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Protein simulations: The absorption spectrum of barnase point mutants
Author(s) -
Somers Ken R.F.,
Krüger Peter,
Bucikiewicz Sylwia,
De Maeyer Marc,
Engelborghs Yves,
Ceulemans Arnout
Publication year - 2004
Publication title -
protein science
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 3.353
H-Index - 175
eISSN - 1469-896X
pISSN - 0961-8368
DOI - 10.1110/ps.04652804
Subject(s) - barnase , molecular dynamics , chemistry , ab initio , conformational isomerism , fluorescence , ab initio quantum chemistry methods , absorption (acoustics) , chemical physics , absorption spectroscopy , computational chemistry , materials science , molecule , physics , ribonuclease , rna , biochemistry , organic chemistry , gene , quantum mechanics , composite material
The near‐UV absorption spectra of barnase double‐point mutants are calculated using a combination of molecular dynamics and ab initio techniques. The atoms of the fluorescent probes are placed in a cloud of point charges, generated by molecular dynamics simulations. Ab initio calculations (CASPT2) are performed on these systems. Three molecular dynamics packages are compared—Amber5.0, CHARMM‐c27b1, and GROMOS96—using indole as the fluorescent probe. It was found that calculated absorption spectra reproduce experimental values very well, provided detailed charge cloud descriptions are included. These calculations further sustain the hypothesis that different tryptophan rotamers can be present in proteins. Molecular dynamics calculations of the double‐point mutants also point to the structural effect of counter ions.