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Protein-protein interactions: Insight from molecular dynamics simulations and nanoparticle tracking analysis

Protein-protein interaction plays an essential role in almost all cellular processes and biological functions. Coupling molecular dynamics (MD) simulations and nanoparticle tracking analysis (NTA) assay offered a simple, rapid, and direct approach in monitoring the protein-protein binding process an...

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Main Authors:	Chong, Wei Lim, Chupradit, Koollawat, Chin, Sek Peng, Khoo, Mai Mai, Khor, Sook Mei, Tayapiwatana, Chatchai, Nimmanpipug, Piyarat, Thongkum, Weeraya, Lee, Vannajan Sanghiran
Format:	Article
Published:	MDPI 2021
Subjects:	QD Chemistry R Medicine RS Pharmacy and materia medica
Online Access:	http://eprints.um.edu.my/34173/
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spelling	my.um.eprints.341732022-09-02T03:20:51Z http://eprints.um.edu.my/34173/ Protein-protein interactions: Insight from molecular dynamics simulations and nanoparticle tracking analysis Chong, Wei Lim Chupradit, Koollawat Chin, Sek Peng Khoo, Mai Mai Khor, Sook Mei Tayapiwatana, Chatchai Nimmanpipug, Piyarat Thongkum, Weeraya Lee, Vannajan Sanghiran QD Chemistry R Medicine RS Pharmacy and materia medica Protein-protein interaction plays an essential role in almost all cellular processes and biological functions. Coupling molecular dynamics (MD) simulations and nanoparticle tracking analysis (NTA) assay offered a simple, rapid, and direct approach in monitoring the protein-protein binding process and predicting the binding affinity. Our case study of designed ankyrin repeats proteins (DARPins)-AnkGAG1D4 and the single point mutated AnkGAG1D4-Y56A for HIV-1 capsid protein (CA) were investigated. As reported, AnkGAG1D4 bound with CA for inhibitory activity; however, it lost its inhibitory strength when tyrosine at residue 56 AnkGAG1D4, the most key residue was replaced by alanine (AnkGAG1D4-Y56A). Through NTA, the binding of DARPins and CA was measured by monitoring the increment of the hydrodynamic radius of the AnkGAG1D4-gold conjugated nanoparticles (AnkGAG1D4-GNP) and AnkGAG1D4-Y56A-GNP upon interaction with CA in buffer solution. The size of the AnkGAG1D4-GNP increased when it interacted with CA but not AnkGAG1D4-Y56A-GNP. In addition, a much higher binding free energy ( increment GB) of AnkGAG1D4-Y56A (-31 kcal/mol) obtained from MD further suggested affinity for CA completely reduced compared to AnkGAG1D4 (-60 kcal/mol). The possible mechanism of the protein-protein binding was explored in detail by decomposing the binding free energy for crucial residues identification and hydrogen bond analysis. MDPI 2021-09 Article PeerReviewed Chong, Wei Lim and Chupradit, Koollawat and Chin, Sek Peng and Khoo, Mai Mai and Khor, Sook Mei and Tayapiwatana, Chatchai and Nimmanpipug, Piyarat and Thongkum, Weeraya and Lee, Vannajan Sanghiran (2021) Protein-protein interactions: Insight from molecular dynamics simulations and nanoparticle tracking analysis. Molecules, 26 (18). ISSN 1420-3049, DOI https://doi.org/10.3390/molecules26185696 <https://doi.org/10.3390/molecules26185696>. 10.3390/molecules26185696
institution	Universiti Malaya
building	UM Library
collection	Institutional Repository
continent	Asia
country	Malaysia
content_provider	Universiti Malaya
content_source	UM Research Repository
url_provider	http://eprints.um.edu.my/
topic	QD Chemistry R Medicine RS Pharmacy and materia medica
spellingShingle	QD Chemistry R Medicine RS Pharmacy and materia medica Chong, Wei Lim Chupradit, Koollawat Chin, Sek Peng Khoo, Mai Mai Khor, Sook Mei Tayapiwatana, Chatchai Nimmanpipug, Piyarat Thongkum, Weeraya Lee, Vannajan Sanghiran Protein-protein interactions: Insight from molecular dynamics simulations and nanoparticle tracking analysis
description	Protein-protein interaction plays an essential role in almost all cellular processes and biological functions. Coupling molecular dynamics (MD) simulations and nanoparticle tracking analysis (NTA) assay offered a simple, rapid, and direct approach in monitoring the protein-protein binding process and predicting the binding affinity. Our case study of designed ankyrin repeats proteins (DARPins)-AnkGAG1D4 and the single point mutated AnkGAG1D4-Y56A for HIV-1 capsid protein (CA) were investigated. As reported, AnkGAG1D4 bound with CA for inhibitory activity; however, it lost its inhibitory strength when tyrosine at residue 56 AnkGAG1D4, the most key residue was replaced by alanine (AnkGAG1D4-Y56A). Through NTA, the binding of DARPins and CA was measured by monitoring the increment of the hydrodynamic radius of the AnkGAG1D4-gold conjugated nanoparticles (AnkGAG1D4-GNP) and AnkGAG1D4-Y56A-GNP upon interaction with CA in buffer solution. The size of the AnkGAG1D4-GNP increased when it interacted with CA but not AnkGAG1D4-Y56A-GNP. In addition, a much higher binding free energy ( increment GB) of AnkGAG1D4-Y56A (-31 kcal/mol) obtained from MD further suggested affinity for CA completely reduced compared to AnkGAG1D4 (-60 kcal/mol). The possible mechanism of the protein-protein binding was explored in detail by decomposing the binding free energy for crucial residues identification and hydrogen bond analysis.
format	Article
author	Chong, Wei Lim Chupradit, Koollawat Chin, Sek Peng Khoo, Mai Mai Khor, Sook Mei Tayapiwatana, Chatchai Nimmanpipug, Piyarat Thongkum, Weeraya Lee, Vannajan Sanghiran
author_facet	Chong, Wei Lim Chupradit, Koollawat Chin, Sek Peng Khoo, Mai Mai Khor, Sook Mei Tayapiwatana, Chatchai Nimmanpipug, Piyarat Thongkum, Weeraya Lee, Vannajan Sanghiran
author_sort	Chong, Wei Lim
title	Protein-protein interactions: Insight from molecular dynamics simulations and nanoparticle tracking analysis
title_short	Protein-protein interactions: Insight from molecular dynamics simulations and nanoparticle tracking analysis
title_full	Protein-protein interactions: Insight from molecular dynamics simulations and nanoparticle tracking analysis
title_fullStr	Protein-protein interactions: Insight from molecular dynamics simulations and nanoparticle tracking analysis
title_full_unstemmed	Protein-protein interactions: Insight from molecular dynamics simulations and nanoparticle tracking analysis
title_sort	protein-protein interactions: insight from molecular dynamics simulations and nanoparticle tracking analysis
publisher	MDPI
publishDate	2021
url	http://eprints.um.edu.my/34173/
_version_	1744649161547972608
score	13.211869

Protein-protein interactions: Insight from molecular dynamics simulations and nanoparticle tracking analysis

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