scholarly journals Checking the pH-Induced Conformational Transition of Prion Protein by Molecular Dynamics Simulations: Effect of Protonation of Histidine Residues

2004 ◽  
Vol 87 (6) ◽  
pp. 3623-3632 ◽  
Author(s):  
Emma Langella ◽  
Roberto Improta ◽  
Vincenzo Barone
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Prion Protein ◽  
Conformational Transition ◽  
Histidine Residues ◽  
Dynamics Simulations

scholarly journals Dominant-negative effects in prion diseases: insights from molecular dynamics simulations on mouse prion protein chimeras

2013 ◽  
Vol 31 (8) ◽  
pp. 829-840 ◽  
Author(s):  
Xiaojing Cong ◽  
Salvatore Bongarzone ◽  
Gabriele Giachin ◽  
Giulia Rossetti ◽  
Paolo Carloni ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Prion Protein ◽  
Prion Diseases ◽  
Dominant Negative ◽  
Negative Effects ◽  
Dynamics Simulations

UNDERSTANDING DIFFERENT LCST LEVELS OF POLY(N-ALKYLACRYLAMIDE)S BY MOLECULAR DYNAMICS SIMULATIONS AND QUANTUM MECHANICS CALCULATIONS

2011 ◽  
Vol 10 (03) ◽  
pp. 359-370 ◽  
Author(s):  
JUAN PANG ◽  
HU YANG ◽  
JING MA ◽  
RONGSHI CHENG
Keyword(s):  
Molecular Dynamics ◽  
Quantum Mechanics ◽  
Aqueous Solutions ◽  
Molecular Dynamics Simulations ◽  
Steric Effect ◽  
Conformational Transition ◽  
Methyl Group ◽  
Branched Chain ◽  
Dynamics Simulations ◽  
Different Levels

Poly(N-alkylacrylamide) is a group of thermo-sensitive polymers that include poly (N-isopropylacrylamide), poly(N-n-propylacrylamide), poly(N-isopropylmethacryl-amide), and so on. The polymers exhibit different levels of lower critical solution temperatures (LCST) in aqueous solutions. In this article, their monomers and oligomers with 10 repeating units are selected, respectively, to demonstrate the cause of different LCST levels of the polymers in aqueous solutions using molecular dynamics simulations and quantum mechanics calculations. The monomers have functional groups of different steric volume that greatly affect the conformational transition of chains and LCST levels of the polymers. A branched chain of N-propyl group in N-isopropylacrylamide and an additional methyl group at α-carbon in N-isopropylmethacrylamide both increase the steric effect, making it more difficult for monomers to draw closer and resulting in higher LCST levels of the polymers. In addition, the simulated results from their corresponding oligomers exhibit the similar trend to those from the monomers.

scholarly journals Misfolding Pathways of the Prion Protein Probed by Molecular Dynamics Simulations

2005 ◽  
Vol 88 (2) ◽  
pp. 1334-1343 ◽  
Author(s):  
Alessandro Barducci ◽  
Riccardo Chelli ◽  
Piero Procacci ◽  
Vincenzo Schettino
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Prion Protein ◽  
Dynamics Simulations
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