  7. Guest-host Relationship of Cyclodextrin and its Pharmacological Benefits
    Alshati F, Alahmed TAA, Sami F, Ali MS, Majeed S, Murtuja S, et al.
    Curr Pharm Des, 2023;29(36):2853-2866.
    PMID: 37946351 DOI: 10.2174/0113816128266398231027100119
    Many methods, including solid dispersion, micellization, and inclusion complexes, have been employed to increase the solubility of potent drugs. Beta-cyclodextrin (βCD) is a cyclic oligosaccharide consisting of seven glucopyranoside molecules, and is a widely used polymer for formulating soluble inclusion complexes of hydrophobic drugs. The enzymatic activity of Glycosyltransferase or α-amylase converts starch or its derivatives into a mixture of cyclodextrins. The βCD units are characterized by α -(1-4) glucopyranose bonds. Cyclodextrins possess certain properties that make them very distinctive because of their toroidal or truncated cage-like supramolecular configurations with multiple hydroxyl groups at each end. This allowed them to encapsulate hydrophobic compounds by forming inclusion complexes without losing their solubility in water. Chemical modifications and newer derivatives, such as methylated βCD, more soluble hydroxyl propyl methyl βCD, and sodium salts of sulfobutylether-βCD, known as dexolve® or captisol®, have envisaged the use of CDs in various pharmaceutical, medical, and cosmetic industries. The successful inclusion of drug complexes has demonstrated improved solubility, bioavailability, drug resistance reduction, targeting, and penetration across skin and brain tissues. This review encompasses the current applications of β-CDs in improving the disease outcomes of antimicrobials and antifungals as well as anticancer and anti-tubercular drugs.
  8. Fulltext Crystallization and preliminary X-ray crystallographic analysis of highly thermostable L2 lipase from the newly isolated Bacillus sp. L2
    Shariff FM, Rahman RN, Ali MS, Chor AL, Basri M, Salleh AB
    Acta Crystallogr Sect F Struct Biol Cryst Commun, 2010 Jun 1;66(Pt 6):715-7.
    PMID: 20516608 DOI: 10.1107/S174430911001482X
    Purified thermostable recombinant L2 lipase from Bacillus sp. L2 was crystallized by the counter-diffusion method using 20% PEG 6000, 50 mM MES pH 6.5 and 50 mM NaCl as precipitant. X-ray diffraction data were collected to 2.7 A resolution using an in-house Bruker X8 PROTEUM single-crystal diffractometer system. The crystal belonged to the primitive orthorhombic space group P2(1)2(1)2(1), with unit-cell parameters a = 87.44, b = 94.90, c = 126.46 A. The asymmetric unit contained one single molecule of protein, with a Matthews coefficient (V(M)) of 2.85 A(3) Da(-1) and a solvent content of 57%.
  9. Fulltext Crystallization and preliminary X-ray crystallographic analysis of a thermostable organic solvent-tolerant lipase from Bacillus sp. strain 42
    Khusaini MS, Rahman RN, Mohamad Ali MS, Leow TC, Basri M, Salleh AB
    Acta Crystallogr Sect F Struct Biol Cryst Commun, 2011 Mar 01;67(Pt 3):401-3.
    PMID: 21393852 DOI: 10.1107/S1744309111002028
    An organic solvent-tolerant lipase from Bacillus sp. strain 42 was crystallized using the capillary-tube method. The purpose of studying this enzyme was in order to better understand its folding and to characterize its properties in organic solvents. By initially solving its structure in the native state, further studies on protein-solvent interactions could be performed. X-ray data were collected at 2.0 Å resolution using an in-house diffractometer. The estimated crystal dimensions were 0.09×0.19×0.08 mm. The crystal belonged to the monoclinic space group C2, with unit-cell parameters a=117.41, b=80.85, c=99.44 Å, β=96.40°.
  10. Fulltext Spray-dried immobilized lipase from Geobacillus sp. strain ARM in sago
    Mohtar NS, Abdul Rahman MB, Mustafa S, Mohamad Ali MS, Raja Abd Rahman RNZ
    PeerJ, 2019;7:e6880.
