2JUE

Solution structure of the all-D kalata B1


Experimental Data Snapshot

  • Method: SOLUTION NMR
  • Conformers Calculated: 50 
  • Conformers Submitted: 20 
  • Selection Criteria: structures with the lowest energy 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

A Synthetic mirror image of kalata B1 reveals that cyclotide activity is independent of a protein receptor.

Sando, L.Henriques, S.T.Foley, F.Simonsen, S.M.Daly, N.L.Hall, K.N.Gustafson, K.R.Aguilar, M.I.Craik, D.J.

(2011) Chembiochem 12: 2456-2462

  • DOI: 10.1002/cbic.201100450

  • PubMed Abstract: 
  • Featuring a circular, knotted structure and diverse bioactivities, cyclotides are a fascinating family of peptides that have inspired applications in drug design. Most likely evolved to protect plants against pests and herbivores, cyclotides also exh ...

    Featuring a circular, knotted structure and diverse bioactivities, cyclotides are a fascinating family of peptides that have inspired applications in drug design. Most likely evolved to protect plants against pests and herbivores, cyclotides also exhibit anti-cancer, anti-HIV, and hemolytic activities. In all of these activities, cell membranes appear to play an important role. However, the question of whether the activity of cyclotides depends on the recognition of chiral receptors or is primarily modulated by the lipid-bilayer environment has remained unknown. To determine the importance of lipid membranes on the activity of the prototypic cyclotide, kalata B1, we synthesized its all-D enantiomer and assessed its bioactivities. After the all-D enantiomer had been confirmed by (1)H NMR to be the structural mirror image of the native kalata B1, it was tested for anti-HIV activity, cytotoxicity, and hemolytic properties. The all-D peptide is active in these assays, albeit with less efficiency; this reveals that kalata B1 does not require chiral recognition to be active. The lower activity than the native peptide correlates with a lower affinity for phospholipid bilayers in model membranes. These results exclude a chiral receptor mechanism and support the idea that interaction with phospholipid membranes plays a role in the activity of kalata B1. In addition, studies with mixtures of L and D enantiomers of kalata B1 suggested that biological activity depends on peptide oligomerization at the membrane surface, which determines affinity for membranes by modulating the association-dissociation equilibrium.


    Organizational Affiliation

    Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, Australia.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Kalata-B1
A
29Oldenlandia affinisMutation(s): 0 
Gene Names: OAK1
Find proteins for P56254 (Oldenlandia affinis)
Go to UniProtKB:  P56254
Small Molecules
Modified Residues  10 Unique
IDChainsTypeFormula2D DiagramParent
DCY
Query on DCY
A
D-PEPTIDE LINKINGC3 H7 N O2 S

--

DPR
Query on DPR
A
D-PEPTIDE LINKINGC5 H9 N O2

--

DSN
Query on DSN
A
D-PEPTIDE LINKINGC3 H7 N O3

--

DVA
Query on DVA
A
D-PEPTIDE LINKINGC5 H11 N O2

--

DTH
Query on DTH
A
D-PEPTIDE LINKINGC4 H9 N O3

--

DLE
Query on DLE
A
D-PEPTIDE LINKINGC6 H13 N O2

--

DGL
Query on DGL
A
D-PEPTIDE LINKINGC5 H9 N O4

--

DSG
Query on DSG
A
D-PEPTIDE LINKINGC4 H8 N2 O3

--

DTR
Query on DTR
A
D-PEPTIDE LINKINGC11 H12 N2 O2

--

DAR
Query on DAR
A
D-PEPTIDE LINKINGC6 H15 N4 O2

--

Experimental Data & Validation

Experimental Data

  • Method: SOLUTION NMR
  • Conformers Calculated: 50 
  • Conformers Submitted: 20 
  • Selection Criteria: structures with the lowest energy 

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2008-08-05
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance
  • Version 1.2: 2015-08-19
    Type: Database references