title: Color modeling of protein optical probes.
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.
authors: Department of Theoretical Chemistry and Biology, School of Biotechnology, Royal Institute of Technology, SE-10691 Stockholm, Sweden. murugan@theochem.kth.se
authors: N Arul
authors: NA
authors: Murugan
authors: Jacob
authors: J
authors: Kongsted
authors: Zilvinas
authors: Z
authors: Rinkevicius
authors: Hans
authors: H
authors: Ågren
mesh_terms: D000042:Absorption; D003116:Color; D007782:Lactoglobulins / Q000737:chemistry*; D008956:Models, Chemical; D056004:Molecular Dynamics Simulation; D055096:Optical Devices; D010078:Oxazines / Q000737:chemistry; D011789:Quantum Theory; D012997:Solvents / Q000737:chemistry
chemical_list: D007782:Lactoglobulins; D010078:Oxazines; D012997:Solvents; C044808:nile red