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All Journal HAYATI Journal of Biosciences Jurnal Agronomi Indonesia (Indonesian Journal of Agronomy) Jurnal Ilmu Pertanian Indonesia Jurnal Fitopatologi Indonesia Jurnal Pengolahan Hasil Perikanan Indonesia Jurnal Akuatika Jurnal Ilmu Dasar Microbiology Indonesia BIOTROPIA - The Southeast Asian Journal of Tropical Biology BERKALA SAINSTEK Biota: Jurnal Ilmiah Ilmu-Ilmu Hayati Indonesian Journal of Agricultural Science Indonesian Journal of Biotechnology Jurnal Perlindungan Tanaman Indonesia Journal of Tropical Biodiversity and Biotechnology UNEJ e-Proceeding JURNAL HAMA DAN PENYAKIT TUMBUHAN TROPIKA ANNALES BOGORIENSES Marine Research in Indonesia Biosaintifika: Journal of Biology & Biology Education Menara Perkebunan International Journal of Environment, Engineering, and Education International Journal of Environment, Engineering & Education International Journal of Oil Palm
Antonius Suwanto
Department Of Biology, Faculty Of Mathematics And Natural Science, IPB University, Bogor, Indonesia
Agriculture, Biological Sciences & Forestry Biochemistry, Genetics & Molecular Biology Chemical Engineering, Chemistry & Bioengineering Chemistry Civil Engineering, Building, Construction & Architecture Control & Systems Engineering Decision Sciences, Operations Research & Management Earth & Planetary Sciences Economics, Econometrics & Finance Education Engineering Environmental Science Immunology & microbiology Materials Science & Nanotechnology Mathematics Medicine & Pharmacology Physics Veterinary

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Journal : UNEJ e-Proceeding

 1 
Molecular Dynamic Simulation for Thermal Stability Properties of Endo β-Mannanase Enzyme Yulandi, Adi; Hermosaningtyas, A A; Sutanto, Sheila; Suwanto, Antonius
UNEJ e-Proceeding Indonesian Protein Society (IPS), International Seminar and Workshop 2014
Publisher : UNEJ e-Proceeding

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Abstract

Endo β-mannanase or mannanase hydrolyse the β-D-1,4 mannopyranoside linkages in β-mannan intomanno-oligosaccharides. Four mannanases, named MAN1, MAN2, MAN3 and MAN4, were isolated from palm kernel meal waste have potential as thermostable mannanases. Series of enzymatic assay to characterize enzyme properties may affect longer time and higher cost. Homology modeling and molecular dynamic simulation are reliable and faster alternative assay to determine enzyme properties by analyzing enzymes’ three-dimensional structure. The structureswere constructed using homology modeling approach using Modeller. Template 2QHA was chosen for having more than 98% sequence similarity with targets. The homology models and template were simulated using molecular dynamics software GROMACS 4.6 for 10 ns production time each at 300 K, 323 K and 353 K. Both targets share the same (β/α)8 TIM barrel folding type similar to template 2QHA The basic analysis of molecular dynamic simulation (root mean square deviation and root mean square fluctuation) showed that both enzymes were thermostable, albeit compared to template 2QHA amino acid residues substitution in samples contribute for different thermostable profile. However, MAN2 was appeared to be more stable at high temperature than other samples. Keywords: endo β-mananase, homology modeling, molecular dynamic simulation
Molecular Dynamic Simulation for Thermal Stability Properties of Endo β-Mannanase Enzyme Adi Yulandi; A A Hermosaningtyas; Sheila Sutanto; Antonius Suwanto
UNEJ e-Proceeding Indonesian Protein Society (IPS), International Seminar and Workshop 2014
Publisher : UPT Penerbitan Universitas Jember

