7TMH

Porous framework formed by assembly of a bipyridyl-conjugated helical peptide

  • Classification: DE NOVO PROTEIN
  • Organism(s): synthetic construct
  • Mutation(s): No 

  • Deposited: 2022-01-19 Released: 2022-04-20 
  • Deposition Author(s): Nguyen, A.I.
  • Funding Organization(s): Department of Energy (DOE, United States)

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 0.80 Å
  • R-Value Free: 0.127 
  • R-Value Work: 0.115 
  • R-Value Observed: 0.117 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 2.0 of the entry. See complete history


Literature

Assembly of pi-Stacking Helical Peptides into a Porous and Multivariable Proteomimetic Framework.

Heinz-Kunert, S.L.Pandya, A.Dang, V.T.Tran, P.N.Ghosh, S.McElheny, D.Santarsiero, B.D.Ren, Z.Nguyen, A.I.

(2022) J Am Chem Soc 144: 7001-7009

  • DOI: https://doi.org/10.1021/jacs.2c02146
  • Primary Citation of Related Structures:  
    7TLS, 7TLU, 7TM1, 7TM2, 7TMA, 7TME, 7TMH, 7TMI, 7TMJ, 7TMK, 7TML

  • PubMed Abstract: 

    The evolution of proteins from simpler, self-assembled peptides provides a powerful blueprint for the design of complex synthetic materials. Previously, peptide-metal frameworks using short sequences (≤3 residues) have shown great promise as proteomimetic materials that exhibit sophisticated capabilities. However, their development has been hindered due to few variable residues and restricted choice of side-chains that are compatible with metal ions. Herein, we developed a noncovalent strategy featuring π-stacking bipyridyl residues to assemble much longer peptides into crystalline frameworks that tolerate even previously incompatible acidic and basic functionalities and allow an unprecedented level of pore variations. Single-crystal X-ray structures are provided for all variants to guide and validate rational design. These materials exhibit hallmark proteomimetic behaviors such as guest-selective induced fit and assembly of multimetallic units. Significantly, we demonstrate facile optimization of the framework design to substantially increase affinity toward a complex organic molecule.


  • Organizational Affiliation

    Department of Chemistry, University of Illinois at Chicago, Chicago, Illinois 60607, United States.


Macromolecules

Find similar proteins by:  Sequence   |   3D Structure  

Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
bipyridyl-conjugated helical peptide11synthetic constructMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
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  • Reference Sequence
Small Molecules
Modified Residues  2 Unique
IDChains TypeFormula2D DiagramParent
AIB
Query on AIB
A
L-PEPTIDE LINKINGC4 H9 N O2ALA
PHI
Query on PHI
A
L-PEPTIDE LINKINGC9 H10 I N O2PHE
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 0.80 Å
  • R-Value Free: 0.127 
  • R-Value Work: 0.115 
  • R-Value Observed: 0.117 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 13.608α = 90
b = 13.513β = 97.094
c = 27.424γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XDSdata scaling
PHASERphasing

Structure Validation

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Entry History & Funding Information

Deposition Data

  • Released Date: 2022-04-20 
  • Deposition Author(s): Nguyen, A.I.

Funding OrganizationLocationGrant Number
Department of Energy (DOE, United States)DE-AC02-06CH11357

Revision History  (Full details and data files)

  • Version 1.0: 2022-04-20
    Type: Initial release
  • Version 1.1: 2022-04-27
    Changes: Database references
  • Version 1.2: 2023-10-18
    Changes: Data collection, Refinement description
  • Version 1.3: 2023-11-15
    Changes: Data collection
  • Version 2.0: 2024-09-25
    Changes: Atomic model, Data collection, Database references, Derived calculations, Polymer sequence, Source and taxonomy, Structure summary