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All Journal HAYATI Journal of Biosciences Journal of Tropical Life Science : International Journal of Theoretical, Experimental, and Applied Life Sciences Biota: Jurnal Ilmiah Ilmu-Ilmu Hayati Biogenesis: Jurnal Ilmiah Biologi Indonesian Journal of Biotechnology Biota Mutiara Medika: Jurnal Kedokteran dan Kesehatan Pharmacon Molecular and Cellular Biomedical Sciences (MCBS) Jurnal Biologi Tropis Jurnal Medik Veteriner Proceedings of the International Conference on Applied Science and Health Global Health Management Journal Biota Jurnal Biomedika JURNAL PERIKANAN TROPIS Narra J Makara Journal of Science Biological Environment and Pollution Rumphius Pattimura Biological Journal Berkala Ilmiah Biologi Kesmas: Jurnal Kesehatan Masyarakat Nasional (National Public Health Journal)
Nastiti Wijayanti
Universitas Gadjah Mada
Agriculture, Biological Sciences & Forestry Biochemistry, Genetics & Molecular Biology Dentistry Earth & Planetary Sciences Education Energy Environmental Science Health Professions Immunology & microbiology Materials Science & Nanotechnology Medicine & Pharmacology Neuroscience Nursing Public Health Veterinary

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In-Silico Optimization of α-agarase for Sustainable Bioprospecting of Agaro-oligosaccharides: In-Silico Optimization of α-agarase for Sustainable Bioprospecting of Agaro-oligosaccharides Hanbal, Mayland Muhammad; Wijayanti, Nastiti; Tsabitah, Khansa; Zulfa, Amania; Tasania, Nadia Nisa; Saksono, Budi
Journal of Tropical Life Science Vol. 15 No. 2
Publisher : Journal of Tropical Life Science

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.11594/gg6mkk56

Abstract

Enzymatic synthesis is a sustainable alternative to chemical methods, offering high substrate specificity, reduced byproducts, and environmentally friendly processes. Despite its advantages, agaro-oligosaccharides (AOS) production largely depends on chemical synthesis due to the limited exploration of α-agarase. Therefore, this study aims to identify, analyze, and redesign a suitable α-agarase candidate for AOS production using in-silico approaches. Biological databases from CAZy, UniProtKB, and PDB, along with journal references, were used to curate α-agarase candidates. Non-catalytic regions were removed to retain only the GH96 catalytic domain, with a His-tag added for easier purification. Subsequently, structural modeling using SWISS-MODEL was performed to facilitate blind docking with CB-Dock2. Modeling also facilitated physicochemical properties predictions incorporating OphPred, Protein-Sol, and SCooP for pH, solubility, and thermal stability. The results showed that AgaA33, obtained from Thalassomonas agarivorans JAMB-A33, was selected due to its high annotation score and optimal temperature. Structural modeling and blind docking confirmed that the functional domains were preserved after redesign. In-silico physicochemical assessments revealed that the redesigned enzyme exhibited improved pH tolerance and thermal stability, despite a slight reduction in solubility. This study showed the use of computational tools for enzyme redesign and showed the potential of α-agarase as a green and sustainable biocatalyst for AOS production. By combining database-driven candidate selection with in-silico structural and functional analyses, these results set the foundation for further optimization of α-agarase to meet industrial needs. Future efforts must focus on improving solubility and refining activity predictions to fully realize the enzyme’s potential for eco-friendly bioprocesses.
Codon Optimization and Epitope Identification of L1 Protein Human Papillomavirus Type 52 for Expression in Lactococcus lactis: Codon Optimization and Epitope Identification L1 Protein HPV52 Prastyowati, Anika; Hakim, Mohamad Saifudin; Wijayanti, Nastiti; Wibawa, Tri
Journal of Tropical Life Science Vol. 15 No. 3
Publisher : Journal of Tropical Life Science

