Efficient sampling of ligand orientations and conformations in free energy calculations using the lambda-dynamics method
Article Abstract:
The lambda-dynamics free energy based simulation method was used to study the binding of 10 five-member ring heterocycle derivatives to an artificial cavity created by mutagenesis inside cytochrome c peroxiade. The examination of lambda-dynamics trajectory of the ligands revealed alternative binding orientations and conformations not detected by crystallography.
Publication Name: Journal of Physical Chemistry B
Subject: Chemicals, plastics and rubber industries
ISSN: 1520-6106
Year: 2000
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Coupling to lysine -13 promotes electron tunneling through carboxylate - terminated alkanethiol self-assembled monolayers to cytochrome c
Article Abstract:
Highly anisotropic electronic coupling is revealed in the electrochemistry of surface-modified cytochrome c that is bound electrostatically to alkanethiol self-assembled monolayers (SAMs). It is shown that lysine -13 is directly involved in coupling the protein to the SAM carboxylate terminus.
Publication Name: Journal of Physical Chemistry B
Subject: Chemicals, plastics and rubber industries
ISSN: 1520-6106
Year: 2003
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