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All Journal HAYATI Journal of Biosciences Jurnal Teknologi Industri Pertanian Indonesian Journal of Biotechnology Journal of Agromedicine and Medical Sciences Journal of Tropical Biodiversity and Biotechnology Manajemen Pendidikan BERITA BIOLOGI JURNAL BIOLOGI INDONESIA Jurnal Teknologi Laboratorium Jurnal RESTI (Rekayasa Sistem dan Teknologi Informasi) Chimica et Natura Acta Indonesian Journal of Chemistry Jurnal Sinergitas PkM & CSR FaST : Jurnal Sains dan Teknologi Walisongo Journal of Chemistry Menara Perkebunan Jurnal Teknik Informatika (JUTIF) Bioinformatics and Biomedical Research Journal Cermin Dunia Kedokteran Indonesian Journal of Life Sciences Makara Journal of Science Makara Journal of Technology Biosaintifika: Journal of Biology & Biology Education Jurnal Bioteknologi & Biosains Indonesia (JBBI) Cermin Dunia Kedokteran Kesmas: Jurnal Kesehatan Masyarakat Nasional (National Public Health Journal) Jurnal Bioteknologi & Biosains Indonesia Berita Biologi
Arli Aditya Parikesit
Department Of Bioinformatics, School Of Life Sciences, Indonesia International Institute For Life Sciences (i3l), Jakarta, Indonesia
Agriculture, Biological Sciences & Forestry Biochemistry, Genetics & Molecular Biology Chemical Engineering, Chemistry & Bioengineering Chemistry Civil Engineering, Building, Construction & Architecture Computer Science & IT Earth & Planetary Sciences Economics, Econometrics & Finance Education Electrical & Electronics Engineering Engineering Environmental Science Health Professions Immunology & microbiology Industrial & Manufacturing Engineering Materials Science & Nanotechnology Mechanical Engineering Medicine & Pharmacology Public Health Social Sciences Other

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Journal : JURNAL BIOLOGI INDONESIA

 1 
Protein Domain Annotation of Plasmodium spp. Circumsporozoite Protein (CSP) Using Hidden Markov Model-based Tools Parikesit, Arli Aditya; Utomo, Didik Huswo; Karimah, Nihayatul
JURNAL BIOLOGI INDONESIA Vol 14, No 2 (2018): JURNAL BIOLOGI INDONESIA
Publisher : Perhimpunan Biologi Indonesia

Show Abstract | Download Original | Original Source | Check in Google Scholar | Full PDF (1310.253 KB) | DOI: 10.14203/jbi.v14i2.3737

Abstract

ABSTRACTPlasmodium sp. Circumsporozoite Protein (CSP) has a crucial role in sporozoite function and hepatocyte invasion. The basic understanding of this protein can reveal the mechanism of action. Protein domain annotation could determine the functional region of the specific protein. This study aimed is to identify the conserved and functional region of circumsporozoite protein using Hidden Markov Model approach. Three samples of CSP was retrieved from UniProt database; Circumsporozoite protein from Plasmodium vivax (P08677), Circumsporozoite protein from Plasmodium malariae (P13815), and Circumsporozoite protein from Plasmodium knowlesi (P02894). All sequenced was reviewed and could be used for further analysis. Multiple Sequences alignment (MSA) was used for analyzing the conserved region. CLUSTAL X software employed to run the MSA of circumsporozoite protein. Protein homology was clustered using MEGA 7.0, and domain annotation was done by the SUPERFAMILY hidden Markov models. The result showed that Circumsporozoite Protein has two specific conserved regions among species. This conserved region indicates the similar function and takes a vital role in their life cycle. Plasmodium  knowlesi and Plasmodium vivax had more similar sequence than Plasmodium malariae. The clustering result based on Circumsporozoite Protein indicates that Plasmodium malariae may have distinct infection mode to the host. The CSP was identified has one domain in C-terminus. Domain family of  CSP was TSP-1 type 1 repeat with high reliability. It can be concluded that conserved domain of Circumsporozoite Protein could reveal its critical role in Malaria Disease. To this end, CSP could be a potential candidate for vaccine development. Keywords: Circumsporozoite, conserved domain, Plasmodium spp, TSP-1 type 1 repeat.  
PROTEIN DOMAIN ANNOTATION OF PLASMODIUM SPP. CIRCUMSPOROZOITE PROTEIN (CSP) USING HIDDEN MARKOV MODEL-BASED TOOLS Parikesit, Arli Aditya; Utomo, Didik Huswo; Karimah, Nihayatul
JURNAL BIOLOGI INDONESIA Vol 14, No 2 (2018): JURNAL BIOLOGI INDONESIA
Publisher : Perhimpunan Biologi Indonesia

