7T03 | pdb_00007t03

NMR structure of a designed cold unfolding four helix bundle

PDB DOI: https://doi.org/10.2210/pdb7T03/pdb
BMRB: 30970

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

Deposited: 2021-11-29 Released: 2022-03-02
Deposition Author(s): Pulavarti, S., Szyperski, T., Yuen, S., Maguire, J., Griffin, J., Kuhlman, B.
Funding Organization(s): National Science Foundation (NSF, United States)

Experimental Data Snapshot

Method: SOLUTION NMR
Conformers Calculated: 100
Conformers Submitted: 20
Selection Criteria: structures with the lowest energy

wwPDB Validation 3D Report Full Report

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

Literature

From Protein Design to the Energy Landscape of a Cold Unfolding Protein.

Pulavarti, S.V.S.R.K., Maguire, J.B., Yuen, S., Harrison, J.S., Griffin, J., Premkumar, L., Esposito, E.A., Makhatadze, G.I., Garcia, A.E., Weiss, T.M., Snell, E.H., Kuhlman, B., Szyperski, T.

(2022) J Phys Chem B 126: 1212-1231

PubMed: 35128921 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1021/acs.jpcb.1c10750
Primary Citation Related Structures:
7T03, 7T2Y

PubMed Abstract:
Understanding protein folding is crucial for protein sciences. The conformational spaces and energy landscapes of cold (unfolded) protein states, as well as the associated transitions, are hardly explored. Furthermore, it is not known how structure relates to the cooperativity of cold transitions, if cold and heat unfolded states are thermodynamically similar, and if cold states play important roles for protein function. We created the cold unfolding 4-helix bundle DCUB1 with a de novo designed bipartite hydrophilic/hydrophobic core featuring a hydrogen bond network which extends across the bundle in order to study the relative importance of hydrophobic versus hydrophilic protein-water interactions for cold unfolding. Structural and thermodynamic characterization resulted in the discovery of a complex energy landscape for cold transitions, while the heat unfolded state is a random coil. Below ∼0 °C, the core of DCUB1 disintegrates in a largely cooperative manner, while a near-native helical content is retained. The resulting cold core-unfolded state is compact and features extensive internal dynamics. Below -5 °C, two additional cold transitions are seen, that is, (i) the formation of a water-mediated, compact, and highly dynamic dimer, and (ii) the onset of cold helix unfolding decoupled from cold core unfolding. Our results suggest that cold unfolding is initiated by the intrusion of water into the hydrophilic core network and that cooperativity can be tuned by varying the number of core hydrogen bond networks. Protein design has proven to be invaluable to explore the energy landscapes of cold states and to robustly test related theories.