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WIREs Comput Mol Sci
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Quantum mechanical/molecular mechanical studies of photophysical properties of fluorescent proteins

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Abstract Light‐responsive proteins are widely employed in bioimaging, for example, fluorescent proteins (FPs), which are comprised of a chromophore centered within a barrel‐shaped protein. FPs exhibit remarkable one‐ and multi‐photon absorption (1PA and MPA, respectively) in addition to their emissive properties. Over the last two decades, many types of quantum mechanical, molecular dynamics, and combined quantum mechanical/molecular‐mechanical (QM/MM) approaches have been employed in the study of the photophysics of FPs. Among the latter, QM/MM approaches have proven to be capable of capturing the strong correlation between FPs' light‐responsive properties and their chromophore–environment interactions. In particular, polarizable embedding QM/MM methods are gaining attention by reason of their outstanding performance in the computation of MPA in FPs. Herein, we discuss the outcomes of some of the investigations performed on the 1PA, MPA, and emissive features of FPs using QM/MM approaches. In addition, critical aspects of the use of QM/MM approaches to study FPs' 1PA and MPA features are described. To those researchers interested in starting to perform MPA computations for FPs using QM/MM methods, this review aims to be a compass to navigate among the relevant available literature. This article is categorized under: Electronic Structure Theory > Combined QM/MM Methods Structure and Mechanism > Computational Biochemistry and Biophysics
Fluorescent proteins (red fluorescent protein DsRed, PDB 1ZGO,7 in this particular case) main components; (a,b) the protein barrel and (c) the chromophore embedded within it. The neighboring amino acids (within 3 Å) from the chromophore are shown in orange
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Cluster used by Kaila et al. for studying GFP,68 which included nine truncated residues and four water molecules (W) around the chromophore (CRO). Labeling is almost entirely based on the cluster model of Schwabe et al.69
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Depiction of the strong dependence of σ2PA (blue squares) versus the corresponding 1PA (red dots) as a function of the permanent electric dipole moment difference between the ground and the first excited state |Δμ10|.57 The inset illustrates a simplified version of the RFP chromophore, which is the primary chromophore in all FPs presented. R‐ corresponds to –CH2–CH2–CO–NH2 in the DsRed FP whereas connections to the protein are indicated as “Protein” (based on the figure previously reported by Drobizhev et al.5)
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Structure and Mechanism > Computational Biochemistry and Biophysics
Electronic Structure Theory > Combined QM/MM Methods

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