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All Journal International Journal of Renewable Energy Development Jurnal Matematika & Sains Journal of Engineering and Technological Sciences Jurnal Kimia Riset Berkala Penelitian Hayati
Akhmaloka Akhmaloka
Departemen Kimia, FMIPA, Institut Teknologi Bandung
Agriculture, Biological Sciences & Forestry Biochemistry, Genetics & Molecular Biology Chemistry Energy Engineering Immunology & microbiology Materials Science & Nanotechnology Mathematics Medicine & Pharmacology

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Journal : Jurnal Kimia Riset

 1 
STUDI BIOINFORMASI URUTAN ASAM AMINO DAN STRUKTUR 3D PROTEIN ALDOLASE KELAS II (AldII) DARI Uncultured Acidilobus sp. Nishia Waya Meray; Suharti Suharti; Akhmaloka Akhmaloka
Jurnal Kimia Riset Vol. 6 No. 2 (2021): Desember
Publisher : Universitas Airlangga, Campus C Mulyorejo, Surabaya, Indonesia

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.20473/jkr.v6i2.31097

Abstract

Pada penelitian sebelumnya fragmen gen 1,9 kb telah berhasil diisolasi dari Kawah Domas, Jawa Barat melalui pendekatan metagenom. Fragmen tersebut diketahui mengandung daerah Open Reading Frame (ORF) utuh dari gen pengkode aldolase kelas II dari uncultured Acidilobus sp. yang kemudian disebut sebagai aldII. Fragmen gen aldII tersebut berhasil diekspresikan menjadi protein termostabil aldolase kelas II yang kemudian disebut sebagai AldII. Penelitian ini bertujuan untuk melakukan studi bioinformasi terhadap protein AldII tersebut. Protein AldII kemudian diketahui memiliki massa molekul ~21,2 kDa dengan rumus molekul C940H1539N261O281S8. Total residu bermuatan negatif (Asp + Glu) sebanyak 22 residu, sedangkan total residu bermuatan positif (Arg + Lys) adalah 18 residu. Nilai pI teoritis AldII sebesar 5,86. Hasil perhitungan indeks kestabilan protein ini adalah 36,61 dan diklasifikasikan sebagai protein yang stabil. Lewat penjajaran dengan homologi terdekat, ditemukan daerah lestari yang dapat menunjukan residu yang mungkin berperan dalam pengikatan logam dan sisi aktif. Prediksi struktur 3D dilakukan secara ab initio, menunjukan adanya 6 struktur β-sheet dan 6 struktur α-heliks. Dengan demikian dapat disimpulkan bahwa protein AldII dari uncultured Acidilobus sp. diduga memiliki aktivitas enzimatik.
3D STRUCTURE AND FUNCTION ANALYSIS OF RECOMBINANT ALDII PROTEIN FROM Uncultured Acidilobus sp. USING I-TASSER Meray, Nishia Waya; Suharti, Suharti; Akhmaloka, Akhmaloka
Jurnal Kimia Riset Vol. 9 No. 1 (2024): June
Publisher : Universitas Airlangga, Campus C Mulyorejo, Surabaya, Indonesia

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.20473/jkr.v9i1.56154

Abstract

The AldII protein is a new recombinant protein produced from a novel gene obtained via a metagenome approach. Previous studies showed that this protein is strong and has the same metal binding aspect as the class II Aldolase enzyme. Aldolase is a valuable enzyme used in pharmaceuticals, food processing, and biochemistry. Further investigation is required to comprehend the structure and function of the AldII protein due to its potential. Researchers will conduct sophisticated bioinformatic analysis on the 3D shape and function prediction of AldII using the I-TASSER webserver from Zhanglab. The AldII protein is a new recombinant protein produced from a novel gene obtained via a metagenome approach. Previous studies showed that this protein is strong and has the same metal binding aspect as the class II Aldolase enzyme. Aldolase is a valuable enzyme used in pharmaceuticals, food processing, and biochemistry. Further investigation is required to comprehend the structure and function of the AldII protein due to its potential. Researchers will conduct sophisticated bioinformatic analysis on the 3D shape and function prediction of AldII using the I-TASSER webserver from Zhanglab. The I-TASSER server is an online tool for the automated prediction of protein structure and annotation of functions based on structure. Analysis of the AldII protein using the I-TASSER webserver shows that this protein has a stable structure with the closest structural homology to deoxyribose-phosphate aldolase from Bacillus thuringiensis with PDB code 6btdA. Additionally, the biological structure analysis shows that this protein shares the biological function of the enzyme L-fuculose-1-phosphate aldolase, which is part of the class II Aldolase enzyme that plays a role in the catabolism of arabinose, L-Fuculose, and Rhamnose. The results align with prior research that states the AldII protein is a stable protein with a catalytic side that is homologous to the class II Aldolase enzyme.
Co-Authors A. Suharto A. Suharto AFAF BAKTIR Ami Soewandi J.S. Arina, Linea Alfa Dewi, Arinta Elvi Restiawaty F Madayanti, F F. M. Warganegara F. M. Warganegara Gani, Kindi Pyta Garaika H. Sutedjo Hadi Sutedjo I. N. Tika I. N. Tika Kurniawati, Katarina Ika M. Sindumarta Meray, Nishia Waya Ni Nyoman Tri Puspaningsih P Aditiawati P. E. Susilowati R. Hertadi RUKMAN HERTADI S. Nurbaiti S. Nurbaiti Safika S, Safika Senam Senam Suharti Suharti Y. Sriwulan M. Yogi Wibisono Budhi