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.11594/jtls.15.03.03

Abstract

Human papillomavirus (HPV) type 52 is among the top three high-risk oncogenic types that are associated with cervical cancer worldwide, especially in Indonesia. Designing a vaccine against HPV using an Lactococcus lactis expression system is a promising strategy, as this bacterium is well-known for its probiotic properties and can be safely utilized as a delivery carrier for oral vaccines. This study aimed to optimize the codon usage of the L1 protein of HPV type 52 for expression in L. lactis expression system and to identify potential epitopes using bioinformatics tools. To determine the codon optimization, the L1 protein sequence of HPV type 52 was retrieved from the National Center for Biotechnology Information (NCBI) database. Furthermore, codon optimization was conducted once the model had been established using OPTIMIZER, Clustal Omega, Restriction Mapper, and the ExPASy tool, based on L. lactis. The final construct was predicted to have a B-cell epitope by Ellipro tools, antigenicity by VaxiJen v.2.0, allergenicity by AllerTOP v.2.0, and toxicity by ToxIBTL. This resulted in a potential vaccine candidate with a Codon Adaptation Index (CAI) of 0.754 and GC content of 39.0%. Identification of epitopes from the optimized gene resulted in two peptide sequences, WRPSEATVYLPPVPVSKVVS and GTLGDPVPGDLYIKGSNSGNTATVQ, as components of the vaccine candidate.
Co-Authors . Sismindari Abdul Rahman Siregar, Abdul Rahman Abrory Agus Cahya Pramana Adelfiani, Adelfiani Adi Sofyan Ansori, Muhammad Aeniah, Siti Agustiningsih Agustiningsih Akira Hosoyama Allimi, Hayu Swari Amalia, Nur Rofika Ayu Shinta Andi Mahendra Andrian, Krisna Noli Anika Prastyowati, Anika Apriliyani, Tia Ardaning Nuriliani ARI SUSILOWATI Ariesti, Wiwin Arif Luthfi Nurul Huda Aris Haryanto Atsushi Yamazoe Aushia Tanzih Al Haq Bambang Hariwiyanto Bambang Retnoaji BUDI SAKSONO Camelia Herdini Ch. Retna Handayani Dafa, Maula Haqul Dafip, Muchamad Dewi Kartikawati Paramita Diani Mentari Dwi Liliek Kusindarta Dyah Widiastuti Eka Putri Empra, Desi Empra, Desi Eka Putri Endar Pertiwi, Anggita ERLIN LISTIYANINGSIH Fajar Sofyantoro Hakim, Mohamad Saifudin Halim, Shuha Ma’muriyah Hanbal, Mayland Muhammad Hendry Tri Sakti Saragih Hera Nirwati Heriyanto, Didik S. Hevi Wihadmadyatami Hideaki Nojiri Ibnu Agus Ariyanto Illiyin, Sirayya Ina Kusrini Jajah Fachiroh, Jajah JAKA WIDADA Juliadmi, Dian Karlina, Ina Karnati, Srikanth Kartika W. Taroeno-Hariadi Kartika, Aprilia I. Lisna Hidayati Mayani, Olvita Mei Ria Santi Michael Kann Moli Podhi, Felisitas Muhammad Adnan Mumtazah, Dzul Fithria Munawir Sazali Murwantoko . Naima, Mirtani Nenny Sri Mulyani Ni Wayan Erly Sintya Dewi Nisa, Mutia Khoirun Nuhamunada, Matin Oktaviana, Shintia Peni Indrayudha Pertiwi, Gian Aditya Pradnya Paramita Pratitis, Visi Endah Primahesa, Alfian Prissandi, Anthera Al Firdaus Priyambada, Fajar Purnomo Hadi Pusparini, Nur Ainun Oktavia Puspitasari, Pinki Anggrahini Putra, Hendy Eka R.C. Hidayat Soesilohadi Rahayu, Sekar Ramadhani, Eka Rarastoeti Pratiwi Retno Murwanti Rinda Binugraheni, Rinda Rohmah, Zuliyati Sadewo, Imran Saeed, Faisal Salamah, Rohmi Samparisna Rumansara, Papuani Saragih, Hendry T. S. S. G. Sari, Ria Vinola Septhya Saribu, Ruth Liananda Citra Dolok Septriani, Nur Indah Septriani, Nur Indah Setiawibawa, Raden Aditya Aryandi Shinta Hartanto Simanungkalit, Eben Ezer Slamet Widiyanto Sofia M. Haryana Sofia Mubarika Haryana Sofyantoro, Fajar Subchan, Aditya Nur Sularsah, Sais Supraitno, Murtiadi Erlan Sutaryo1 S, Sutaryo1 T. Trijoko T.S.S.G. Saragih, Hendry Tasania, Nadia Nisa Titis Widowati, Titis To'bungan, Nelsiani Tri Rini Nuringtyas Tri Wibawa Triska Desi Sundari Tsabitah, Khansa Wulansari, Riska Yundari, Yundari Zulfa, Amania Zulfadhli Zulfadhli Zumrotus Sholichah Zusrina, Laili Mufli ‘Aliyah, Siti Hamidatul