Protein simulations: The absorption spectrum of barnase point mutants

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) a...

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Bibliographic Details
Published in:Protein science 2004-07, Vol.13 (7), p.1823-1831
Main Authors: Somers, Ken R.F., Krüger, Peter, Bucikiewicz, Sylwia, De Maeyer, Marc, Engelborghs, Yves, Ceulemans, Arnout
Format: Article
Language:English
Subjects:
ab initio
absorption
Bacillus - enzymology
Bacillus - genetics
Bacterial Proteins - chemistry
Bacterial Proteins - genetics
barnase
CASPT2
force field
molecular dynamics
Point Mutation
Protein Structure, Tertiary
Ribonucleases - chemistry
Ribonucleases - genetics
Software
Spectrophotometry
Tryptophan - chemistry
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Summary: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.
ISSN:0961-8368
1469-896X
DOI:10.1110/ps.04652804