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

Abstract

Endo β-mannanase or mannanase hydrolyse the β-D-1,4 mannopyranoside linkages in β-mannan intomanno-oligosaccharides. Four mannanases, named MAN1, MAN2, MAN3 and MAN4, were isolated from palm kernel meal waste have potential as thermostable mannanases. Series of enzymatic assay to characterize enzyme properties may affect longer time and higher cost. Homology modeling and molecular dynamic simulation are reliable and faster alternative assay to determine enzyme properties by analyzing enzymes’ three-dimensional structure. The structureswere constructed using homology modeling approach using Modeller. Template 2QHA was chosen for having more than 98% sequence similarity with targets. The homology models and template were simulated using molecular dynamics software GROMACS 4.6 for 10 ns production time each at 300 K, 323 K and 353 K. Both targets share the same (β/α)8 TIM barrel folding type similar to template 2QHA The basic analysis of molecular dynamic simulation (root mean square deviation and root mean square fluctuation) showed that both enzymes were thermostable, albeit compared to template 2QHA amino acid residues substitution in samples contribute for different thermostable profile. However, MAN2 was appeared to be more stable at high temperature than other samples. Keywords: endo β-mananase, homology modeling, molecular dynamic simulation
Co-Authors . EFRIWATI . Melani . NURHAIMI-HARIS A A Hermosaningtyas A A Hermosaningtyas, A A ADI YULANDI Agus PURWANTARA Agus Purwito Agustin Wydia Gunawan Agustina, Delia Alfred Michael ALINA AKHDIYA RUSMANA AMARILA MALIK AMARILA MALIK Andi Khaeruni Andi Khaeruni Andreas Adhi Satya Andreas Adhi Satya ANJA MERYANDINI Anja Meryandini ARI SUSILOWATI Arifudin Rafif , Muhammad Ghildan Arild Ranlym Arifin Arina Amalia Putri Aris Tjahjoleksono Aris Tri Wahyudi ARTINI PANGASTUTI Asmini Budiani Basil J NIKOLAU BIBIANA W LAY BUDI TJAHJONO Budi Tjahjono Budi Tjahjono BUDI TJAHJONO Budinarta, Widyah C Hanny Wijaya CAHYA PRIHATNA Cahya Prihatna Cahya Prihatna CECILIA ANNA SEUMAHU CECILIA ANNA SEUMAHU DEBORA HADISUSANTO Delia Agustina Desniar - - DIAH ISKANDRIATI DIANA ELIZABETH WATURANGI Djoko Santoso Dondin Sajuthi DWI SURYANTO Dyah Kusuma Anggraini Edi Husen Edi Husen EDI HUSEN ERNIN HIDAYATI ESTI PUSPITASARI Esti Puspitasari ESTI PUSPITASARI Esti Utarti Eunice Limantara EVELINE AYU Felicia Felicia Felicia Kartawidjajaputra Ferymon Mahulette Ferymon Mahulette Ferymon Mahulette, Ferymon G. A. Wattimena Gayuh Rahayu Griselda Griselda Griselda Herman Natadiputri Griselda, Griselda Hajrial ASWIDINNOO HAJRIAL ASWIDINNOOR Hariyatun Hariyatun Hariyatun, Hariyatun Hermosaningtyas, Anastasia Aliesa Iman Rusmana Inez H.S. Loeddin Suharsono It Jamilah IVAN HANJAYA JOANITA SADELI KATHARINA JESSICA Kusharyoto, Wien Lilis Nuraida Linda Wati LISTYA UTAMI KARMAWAN Ludovika Jessica Virginia MAGGY T HENAWIDJAJA Maggy T Suhartono Maggy T Suhartono Maggy T. Suhartono MAGGY T. SUHARTONO MAGGY T. SUHARTONO MAGGY THENAWIJAYA SUHARTONO Maria Dita Febriani Lumban Gaol Maria Indah Purnamasari Maria Indah Purnamasari Maria Indah Purnamasari Maria Sugiharti Meity S. Sinaga MEITY SURADJI SINAGA Muhamad Azwar Syah Muhammad Agus Muljanto MUHAMMAD ZAIRIN Jr. Ni Nyoman Tri Puspaningsih NISA RACHMANIA MUBARIK NURITA TORUAN-MATHIUS NURUL AINI PRIHASTO SETYANTO Prihasto Setyanto Prihatna , Cahya Puspitasari, Esti QURROTA A’YUN R. Sapto Hendri Boedi Soesatyo Raden Ajie Syahbarie RAHAYU WIDYASTUTI RASTI SARASWATI RASTI SARASWATI Rasti Saraswati Rasti Saraswati RATIH DEWI HASTUTI RATNA SETYANINGSIH RATNA SETYANINGSIH RIDWAN AFFANDI Rika Indri Astuti ROB HARLING ROHANI CINTA BADIA GINTING Rustam, Yepy Hardi Satya, Andreas Adhi Sheila Sutanto Sheila Sutanto, Sheila SUMARDI Suryo Wiyono SUSAN SOKA SUSILOWATI1 SUSILOWATI1 T RESNAWATI P URWADARIA Tan Watumesa Agustina TARUNI SRI PRAWAST MIEN KAOMINI ANY ARYANI DEDY DURYADI SOLIHIN Tati Barus TEMMY DESILIYARNI TRESNAWATI PURWADARIA VICKY MEICY WALTER ERDELEN WIDANARNI WIDANARNI Widanarni Widanarni Wien Kusharyoto Yasinta Ratna Esti Wulandari Yepy Hardi Rustam Yogiara Yogiara YULIN LESTARI Yusminah Hala