1S1O

NMR Structure of a D,L Alternating pentadecamer of norleucine: double antiparallel beta-helix


Experimental Data Snapshot

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

wwPDB Validation 3D Report Full Report


This is version 1.4 of the entry. See complete history

Literature

Solution structure of a D,L-alternating oligonorleucine as a model of double-stranded antiparallel beta-helix.

Navarro, E.Fenude, E.Celda, B.

(2002) Biopolymers 64: 198-209

  • DOI: 10.1002/bip.10172

  • PubMed Abstract: 
  • Conformational characteristics of alternating D,L linear peptides are of particular interest because of their capacity to form transmembrane channels with different transport properties, as some natural antibiotics do. Single- and double-stranded bet ...

    Conformational characteristics of alternating D,L linear peptides are of particular interest because of their capacity to form transmembrane channels with different transport properties, as some natural antibiotics do. Single- and double-stranded beta-helical structures are common for alternating D,L peptides. The stability of the beta-helix depends on several structural factors, such as the backbone peptide length, type and position of side chains, and nature of terminal groups. The NMR and molecular dynamics solution conformation of a synthetic alternating D,L-oligopeptide with 15 norleucines (XVMe) has been used as a model to get insight in to the conformational features of double-stranded beta-helix structures. The NH chemical shift values (delta(NH)) and long-range nuclear Overhauser effects (NOE) cross peaks, in particular interstrand connectivities, clearly point to an antiparallel double-stranded beta-helix for the XVMe major conformation in solution. An extensive set of distances (from NOE cross peaks) and H-bonds (from delta(NH)) has been included in the molecular dynamics calculations. The experimental NMR data and theoretical calculations clearly indicate that the most probable conformation of XVMe in solution is a double-strand antiparallel beta(5.6) increasing decreasing-helix structure.


    Organizational Affiliation

    Departamento de Química Física, Facultat de Químicas, Universitat de Valencia, C/Dr. Moliner,50, 46100-Burjassot (Valencia), Spain.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
BOC-L-NLE-(D-NLE-L-NLE)5-D-NLE(METHYL)-L-NLE-D-NLE-L-NLE METHYL ESTER
A, B
16N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Small Molecules
Biologically Interesting Molecules 1 Unique
IDChainsNameType/Class2D Diagram3D Interactions
PRD_000109
Query on PRD_000109
ABOC-L-NLE-(D-NLE-L-NLE)5-D-NLE(METHYL)-L-NLE-D-NLE-L-NLE METHYL ESTERPolypeptide / Antibiotic

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Experimental Data & Validation

Experimental Data

  • Method: SOLUTION NMR
  • Conformers Calculated: 50 
  • Conformers Submitted: 
  • 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: 2004-02-24
    Type: Initial release
  • Version 1.1: 2008-04-29
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance
  • Version 1.3: 2012-09-19
    Type: Non-polymer description, Structure summary
  • Version 1.4: 2012-12-12
    Type: Other