scholarly journals The Reactivity and Structural Dynamics of Supported Metal Nanoclusters Using Electron Microscopy, in situ X-Ray Spectroscopy, Electronic Structure Theories, and Molecular Dynamics Simulations.

2008 ◽  
Author(s):  
Judith C. Yang ◽  
Duane Johnson, Anatoly Frenkel Ralph G. Nuzzo
Keyword(s):  
Electron Microscopy ◽  
Molecular Dynamics ◽  
Electronic Structure ◽  
Molecular Dynamics Simulations ◽  
Structural Dynamics ◽  
Metal Nanoclusters ◽  
X Ray ◽  
Dynamics Simulations ◽  
Supported Metal

scholarly journals Examinations of tRNA Range of Motion Using Simulations of Cryo-EM Microscopy and X-Ray Data

2011 ◽  
Vol 2011 ◽  
pp. 1-11 ◽  
Author(s):  
Thomas R. Caulfield ◽  
Batsal Devkota ◽  
Geoffrey C. Rollins
Keyword(s):  
Electron Microscopy ◽  
Molecular Dynamics ◽  
Range Of Motion ◽  
Molecular Dynamics Simulations ◽  
Conformational Space ◽  
X Ray ◽  
Maxwell’S Demon ◽  
Density Maps ◽  
Maxwell's Demon ◽  
Dynamics Simulations

We examined tRNA flexibility using a combination of steered and unbiased molecular dynamics simulations. Using Maxwell's demon algorithm, molecular dynamics was used to steer X-ray structure data toward that from an alternative state obtained from cryogenic-electron microscopy density maps. Thus, we were able to fit X-ray structures of tRNA onto cryogenic-electron microscopy density maps for hybrid states of tRNA. Additionally, we employed both Maxwell's demon molecular dynamics simulations and unbiased simulation methods to identify possible ribosome-tRNA contact areas where the ribosome may discriminate tRNAs during translation. Herein, we collected >500 ns of simulation data to assess the global range of motion for tRNAs. Biased simulations can be used to steer between known conformational stop points, while unbiased simulations allow for a general testing of conformational space previously unexplored. The unbiased molecular dynamics data describes the global conformational changes of tRNA on a sub-microsecond time scale for comparison with steered data. Additionally, the unbiased molecular dynamics data was used to identify putative contacts between tRNA and the ribosome during the accommodation step of translation. We found that the primary contact regions were H71 and H92 of the 50S subunit and ribosomal proteins L14 and L16.

How does growth hormone releasing hexapeptide self-assemble in nanotubes?

Soft Matter ◽  
2014 ◽  
Vol 10 (46) ◽  
pp. 9260-9269 ◽  
Author(s):  
Héctor Santana ◽  
Cesar L. Avila ◽  
Ingrid Cabrera ◽  
Rolando Páez ◽  
Viviana Falcón ◽  
...  
Keyword(s):  
Electron Microscopy ◽  
Molecular Dynamics ◽  
Growth Hormone ◽  
Molecular Dynamics Simulations ◽  
Small Angle ◽  
X Ray ◽  
X Ray Scattering ◽  
Hollow Cylinders ◽  
Dynamics Simulations ◽  
Ray Scattering

Growth hormone releasing peptide-6 self-assembles into long hollow-cylinders, as evidenced by electron microscopy, small-angle X-ray scattering and molecular dynamics simulations.

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