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Molecular dynamics study of femtosecond events in photoactive yellow protein after photoexcitation of the chromophore
Author(s) -
Yamato Takahisa,
Niimura Nobuo,
Go Nobuhiro
Publication year - 1998
Publication title -
proteins: structure, function, and bioinformatics
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 1.699
H-Index - 191
eISSN - 1097-0134
pISSN - 0887-3585
DOI - 10.1002/(sici)1097-0134(19980815)32:3<268::aid-prot2>3.0.co;2-e
Subject(s) - photoexcitation , chromophore , femtosecond , photochemistry , dynamics (music) , molecular dynamics , chemistry , chemical physics , materials science , excited state , physics , optics , computational chemistry , laser , atomic physics , acoustics
Molecular dynamics simulations were carried out to study what happens in a photoreceptor protein, photoactive yellow protein (PYP), immediately after the vertical transition of the chromophore from the ground to the excited state. A photon absorption simulation was performed to investigate the movement of amino acid residues upon photoexcitation. To calculate the excited state of the chromophore, SCF‐CI calculation was carried out with INDO/S Hamiltonian. We observed that some amino acid residues have strong interactions with the chromophore. Most of these amino acid residues are conserved in PYPs from three different species of bacteria. This observation indicates the biological importance of these residues. Proteins 32:268–275, 1998. © 1998 Wiley‐Liss, Inc.