Simulation of folding pathway studies of trp-cage miniprotein, amyloid A4 peptide, and a-conotoxin RgIA peptide

Protein is a sequence of a linear chain of amino acids. Protein folding is a physical process by which the linear chains of amino acid fold into its functional tertiary structures. Misfolding of a protein will lead to the problem such as diseases (cancer and influenza) in protein function. Discovery...

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Main Author:	Mohamed Tap, Fatahiya
Format:	Thesis
Published:	2013
Subjects:	QP Physiology
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id	my-utm-ep.41719
record_format	uketd_dc
spelling	my-utm-ep.417192020-06-28T04:27:52Z Simulation of folding pathway studies of trp-cage miniprotein, amyloid A4 peptide, and a-conotoxin RgIA peptide 2013 Mohamed Tap, Fatahiya QP Physiology Protein is a sequence of a linear chain of amino acids. Protein folding is a physical process by which the linear chains of amino acid fold into its functional tertiary structures. Misfolding of a protein will lead to the problem such as diseases (cancer and influenza) in protein function. Discovery of protein folding will help the biologist to find the cause of misfolding and also assist the drug designer to find the cure for related diseases. Therefore the objective of this study is to investigate the folding pathways of Trp-cage miniprotein, Amyloid A4 peptide, and a-conotoxin RgIA. The folding process was simulated using molecular dynamics (MD) simulation in both explicit and implicit solvent. Amyloid A4 peptide (350ns) and a-conotoxin (800ns) were simulated in implicit solvent, while the simulation for Trp-cage (150ns) and a-conotoxin (200ns) were performed in explicit solvent method. The simulations produced a huge number of trajectories which were further analysed based on their root mean squared deviation (RMSD) values. The RMSD values showed that these trajectories approaching their simulated native structure (NMRMD). Besides that, a few crucial formations of hydrogen bond, disulfide bond, and salt bridge were involved in stabilizing the folding process. The best structure was identified by clustering all the trajectories based on RMSD, solvent accessible surface area (SASA), van der Waals interaction, electrostatic interactions and total energy of each trajectory. The best structure for Trp-cage miniprotein, Amyloid A4 peptide, a-conotoxin with implicit solvent and, a-conotoxin with explicit solvent were extracted at 79.76 ns, 224.85 ns, 184.20, and 104.20 ns, respectively. 2013 Thesis http://eprints.utm.my/id/eprint/41719/ masters Universiti Teknologi Malaysia, Faculty of Chemical Engineering Faculty of Chemical Engineering
institution	Universiti Teknologi Malaysia
collection	UTM Institutional Repository
topic	QP Physiology
spellingShingle	QP Physiology Mohamed Tap, Fatahiya Simulation of folding pathway studies of trp-cage miniprotein, amyloid A4 peptide, and a-conotoxin RgIA peptide
description	Protein is a sequence of a linear chain of amino acids. Protein folding is a physical process by which the linear chains of amino acid fold into its functional tertiary structures. Misfolding of a protein will lead to the problem such as diseases (cancer and influenza) in protein function. Discovery of protein folding will help the biologist to find the cause of misfolding and also assist the drug designer to find the cure for related diseases. Therefore the objective of this study is to investigate the folding pathways of Trp-cage miniprotein, Amyloid A4 peptide, and a-conotoxin RgIA. The folding process was simulated using molecular dynamics (MD) simulation in both explicit and implicit solvent. Amyloid A4 peptide (350ns) and a-conotoxin (800ns) were simulated in implicit solvent, while the simulation for Trp-cage (150ns) and a-conotoxin (200ns) were performed in explicit solvent method. The simulations produced a huge number of trajectories which were further analysed based on their root mean squared deviation (RMSD) values. The RMSD values showed that these trajectories approaching their simulated native structure (NMRMD). Besides that, a few crucial formations of hydrogen bond, disulfide bond, and salt bridge were involved in stabilizing the folding process. The best structure was identified by clustering all the trajectories based on RMSD, solvent accessible surface area (SASA), van der Waals interaction, electrostatic interactions and total energy of each trajectory. The best structure for Trp-cage miniprotein, Amyloid A4 peptide, a-conotoxin with implicit solvent and, a-conotoxin with explicit solvent were extracted at 79.76 ns, 224.85 ns, 184.20, and 104.20 ns, respectively.
format	Thesis
qualification_level	Master's degree
author	Mohamed Tap, Fatahiya
author_facet	Mohamed Tap, Fatahiya
author_sort	Mohamed Tap, Fatahiya
title	Simulation of folding pathway studies of trp-cage miniprotein, amyloid A4 peptide, and a-conotoxin RgIA peptide
title_short	Simulation of folding pathway studies of trp-cage miniprotein, amyloid A4 peptide, and a-conotoxin RgIA peptide
title_full	Simulation of folding pathway studies of trp-cage miniprotein, amyloid A4 peptide, and a-conotoxin RgIA peptide
title_fullStr	Simulation of folding pathway studies of trp-cage miniprotein, amyloid A4 peptide, and a-conotoxin RgIA peptide
title_full_unstemmed	Simulation of folding pathway studies of trp-cage miniprotein, amyloid A4 peptide, and a-conotoxin RgIA peptide
title_sort	simulation of folding pathway studies of trp-cage miniprotein, amyloid a4 peptide, and a-conotoxin rgia peptide
granting_institution	Universiti Teknologi Malaysia, Faculty of Chemical Engineering
granting_department	Faculty of Chemical Engineering
publishDate	2013
_version_	1747816604103606272

Simulation of folding pathway studies of trp-cage miniprotein, amyloid A4 peptide, and a-conotoxin RgIA peptide

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