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Protein Science (2004), 13:1823-1831. Published by Cold Spring Harbor Laboratory Press. Copyright © 2004 The Protein Society
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Protein simulations: The absorption spectrum of barnase point mutants

Ken R.F. Somers, Peter Krüger, Sylwia Bucikiewicz, Marc De Maeyer, Yves Engelborghs and Arnout Ceulemans

Department of Chemistry, University of Leuven, Celestijnenlaan 200 F, B-3001 Leuven, Belgium

(RECEIVED January 23, 2004; FINAL REVISION March 31, 2004; ACCEPTED April 8, 2004)



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.

Keywords: barnase; absorption; molecular dynamics; force field; ab initio; CASPT2

Reprint requests to: Arnout Ceulemans, Department of Chemistry, University of Leuven, B-3001 Leuven, Belgium; e-mail: arnout.ceulemans{at}chem.kuleuven.ac.be; fax: + 32 16 32 73 92.

Article and publication are at http://www.proteinscience.org/cgi/doi/10.1110/ps.04652804.

Supplemental material: see www.proteinscience.org


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S. L. C. Moors, M. Hellings, M. De Maeyer, Y. Engelborghs, and A. Ceulemans
Tryptophan Rotamers as Evidenced by X-Ray, Fluorescence Lifetimes, and Molecular Dynamics Modeling
Biophys. J., August 1, 2006; 91(3): 816 - 823.
[Abstract] [Full Text] [PDF]


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