Pairwise decomposition of residue interaction energies of single chain Fv with HIV-1 p17 epitope variants

Computational assisted modeling was carried out to investigate the importance of specific residues in the binding site of scFv. In this study, scFv against HIV-1 epitope at the C-terminal on p17 (scFv anti-p17) was used as a candidate molecule for evaluating the method. The wild-type p17 and its nin...

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Main Authors: Vannajan Sanghiran Lee, Panthip Tue-ngeun, Sawitree Nangola, Kuntida Kitidee, Jitrayut Jitonnom, Piyarat Nimmanpipug, Supat Jiranusornkul, Chatchai Tayapiwatana
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Published: 2018
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http://cmuir.cmu.ac.th/jspui/handle/6653943832/50598
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spelling th-cmuir.6653943832-505982018-09-04T04:47:50Z Pairwise decomposition of residue interaction energies of single chain Fv with HIV-1 p17 epitope variants Vannajan Sanghiran Lee Panthip Tue-ngeun Sawitree Nangola Kuntida Kitidee Jitrayut Jitonnom Piyarat Nimmanpipug Supat Jiranusornkul Chatchai Tayapiwatana Biochemistry, Genetics and Molecular Biology Immunology and Microbiology Computational assisted modeling was carried out to investigate the importance of specific residues in the binding site of scFv. In this study, scFv against HIV-1 epitope at the C-terminal on p17 (scFv anti-p17) was used as a candidate molecule for evaluating the method. The wild-type p17 and its nine natural mutants were docked with scFv anti-p17. Potential mean force (PMF) scores predicted the most favorable binding interaction, and the correlation agreed well with the corresponding activity data from the peptide based ELISA. In the interaction with solvent molecules, the 3D structures of scFv anti-p17 and selected peptide epitopes were further investigated by molecular dynamics (MDs) simulation with the AMBER 9 program. Post-processing of the snapshot at equilibrium was performed to evaluate the binding free energy and pairwise decomposition or residue-based energy calculation of complexes in solution using the Molecular Mechanics Poisson-Boltzmann Surface Area (MM-PBSA) protocol. Our results demonstrated that the specific residues located in the complementary determining regions (CDRs) of scFv anti-p17, MET100, LYS101, ASN169, HIS228, and LEU229, play a crucial role in the effective binding interaction with the absolute relative decomposed energy more than 2.00 kcal/mol in comparison to the original substrate. © 2009 Elsevier Ltd. All rights reserved. 2018-09-04T04:42:47Z 2018-09-04T04:42:47Z 2010-02-01 Journal 01615890 2-s2.0-74849100500 10.1016/j.molimm.2009.11.021 https://www.scopus.com/inward/record.uri?partnerID=HzOxMe3b&scp=74849100500&origin=inward http://cmuir.cmu.ac.th/jspui/handle/6653943832/50598
institution Chiang Mai University
building Chiang Mai University Library
country Thailand
collection CMU Intellectual Repository
topic Biochemistry, Genetics and Molecular Biology
Immunology and Microbiology
spellingShingle Biochemistry, Genetics and Molecular Biology
Immunology and Microbiology
Vannajan Sanghiran Lee
Panthip Tue-ngeun
Sawitree Nangola
Kuntida Kitidee
Jitrayut Jitonnom
Piyarat Nimmanpipug
Supat Jiranusornkul
Chatchai Tayapiwatana
Pairwise decomposition of residue interaction energies of single chain Fv with HIV-1 p17 epitope variants
description Computational assisted modeling was carried out to investigate the importance of specific residues in the binding site of scFv. In this study, scFv against HIV-1 epitope at the C-terminal on p17 (scFv anti-p17) was used as a candidate molecule for evaluating the method. The wild-type p17 and its nine natural mutants were docked with scFv anti-p17. Potential mean force (PMF) scores predicted the most favorable binding interaction, and the correlation agreed well with the corresponding activity data from the peptide based ELISA. In the interaction with solvent molecules, the 3D structures of scFv anti-p17 and selected peptide epitopes were further investigated by molecular dynamics (MDs) simulation with the AMBER 9 program. Post-processing of the snapshot at equilibrium was performed to evaluate the binding free energy and pairwise decomposition or residue-based energy calculation of complexes in solution using the Molecular Mechanics Poisson-Boltzmann Surface Area (MM-PBSA) protocol. Our results demonstrated that the specific residues located in the complementary determining regions (CDRs) of scFv anti-p17, MET100, LYS101, ASN169, HIS228, and LEU229, play a crucial role in the effective binding interaction with the absolute relative decomposed energy more than 2.00 kcal/mol in comparison to the original substrate. © 2009 Elsevier Ltd. All rights reserved.
format Journal
author Vannajan Sanghiran Lee
Panthip Tue-ngeun
Sawitree Nangola
Kuntida Kitidee
Jitrayut Jitonnom
Piyarat Nimmanpipug
Supat Jiranusornkul
Chatchai Tayapiwatana
author_facet Vannajan Sanghiran Lee
Panthip Tue-ngeun
Sawitree Nangola
Kuntida Kitidee
Jitrayut Jitonnom
Piyarat Nimmanpipug
Supat Jiranusornkul
Chatchai Tayapiwatana
author_sort Vannajan Sanghiran Lee
title Pairwise decomposition of residue interaction energies of single chain Fv with HIV-1 p17 epitope variants
title_short Pairwise decomposition of residue interaction energies of single chain Fv with HIV-1 p17 epitope variants
title_full Pairwise decomposition of residue interaction energies of single chain Fv with HIV-1 p17 epitope variants
title_fullStr Pairwise decomposition of residue interaction energies of single chain Fv with HIV-1 p17 epitope variants
title_full_unstemmed Pairwise decomposition of residue interaction energies of single chain Fv with HIV-1 p17 epitope variants
title_sort pairwise decomposition of residue interaction energies of single chain fv with hiv-1 p17 epitope variants
publishDate 2018
url https://www.scopus.com/inward/record.uri?partnerID=HzOxMe3b&scp=74849100500&origin=inward
http://cmuir.cmu.ac.th/jspui/handle/6653943832/50598
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