7L96 | pdb_00007l96

Connecting hydrophobic surfaces in cyclic peptides increases membrane permeability

• PDB DOI: https://doi.org/10.2210/pdb7L96/pdb
• BMRB: 30838

• Classification: PEPTIDE BINDING PROTEIN
• Organism(s): Homo sapiens
• Mutation(s): No 


• Deposited: 2021-01-02 Released: 2023-08-09 
• Deposition Author(s): Hoang, H.N.

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Experimental Data Snapshot

• Method: SOLUTION NMR
• Conformers Calculated: 50 
• Conformers Submitted: 5 
• Selection Criteria: structures with the lowest energy 

Literature

Connecting Hydrophobic Surfaces in Cyclic Peptides Increases Membrane Permeability.

Hoang, H.N., Hill, T.A., Fairlie, D.P.

(2021) Angew Chem Int Ed Engl 60: 8385-8390

• PubMed: 33185961 
• DOI: https://doi.org/10.1002/anie.202012643
• Primary Citation Related Structures: 
  7L96, 7L98, 7L9D


• PubMed Abstract: 
  

  N- or C-methylation in natural and synthetic cyclic peptides can increase membrane permeability, but it remains unclear why this happens in some cases but not others. Here we compare three-dimensional structures for cyclic peptides from six families, including isomers differing only in the location of an N- or Cα-methyl substituent. We show that a single methyl group only increases membrane permeability when it connects or expands hydrophobic surface patches. Positional isomers, with the same molecular weight, hydrogen bond donors/acceptors, rotatable bonds, calculated LogP, topological polar surface area, and total hydrophobic surface area, can have different membrane permeabilities that correlate with the size of the largest continuous hydrophobic surface patch. These results illuminate a key local molecular determinant of membrane permeability.

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Organizational Affiliation: 
• Division of Chemistry and Structural Biology and ARC Centre of Excellence for Innovations in Peptide and Protein Science, Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD 4072, Australia.
ARC Centre of Excellence in Advanced Molecular Imaging, Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, 4072, Australia.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 0.74 kDa 
• Atom Count: 52 
• Modeled Residue Count: 6 
• Deposited Residue Count: 6 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cyclic peptide LEU-DLE-LEU-LEU-DPR-N9K	A	6	Homo sapiens	Mutation(s): 0

Small Molecules

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
DLE	A	D-PEPTIDE LINKING	C6 H13 N O2		--
DPR	A	D-PEPTIDE LINKING	C5 H9 N O2		--
YNM	A	L-PEPTIDE LINKING	C10 H13 N O3		TYR

Experimental Data & Validation

Experimental Data

• Method: SOLUTION NMR
• Conformers Calculated: 50 
• Conformers Submitted: 5 
• Selection Criteria: structures with the lowest energy 

Structure Validation

Entry History 

Deposition Data

• Released Date: 2023-08-09 
Deposition Author(s): Hoang, H.N.

Revision History  

• Version 1.0: 2023-08-09
  Type: Initial release
  
• Version 2.0: 2023-11-15
  Changes: Atomic model, Data collection, Derived calculations
• Version 3.0: 2025-12-24
  Changes: Atomic model, Data collection, Database references, Derived calculations, Non-polymer description, Polymer sequence, Structure summary