Water Dynamics:  Vibrational Echo Correlation Spectroscopy and Comparison to Molecular Dynamics Simulations

2004 ◽  
Vol 108 (7) ◽  
pp. 1107-1119 ◽  
Author(s):  
John B. Asbury ◽  
Tobias Steinel ◽  
C. Stromberg ◽  
S. A. Corcelli ◽  
C. P. Lawrence ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Correlation Spectroscopy ◽  
Water Dynamics ◽  
Dynamics Simulations ◽  
Vibrational Echo

scholarly journals Anomalous dynamics of water at the octopeptide lanreotide surface

RSC Advances ◽  
2020 ◽  
Vol 10 (56) ◽  
pp. 33903-33910
Author(s):  
Florian Pinzan ◽  
Franck Artzner ◽  
Aziz Ghoufi
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Water Dynamics ◽  
Atomistic Simulations ◽  
Hydration State ◽  
Dynamics Simulations ◽  
Anomalous Dynamics ◽  
Cyclic Octapeptide

Molecular dynamics simulations of a hydrated mutated lanreotide, a cyclic octapeptide, were carried out to characterize its hydration state. We studied the water dynamics close to the peptide using atomistic simulations.

scholarly journals Hydration water mobility is enhanced around tau amyloid fibers

2015 ◽  
Vol 112 (20) ◽  
pp. 6365-6370 ◽  
Author(s):  
Yann Fichou ◽  
Giorgio Schirò ◽  
François-Xavier Gallat ◽  
Cedric Laguri ◽  
Martine Moulin ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Neutron Scattering ◽  
Molecular Dynamics Simulations ◽  
Fiber Formation ◽  
Human Protein ◽  
Water Dynamics ◽  
Hydration Water ◽  
Water Mobility ◽  
Intrinsically Disordered ◽  
Dynamics Simulations

The paired helical filaments (PHF) formed by the intrinsically disordered human protein tau are one of the pathological hallmarks of Alzheimer disease. PHF are fibers of amyloid nature that are composed of a rigid core and an unstructured fuzzy coat. The mechanisms of fiber formation, in particular the role that hydration water might play, remain poorly understood. We combined protein deuteration, neutron scattering, and all-atom molecular dynamics simulations to study the dynamics of hydration water at the surface of fibers formed by the full-length human protein htau40. In comparison with monomeric tau, hydration water on the surface of tau fibers is more mobile, as evidenced by an increased fraction of translationally diffusing water molecules, a higher diffusion coefficient, and increased mean-squared displacements in neutron scattering experiments. Fibers formed by the hexapeptide 306VQIVYK311 were taken as a model for the tau fiber core and studied by molecular dynamics simulations, revealing that hydration water dynamics around the core domain is significantly reduced after fiber formation. Thus, an increase in water dynamics around the fuzzy coat is proposed to be at the origin of the experimentally observed increase in hydration water dynamics around the entire tau fiber. The observed increase in hydration water dynamics is suggested to promote fiber formation through entropic effects. Detection of the enhanced hydration water mobility around tau fibers is conjectured to potentially contribute to the early diagnosis of Alzheimer patients by diffusion MRI.

Ultrafast Dynamics of Myoglobin without the Distal Histidine:  Stimulated Vibrational Echo Experiments and Molecular Dynamics Simulations

2005 ◽  
Vol 109 (35) ◽  
pp. 16959-16966 ◽  
Author(s):  
Ilya J. Finkelstein ◽  
Anne Goj ◽  
Brian L. McClain ◽  
Aaron M. Massari ◽  
Kusai A. Merchant ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Ultrafast Dynamics ◽  
Dynamics Simulations ◽  
Vibrational Echo

The Influence of Aqueous versus Glassy Solvents on Protein Dynamics:  Vibrational Echo Experiments and Molecular Dynamics Simulations

2005 ◽  
Vol 127 (41) ◽  
pp. 14279-14289 ◽  
Author(s):  
Aaron M. Massari ◽  
Ilya J. Finkelstein ◽  
Brian L. McClain ◽  
Anne Goj ◽  
Xin Wen ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Protein Dynamics ◽  
Dynamics Simulations ◽  
Vibrational Echo

scholarly journals Correlation Spectroscopy and Molecular Dynamics Simulations to Study the Structural Features of Proteins

PLoS ONE ◽  
2013 ◽  
Vol 8 (6) ◽  
pp. e64840 ◽  
Author(s):  
Antonio Varriale ◽  
Anna Marabotti ◽  
Giampiero Mei ◽  
Maria Staiano ◽  
Sabato D’Auria
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Structural Features ◽  
Correlation Spectroscopy ◽  
Dynamics Simulations
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