Primary Citation PubMed: 23373469
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An Anisotropic Coarse-Grained Model for Proteins Based On Gay-Berne and Electric Multipole Potentials.
(2014) J Chem Theory Comput 10
PubMed: 24659927 | PubMedCentral: PMC3958967 | DOI: 10.1021/ct400974z
Actinobacterial transcription factor RdpA (PDB ID 2M6O) 63 is a small protein (48 amino acid residues) consisting of two antiparallel β-sheets; 2-mercaptophenol-α3C (PDB ID 2LXY) 64 is... a three α helix-bundle protein of 67 amino acid residues.
Figure 13 (A) RMSD values of the backbone Cα atoms from the crystal structure (PDB ID 2LXY) and (B) RMSF values of the backbone Cα atoms were calculated using AMBER 03 atomistic force field (in black) and GBEMP coarse-grained force field (in red).
Molecular Dynamics Simulations of Proteins In this work, we attempt to apply the GBEMP model to study the dynamics of two test cases of proteins (PDB IDs 2M6O and 2LXY), 63 , 64 which have different secondary structures and sizes.
Publication Year: 2014
Photochemical tyrosine oxidation in the structurally well-defined ?3Y protein: proton-coupled electron transfer and a long-lived tyrosine radical.
(2014) J Am Chem Soc 136
PubMed: 25121576 | PubMedCentral: PMC4195373 | DOI: 10.1021/ja503348d
The radical site (residue 32, labeled X) is placed in an internal position in the middle of the central helix and occupied by (b and e) Y32 in α 3 Y (PDB ID 2MI7), (c) W32 in α 3 W (PD... ID 1LQ7), 29 and (d) 2-mercaptophenol (2MP) in 2MP-α 3 C (PDB ID 2LXY).
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