9DM3 image
Entry Detail
PDB ID:
9DM3
Keywords:
Title:
De novo design of proteins that bind naphthalenediimides, powerful photooxidants with tunable photophysical properties
Biological Source:
Source Organism:
Host Organism:
PDB Version:
Deposition Date:
2024-09-12
Release Date:
2025-03-05
Method Details:
Experimental Method:
Conformers Calculated:
10
Conformers Submitted:
10
Selection Criteria:
all calculated structures submitted
Macromolecular Entities
Polymer Type:polypeptide(L)
Description:naphthalenediimide binding protein
Chain IDs:A
Chain Length:132
Number of Molecules:1
Biological Source:Helicana
Ligand Molecules
Primary Citation
De Novo Design of Proteins That Bind Naphthalenediimides, Powerful Photooxidants with Tunable Photophysical Properties.
J.Am.Chem.Soc. 147 7849 7858 (2025)
PMID: 39982408 DOI: 10.1021/jacs.4c18151

Abstact

De novo protein design provides a framework to test our understanding of protein function and build proteins with cofactors and functions not found in nature. Here, we report the design of proteins designed to bind powerful photooxidants and the evaluation of the use of these proteins to generate diffusible small-molecule reactive species. Because excited-state dynamics are influenced by the dynamics and hydration of a photooxidant's environment, it was important to not only design a binding site but also to evaluate its dynamic properties. Thus, we used computational design in conjunction with molecular dynamics (MD) simulations to design a protein, designated NBP (NDI Binding Protein), that held a naphthalenediimide (NDI), a powerful photooxidant, in a programmable molecular environment. Solution NMR confirmed the structure of the complex. We evaluated two NDI cofactors in this de novo protein using ultrafast pump-probe spectroscopy to evaluate light-triggered intra- and intermolecular electron transfer function. Moreover, we demonstrated the utility of this platform to activate multiple molecular probes for protein labeling.

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