    PMID: 31183251 DOI: 10.7717/peerj.6880
    Sago starch is traditionally used as food especially in Southeast Asia. Generally, sago is safe for consumption, biodegradable, easily available and inexpensive. Therefore, this research was done to expand the potential of sago by using it as a support for enzyme immobilization. In this study, ARM lipase, which was isolated from Geobacillus sp. strain ARM, was overexpressed in Escherichia coli system and then purified using affinity chromatography. The specific activity of the pure enzyme was 650 U/mg, increased 7 folds from the cell lysate. The purified enzyme was immobilized in gelatinized sago and spray-dried by entrapment technique in order to enhance the enzyme operational stability for handling at high temperature and also for storage. The morphology of the gelatinized sago and immobilized enzyme was studied by scanning electron microscopy. The results showed that the spray-dried gelatinized sago was shrunken and became irregular in structure as compared to untreated sago powder. The surface areas and porosities of spray-dried gelatinized sago with and without the enzyme were analyzed using BET and BJH method and have shown an increase in surface area and decrease in pore size. The immobilized ARM lipase showed good performance at 60-80  °C, with a half-life of 4 h and in a pH range 6-9. The immobilized enzyme could be stored at 10 °C with the half-life for 9 months. Collectively, the spray-dried immobilized lipase shows promising capability for industrial uses, especially in food processing.
  11. Fulltext Quantification of Berberine in Berberis vulgaris L. Root Extract and Its Curative and Prophylactic Role in Cisplatin-Induced In Vivo Toxicity and In Vitro Cytotoxicity
    Ahmad S, Hussain A, Hussain A, Abdullah I, Ali MS, Froeyen M, et al.
    Antioxidants (Basel), 2019 Jun 19;8(6).
    PMID: 31248160 DOI: 10.3390/antiox8060185
    Cisplatin is amongst the most potent chemotherapeutic drugs with applications in more than 50% of cancer treatments, but dose-dependent side effects limit its usefulness. Berberis vulgaris L. (B. vulgaris) has a proven role in several therapeutic applications in the traditional medicinal system. High-performance liquid chromatography was used to quantify berberine, a potent alkaloid in the methanolic root extract of B. vulgaris (BvRE). Berberine chloride in BvRE was found to be 10.29% w/w. To assess the prophylactic and curative protective effects of BvRE on cisplatin-induced nephrotoxicity, hepatotoxicity, and hyperlipidemia, in vivo toxicity trials were carried out on 25 healthy male albino Wistar rats (130-180 g). Both prophylactic and curative trials included a single dose of cisplatin (4 mg/kg, i.p.) and nine doses of BvRE (500 mg/kg/day, orally). An array of marked toxicity effects appeared in response to cisplatin dosage evident by morphological condition, biochemical analysis of serum (urea, creatinine, total protein, alanine transaminase, aspartate transaminase, total cholesterol, and triglyceride), and organ tissue homogenates (malondialdehyde and catalase). Statistically-significant (p < 0.05) variations were observed in various parameters. Moreover, histological studies of liver and kidney tissues revealed that the protective effect of BvRE effectively minimized and reversed nephrotoxic, hepatotoxic, and hyperlipidemic effects caused by cisplatin in both prophylactic and curative groups with relatively promising ameliorative effects in the prophylactic regimen. The in vitro cell viability effect of cisplatin, BvRE, and their combination was determined on HeLa cells using the tetrazolium (MTT) assay. MTT clearly corroborated that HeLa cells appeared to be less sensitive to cisplatin and berberine individually, while the combination of both at the same concentrations resulted in growth inhibition of HeLa cells in a remarkable synergistic way. The present study validated the use of BvRE as a protective agent in combination therapy with cisplatin.
  12. Fulltext Molecular Cloning and Functional Expression of a Δ9- Fatty Acid Desaturase from an Antarctic Pseudomonas sp. A3
    Garba L, Mohamad Ali MS, Oslan SN, Rahman RN
    PLoS One, 2016;11(8):e0160681.
