6B17

Design of a short thermally stable alpha-helix embedded in a macrocycle


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.25 Å
  • R-Value Free: 0.148 
  • R-Value Work: 0.132 
  • R-Value Observed: 0.133 

wwPDB Validation 3D Report Full Report



Literature

Design of a Short Thermally Stable alpha-Helix Embedded in a Macrocycle.

Wu, H.Acharyya, A.Wu, Y.Liu, L.Jo, H.Gai, F.DeGrado, W.F.

(2018) Chembiochem 19: 902-906

  • DOI: 10.1002/cbic.201800026
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • Although helices play key roles in peptide-protein and protein-protein interactions, the helical conformation is generally unstable for short peptides (10-15 residues) in aqueous solution in the absence of their binding partners. Thus, stabilizing th ...

    Although helices play key roles in peptide-protein and protein-protein interactions, the helical conformation is generally unstable for short peptides (10-15 residues) in aqueous solution in the absence of their binding partners. Thus, stabilizing the helical conformation of peptides can lead to increases in binding potency, specificity, and stability towards proteolytic degradation. Helices have been successfully stabilized by introducing side chain-to-side chain crosslinks within the central portion of the helix. However, this approach leaves the ends of the helix free, thus leading to fraying and exposure of the non-hydrogen-bonded amide groups to solvent. Here, we develop a "capped-strapped" peptide strategy to stabilize helices by embedding the entire length of the helix within a macrocycle, which also includes a semirigid organic template as well as end-capping interactions. We have designed a ten-residue capped-strapped helical peptide that behaves like a miniprotein, with a cooperative thermal unfolding transition and T m ≈70 °C, unprecedented for helical peptides of this length. The NMR structure determination confirmed the design, and X-ray crystallography revealed a novel quaternary structure with implications for foldamer design.


    Organizational Affiliation

    Department of Pharmaceutical Chemistry, University of California, San Francisco, CA, 94158, USA.



Macromolecules
  • Find similar proteins by: Sequence   |   Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Capped-strapped peptide
A, B, C, D, E, F
15synthetic constructMutation(s): 0 
Protein Feature View
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
B0I
Query on B0I

Download CCD File 
A, B, C, D, E, F
3,3'-dimethyl-1,1'-biphenyl
C14 H14
GVEDOIATHPCYGS-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.25 Å
  • R-Value Free: 0.148 
  • R-Value Work: 0.132 
  • R-Value Observed: 0.133 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 36.758α = 90
b = 35.583β = 118.88
c = 38.076γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2018-02-21
    Type: Initial release
  • Version 1.1: 2018-05-16
    Changes: Data collection, Database references
  • Version 2.0: 2020-03-04
    Changes: Atomic model, Data collection, Database references, Derived calculations, Polymer sequence, Refinement description, Source and taxonomy, Structure summary