1VM4

Solution structure of an antibacterial and antitumor peptide designed based on the N-terminal membrane anchor of E. coli enzyme IIA (Glucose)


Experimental Data Snapshot

  • Method: SOLUTION NMR
  • Conformers Calculated: 100 
  • Conformers Submitted: 
  • Selection Criteria: No NOE violations greater than 0.50, rms difference for bond deviations from ideality less than 0.01 A, rms difference for angle deviations from ideality less than 5 degrees, Structures with the lowerest energies in the ensemble. 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Correlation of Three-dimensional Structures with the Antibacterial Activity of a Group of Peptides Designed Based on a Nontoxic Bacterial Membrane Anchor.

Wang, G.Li, Y.Li, X.

(2005) J Biol Chem 280: 5803-5811

  • DOI: 10.1074/jbc.M410116200
  • Primary Citation of Related Structures:  
    1VM5, 1VM4, 1VM3, 1VM2

  • PubMed Abstract: 
  • To understand the functional differences between a nontoxic membrane anchor corresponding to the N-terminal sequence of the Escherichia coli enzyme IIA(Glc) and a toxic antimicrobial peptide aurein 1.2 of similar sequence, a series of peptides was designed to bridge the gap between them ...

    To understand the functional differences between a nontoxic membrane anchor corresponding to the N-terminal sequence of the Escherichia coli enzyme IIA(Glc) and a toxic antimicrobial peptide aurein 1.2 of similar sequence, a series of peptides was designed to bridge the gap between them. An alteration of a single residue of the membrane anchor converted it into an antibacterial peptide. Circular dichroism spectra indicate that all peptides are disordered in water but helical in micelles. Structures of the peptides were determined in membrane-mimetic micelles by solution NMR spectroscopy. The quality of the distance-based structures was improved by including backbone angle restraints derived from a set of chemical shifts ((1)H(alpha), (15)N, (13)C(alpha), and (13)C(beta)) from natural abundance two-dimensional heteronuclear correlated spectroscopy. Different from the membrane anchor, antibacterial peptides possess a broader and longer hydrophobic surface, allowing a deeper penetration into the membrane, as supported by intermolecular nuclear Overhauser effect cross-peaks between the peptide and short chain dioctanoyl phosphatidylglycerol. An attempt was made to correlate the NMR structures of these peptides with their antibacterial activity. The activity of this group of peptides does not correlate exactly with helicity, amphipathicity, charge, the number of charges, the size of the hydrophobic surface, or hydrophobic transfer free energy. However, a correlation is established between the peptide activity and membrane perturbation potential, which is defined by interfacial hydrophobic patches and basic residues in the case of cationic peptides. Indeed, (31)P solid state NMR spectroscopy of lipid bilayers showed that the extent of lipid vesicle disruption by these peptides is proportional to their membrane perturbation potential.


    Organizational Affiliation

    Structure-Fun Laboratory, Eppley Institute for Research in Cancer and Allied Diseases, University of Nebraska Medical Center, Omaha, NE 68198-6805, USA.



Macromolecules
  • Find similar proteins by:  Sequence   |   Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
peptide A4A14synthetic constructMutation(s): 0 
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: SOLUTION NMR
  • Conformers Calculated: 100 
  • Conformers Submitted: 
  • Selection Criteria: No NOE violations greater than 0.50, rms difference for bond deviations from ideality less than 0.01 A, rms difference for angle deviations from ideality less than 5 degrees, Structures with the lowerest energies in the ensemble. 
  • OLDERADO: 1VM4 Olderado

Structure Validation

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Entry History 

Deposition Data

  • Deposited Date: 2004-08-31 
  • Released Date: 2004-12-07 
  • Deposition Author(s): Wang, G., Li, X.

Revision History  (Full details and data files)

  • Version 1.0: 2004-12-07
    Type: Initial release
  • Version 1.1: 2008-04-26
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2020-06-24
    Changes: Database references, Derived calculations, Source and taxonomy