NDLI: Red fluorescent protein DsRed: Parametrization of its chromophore as an amino acid residue for computer modeling in the OPLS-AA force field

Content Provider	Springer Nature Link
Author	Dmitrienko, D. V. Vrzheshch, E. P. Drutsa, V. L. Vrzheshch, P. V.
Copyright Year	2006
Abstract	Topology of the neutral form of the DsRed fluorescent protein chromophore as a residue of [(4-cis)-2-[(1-cis)-4-amino-4-oxobutanimidoyl]-4-(4-hydroxybenzylidene)-5-oxo-4,5-dihydro-1H-imidazol-1-yl]acetic acid was calculated with OPLS-AA force field. Use of this topology and molecular dynamics simulation allows calculating the parameters of proteins that contain such residue in their polypeptide chains. The chromophore parameters were obtained by ab initio (RHF/6-31G**) quantum chemical calculations applying density functional theory (B3LYP). Using this chromophore, we have calculated the molecular dynamics trajectory of tetrameric fluorescent protein DsRed in solution at 300 K (4 nsec). Correctness of the chromophore parametrization was revealed by comparison of quantitative characteristics of the chromophore structure obtained from the molecular dynamic simulations of DsRed protein with the quantitative characteristics of the chromophore based on the crystallographic X-ray data of fluorescent protein DsRed (PDB ID: 1ZGO, 1G7K, and 1GGX), and also with the quantitative characteristics of the chromophore obtained by quantum chemical calculations. Inclusion of the neutral form of DsRed protein chromophore topology into the OPLS-AA force field yielded the extended force field OPLS-AA/DsRed. This force field can be used for molecular dynamics calculations of proteins containing the DsRed chromophore. The parameter set presented in this study can be applied for similar extension in any other force fields.
Starting Page	1133
Ending Page	1152
Page Count	20
File Format	PDF
ISSN	00062979
Journal	Biochemistry (Moscow)
Volume Number	71
Issue Number	10
e-ISSN	16083040
Language	English
Publisher	Nauka/Interperiodica
Publisher Date	2006-01-01
Publisher Place	Moscow
Access Restriction	One Nation One Subscription (ONOS)
Subject Keyword	red fluorescent protein DsRed chromophore quantum chemical calculations topology OPLS-AA molecular dynamics Biomedicine general Bioorganic Chemistry Biochemistry Microbiology
Content Type	Text
Resource Type	Article
Subject	Biochemistry Biophysics Geriatrics and Gerontology

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