title: Protein simulations: the absorption spectrum of barnase point mutants.
abstract: 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.
authors.affiliation: Department of Chemistry, University of Leuven, B-3001 Leuven, Belgium.
authors.forename: Ken R F
authors.initials: KR
authors.lastname: Somers
authors.forename: Peter
authors.initials: P
authors.lastname: Krüger
authors.forename: Sylwia
authors.initials: S
authors.lastname: Bucikiewicz
authors.forename: Marc
authors.initials: M
authors.lastname: De Maeyer
authors.forename: Yves
authors.initials: Y
authors.lastname: Engelborghs
authors.forename: Arnout
authors.initials: A
authors.lastname: Ceulemans
mesh_terms: D001407:Bacillus / Q000201:enzymology* / Q000235:genetics; D001426:Bacterial Proteins / Q000737:chemistry* / Q000235:genetics; D017354:Point Mutation; D017434:Protein Structure, Tertiary; D012260:Ribonucleases / Q000737:chemistry* / Q000235:genetics; D012984:Software; D013053:Spectrophotometry; D014364:Tryptophan / Q000737:chemistry*
chemical_list: D001426:Bacterial Proteins; D014364:Tryptophan; D012260:Ribonucleases; C019760:Bacillus amyloliquefaciens ribonuclease