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Molecular dynamics simulation of the aggregation of the core‐recognition motif of the islet amyloid polypeptide in explicit water
The formation of amyloid fibrils is associated with major human diseases. Nevertheless, the molecular mechanism that directs the nucleation of these fibrils is not fully understood. Here, we usedExpand
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Molecular dynamics simulation of sperm whale myoglobin: effects of mutations and trapped CO on the structure and dynamics of cavities.
The results of extended (80-ns) molecular dynamics simulations of wild-type and YQR triple mutant of sperm whale deoxy myoglobin in water are reported and compared with the results of the simulationExpand
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Essential dynamics: foundation and applications
TLDR
Collective coordinates, as obtained by a principal component analysis of atomic fluctuations, are commonly used to predict a low‐dimensional subspace in which essential protein motion is expected to take place. Expand
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Aggregation of small peptides studied by molecular dynamics simulations
Peptides and proteins tend to aggregate under appropriate conditions. The amyloid fibrils that are ubiquitously found among these structures are associated with major human diseases like Alzheimer'sExpand
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Dynamical fingerprints for probing individual relaxation processes in biomolecular dynamics with simulations and kinetic experiments
  • F. Noé, S. Doose, +4 authors J. Smith
  • Chemistry, Medicine
  • Proceedings of the National Academy of Sciences
  • 2 March 2011
There is a gap between kinetic experiment and simulation in their views of the dynamics of complex biomolecular systems. Whereas experiments typically reveal only a few readily discernibleExpand
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β‐Hairpin conformation of fibrillogenic peptides: Structure and α‐β transition mechanism revealed by molecular dynamics simulations
Understanding the conformational transitions that trigger the aggregation and amyloidogenesis of otherwise soluble peptides at atomic resolution is of fundamental relevance for the design ofExpand
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The reversible opening of water channels in cytochrome c modulates the heme iron reduction potential.
Dynamic protein-solvent interactions are fundamental for life processes, but their investigation is still experimentally very demanding. Molecular dynamics simulations up to hundreds of nanosecondsExpand
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Common folding mechanism of a beta-hairpin peptide via non-native turn formation revealed by unbiased molecular dynamics simulations.
The folding of a 15-residue beta-hairpin peptide (Peptide 1) is characterized using multiple unbiased, atomistic molecular dynamics (MD) simulations. Fifteen independent MD trajectories, each 2.5Expand
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Investigating the accessibility of the closed domain conformation of citrate synthase using essential dynamics sampling.
A molecular dynamics study of pig heart citrate synthase is presented that aims to directly address the question of whether, for this enzyme, the ligand-induced closed domain conformation isExpand
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Charge-based interactions between peptides observed as the dominant force for association in aqueous solution.
The process by which proteins fold in solution into their biologically functional forms is still not well understood despite intense research. The association of hydrophobic amino acid side chains inExpand
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