1NT5

F1-Gramicidin A in Sodium Dodecyl Sulfate Micelles (NMR)


Experimental Data Snapshot

  • Method: SOLUTION NMR
  • Conformers Submitted: 

wwPDB Validation   3D Report Full Report


This is version 2.0 of the entry. See complete history


Literature

The Structure, Cation Binding, Transport, and Conductance of Gly15-Gramicidin a Incorporated Into Sds Micelles and Pc/Pg Vesicles.

Sham, S.S.Shobana, S.Townsley, L.E.Jordan, J.B.Fernandez, J.Q.Andersen, O.S.Greathouse, D.V.Hinton, J.F.

(2003) Biochemistry 42: 1401

  • DOI: https://doi.org/10.1021/bi0204286
  • Primary Citation of Related Structures:  
    1NG8, 1NT5, 1NT6

  • PubMed Abstract: 

    To further investigate the effect of single amino acid substitution on the structure and function of the gramicidin channel, an analogue of gramicidin A (GA) has been synthesized in which Trp(15) is replaced by Gly in the critical aqueous interface and cation binding region. The structure of Gly(15)-GA incorporated into SDS micelles has been determined using a combination of 2D-NMR spectroscopy and molecular modeling. Like the parent GA, Gly(15)-GA forms a dimeric channel composed of two single-stranded, right-handed beta(6.3)-helices joined by hydrogen bonds between their N-termini. The replacement of Trp(15) by Gly does not have a significant effect on backbone structure or side chain conformations with the exception of Trp(11) in which the indole ring is rotated away from the channel axis. Measurement of the equilibrium binding constants and Delta G for the binding of monovalent cations to GA and Gly(15)-GA channels incorporated into PC vesicles using (205)Tl NMR spectroscopy shows that monovalent cations bind much more weakly to the Gly(15)-GA channel entrance than to GA channels. Utilizing the magnetization inversion transfer NMR technique, the transport of Na(+) ions through GA and Gly(15)-GA channels incorporated into PC/PG vesicles has been investigated. The Gly(15) substitution produces an increase in the activation enthalpy of transport and thus a significant decrease in the transport rate of the Na(+) ion is observed. The single-channel appearances show that the conducting channels have a single, well-defined structure. Consistent with the NMR results, the single-channel conductances are reduced by 30% and the lifetimes by 70%. It is concluded that the decrease in cation binding, transport, and conductance in Gly(15)-GA results from the removal of the Trp(15) dipole and, to a lesser extent, the change in orientation of Trp(11).


  • Organizational Affiliation

    Department of Chemistry and Biochemistry, University of Arkansas, Fayetteville, Arkansas 72701, and Department of Physiology and Biophysics, Cornell University, Weill Medical College, New York, New York 10021.


Macromolecules

Find similar proteins by:  Sequence   |   3D Structure  

Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
GRAMICIDIN A
A, B
16Brevibacillus brevisMutation(s): 1 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
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  • Reference Sequence
Small Molecules
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
QPH
Query on QPH
A, B
L-PEPTIDE LINKINGC10 H11 N O3PHE
Biologically Interesting Molecules (External Reference) 1 Unique
Entity ID: 1
IDChains NameType/Class2D Diagram3D Interactions
PRD_001127
Query on PRD_001127
A, B
GRAMICIDIN APolypeptide / Antibiotic
Experimental Data & Validation

Experimental Data

  • Method: SOLUTION NMR
  • Conformers Submitted: 

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2003-02-11
    Type: Initial release
  • Version 1.1: 2011-06-14
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2011-07-27
    Changes: Atomic model, Database references, Derived calculations, Non-polymer description, Structure summary
  • Version 1.4: 2012-12-12
    Changes: Structure summary
  • Version 1.5: 2013-07-10
    Changes: Structure summary
  • Version 2.0: 2023-11-15
    Changes: Atomic model, Data collection, Database references, Derived calculations