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All Journal HAYATI Journal of Biosciences Jurnal Matematika & Sains Indonesian Journal of Biotechnology Biology, Medicine, & Natural Product Chemistry Jurnal Informatika Indonesian Journal of Chemistry CHEESA: Chemical Engineering Research Articles Indonesian Journal of Chemical Analysis (IJCA) Jurnal Ilmiah Farmako Bahari Scientific Contribution Oil and Gas

RUKMAN HERTADI

Institut Teknologi Bandung

Author-ID : 280901

Agriculture, Biological Sciences & Forestry Biochemistry, Genetics & Molecular Biology Chemical Engineering, Chemistry & Bioengineering Chemistry Computer Science & IT Earth & Planetary Sciences Energy Engineering Environmental Science Health Professions Immunology & microbiology Materials Science & Nanotechnology Mathematics Medicine & Pharmacology Public Health

Published : 17 Documents Claim Missing Document

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Molecular Genetic Analysis of sup45 Paromomycin Hypersensitive Mutants In Saccharomyces cerevisiae Rukman Hertadi; Hadi Sutedjo; Akhmaloka Akhmaloka
Jurnal Matematika & Sains Vol 6, No 2 (2001)
Publisher : Institut Teknologi Bandung

Show Abstract | Download Original | Original Source | Check in Google Scholar

Translation termination in Saccharomyces cerevisiae is mediated by eRF-1 and eRF-3 protein encoded by SUP45 and SUP35 gene respectively. To probe more detail concerning the mechanism of translation termination in this organisms, the structure-function of the eRF-1 protein was studied by analyzing of sup45 mutants. In this study, we used three paramomycin hyper sensitive mutants, namely sup45-23, sup45-24 and sup45-38. Phenotypic characterization and quantitation of allosuppresor level showed that the mutants were allele specific mutants. Cloning and sequencing of the sup45 genes from these mutants showed that the sup45-23 exhibited Met48ATG â Ile48Ala and Gly431GGT â Gly431GGA mutation. While sup45-24 and sup45-38 exhibited single silent mutation, Gly431GGT â Gly431GGA . The structure-function analysis of sup45 gene of these mutant suggested that phenotypic mutants were not only due to the alteration of amino acid of eRF-1 protein in the cells.

Intramolecular Forces Density in Mesophilic and Thermophilic Proteins: Amino Acid Clusters Based Study Rukman Hertadi; Minoru Kanehisa
Jurnal Matematika & Sains Vol 12, No 3 (2007)
Publisher : Institut Teknologi Bandung

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Thermostability of (hyper)thermophilic enzymes has been taken as an advantage in industry to enhance biochemicalreactions at elevated temperature. Factors responsible for the thermostability in this class of proteins, however, stillremain unclear despite the many works that have been done to elucidate such factors by performing variouscomparative studies to homologous pairs of (hyper)thermophilic and mesophilic proteins. In the current work, weelucidated the factors by comparing intramolecular forces density in tertiary structure of mesophilic and(hyper)thermophilic proteins in terms of the content of various types of amino acid clusters. A graph spectral methodwas employed to probe the charged, hydrophobic and aromatic clusters in each tertiary structure of all classes ofthermophilic proteins used in our study. Our results revealed that mesophilic and (hyper)thermophilic proteins containsimilar level of all types of amino clusters, thereby stabilized with similar level of high-density intramolecular forces,but the former contain a higher number of non-cluster residues and less stabilized by electrostatic interactions, therebymore sensitive to heat.

Cloning, Expression, and In Silico Analysis of Class IV Poly-(R)-3-hydroxybutyrate Genes from New Strain of Bacillus thuringiensis TH-01 Zuhdina Sabiqoh; Rukman Hertadi; Enny Ratnaningsih
HAYATI Journal of Biosciences Vol. 29 No. 3 (2022): May 2022
Publisher : Bogor Agricultural University, Indonesia