    PMID: 27494717 DOI: 10.1371/journal.pone.0160681
    Fatty acid desaturase enzymes play an essential role in the synthesis of unsaturated fatty acids. Pseudomonas sp. A3 was found to produce a large amount of palmitoleic and oleic acids after incubation at low temperatures. Using polymerase Chain Reaction (PCR), a novel Δ9- fatty acid desaturase gene was isolated, cloned, and successfully expressed in Escherichia coli. The gene was designated as PA3FAD9 and has an open reading frame of 1,185 bp which codes for 394 amino acids with a predicted molecular weight of 45 kDa. The activity of the gene product was confirmed via GCMS, which showed a functional putative Δ9-fatty acid desaturase capable of increasing the total amount of cellular unsaturated fatty acids of the E. coli cells expressing the gene. The results demonstrate that the cellular palmitoleic acids have increased two-fold upon expression at 15°C using only 0.1 mM IPTG. Therefore, PA3FAD9 from Pseudomonas sp.A3 codes for a Δ9-fatty acid desaturase-like protein which was actively expressed in E. coli.
  13. Night eating and its relationship with BMI, stress, sleep quality and duration of study among university students
    Emmy HKI, Boleh NC, Ali MS, Jakiwa J, Mardiyati NL, Ahmad MF
    Med J Malaysia, 2024 Mar;79(Suppl 1):134-139.
    PMID: 38555898
    INTRODUCTION: Night eating is a very common dietary behaviour among university students. This study aims to investigate the relationship between night eating and BMI, stress, sleep quality and duration of study among university students.

    MATERIALS AND METHODS: A total of 385 university students including foundation and undergraduate students took part in this study. Self-administered online surveys were used to obtain sociodemographic data, and anthropometry measurements including weight and height, night eating during studying, duration of the study, opinion on eating and academic performance, sleep quality, level of depression, anxiety, and stress of the respondents. Questionnaires were validated and IBM SPSS Statistics Software version 26.0 was used to analyse categorical and continuous variables.

    RESULTS: The findings showed that there was an association between night eaters and coffee consumption with BMI (p<0.001) and sleep quality (p<0.05). However, there was no association (p>0.05) found between the types of food eaten during night studying and the mean duration of the study. The results showed drinking coffee had an association with depression, anxiety, and stress (p<0.05) among Malaysian university students.

    CONCLUSION: Coffee consumption was common among undergraduate students during studying. Awareness of the risk of overconsumption of caffeine intake should be implemented in the future. However, this study did not include all types of food choices and drinks. Thus, frequency of eating energy dense food during night studying among students should be conducted in the future.

  14. Fulltext Mechanistic Studies of the Antiallergic Activity of Phyllanthus amarus Schum. & Thonn. and Its Compounds
    Abd Rani NZ, Lam KW, Jalil J, Mohamad HF, Mat Ali MS, Husain K
    Molecules, 2021 Jan 28;26(3).
    PMID: 33525733 DOI: 10.3390/molecules26030695
    Phyllanthus amarus Schum. & Thonn. (Phyllanthaceae) is a medicinal plant that is commonly used to treat diseases such as asthma, diabetes, and anemia. This study aimed to examine the antiallergic activity of P. amarus extract and its compounds. The antiallergic activity was determined by measuring the concentration of allergy markers release from rat basophilic leukemia (RBL-2H3) cells with ketotifen fumarate as the positive control. As a result, P. amarus did not stabilize mast cell degranulation but exhibited antihistamine activity. The antihistamine activity was evaluated by conducting a competition radioligand binding assay on the histamine 1 receptor (H1R). Four compounds were identified from the high performance liquid chromatography (HPLC) analysis which were phyllanthin (1), hypophyllanthin (2), niranthin (3), and corilagin (4). To gain insights into the binding interactions of the most active compound hypophyllanthin (2), molecular docking was conducted and found that hypophyllanthin (2) exhibited favorable binding in the H1R binding site. In conclusion, P. amarus and hypophyllanthin (2) could potentially exhibit antiallergic activity by preventing the activation of the H1 receptor.
  15. Bibliometric analysis and thematic review of Candida pathogenesis: Fundamental omics to applications as potential antifungal drugs and vaccines
    Lim SJ, Muhd Noor ND, Sabri S, Mohamad Ali MS, Salleh AB, Oslan SN
    Med Mycol, 2024 Jan 09;62(1).