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.14203/jbi.v14i2.3737

Abstract

ABSTRACTPlasmodium sp. Circumsporozoite Protein (CSP) has a crucial role in sporozoite function and hepatocyte invasion. The basic understanding of this protein can reveal the mechanism of action. Protein domain annotation could determine the functional region of the specific protein. This study aimed is to identify the conserved and functional region of circumsporozoite protein using Hidden Markov Model approach. Three samples of CSP was retrieved from UniProt database; Circumsporozoite protein from Plasmodium vivax (P08677), Circumsporozoite protein from Plasmodium malariae (P13815), and Circumsporozoite protein from Plasmodium knowlesi (P02894). All sequenced was reviewed and could be used for further analysis. Multiple Sequences alignment (MSA) was used for analyzing the conserved region. CLUSTAL X software employed to run the MSA of circumsporozoite protein. Protein homology was clustered using MEGA 7.0, and domain annotation was done by the SUPERFAMILY hidden Markov models. The result showed that Circumsporozoite Protein has two specific conserved regions among species. This conserved region indicates the similar function and takes a vital role in their life cycle. Plasmodium  knowlesi and Plasmodium vivax had more similar sequence than Plasmodium malariae. The clustering result based on Circumsporozoite Protein indicates that Plasmodium malariae may have distinct infection mode to the host. The CSP was identified has one domain in C-terminus. Domain family of  CSP was TSP-1 type 1 repeat with high reliability. It can be concluded that conserved domain of Circumsporozoite Protein could reveal its critical role in Malaria Disease. To this end, CSP could be a potential candidate for vaccine development. Keywords: Circumsporozoite, conserved domain, Plasmodium spp, TSP-1 type 1 repeat.  
Co-Authors Adi Sofyan Ansori, Muhammad Albert Widjaja Aldino Hafidzhah, Muhammad Alhussain, Shaheer Alyaa Farrah Dibha Angelique, Priscilla Arif Nur Muhammad Ansori Bernard, Stefanus Bhat, Nausheen Burkov, Pavel Chandra, Nelson David Agustriawan Dedy Sugiono Deidre Valeska, Margareta Derkho, Marina Dian, Farida Aryani Didik Huswo Utomo Dito Anurogo Dito Anurogo Dito Anurogo Dito ANUROGO Dito Anurogo Dito Anurogo Dito Anurogo, Dito Ema Utami Ezra Bernandus Wijaya Fugaha, Daniel Ryan Gabriela, Vania Gabriele Mustika Kresnia Gabriella Patricia Adisurja Hafidzhah, Muhammad Aldino Heerlie, Devita Mayanda Herdiansyah, Mochammad Aqilah Hutapea, Hotma Martogi Lorensi Imron Imron Jakhmola, Vikash Jeremias Ivan Josephine, Evalina Junaida Astina Karimah, Nihayatul Karimah, Nihayatul Kharisma, Viol Dhea KUSRINI Kusrini, Kusrini Maksim Rebezov Margareta Deidre Valeska Margaretha, Febrina Maria Kiseleva Maulani Wijaya, Renadya Miko Wahyono, Tri Yunis Muhammad Aldino Hafidzhah Muhammad Aldino Handzhah Muhammad Hermawan Widyananda Murtadlo, Ahmad Affan Ali Nadezhda Kenijz Natalia Satya, Putri Gabriella Angel Nelda Aprilia Salim Nihayatul Karimah Patricia Adisurja, Gabriella Patricia, Gabriella Posa, Gabrielle Ann Villar Prakoso, Muhammad Ja'far Pratama, Rico Alexander Putri Gabriella Angel Natalia Satya Rahadian Zainul Ramanto, Kevin Nathanael Ratnasari, Nanda Risqia Pradana Renadya Maulani Wijaya Ridarto, Afif Maulana Yusuf Riza A PUTRANTO Rizky Nurdiansyah Rizky, Wahyu Choirur Ryan Fugaha, Daniel Ryan Wijaya Ryan Wijaya, Ryan Satrio Wibowo Scherbakov, Pavel Sepiashvili, Ekaterina Shemuel, Josia Sofy Permana Sri Wahyuningsih Stefanus Bernard Sudaryo, Mondastri Korib Sugiono, Dedy Svetlana Artyukhova Tambunan, Usman Sumo Friend Teguh Hari Sucipto, Teguh Hari Theo A Tochary Tochary, Theo A. Usman Sumo Friend Tambunan Utomo, Didik Huswo Utomo, Didik Huswo Vikash Jakhmola Viol Dhea Kharisma Wicaksono, Adhityo Wijaya, Renadya Maulani Yanuargi, Bayu Yulia Matrosova