8XYV | pdb_00008xyv

De novo designed protein 0705-5

PDB DOI: https://doi.org/10.2210/pdb8XYV/pdb

Classification: DE NOVO PROTEIN
Organism(s): synthetic construct
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2024-01-20 Released: 2024-10-02
Deposition Author(s): Liu, J.L., Guo, Z., Lai, L.H.
Funding Organization(s): National Natural Science Foundation of China (NSFC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.81 Å
R-Value Free:
0.259 (Depositor), 0.297 (DCC)
R-Value Work:
0.216 (Depositor)
R-Value Observed:
0.219 (Depositor)

Starting Model: in silico
View more details

wwPDB Validation 3D Report Full Report

This is version 1.2 of the entry. See complete history.

Literature

All-Atom Protein Sequence Design Based on Geometric Deep Learning.

Liu, J., Guo, Z., You, H., Zhang, C., Lai, L.

(2024) Angew Chem Int Ed Engl 63: e202411461-e202411461

PubMed: 39295564 Search on PubMed
DOI: https://doi.org/10.1002/anie.202411461
Primary Citation Related Structures:
8XYR, 8XYS, 8XYT, 8XYU, 8XYV, 8XYW

PubMed Abstract:
Designing sequences for specific protein backbones is a key step in creating new functional proteins. Here, we introduce GeoSeqBuilder, a deep learning framework that integrates protein sequence generation with side chain conformation prediction to produce the complete all-atom structures for designed sequences. GeoSeqBuilder uses spatial geometric features from protein backbones and explicitly includes three-body interactions of neighboring residues. GeoSeqBuilder achieves native residue type recovery rate of 51.6%, comparable to ProteinMPNN and other leading methods, while accurately predicting side chain conformations. We first used GeoSeqBuilder to design sequences for thioredoxin and a hallucinated three-helical bundle protein. All the 15 tested sequences expressed as soluble monomeric proteins with high thermal stability, and the 2 high-resolution crystal structures solved closely match the designed models. The generated protein sequences exhibit low similarity (minimum 23%) to the original sequences, with significantly altered hydrophobic cores. We further redesigned the hydrophobic core of glutathione peroxidase 4, and 3 of the 5 designs showed improved enzyme activity. Although further testing is needed, the high experimental success rate in our testing demonstrates that GeoSeqBuilder is a powerful tool for designing novel sequences for predefined protein structures with atomic details. GeoSeqBuilder is available at https://github.com/PKUliujl/GeoSeqBuilder.