    PMID: 38061839 DOI: 10.1093/mmy/myad126
    Invasive candidiasis caused by the pathogenic Candida yeast species has resulted in elevating global mortality. The pathogenicity of Candida spp. is not only originated from its primary invasive yeast-to-hyphal transition; virulence factors (transcription factors, adhesins, invasins, and enzymes), biofilm, antifungal drug resistance, stress tolerance, and metabolic adaptation have also contributed to a greater clinical burden. However, the current research theme in fungal pathogenicity could hardly be delineated with the increasing research output. Therefore, our study analysed the research trends in Candida pathogenesis over the past 37 years via a bibliometric approach against the Scopus and Web of Science databases. Based on the 3993 unique documents retrieved, significant international collaborations among researchers were observed, especially between Germany (Bernhard Hube) and the UK (Julian Naglik), whose focuses are on Candida proteinases, adhesins, and candidalysin. The prominent researchers (Neils Gow, Alistair Brown, and Frank Odds) at the University of Exeter and the University of Aberdeen (second top performing affiliation) UK contribute significantly to the mechanisms of Candida adaptation, tolerance, and stress response. However, the science mapping of co-citation analysis performed herein could not identify a hub representative of subsequent work since the clusters were semi-redundant. The co-word analysis that was otherwise adopted, revealed three research clusters; the cluster-based thematic analyses indicated the severeness of Candida biofilm and antifungal resistance as well as the elevating trend on molecular mechanism elucidation for drug screening and repurposing. Importantly, the in vivo pathogen adaptation and interactions with hosts are crucial for potential vaccine development.
  16. Advancements in Perovskite-Based Cathode Materials for Solid Oxide Fuel Cells: A Comprehensive Review
    Samreen A, Ali MS, Huzaifa M, Ali N, Hassan B, Ullah F, et al.
    Chem Rec, 2024 Jan;24(1):e202300247.
    PMID: 37933973 DOI: 10.1002/tcr.202300247
    The high-temperature solid oxide fuel cells (SOFCs) are the most efficient and green conversion technology for electricity generation from hydrogen-based fuel as compared to conventional thermal power plants. Many efforts have been made to reduce the high operating temperature (>800 °C) to intermediate/low operating temperature (400 °C
  17. Catalytically active inclusion bodies as a potential tool for biotechnology
    Bello MN, Sabri S, Mohd Yahaya N, Mohd Shariff F, Mohamad Ali MS
    Biotechnol Appl Biochem, 2024 Dec;71(6):1235-1242.
    PMID: 38863240 DOI: 10.1002/bab.2624
    The initial assumption that viewed inclusion bodies as a hindrance to the efficient production of protein is no longer held due to the emergence of catalytically active inclusion bodies (CatIBs). Recent studies revealed their potential to be used in free form or immobilized as biocatalysts. The curiosity to acquire suitable catalysts has remained the measure of concern for researchers and industrialists. Numerous processes and production in various sectors of food industries, petroleum, pharmaceutical, cosmetics, and many others are still searching for a robust catalyst with outstanding features such as recyclability, resistance to pH, as well as temperature. CatIBs are forms of inclusion bodies that possess catalytic activity, which can improve catalysis efficiency, stability, and recyclability. One of the advantages of CatIBs is their potential to be used as catalysts for numerous bioprocesses when generated by an enzyme. These aggregates can efficiently be used as a replacement for traditional enzyme immobilization. This review tends to focus on the possibility of its application in various processes. The novelty of this review is that it considered the production of CatIBs both from artificial and natural perspectives, as well as how to improve it. Inclusion bodies' immobilization may provide an efficient alternative in the area of biocatalysis, and hence it will improve industrial sectors and substantially provide a means of achieving excellent performance in the near future.
  18. Features of the rare pathogen Meyerozyma guilliermondii strain SO and comprehensive in silico analyses of its adherence-contributing virulence factor agglutinin-like sequences
    Lim SJ, Muhd Noor ND, Sabri S, Mohamad Ali MS, Salleh AB, Oslan SN
    J Biomol Struct Dyn, 2025 Apr;43(7):3728-3748.
