Prediction of Fluorophore Brightness in Designed Mini Fluorescence Activating Proteins

Prediction of Fluorophore Brightness in Designed Mini Fluorescence Activating Proteins

The de novo computational design of proteins with predefined three-dimensional structure is becoming much more routine due to advancements both in force fields and algorithms. However, creating designs with functions beyond folding is more challenging. In that regard, the recent design of small beta...

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Bibliographic Details
Published in:Journal of chemical theory and computation Vol. 18; no. 5; pp. 3190 - 3203
Main Authors: Hostetter, Emma R., Keyes, Jeffrey R., Poon, Ivy, Nguyen, Justin P., Nite, Jacob M., Jimenez Hoyos, Carlos A., Smith, Colin A.
Format: Journal Article
Language:English
Published: United States American Chemical Society 10-05-2022
Subjects:
Algorithms
Biomolecular Systems
Brightness
Chromophores
Design
Dihedral angle
Excitation
Fluorescence
Fluorescent Dyes - chemistry
Green Fluorescent Proteins - chemistry
Ligands
Molecular Conformation
Molecular dynamics
Molecular Dynamics Simulation
Proteins
Quantum mechanics
Rotation
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Summary:The de novo computational design of proteins with predefined three-dimensional structure is becoming much more routine due to advancements both in force fields and algorithms. However, creating designs with functions beyond folding is more challenging. In that regard, the recent design of small beta barrel proteins that activate the fluorescence of an exogenous small molecule chromophore (DFHBI) is noteworthy. These proteins, termed mini fluorescence activating proteins (mFAPs), have been shown to increase the brightness of the chromophore more than 100-fold upon binding to the designed ligand pocket. The design process created a large library of variants with different brightness levels but gave no rational explanation for why one variant was brighter than another. Here, we use quantum mechanics and molecular dynamics simulations to investigate how molecular flexibility in the ground and excited states influences brightness. We show that the ability of the protein to resist dihedral angle rotation of the chromophore is critical for predicting brightness. Our simulations suggest that the mFAP/DFHBI complex has a rough energy landscape, requiring extensive ground-state sampling to achieve converged predictions of excited-state kinetics. While computationally demanding, this roughness suggests that mFAP protein function can be enhanced by reshaping the energy landscape toward conformations that better resist DFHBI bond rotation.
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ISSN:1549-9618
1549-9626
DOI:10.1021/acs.jctc.1c00748