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Cloning of acetyl-CoA acetyltransferase gene from Halomonas elongata BK-AG18 and in silico analysis of its gene product Yuliastri, Ni Putu; Ratnaningsih, Enny; Hertadi, Rukman
Indonesian Journal of Biotechnology Vol 22, No 1 (2017)
Publisher : Universitas Gadjah Mada

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Abstract

Polyhydroxybutyrate (PHB) is a biodegradable polymer that can be used as a substitute for petrochemical plastics. Bacteria accumulate PHB in their cells as carbon and energy reserves because of unbalanced growth conditions.  This study aimed to amplify phbA from the chromosomal DNA of Halomonas elongata BK-AG18, a PHB-producing bacterium that was previously isolated from the Bledug Kuwu mud crater of Central Java, Indonesia. The obtained phbA amplicon was 1176 bp. This fragment was cloned into a pGEM-T Easy cloning vector and used to transform Eschericia coli TOP10. The recombinant colonies were selected using blue-white screening, confirmed by size screening, reconfirmed by re-PCR, and sequenced. When putative phbA sequences were aligned with H. elongata DSM2581 chromosome using BLASTN, this sequence showed 99% identity. The deduced amino acid sequences of this clone showed 100% identity to PhbA of  H. elongata DSM2581, suggesting that the obtained cloned fragment is a  phbA  gene. The 3D structure predicted by I-TASSER showed that PhbA of H. elongata  BK-AG18 had a high similarity to the acetyl CoA acetyltransferase structure of  Ralstonia eutropha H16. PhbA of H. elongata BK-AG18 possesses three catalytic residues, namely Cys88, His348, and Cys378.
Bioconversion of Glycerol to Biosurfactant by Halophilic Bacteria Halomonas elongata BK-AG18 Alvionita, Mieke; Hertadi, Rukman
Indonesian Journal of Chemistry Vol 19, No 1 (2019)
Publisher : Universitas Gadjah Mada

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Abstract

The increasing production of biodiesel is typically followed by the increasing number of glycerol as co-product. The abundance of glycerol will cause an environmental problem since it can be used as the carbon source for bacterial growth including pathogenic bacteria. In this study, four moderate halophilic bacteria indigenous from Bledug Kuwu Mud Crater, Central Java, Indonesia were screened based on their capability to bioconvert glycerol to biosurfactant. This study found Halomonas elongata BK-AG18 as the potential bacterium that able to perform such bioconversion. The optimum condition for the bioconversion of glycerol into biosurfactant was attained when the bacterial inoculum was grown in the medium containing 2% (v/v) glycerol, 0.3% (w/v) urea, and 5% (w/v) NaCl at 35 °C and pH 6. The resulted biosurfactant has emulsification index (EI24) about 53.6% and CMC about 275 mg/L. Preliminary structural analysis using FTIR and 1H-NMR indicated that biosurfactant produced by H. elongata BK-AG18 was likely a glycolipid type. The biosurfactants have antibacterial activity against Staphylococcus aureus with a minimum inhibitory concentration of 433 mg/L. Our study thus showed that H. elongata BK-AG18 was the potential halophilic bacteria that can bioconvert glycerol into glycolipid type of biosurfactant with antibacterial activity.
Bioconversion of Palm Oil into Biosurfactant by Halomonas meridiana BK-AB4 for the Application of Corrosion Inhibitor Sari, Ira Prima; Basyiruddin, Muhammad Imam; Hertadi, Rukman
Indonesian Journal of Chemistry Vol 18, No 4 (2018)
Publisher : Universitas Gadjah Mada

