9J7T

De Novo Designed Cell-Penetrating Peptide Self-Assembly Featuring Distinctive Tertiary Structure

Summary for 9J7T

• Entry DOI: 10.2210/pdb9j7t/pdb
• Descriptor: LKa14, GLYCEROL (3 entities in total)
• Functional Keywords: cpp, protein design, peptide self-assembly, amphipathic peptides, cell-penetration, de novo protein
• Biological source: synthetic construct
• Total number of polymer chains: 24
• Total formula weight: 41088.92

Authors

Park, J.,Hyun, S.,Lee, S.J. (deposition date: 2024-08-19, release date: 2024-09-04, Last modification date: 2024-10-16)

Primary citation

Park, J.,Hyun, S.,Lee, S.J.
De Novo Designed Cell-Penetrating Peptide Self-Assembly Featuring Distinctive Tertiary Structure
Acs Omega, 9:32991-32999, 2024

PubMed Abstract: Recent attention has focused on the design of proteins, paralleling advancements in biopharmaceuticals. Achieving protein designs with both structure and function poses a significant challenge, particularly considering the importance of quaternary structures, such as oligomers, in protein function. The cell penetration properties of peptides are of particular interest as they involve the penetration of large molecules into cells. We previously suggested a link between the oligomerization propensity of amphipathic peptides and their cell penetration abilities, yet concrete evidence at cellular-relevant concentrations was lacking due to oligomers' instability. In this study, we sought to characterize oligomerization states using various techniques, including X-ray crystallography, acceptor photobleaching Förster resonance energy transfer (FRET), native mass spectrometry (MS), and differential scanning calorimetry (DSC), while exploring the function related to oligomer status. X-ray crystallography revealed the atomic structures of oligomers formed by LK-3, a bis-disulfide bridged dimer with amino acid sequence LKKLCLKLKKLCKLAG, and its derivatives, highlighting the formation of hexamers, specifically the trimer of dimers, which exhibited a stable hydrophobic core. FRET experiments showed that LK-3 oligomer formation was associated with cell penetration. Native MS confirmed higher-order oligomers of LK-3, while an intriguing finding was the enhanced cell-penetrating capability of a 1:1 mixture of l/d-peptide dimers compared to pure enantiomers. DSC analysis supported the notion that this enantiomeric mixture promotes the formation of functional oligomers, crucial for cell penetration. In conclusion, our study provides direct evidence that amphipathic peptide LK-3 forms oligomers at low nanomolar concentrations, underscoring their significance in cell penetration behavior.

PubMed: 39100342
DOI: 10.1021/acsomega.4c04004

Experimental method

X-RAY DIFFRACTION (1.92 Å)