    PMID: 38189364 DOI: 10.1080/07391102.2023.2300757
    Meyerozyma guilliermondii is a rare yeast pathogen contributing to the deadly invasive candidiasis. M. guilliermondii strain SO, as a promising protein expression host, showed 99% proteome similarity with the clinically isolated ATCC 6260 (type strain) in a recent comparative genomic analysis. However, their in vitro virulence features and in vivo pathogenicity were uncharacterized. This study aimed to characterize the in vitro and in vivo pathogenicity of M. guilliermondii strain SO and analyze its Als proteins (MgAls) via comprehensive bioinformatics approaches. M. guilliermondii strain SO showed lower and higher sensitivity towards β-mercaptoethanol and lithium, respectively than the avirulent S. cerevisiae but exhibited the same tolerance towards cell wall-perturbing Congo Red with C. albicans. With 7.5× higher biofilm mass, M. guilliermondii strain SO also demonstrated 75% higher mortality rate in the zebrafish embryos with a thicker biofilm layer on the chorion compared to the avirulent S. cerevisiae. Being one of the most important Candida adhesins, sequence and structural analyses of four statistically identified MgAls showed that MgAls1056 was predicted to exhibit the most conserved amyloid-forming regions, tandem repeat domain and peptide binding cavity (PBC) compared to C. albicans Als3. Favoured from the predicted largest ligand binding site and druggable pockets, it showed the highest affinity towards hepta-threonine. Non-PBC druggable pockets in the most potent virulence contributing MgAls1056 provide new insights into developing antifungal drugs targeting non-albicans Candida spp. Virtual screening of available synthetic or natural bioactive compounds and MgAls1056 deletion from the fungal genome should be further performed and validated experimentally.
  19. Characterisation and molecular dynamic simulations of J15 asparaginase from Photobacterium sp. strain J15
    Yaacob MA, Hasan WA, Ali MS, Rahman RN, Salleh AB, Basri M, et al.
    Acta Biochim. Pol., 2014;61(4):745-52.
    PMID: 25337608
    Genome mining revealed a 1011 nucleotide-long fragment encoding a type I L-asparaginase (J15 asparaginase) from the halo-tolerant Photobacterium sp. strain J15. The gene was overexpressed in pET-32b (+) vector in E. coli strain Rosetta-gami B (DE3) pLysS and purified using two-step chromatographic methods: Ni(2+)-Sepharose affinity chromatography and Q-Sepharose anion exchange chromatography. The final specific activity and yield of the enzyme achieved from these steps were 20 U/mg and 49.2%, respectively. The functional dimeric form of J15-asparaginase was characterised with a molecular weight of ~70 kDa. The optimum temperature and pH were 25°C and pH 7.0, respectively. This protein was stable in the presence of 1 mM Ni(2+) and Mg(2+), but it was inhibited by Mn(2+), Fe(3+) and Zn(2+) at the same concentration. J15 asparaginase actively hydrolysed its native substrate, l-asparagine, but had low activity towards l-glutamine. The melting temperature of J15 asparaginase was ~51°C, which was determined using denatured protein analysis of CD spectra. The Km, Kcat, Kcat/Km of J15 asparaginase were 0.76 mM, 3.2 s(-1), and 4.21 s(-1) mM(-1), respectively. Conformational changes of the J15 asparaginase 3D structure at different temperatures (25°C, 45°C, and 65°C) were analysed using Molecular Dynamic simulations. From the analysis, residues Tyr₂₄ , His₂₂, Gly₂₃, Val₂₅ and Pro₂₆ may be directly involved in the 'open' and 'closed' lid-loop conformation, facilitating the conversion of substrates during enzymatic reactions. The properties of J15 asparaginase, which can work at physiological pH and has low glutaminase activity, suggest that this could be a good candidate for reducing toxic effects during cancer treatment.
  20. A comparative analysis of microgravity and earth grown thermostable T1 lipase crystals using HDPCG apparatus
    Abd Rahman RN, Ali MS, Sugiyama S, Leow AT, Inoue T, Basri M, et al.
    Protein Pept Lett, 2015;22(2):173-9.
    PMID: 25329331
    Geobacillus zalihae sp. nov., which produces a putative thermostable lipase, represents a novel species, with type strain T1. The characterisation of this intrinsically thermostable T1 lipase either physicochemically or structurally is an important task. The crystallisation of T1lipase in space was carried out using a High-Density Protein Crystal Growth (HDPCG) apparatus with the vapour diffusion method, and X-ray diffraction data were collected. The microgravity environment has improved the size and quality of the crystals as compared to earth grown crystal. The effect of microgravity on the crystallisation of T1 lipase was clearly evidenced by the finer atomic details at 1.35 A resolution. Better electron densities were observed overall compared with the Earth-grown crystals, and comparison shows the subtle but distinct conformations around Na(+) ion binding site stabilized via cation-π interactions. This approach could be useful for solving structure and function of lipases towards exploiting its potentials to various industrial applications.
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