2DCX | pdb_00002dcx

NMR solution structure of the Dermaseptin antimicrobial peptide analog NC12-K4S4(1-13)a


Experimental Data Snapshot

  • Method: SOLUTION NMR
  • Conformers Calculated: 50 
  • Conformers Submitted: 15 
  • Selection Criteria: structures with the lowest energy, structures with the least restraint violations 

wwPDB Validation 3D Report Full Report

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This is version 2.0 of the entry. See complete history

Literature

Consequences of N-acylation on structure and membrane binding properties of dermaseptin derivative k4-s4-(1-13)

Shalev, D.E.Rotem, S.Fish, A.Mor, A.

(2006) J Biological Chem 281: 9432-9438

  • DOI: https://doi.org/10.1074/jbc.M513051200
  • Primary Citation Related Structures: 
    2DCX, 2DD6

  • PubMed Abstract: 

    Acyl conjugation to antimicrobial peptides is known to enhance antimicrobial properties. Here, we investigated the consequences of aminolauryl (NC(12)) conjugation to the dermaseptin derivative K(4)-S4-(1-13) (P) on binding properties to bilayer models mimicking bacterial plasma membrane, which is often cited as the ultimate site of action. Isothermal titration calorimetry revealed that acylation was responsible for enhancing the binding affinity of NC(12)-P compared with P (K = 13 x 10(5) and 1.5 x 10(5) m(-1), respectively). Surface plasmon resonance measurements confirmed the isothermal titration calorimetry results (K(app) = 12.6 x 10(5) and 1.53 x 10(5) m(-1), respectively) and further indicated that enhanced adhesion affinity (K(adhesion) = 3 x 10(5) and 1 x 10(5) m(-1), respectively) was coupled to enhanced tendency to insert within the bilayer (K(insertion) = 4.5 and 1.5, respectively). To gain insight into the molecular basis for these observations, we investigated the three-dimensional structures in the presence of dodecylphosphocholine using NMR. The ensemble of NMR-calculated structures (backbone root mean square deviation <0.6 A) showed that the acyl moiety was responsible for a significant molecular reorganization, possibly affecting the electrostatic potential distribution in NC(12)-P relative to that of P. The combined data present compelling evidence in support of the hypothesis that N-acylation affects antimicrobial properties by modifying the secondary structure of the peptide in a manner that facilitates contact with the membrane and consequently increases its disruption.


  • Organizational Affiliation
    • Wolfson Centre for Applied Structural Biology, Hebrew University of Jerusalem, Safra Campus, Givat Ram, 91904 Jerusalem, Israel.

Macromolecule Content 

  • Total Structure Weight: 1.73 kDa 
  • Atom Count: 121 
  • Modeled Residue Count: 14 
  • Deposited Residue Count: 14 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:  Sequence   |   3D Structure  
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Dermaseptin-414N/AMutation(s): 1 
UniProt
Find proteins for P80280 (Phyllomedusa sauvagei)
Explore P80280 
Go to UniProtKB:  P80280
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP80280
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
DOA

Query on DOA



Download:Ideal Coordinates CCD File
B [auth A]12-AMINO-DODECANOIC ACID
C12 H25 N O2
PBLZLIFKVPJDCO-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: SOLUTION NMR
  • Conformers Calculated: 50 
  • Conformers Submitted: 15 
  • Selection Criteria: structures with the lowest energy, structures with the least restraint violations 

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2006-02-28
    Type: Initial release
  • Version 1.1: 2008-04-30
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2021-11-10
    Changes: Data collection, Database references, Derived calculations
  • Version 2.0: 2023-11-15
    Changes: Atomic model, Data collection