Issue 3, 2012
From the journal:

Physical Chemistry Chemical Physics

Color modeling of protein optical probes†

N. Arul Murugan,*a   Jacob Kongsted,b   Zilvinas Rinkeviciusac  and  Hans Ågrena  

* Corresponding authors

a Department of Theoretical Chemistry and Biology, School of Biotechnology, Royal Institute of Technology, SE-10691 Stockholm, Sweden
E-mail: murugan@theochem.kth.se

b Department of Physics and Chemistry, University of Southern Denmark, Campusvej 55, DK-5230 Odense M, Denmark

c Swedish e-Science Research Center (SeRC), Royal Institute of Technology, SE-100 44 Stockholm, Sweden

Abstract

We present a strategy for modeling optical probes within heterogeneous environments of restricted dimension. The method is based on a multiphysics approach comprising sequential structure modeling by means of hybrid Car–Parrinello molecular dynamics and property modeling by means of quantum mechanics/molecular mechanics response theory. For demonstration we address the structural and optical properties of nile red within the β-lacto globulin protein. We consider the cases with the probe situated on the surface or within the cavity of the protein, or embedded in a water solvent. We find the absorption properties of the probe to be highly dependent on its position relative to the protein. Structural rearrangements of the optical probe are found to contribute significantly to these environmental effects.

Graphical abstract: Color modeling of protein optical probes

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Article information

DOI
https://doi.org/10.1039/C1CP23060C
Article type
Communication
Submitted
27 Sep 2011
Accepted
16 Nov 2011
First published
01 Dec 2011

Phys. Chem. Chem. Phys., 2012,14, 1107-1112

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Color modeling of protein optical probes

N. A. Murugan, J. Kongsted, Z. Rinkevicius and H. Ågren, Phys. Chem. Chem. Phys., 2012, 14, 1107 DOI: 10.1039/C1CP23060C

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