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All Journal Journal of Tropical Life Science : International Journal of Theoretical, Experimental, and Applied Life Sciences JURNAL KIMIA SAINS DAN APLIKASI Chem Info WAPFI (Wahana Pendidikan Fisika) Phi : Jurnal Pendidikan Fisika dan Terapan JURNAL ILMIAH PENDIDIKAN FISIKA AL BIRUNI Jurnal Penelitian dan Pembelajaran IPA Jurnal Penelitian Pendidikan IPA (JPPIPA) INDONESIAN JOURNAL OF APPLIED PHYSICS Indonesian Journal of Chemistry ORBITA: Jurnal Pendidikan dan Ilmu Fisika JPF : JURNAL PENDIDIKAN FISIKA Molekul: Jurnal Ilmiah Kimia Greensphere: Journal of Environmental Chemistry Journal of Educational Sciences Jurnal Pendidikan MIPA
Parsaoran Siahaan
Department Of Chemistry, Faculty Of Sciences And Mathematics, Diponegoro University, Jl. Prof. H. Soedarto, S.H., Tembalang, Semarang 50275, Indonesia
Religion Agriculture, Biological Sciences & Forestry Humanities Astronomy Biochemistry, Genetics & Molecular Biology Chemical Engineering, Chemistry & Bioengineering Chemistry Earth & Planetary Sciences Education Electrical & Electronics Engineering Energy Engineering Environmental Science Library & Information Science Materials Science & Nanotechnology Physics Social Sciences Other

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Structural Stability of ADTC5 Peptide: Conformational Insights into Dynamics and Its Binding Mode Siahaan, Parsaoran; Prasasty, Vivitri Dewi; Simanjuntak, Bungaran David; Hildayani, Suci; Anam, Khairul
Journal of Tropical Life Science Vol 7, No 2 (2017)
Publisher : Journal of Tropical Life Science

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.11594/jtls.07.02.09

Abstract

The cyclic structure of ADTC5 (Ac-CDTPPVC-NH2) peptide is known has ability to modulate homo dimer E-cadherin interactions to form adherens junction at the intercellular junction.  The ability to inhibit E-cadherin interaction has become important to increase paracellular porosity in delivering drug molecules to the target cell. There are two types of ADTC5 state: opened-cyclic state (OCS) and closed-cyclic state (CCS). OCS of ADTC5 is affected by distance constraint and CCS is formed by disulfide bond from terminal cysteines through force restraint. The aim of this research is to investigate the inhibition activity of ADTC5 peptide upon E-cadherin. Here we used molecular docking and molecular dynamics approaches. The structure of ADTC5 peptide was generated by PyMOL program. GROMACS v4.5.5 was utilized to simulate molecular dynamics. The optimized ADTC5 molecule was placed in aqueous or polar condition at physiological pH. Furthermore, ADTC5 was docked with EC1-EC2 coupled domain of E-cadherin using AutoDock 4.2 and be refined using molecular dynamic (MD). The result showed that CCS ADTC5 peptide has stronger affinity and more stable interaction with EC1-EC2 coupled domain than the OCS one.
Structural Stability of ADTC5 Peptide: Conformational Insights into Dynamics and Its Binding Mode Parsaoran Siahaan; Vivitri Dewi Prasasty; Bungaran David Simanjuntak; Suci Hildayani; Khairul Anam
Journal of Tropical Life Science Vol. 7 No. 2 (2017)
Publisher : Journal of Tropical Life Science

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.11594/jtls.07.02.09

Abstract

The cyclic structure of ADTC5 (Ac-CDTPPVC-NH2) peptide is known has ability to modulate homo dimer E-cadherin interactions to form adherens junction at the intercellular junction.  The ability to inhibit E-cadherin interaction has become important to increase paracellular porosity in delivering drug molecules to the target cell. There are two types of ADTC5 state: opened-cyclic state (OCS) and closed-cyclic state (CCS). OCS of ADTC5 is affected by distance constraint and CCS is formed by disulfide bond from terminal cysteines through force restraint. The aim of this research is to investigate the inhibition activity of ADTC5 peptide upon E-cadherin. Here we used molecular docking and molecular dynamics approaches. The structure of ADTC5 peptide was generated by PyMOL program. GROMACS v4.5.5 was utilized to simulate molecular dynamics. The optimized ADTC5 molecule was placed in aqueous or polar condition at physiological pH. Furthermore, ADTC5 was docked with EC1-EC2 coupled domain of E-cadherin using AutoDock 4.2 and be refined using molecular dynamic (MD). The result showed that CCS ADTC5 peptide has stronger affinity and more stable interaction with EC1-EC2 coupled domain than the OCS one.
Co-Authors A. Suhandi A.F.C Wijaya A.F.C. Wijaya Achmad Samsudin Ade Rahmani ADI YULANDI Agus Subagio Amsor, Amsor Anam, M. Khairul Anggi Hanif Setyadin Anugrah Ricky Wijaya Anugrah, Daru Seto Bagus ARIF HIDAYAT Asep Saefullah Atiatul Manna Ayub Indra Badri Rahmatulloh Bambang Cahyono Bani Amanullah Prasojo Bungaran David Simanjuntak Choiril Azmiyawati Cynthia L. Radiman Cynthia L. Radiman Desita Triana Dieter Ziessow Dieter Ziessow Diky Yopianto Dwi Hudiyanti Dwi Hudiyanti E. Suhendi Efendi, Ridwan Eka Liandari Endang Sawitri Endi Suhendi Ermawati Dewi Ermawati Dewi, Ermawati Farach, Nurul Febriani Sinambela Friska, Reski Ivon Fungky Iqlima Nasyidiah Gadis Argi Kiranti Hendri Widiyandari Heni Rusnayati Heny Ekawati Haryono Hildayani, Suci I Gusti Bagus Wiksuana Ida Kaniawati Ika Mustika Sari Imelda F. Saragih Isnaini Isnaini Isnaini Isnaini Khafidhoh Nurul Aini, Khafidhoh Nurul Khairul Anam KL Putri Laura Virdy Darmalim Liana Dewi Nuratikah Marchelia Dwi Yanthi Marlyn Dian Laksitorini Marlyn Dian Laksitorini Marta J. Sipangkar Mohd Hafiz Dzarfan Othman Mr Sumar Hendayana Muhamad A. Martoprawiro Muhamad A. Martoprawiro Muhammad Cholid Djunaidi Nadira Cahyaning Mentari Nanik Wijayanti Nastiti Nastiti Nia Kurniasih Nor Basid Adiwibawa Prasetya Nurbani, Anggita Repsi Nurwarrohman Andre Sasongko Parlindungan Sinaga Permono Adi Putro Purwanto, Purwanto Putra Habib Dhitareka Redemtus Heru Tjahjana Restina Septiani Retno Ariadi Lusiana Rikno Budiyanto Risda Destari Royhanshah, Moch Freskha Fauzi Sasmita, Dedi Sekar Kusuma Dewi Simanjuntak, Bungaran David Sri Haryanti Suci Hildayani Suci Zulaikha Hildayani Suhartana Suhartana Susanto Imam Rahayu Susanto Imam Rahayu Tantri Nevi Astuti Taufik Rahman Tri Endro Pranowo Tri Windarti Unang Purwana Ustera Octovindra Wiedyanto Vina Rilantinawati Vivitri Dewi Prasasty Wahyu Setiabudi Wawan Setiawan Wempie Gressangga Yanthi, Marchelia Dwi Yenni, Rozi Prima Yunina Surtiana