Free Energy of Binding of Coiled-Coil Complexes with Different Electrostatic Environments: The Influence of Force Field Polarisation and Capping

doi:10.1007/s13659-014-0036-0

Natural Products and Bioprospecting ›› 2014, Vol. 4 ›› Issue (5): 285-295.DOI: 10.1007/s13659-014-0036-0

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Free Energy of Binding of Coiled-Coil Complexes with Different Electrostatic Environments: The Influence of Force Field Polarisation and Capping

Zhi-Li Zuo¹, Ling Guo², Ricardo L. Mancera³

1. State Key Laboratory of Phytochemistry and Plant Resources in West China, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China;
2. College of Animal Husbandry & Veterinary, Liaoning Medical University, Jinzhou 121001, China;
3. School of Biomedical Sciences, CHIRI Biosciences, Curtin University, GPO Box U1987, Perth, WA 6845, Australia

Received:2014-07-29 Revised:2014-08-08 Online:2018-02-11 Published:2014-10-24
Supported by:
This work was supported by the State Key Laboratory of Phytochemistry and Plant Resources in West China, Kunming Institute of Botany, Chinese Academy of Sciences(P2013-ZZ05). We also thank National Supercomputing Center of Jinan to provid the computational resource.

Free Energy of Binding of Coiled-Coil Complexes with Different Electrostatic Environments: The Influence of Force Field Polarisation and Capping

Zhi-Li Zuo¹, Ling Guo², Ricardo L. Mancera³

1. State Key Laboratory of Phytochemistry and Plant Resources in West China, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China;
2. College of Animal Husbandry & Veterinary, Liaoning Medical University, Jinzhou 121001, China;
3. School of Biomedical Sciences, CHIRI Biosciences, Curtin University, GPO Box U1987, Perth, WA 6845, Australia

通讯作者: Zhi-Li Zuo,e-mail:zuozhili@mail.kib.ac.cn;Ricardo L.Mancera,e-mail:r.mancera@curtin.edu.au
基金资助:
This work was supported by the State Key Laboratory of Phytochemistry and Plant Resources in West China, Kunming Institute of Botany, Chinese Academy of Sciences(P2013-ZZ05). We also thank National Supercomputing Center of Jinan to provid the computational resource.

Abstract

Abstract: Coiled-coils are well known protein-protein interaction motifs, with the leucine zipper region of activator protein-1(AP-1) consisting of the c-Jun and c-Fos proteins being a typical example. Molecular dynamics(MD) simulations using the MM/GBSA method have been used to predict the free energy of interaction of these proteins. The influence of force field polarisation and capping on the predicted free energy of binding of complexes with different electrostatic environments(net charge) were investigated. Although both force field polarisation and peptide capping are important for the prediction of the absolute free energy of binding, peptide capping has the largest influence on the predicted free energy of binding. Polarisable simulations appear better suited to determine structural properties of the complexes of these proteins while non-polarisable simulations seem to give better predictions of the associated free energies of binding.

Key words: Free energy of binding, c-Fos, c-Jun, Leucine zipper, Molecular dynamics, MM/GBSA, Coiled-coil

摘要： Coiled-coils are well known protein-protein interaction motifs, with the leucine zipper region of activator protein-1(AP-1) consisting of the c-Jun and c-Fos proteins being a typical example. Molecular dynamics(MD) simulations using the MM/GBSA method have been used to predict the free energy of interaction of these proteins. The influence of force field polarisation and capping on the predicted free energy of binding of complexes with different electrostatic environments(net charge) were investigated. Although both force field polarisation and peptide capping are important for the prediction of the absolute free energy of binding, peptide capping has the largest influence on the predicted free energy of binding. Polarisable simulations appear better suited to determine structural properties of the complexes of these proteins while non-polarisable simulations seem to give better predictions of the associated free energies of binding.

关键词: Free energy of binding, c-Fos, c-Jun, Leucine zipper, Molecular dynamics, MM/GBSA, Coiled-coil

Zhi-Li Zuo, Ling Guo, Ricardo L. Mancera. Free Energy of Binding of Coiled-Coil Complexes with Different Electrostatic Environments: The Influence of Force Field Polarisation and Capping[J]. Natural Products and Bioprospecting, 2014, 4(5): 285-295.

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Free Energy of Binding of Coiled-Coil Complexes with Different Electrostatic Environments: The Influence of Force Field Polarisation and Capping

Free Energy of Binding of Coiled-Coil Complexes with Different Electrostatic Environments: The Influence of Force Field Polarisation and Capping

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