2N8D | pdb_00002n8d

In silico designed antimicrobial peptide Lavracin

• PDB DOI: https://doi.org/10.2210/pdb2N8D/pdb
• BMRB: 25846

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


• Deposited: 2015-10-13 Released: 2017-01-18 
• Deposition Author(s): Pillong, M., Blatter, M., Schneider, G.

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Experimental Data Snapshot

• Method: SOLUTION NMR
• Conformers Calculated: 20 
• Conformers Submitted: 20 
• Selection Criteria: target function 

Literature

Rational Design of Membrane-Pore-Forming Peptides.

Pillong, M., Hiss, J.A., Schneider, P., Lin, Y.C., Posselt, G., Pfeiffer, B., Blatter, M., Muller, A.T., Bachler, S., Neuhaus, C.S., Dittrich, P.S., Altmann, K.H., Wessler, S., Schneider, G.

(2017) Small 13

• PubMed: 28799716 
• DOI: https://doi.org/10.1002/smll.201701316
• Primary Citation Related Structures: 
  2N8D


• PubMed Abstract: 
  

  Specific interactions of peptides with lipid membranes are essential for cellular communication and constitute a central aspect of the innate host defense against pathogens. A computational method for generating innovative membrane-pore-forming peptides inspired by natural templates is presented. Peptide representation in terms of sequence- and topology-dependent hydrophobic moments is introduced. This design concept proves to be appropriate for the de novo generation of first-in-class membrane-active peptides with the anticipated mode of action. The designed peptides outperform the natural template in terms of their antibacterial activity. They form a kinked helical structure and self-assemble in the membrane by an entropy-driven mechanism to form dynamically growing pores that are dependent on the lipid composition. The results of this study demonstrate the unique potential of natural template-based peptide design for chemical biology and medicinal chemistry.

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Organizational Affiliation: 
• Department of Chemistry and Applied Biosciences, ETH Zurich, 8093, Zurich, Switzerland.
Department of Molecular Biology, University of Salzburg, 5020, Salzburg, Austria.
Department of Biosystems Science and Engineering, ETH Zurich, 8093, Zurich, Switzerland.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 2.25 kDa 
• Atom Count: 160 
• Modeled Residue Count: 21 
• Deposited Residue Count: 21 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
antimicrobial peptide Lavracin	A	21	synthetic construct	Mutation(s): 0

Experimental Data & Validation

Experimental Data

• Method: SOLUTION NMR
• Conformers Calculated: 20 
• Conformers Submitted: 20 
• Selection Criteria: target function 

Structure Validation

Entry History 

Deposition Data

• Released Date: 2017-01-18 
Deposition Author(s): Pillong, M., Blatter, M., Schneider, G.

Revision History  

• Version 1.0: 2017-01-18
  Type: Initial release
  
• Version 1.1: 2017-08-30
  Changes: Database references
• Version 1.2: 2022-08-24
  Changes: Data collection, Database references, Derived calculations
• Version 1.3: 2023-06-14
  Changes: Other
• Version 1.4: 2024-11-06
  Changes: Data collection, Database references, Structure summary