8VP7 | pdb_00008vp7

UIC-13-BIF-A4(Dab) extension of UIC-1

PDB DOI: https://doi.org/10.2210/pdb8VP7/pdb

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

Deposited: 2024-01-16 Released: 2024-08-07
Deposition Author(s): Ganatra, P.
Funding Organization(s): Department of Energy (DOE, United States)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.48 Å
R-Value Free:
0.206 (Depositor), 0.203 (DCC)
R-Value Work:
0.151 (Depositor), 0.149 (DCC)
R-Value Observed:
0.154 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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

Literature

Diverse Proteomimetic Frameworks via Rational Design of pi-Stacking Peptide Tectons.

Ganatra, P., Wang, D.F., Ganatra, V., Dang, V.T., Nguyen, A.I.

(2024) J Am Chem Soc 146: 22236-22246

PubMed: 39096501 Search on PubMed
DOI: https://doi.org/10.1021/jacs.4c03094
Primary Citation Related Structures:
8VOG, 8VP7, 8VPC, 8VPD, 8VPE, 8VPJ, 8VPS, 8VPT, 8VPX, 8VPY, 8VPZ, 8VQ0, 8VSF, 8VT8, 8VW7, 8VW8, 8VXS

PubMed Abstract:
Peptide-based frameworks aim to integrate protein architecture into solid-state materials using simpler building blocks. Despite the growing number of peptide frameworks, there are few strategies to rationally engineer essential properties like pore size and shape. Designing peptide assemblies is generally hindered by the difficulty of predicting complex networks of weak intermolecular interactions. Peptides conjugated to polyaromatic groups are a unique case where assembly appears to be strongly driven by π-π interactions, suggesting that rationally adjusting the geometry of the π-stackers could create novel structures. Here, we report peptide elongation as a simple mechanism to predictably tune the angle between the π-stacking groups to produce a remarkable diversity of pore shapes and sizes, including some that are mesoporous. Notably, rapid jumps in pore size and shape can occur with just a single amino acid insertion. The geometry of the π-stacking residues also significantly influences framework structure, representing an additional dimension for tuning. Lastly, sequence identity can also indirectly modulate the π-π interactions. By correlating each of these factors with detailed crystallographic data, we find that, despite the complexity of peptide structure, the shape and polarity of the tectons are straightforward predictors of framework structure. These guidelines are expected to accelerate the development of advanced porous materials with protein-like capabilities.

Organizational Affiliation

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

Macromolecule Content

Total Structure Weight: 6.67 kDa
Atom Count: 518
Modeled Residue Count: 60
Deposited Residue Count: 60
Unique protein chains: 1

Macromolecules

Find similar proteins by: Sequence | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
UIC-13-BIF-A4(Dab)	A, B, C, D	15	synthetic construct	Mutation(s): 0

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
CCN Query on CCN Download:Ideal Coordinates CCD File SDF format, chain E [auth B] MOL2 format, chain E [auth B] mmCIF format, chain E [auth B]	E [auth B]	ACETONITRILE C₂ H₃ N WEVYAHXRMPXWCK-UHFFFAOYSA-N		Interactions Focus chain E [auth B] Interactions & Density Focus chain E [auth B]

Modified Residues 2 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
AIB Query on AIB	A, B, C, D	L-PEPTIDE LINKING	C₄ H₉ N O₂		ALA
DAB Query on DAB	A, B, C, D	L-PEPTIDE LINKING	C₄ H₁₀ N₂ O₂		ALA