Illuminating the origins of spectral properties of green fluorescent proteins via proteochemometric and molecular modeling

Abstract

Green fluorescent protein (GFP) has immense utility in biomedical imaging owing to its autofluorescent nature. In efforts to broaden the spectral diversity of GFP, there have been several reports of engineered mutants via rational design and random mutagenesis. Understanding the origins of spectral properties of GFP could be achieved by means of investigating its structure-activity relationship. The first quantitative structure-property relationship study for modeling the spectral properties, particularly the excitation and emission maximas, of GFP was previously proposed by us some years ago in which quantum chemical descriptors were used for model development. However, such simplified model does not consider possible effects that neighboring amino acids have on the conjugated π-system of GFP chromophore. This study describes the development of a unified proteochemometric model in which the GFP chromophore and amino acids in its vicinity are both considered in the same model. The predictive performance of the model was verified by internal and external validation as well as Y-scrambling. Our strategy provides a general solution for elucidating the contribution that specific ligand and protein descriptors have on the investigated spectral property, which may be useful in engineering novel GFP variants with desired characteristics.

FPredX: Interpretable models for the prediction of spectral maxima, brightness, and oligomeric states of fluorescent proteins

“…21 For spectral properties of fluorophores and FPs, previous studies focused on the application of quantum chemical descriptors to describe the quantitative structure-activity relationship (QSAR) to spectral maxima and quantum yield, [22][23][24][25] with excellent results when trained with machine learning models. [26][27][28] Quantum chemical methods [29][30][31][32] and molecular dynamics simulation [33][34][35][36] were used to model the effect of non-chromophore residues on the spectral properties of FPs. Yet, a sequence-based model that generalizes the correlation between the currently expanded number of FP variants to their spectral properties is to be developed, which should be a valuable tool for FP design.…”