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

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

scholarly journals Active-site protein dynamics and solvent accessibility in nativeAchromobacter cycloclastescopper nitrite reductase

IUCrJ ◽  
2017 ◽  
Vol 4 (4) ◽  
pp. 495-505 ◽  
Author(s):  
Kakali Sen ◽  
Sam Horrell ◽  
Demet Kekilli ◽  
Chin W. Yong ◽  
Thomas W. Keal ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Protein Dynamics ◽  
Nitrite Reductase ◽  
Active Site ◽  
Solvent Accessibility ◽  
Nitrite Reduction ◽  
Protonation State ◽  
Dynamics Simulations

Microbial nitrite reductases are denitrifying enzymes that are a major component of the global nitrogen cycle. Multiple structures measured from one crystal (MSOX data) of copper nitrite reductase at 240 K, together with molecular-dynamics simulations, have revealed protein dynamics at the type 2 copper site that are significant for its catalytic properties and for the entry and exit of solvent or ligands to and from the active site. Molecular-dynamics simulations were performed using different protonation states of the key catalytic residues (AspCATand HisCAT) involved in the nitrite-reduction mechanism of this enzyme. Taken together, the crystal structures and simulations show that the AspCATprotonation state strongly influences the active-site solvent accessibility, while the dynamics of the active-site `capping residue' (IleCAT), a determinant of ligand binding, are influenced both by temperature and by the protonation state of AspCAT. A previously unobserved conformation of IleCATis seen in the elevated temperature series compared with 100 K structures. DFT calculations also show that the loss of a bound water ligand at the active site during the MSOX series is consistent with reduction of the type 2 Cu atom.

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
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