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.4308/hjb.29.3.310-319

Poly-(R)-3-hydroxybutyrate (PHB) is a bioplastic derivative of polyhydroxyalkanoate (PHA) which can be synthesized by bacteria under certain growth conditions. Previous study has reported a new strain of Bacillus thuringiensis TH-01 isolated from thermite, which found to accumulate PHB. This research aimed to clone PHB biosynthesis genes from B. thuringiensis TH-01 and study its expression as well as predict the tertiary structure of the enzymes. The clone of phaA gene, which encodes PhaA, was obtained as 1182 bp. On the other hand, 2546 bp clone of phaRBC gene cluster was obtained to consist of 744 bp phaB, 1086 bp phaC, and 483 bp phaR, encoding respective PhaB, PhaC, and PhaR proteins. In silico analysis indicated that PhaA, PhaB, PhaC, and PhaR, revealed to have 393, 247, 361, and 160 amino acid, respectively. The predicted model of PhaA, PhaB, and PhaC showed dominant structure of α/β folding motif, while PhaR was dominated by a helix-loop-helix motif. The catalytic residues of PhaA were Cys88, His349, and Cys379, whereas the catalytic residues of PhaB were Ser142, Tyr155, and Lys159. These catalytic residues were identical to those residues obtained in other PHB biosynthetic enzymes reported elsewhere, confirming that our clones were of PHB biosynthetic genes.

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

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 Mieke Alvionita; Rukman Hertadi
Indonesian Journal of Chemistry Vol 19, No 1 (2019)
Publisher : Universitas Gadjah Mada

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 Ira Prima Sari; Muhammad Imam Basyiruddin; Rukman Hertadi
Indonesian Journal of Chemistry Vol 18, No 4 (2018)
Publisher : Universitas Gadjah Mada

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%.

Estimating Factors Determining Emulsification Capability of Surfactant-Like Peptide with Coarse-Grained Molecular Dynamics Simulation Tegar Wijaya; Rukman Hertadi
Indonesian Journal of Chemistry Vol 19, No 3 (2019)
Publisher : Universitas Gadjah Mada

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.

Levan Produced by the Halophilic Bacterium Bacillus licheniformis BK1 as a Nanoparticle for Protein Immobilization Ira Oktavia; Aidah Nur Fithriah; Nur Umriani Permatasari; Enny Ratnaningsih; Rukman Hertadi
Indonesian Journal of Chemistry Vol 20, No 3 (2020)
Publisher : Universitas Gadjah Mada

This study examined the potential of levan from the halophilic bacterium Bacillus licheniformis BK1 as a nanoparticle system for protein immobilization. Levan produced by B. licheniformis BK1 was obtained by incubating the bacterium in the optimized Belghith medium, containing 15% (w/v) sucrose, 7.5% (w/v) NaCl and pH 8, in a rotary shaker at 150 rpm for 16 h, at 40 °C. The structure of the levan produced was verified by FTIR and NMR. It appeared that the levan had the same structure as that from Erwinia herbicola. The obtained levan was then used as a nanoparticle system to immobilize BSA and lysozyme proteins. The BSA-nanoparticle had a non-spherical shape with a surface charge of about -4.72 mV and a size distribution in the range of 83–298 nm. In contrast, the lysozyme-nanoparticle exhibited more spherical shapes with a surface charge of -2.57 mV and 206–285 nm size distribution. The efficiency of immobilization was about 74.26% and 81.77% for BSA and lysozyme, respectively. The study thus shows that levan produced by B. licheniformis BK1 can be used as a nanoparticle system for protein immobilization.

Ability of Ectoine to Stabilize Lipase against Elevated Temperatures and Methanol Concentrations I Putu Parwata; Deana Wahyuningrum; Sony Suhandono; Rukman Hertadi
Indonesian Journal of Chemistry Vol 21, No 2 (2021)
Publisher : Universitas Gadjah Mada

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.22146/ijc.54931

Ectoine is one of the compatible organic molecules that can protect the protein from heating, freezing, and chemicals contact. This study aims to investigate the ability of ectoine to stabilize lipase on heating and in methanol treatments as an effort to provide a stable biocatalyst for the production of biodiesel. Various ectoine concentrations were added to lipase solutions, then the mixture was heated, and the residual activity of the lipase was determined. Similar steps were also conducted for methanol treatment. The results showed that ectoine maintained and even improved the catalytic activity of lipase after treatment with either heat or methanol. The addition of ectoine to a final concentration of 110 to 150 mM could maintain lipase activity up to 80% when heating to approximately 95 °C. Additionally, more than 20% of lipase activity increased on heating to temperatures below 75 °C in the presence of ectoine at a final concentration of 25 to 120 mM. Meanwhile, after incubation in methanol at a level of around 84% (v/v), the activity of lipase containing 40–90 mM ectoine was maintained. These results demonstrated that ectoine was highly effective in protecting lipase from heat and methanol.

