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Investigation of the structural preference and flexibility of the loop residues in amyloid fibrils of the HET-s prion

The structural variability of a 16-residue loop (residues 246261) which is in part disordered and connects two layers of the -solenoid formed by the prion-form of HET-s and its prion domain HET-s(218289) is investigated using molecular dynamics computer simulation. A system of three HET-s(218289) mo... Full description

Journal Title: Physical Chemistry Chemical Physics 2016, Vol.18(8), pp.5860-5866
Main Author: Dolenc, Joica
Other Authors: Meier, Beat H. , Rusu, Victor H. , Van Gunsteren, Wilfred F.
Format: Electronic Article Electronic Article
Language:
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ID: ISSN: 1463-9076 ; E-ISSN: 1463-9084 ; DOI: 10.1039/c6cp00057f
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recordid: rscc6cp00057f
title: Investigation of the structural preference and flexibility of the loop residues in amyloid fibrils of the HET-s prion
format: Article
creator:
  • Dolenc, Joica
  • Meier, Beat H.
  • Rusu, Victor H.
  • Van Gunsteren, Wilfred F.
subjects:
  • Mathematical Models
  • Data Processing
  • Prion Protein
  • Molecular Dynamics
  • Fibrils
  • Amyloid
  • Prions
ispartof: Physical Chemistry Chemical Physics, 2016, Vol.18(8), pp.5860-5866
description: The structural variability of a 16-residue loop (residues 246261) which is in part disordered and connects two layers of the -solenoid formed by the prion-form of HET-s and its prion domain HET-s(218289) is investigated using molecular dynamics computer simulation. A system of three HET-s(218289) molecules in a -sheet structure as in the fibril is simulated in aqueous solution. The trajectory structures appear to be consistent with the C chemical shift data obtained. In order to delineate the influence of the -sheet core of the fibril upon the structural variability of the loop, the latter is also simulated without the -sheet core, but with its N- and C-terminal residues restrained at their positions in the fibril. The analysis of the trajectories shows that the structural variability of the loop is restricted by the -sheet core, least at its N-terminal end and most in the middle of the trimer.
language:
source:
identifier: ISSN: 1463-9076 ; E-ISSN: 1463-9084 ; DOI: 10.1039/c6cp00057f
fulltext: fulltext
issn:
  • 1463-9076
  • 1463-9084
  • 14639084
  • 14639076
url: Link


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titleInvestigation of the structural preference and flexibility of the loop residues in amyloid fibrils of the HET-s prion
creatorDolenc, Joica ; Meier, Beat H. ; Rusu, Victor H. ; Van Gunsteren, Wilfred F.
ispartofPhysical Chemistry Chemical Physics, 2016, Vol.18(8), pp.5860-5866
identifier
descriptionThe structural variability of a 16-residue loop (residues 246261) which is in part disordered and connects two layers of the -solenoid formed by the prion-form of HET-s and its prion domain HET-s(218289) is investigated using molecular dynamics computer simulation. A system of three HET-s(218289) molecules in a -sheet structure as in the fibril is simulated in aqueous solution. The trajectory structures appear to be consistent with the C chemical shift data obtained. In order to delineate the influence of the -sheet core of the fibril upon the structural variability of the loop, the latter is also simulated without the -sheet core, but with its N- and C-terminal residues restrained at their positions in the fibril. The analysis of the trajectories shows that the structural variability of the loop is restricted by the -sheet core, least at its N-terminal end and most in the middle of the trimer.
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subjectMathematical Models ; Data Processing ; Prion Protein ; Molecular Dynamics ; Fibrils ; Amyloid ; Prions;
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titleInvestigation of the structural preference and flexibility of the loop residues in amyloid fibrils of the HET-s prion
descriptionThe structural variability of a 16-residue loop (residues 246261) which is in part disordered and connects two layers of the -solenoid formed by the prion-form of HET-s and its prion domain HET-s(218289) is investigated using molecular dynamics computer simulation. A system of three HET-s(218289) molecules in a -sheet structure as in the fibril is simulated in aqueous solution. The trajectory structures appear to be consistent with the C chemical shift data obtained. In order to delineate the influence of the -sheet core of the fibril upon the structural variability of the loop, the latter is also simulated without the -sheet core, but with its N- and C-terminal residues restrained at their positions in the fibril. The analysis of the trajectories shows that the structural variability of the loop is restricted by the -sheet core, least at its N-terminal end and most in the middle of the trimer.
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titleInvestigation of the structural preference and flexibility of the loop residues in amyloid fibrils of the HET-s prion
authorDolenc, Joica ; Meier, Beat H. ; Rusu, Victor H. ; Van Gunsteren, Wilfred F.
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abstractThe structural variability of a 16-residue loop (residues 246261) which is in part disordered and connects two layers of the -solenoid formed by the prion-form of HET-s and its prion domain HET-s(218289) is investigated using molecular dynamics computer simulation. A system of three HET-s(218289) molecules in a -sheet structure as in the fibril is simulated in aqueous solution. The trajectory structures appear to be consistent with the C chemical shift data obtained. In order to delineate the influence of the -sheet core of the fibril upon the structural variability of the loop, the latter is also simulated without the -sheet core, but with its N- and C-terminal residues restrained at their positions in the fibril. The analysis of the trajectories shows that the structural variability of the loop is restricted by the -sheet core, least at its N-terminal end and most in the middle of the trimer.
doi10.1039/c6cp00057f
pages5860-5866
date2016-02-17