DESIGN OF &lt;i&gt;CANDIDA ANTARCTICA&lt;/i&gt; LIPASE B THERMOSTABILITY IMPROVEMENT BY INTRODUCING EXTRA DISULFIDE BOND INTO THE ENZYME

Tambunan,

doi:10.3844/ojbsci.2014.108.118

Cited by 12 publications

(8 citation statements)

References 71 publications

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“…CALB is hydrolyzing enzyme that works on the ester bonds of carboxyl esters as a means to degrade lipid polymers. 48,49 It is already applied in a wide range of fields, such as agriculture, food, environment, and others. The main problem that revealed in CALB optimization is the difficulties to reach an optimum condition in the harsh temperature of the bioreactor.…”

Section: Food Supplements Productionmentioning

confidence: 99%

Computational Protein Design in Green Chemistry

Parikesit¹,

Tambunan²

2018

RJC

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The application of computational design of protein is mainly seen in the mutations of its active sites for increasing the reliability of that particular protein. Two essential examples from our groups are the stability improvement of riboflavin synthase and lipase enzyme. Specific mutations were introduced to their active and binding sites. Thus, by running molecular dynamics simulations, it is confirmed that the mutations improve the protein stability significantly. However, as the future of green chemistry is eventually aligned with nanotechnology, the atomic and even the subatomic features of the protein improvement will be put into the discussion. Nanotechnology is nowadays could not separate by the computational procedures. Besides molecular dynamics, finding the binding and active sites, as well as their chemical interactions, are important aspects of the nano-based computational design. In this respect, it could be related that the bioinformatics tools in Green Chemistry should be aligned with nanotechnology to produce finegrained protein design that environmentally friendly.

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Section: Food Supplements Productionmentioning

confidence: 99%

Computational Protein Design in Green Chemistry

Parikesit¹,

Tambunan²

2018

RJC

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“…Vu et al (2011) melakukan mutasi dengan radiasi gamma dan N-methyl-N'-nitro-Nnitrosoguanidine (NTG) untuk meningkatkan produksi selulase. Mutasi juga dapat diprediksi dengan metode bioinformatika, seperti yang dilakukan oleh Tambunan et al (2014) terhadap Candida antartica yang menghasilkan lipase.…”

Section: Pendahuluanunclassified

OPTIMASI DAN PEMEKATAN LIPASE Bacillus halodurans CM1

Aisyah

Mangunwardoyo

Trismilah

et al. 2017

Al-Kauniyah J. Biol.

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Lipase diketahui memiliki peranan penting dalam bidang industri. Produksi lipase dapat dihasilkan oleh kapang, khamir, dan bakteri. Penelitian bertujuan untuk meningkatkan aktivitas lipase yang dihasilkan oleh Bacillus halodurans CM1. Aktivitas lipase dapat ditingkatkan dengan optimasi komposisi media, mutasi bakteri dengan radiasi gamma dan N-methyl-N'-nitro-N-nitrosoguanidine (NTG). Enzim yang dihasilkan dipekatkan dengan metode stirred-cell ultrafiltration (UF)ammonium sulfat dan UF-Polyethylene glycol (PEG). Uji aktivitas dilakukan pada tujuh media yang berbeda untuk mendapatkan media produksi. Delapan variabel komposisi media dioptimasi dengan rancangan Plackett-Burman. Bakteri dimutasi dengan radiasi gamma dosis 0,1-0,4 kGy dan NTG 0,05-0,15 mg/mL dengan waktu inkubasi 1-3 jam. Hasil penelitian menunjukkan bahwa media produksi yang digunakan berdasarkan optimasi media dan komposisi media Plackett-Burman adalah media dasar Bora & Bora yang mengandung 0,5% palm oil (PO) dan 0,09% CaCl 2. Aktivitas lipase optimal diproduksi oleh bakteri hasil mutasi dengan NTG 0,1 mg/mL yang diinkubasi selama 3 jam. Pemekatan enzim UF-ammonium sulfat dan UF-PEG mampu meningkatkan aktivitas enzim lipase sebesar 18,44%.

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“…Energy minimization was then performed with a MMFF94x forcefield, born salvation, and RMS gradient of 0.05 kcal/(mol Å ) (1 kcal/(mol Å ) = 41.8 kJ/(mol nm)). The default parameters were utilized [30] . The molecular dynamics simulations of the ligand inhibitor were performed by MOE 2008.10.…”

Section: Molecular Dynamics Simulationmentioning

confidence: 99%

Designing cyclopentapeptide inhibitor of neuraminidase H5N1 virus through molecular and pharmacology simulations

Tambunan

Parikesit

Unadi

et al. 2015

Tsinghua Sci. Technol.

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Highly Pathogenic Avian Influenza (HPAI) H5N1 has attracted much attention as a potential pandemic virus in humans, which makes death inevitable in humans. Neuraminidase (NA) has an important role in viral replication. Thus, it is an attractive target when designing anti-influenza virus drug. However, evolving viruses cause some anti-viral drugs to be ineffective, as they show resistance to them. Selection of peptides as drug candidates is important for the peptide-receptor activity and good selectivity. Cyclic bonds in the peptide ligand design aim to improve the stability of the system and remove the obstacles in drug metabolism. The design is based on the polarity of the ligand and amino acid residues in the active site of NA. The results are 4200 cyclic pentapeptides as potential lead compounds. Docking simulations were conducted using MOE 2008.10 and were screened based on the value of the binding energy (G binding). ADME-Tox prediction assay was conducted on the selected ligands. Intra-and inter-molecular interactions, as well as changes in the form of bonds, were tested by molecular dynamics simulations at temperatures of 310 K and 312 K. The results of the docking simulations and toxicity prediction assay show that there are two ligands that have a residual interaction with the target protein: CLDRC and CIWRC. These two ligands have G binding values of-40.5854 and-39.9721 kcal/mol (1 kcal/mol = 4.18 kJ/mol). These ligands are prone to be mutagenic and carcinogenic, and they have a good oral bioavailability. The results show that the molecular dynamics of both ligand CLDRC and CIWRC are more feasible at the temperature of 312 K. At the end, both CIWRC and CLDRC ligands can be used as the drug candidates against H5N1 virus.

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DESIGN OF <i>CANDIDA ANTARCTICA</i> LIPASE B THERMOSTABILITY IMPROVEMENT BY INTRODUCING EXTRA DISULFIDE BOND INTO THE ENZYME

Cited by 12 publications

References 71 publications

Computational Protein Design in Green Chemistry

Computational Protein Design in Green Chemistry

OPTIMASI DAN PEMEKATAN LIPASE Bacillus halodurans CM1

Designing cyclopentapeptide inhibitor of neuraminidase H5N1 virus through molecular and pharmacology simulations

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