7MP7 | pdb_00007mp7

Rules for designing protein fold switches and their implications for the folding code

• PDB DOI: https://doi.org/10.2210/pdb7MP7/pdb
• BMRB: 30904

• Classification: DE NOVO PROTEIN
• Organism(s): Thermus thermophilus
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2021-05-04 Released: 2022-05-18 
• Deposition Author(s): He, Y., Chen, Y., Ruan, B., Choi, J., Chen, Y., Motabar, D., Solomon, T., Simmerman, R., Kauffman, T., Gallagher, T., Bryan, P., Orban, J.

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Experimental Data Snapshot

• Method: SOLUTION NMR
• Conformers Calculated: 1000 
• Conformers Submitted: 10 
• Selection Criteria: structures with the lowest energy 

Literature

Design and characterization of a protein fold switching network.

Ruan, B., He, Y., Chen, Y., Choi, E.J., Chen, Y., Motabar, D., Solomon, T., Simmerman, R., Kauffman, T., Gallagher, D.T., Orban, J., Bryan, P.N.

(2023) Nat Commun 14: 431-431

• PubMed: 36702827 
• DOI: https://doi.org/10.1038/s41467-023-36065-3
• Primary Citation Related Structures: 
  7MN1, 7MN2, 7MP7, 7MQ4, 9A1B, 9A1C, 9A1D


• PubMed Abstract: 
  

  To better understand how amino acid sequence encodes protein structure, we engineered mutational pathways that connect three common folds (3α, β-grasp, and α/β-plait). The structures of proteins at high sequence-identity intersections in the pathways (nodes) were determined using NMR spectroscopy and analyzed for stability and function. To generate nodes, the amino acid sequence encoding a smaller fold is embedded in the structure of an ~50% larger fold and a new sequence compatible with two sets of native interactions is designed. This generates protein pairs with a 3α or β-grasp fold in the smaller form but an α/β-plait fold in the larger form. Further, embedding smaller antagonistic folds creates critical states in the larger folds such that single amino acid substitutions can switch both their fold and function. The results help explain the underlying ambiguity in the protein folding code and show that new protein structures can evolve via abrupt fold switching.

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Organizational Affiliation: 
• Potomac Affinity Proteins, 11305 Dunleith Pl, North Potomac, MD, 20878, USA.
Institute for Bioscience and Biotechnology Research, University of Maryland, 9600 Gudelsky Drive, Rockville, MD, 20850, USA.
Department of Bioengineering, University of Maryland, College Park, MD, 20742, USA.
Department of Chemistry and Biochemistry, University of Maryland, College Park, MD, 20742, USA.
National Institute of Standards and Technology and the University of Maryland, 9600 Gudelsky Drive, Rockville, MD, 20850, USA.
Institute for Bioscience and Biotechnology Research, University of Maryland, 9600 Gudelsky Drive, Rockville, MD, 20850, USA. [e-mail].
Department of Chemistry and Biochemistry, University of Maryland, College Park, MD, 20742, USA. [e-mail].
Potomac Affinity Proteins, 11305 Dunleith Pl, North Potomac, MD, 20878, USA. [e-mail].
Institute for Bioscience and Biotechnology Research, University of Maryland, 9600 Gudelsky Drive, Rockville, MD, 20850, USA. [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 10.07 kDa 
• Atom Count: 711 
• Modeled Residue Count: 87 
• Deposited Residue Count: 87 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Sb3	A	87	Thermus thermophilus	Mutation(s): 0

Experimental Data & Validation

Experimental Data

• Method: SOLUTION NMR
• Conformers Calculated: 1000 
• Conformers Submitted: 10 
• Selection Criteria: structures with the lowest energy 

Structure Validation

Entry History 

Deposition Data

• Released Date: 2022-05-18 
Deposition Author(s): He, Y., Chen, Y., Ruan, B., Choi, J., Chen, Y., Motabar, D., Solomon, T., Simmerman, R., Kauffman, T., Gallagher, T., Bryan, P., Orban, J.

Revision History  

• Version 1.0: 2022-05-18
  Type: Initial release
  
• Version 1.1: 2023-05-31
  Changes: Database references
• Version 1.2: 2023-06-07
  Changes: Other
• Version 1.3: 2024-05-15
  Changes: Data collection, Database references