Internal dynamics of green fluorescent protein
Article Abstract:
The behavior of the wild-type green fluorescent protein (GFP) from Aequorea victoria has been studied through a 1 ns molecular dynamic simulation. GFP is being used as a protein marker in live cells that can be detected by fluorescence spectroscopy. Results show the protein to be rigid not only on its cylindrical beta-barrel chromophore but also on the surrounding atomic area. A tight H-bond network has been observed to have been formed by six internal water molecules.
Publication Name: Journal of Physical Chemistry B
Subject: Chemicals, plastics and rubber industries
ISSN: 1520-6106
Year: 1999
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Can principle components yield a dimension reduced description of protein dynamics on long time scales?
Article Abstract:
The suitability of principal component analysis (PCA) to produce slow collective coordinates for use within a dimension reduced description of conformational motions in proteins is assessed. Detailed analyses of molecular dynamics trajectories and crystallographic data indicate that simulations of a few nanoseconds should generally provide a stable and statistically reliable definition of the essential and near constraints subspaces.
Publication Name: Journal of Physical Chemistry B
Subject: Chemicals, plastics and rubber industries
ISSN: 1520-6106
Year: 2006
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Energetics and dynamics in MbCN:[CN.sup.-]-vibrational relaxation from molecular dynamics simulations
Article Abstract:
Atomistic simulations are used to investigate the dynamics of the cyanide anion bound to sperm-whale myoglobin. Findings support the hypothesis that the experimentally observed relaxation rate reflects the repopulation of the electronic ground state.
Publication Name: Journal of Physical Chemistry B
Subject: Chemicals, plastics and rubber industries
ISSN: 1520-6106
Year: 2007
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