Oral Presentation The 48th Lorne Conference on Protein Structure and Function 2023

Reshaping the Energy Landscapes of de novo Designed Fluorescent Proteins (#10)

Justin P Nguyen 1 , Colleen Carrigan 1 , Hector J Cardenas 1 2 , Tyla Holoman 1 3 , Meagan E MacDonald 1 , Colin A Smith 1
  1. Wesleyan University, Middletown, CT, United States
  2. University of North Carolina Wilmington, Wilmington, NC, USA
  3. University of Maryland, College Park, MD, USA

The de novo computational design of proteins with predefined three-dimensional structure is becoming much more routine due to advancements in both 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 particularly noteworthy(1,2). 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 (MD) simulations to reveal how molecular flexibility in the ground and excited states determines brightness(3). We show that the ability of the protein to resist dihedral angle rotation of the chromophore is critical for predicting brightness. Our simulations indicate that the mFAP/DFHBI complex has a rough energy landscape, with an ensemble of macrostates each having widely varying function. This roughness suggests that mFAP protein function can be enhanced by reshaping the energy landscape towards conformations that better resist DFHBI bond rotation. We have found that the presence of specific side chain rotamers is particularly important for determining how well a given macrostate stabilizes the DFHBI. Through directed MD simulations, we have shown that the relationship involves causation and not merely correlation. To enable reshaping of the energy landscape towards highly functional macrostates, we have developed a novel design algorithm coupling MD simulations with Rosetta sequence design calculations. We report on our progress towards using this algorithm to create new mFAP designs and experimentally validate them. The approach and algorithm are very general, with applications not only in this system but also to the prediction of allosterically acting second- and third-shell mutations and eventually enzyme design.

  1. Dou, J.; Vorobieva, A. A.; Sheffler, W.; Doyle, L. A.; Park, H.; Bick, M. J.; Mao, B.; Foight, G. W.; Lee, M. Y.; Gagnon, L. A.; Carter, L.; Sankaran, B.; Ovchinnikov, S.; Marcos, E.; Huang, P.-S.; Vaughan, J. C.; Stoddard, B. L.; Baker, D. De novo design of a fluorescence-activating β-barrel. Nature 2018, 561, 485–491, https://doi.org/10.1038/s41586-018-0509-0
  2. Klima, J. C.; Doyle, L. A.; Lee, J. D.; Rappleye, M.; Gagnon, L. A.; Lee, M. Y.; Barros, E. P.; Vorobieva, A. A.; Dou, J.; Bremner, S.; Quon, J. S.; Chow, C. M.; Carter, L.; Mack, D. L.; Amaro, R. E.; Vaughan, J. C.; Berndt, A.; Stoddard, B. L.; Baker, D. Incorporation of sensing modalities into de novo designed fluorescence-activating proteins. Nat. Commun. 2021, 12, 856, https://doi.org/10.1038/s41467-020-18911-w
  3. Hostetter, E. R.; Keyes, J. R.; Poon I.; Nguyen, J. P.; Nite, J. M.; Molecular Modeling and Design Class, Jimenez-Hoyos, C. A., Smith, C. A. Journal of Chemical Theory and Computation 2022 18, 3190-3203, https://doi.org10.1021/acs.jctc.1c00748