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Abstract

Biosurfactant is environmentally friendly surfactant produced by a certain microorganism in a lipid-rich medium. A previous study has shown that Halomonas meridiana BK-AB4 had the potential of a moderately halophilic bacterium in converting olive oil into biosurfactant. In the present study, the effect of changing the carbon source from olive oil into cheaper and more abundant vegetable oil, which is palm oil, for the production of the biosurfactant was evaluated. The study began by optimizing the production medium with varying the nitrogen source, the concentration of palm oil and pH. The optimum condition of biosurfactant production was observed in the medium consisted of 0.6% (w/v) of urea, 2% (v/v) of palm oil and pH 9. The resulted biosurfactant was stable at pH 7–10 and in the salt concentration of 6–15%. Biosurfactant activity in lowering air-water surface tension was measured using the Du Noüy ring method, and the value of critical micelle concentration (CMC) was about 233 ppm. At this point, the surface tension of water dropped from 68.3 to 49.8 dyne/cm. Preliminary structural analysis by using FTIR technique suggested that the resulted biosurfactant has -OH, -C-H aliphatic C=C, H-C-C and C=O groups in its structure, which is similar to that of the fatty-acid type of biosurfactant. The potential of biosurfactant as a metal corrosion inhibitor was evaluated by using electrochemical impedance spectroscopy (EIS) that measured at 30 °C. The measurement revealed that the highest inhibition level was observed at the biosurfactant concentration about 200 ppm that corresponds to the inhibition level about 53.23%.
IN SILICO POTENTIAL ANALYSIS OF X6D MODEL OF PEPTIDE SURFACTANT FOR ENHANCED OIL RECOVERY Sari, Cut Nanda; Usman, Usman; Hertadi, Rukman; Wijaya, Tegar Nurwahyu; Herlina, Leni; Suliandari, Ken Sawitri; Syafrizal, Syafrizal; Kristiawan, Onie
Scientific Contributions Oil and Gas Vol 39, No 2 (2016)
Publisher : Scientific Contributions Oil and Gas

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Abstract

Peptides and their derivatives can be applied in enhanced oil recovery (EOR) due to their ability to form an emulsion with hydrophobic molecules. However, peptide research for EOR application, either theoretical or computational studies, is still limited. The purpose of this research is to analyse the potency of the X6D model of surfactant peptide for EOR by molecular dynamics simulations in oil-water interface. Molecular dynamics simulation using GROMACS Software with Martini force field can assess a peptide’s ability for self-assembly and emulsification on a microscopic scale. Molecular dynamics simulations combined with coarse grained models will give information about the dynamics of peptide molecules in oil-water interface and the calculation of interfacial tension value. Four designs of X6D model: F6D, L6D, V6D, and I6D are simulated on the oil-water interface. The value of interfacial tension from simulation show the trend of F6D L6D > I6D > V6D. The results indicate that V6D has the greatest reduction in interfacial tension and has the stability until 90°C with the salinity of at least 1M NaCl.
Estimating Factors Determining Emulsification Capability of Surfactant-Like Peptide with Coarse-Grained Molecular Dynamics Simulation Wijaya, Tegar; Hertadi, Rukman
Indonesian Journal of Chemistry Vol 19, No 3 (2019)
Publisher : Universitas Gadjah Mada

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Abstract

The ability of surfactant-like peptides to emulsify oil has become the main focus of our current study. We predicted the ability of a series of surfactant-like peptides (G6D, A6D, M6D, F6D, L6D, V6D, and I6D) to emulsify decane molecules using coarse-grained molecular dynamics simulations. A 1-μs simulation of each peptide was carried out at 298 K and 1 atm using MARTINI force field. Simulation system was constructed to consist of 100 peptide molecules, 20 decane molecules, water, antifreeze particles and neutralizing ions in a random configuration. Out of seven tested peptides, M6D, F6D, L6D, V6D, and I6D were able to form emulsion while G6D and A6D self-assembled to order b-strands. A higher hydropathy index of amino acids constituting the hydrophobic tail renders the formation of an emulsion by peptides more likely. By calculating contact number between peptides and decanes, we found that emulsion stability and geometry depends on the structure of amino acids constituting the hydrophobic tail. Analysis of simulation trajectory revealed that emulsions are formed by small nucleation following by fusion to form a bigger emulsion. This study reveals the underlying principle at the molecular level of surfactant peptide ability to form an emulsion with hydrophobic molecules.