Pengaruh Jenis Sumber Nitrogen Pada Produksi Biosurfaktan Oleh Bakteri Halofil Mieke Alvionita; Rukman Hertadi
Indonesian Journal of Chemical Analysis (IJCA) Vol. 4 No. 1 (2021): Indonesian Journal of Chemical Analysis
Publisher : Universitas Islam Indonesia

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.20885/ijca.vol4.iss1.art2

Bakteri halofil merupakan bakteri yang membutuhkan NaCl untuk pertumbuhannya. Salah satu potensi bakteri halofil adalah dapat menghasilkan biosurfaktan yang aktif pada konsentrasi garam yang tinggi. Oleh karena itu, biosurfaktan tersebut dapat diaplikasikan dalam industri minyak terutama pada bidang enhanced oil recovery (EOR). Selain itu, biosurfaktan diketahui secara luas diaplikasikan dalam industri farmasi dan makanan. Sifatnya yang lebih ramah lingkungan dibandingkan dengan surfaktan sintetis menyebabkan ketertarikan untuk produksi biosurfaktan dalam skala besar semakin meningkat. Salah satu cara untuk meningkatkan produksi biosurfaktan adalah dengan melakukan optimasi sumber nitrogen pada medium produksi. Oleh karena itu penelitian ini bertujuan untuk mengetahui sumber nitrogen terbaik yang dapat digunakan untuk produksi biosurfaktan secara optimal. Penelitian ini menggunakan lima jenis sumber nitrogen antara lain urea, NH4Cl, NaNO3, (NH4)2SO4, dan KNO3 sedangkan jenis bakteri halofil yang digunakan adalah Halomonas elongata BK-AG18. Hasil penelitian ini menunjukkan bahwa urea merupakan sumber nitrogen terbaik yang digunakan untuk medium produksi biosurfaktan. Hal ini ditunjukkan dari hasil yang diperoleh dari diameter penyebaran minyak sebesar 3 cm.

Co-Authors Aang Suhendar Agung Wahyu Setiawan Agus Dana Permana Aidah Nur Fithriah Akhmaloka Akhmaloka Alli, Yani F Alvionita, Mieke CUT NANDA SARI Deana Wahyuningrum DEBBIE SOEFIE RETNONINGRUM Dewi, Andi Alfira Ratna Faradisa Dhini Annisa Rahmasari Kanto Dimitri Mahayana Enny Ratnaningsih Enny Ratnaningsih Enny Ratnaningsih ERNAWATI ARIFIN GIRI-RACHMAN Fazli, Rahmat Rizki Hadi Sutedjo HERLINA, LENI I Putu Parwata Ira Oktavia Ira Prima Sari Ira Puspasari Ken Sawitri Suliandari KRISTIAWAN, ONIE LENI HERLINA Meredita Susanty Minoru Kanehisa Muhammad Imam Basyiruddin Ni Putu Yuliastri Nilam Fitriah Novia Syari Intan Nur Umriani Permatasari ONIE KRISTIAWAN Putri Ayu Fajar Rose, Tasyang Oktavia SARI, CUT NANDA Sony Suhandono Suhendar, Aang Suliandari, Ken Sawitri syafrizal Syafrizal Syafrizal Tan, Marselina Irasonia Tati Latifah Erawati Rajab Tegar Nurwahyu Wijaya Tegar Wijaya Usman Usman Usman Wijaya, Tegar Nurwahyu Wojciechowska, Gladys Emmanuella Putri Yani F Alli Yuliana, Cut Zakaria, Hasballah Zuhdina Sabiqoh

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