1FME

SOLUTION STRUCTURE OF FSD-EY, A NOVEL PEPTIDE ASSUMING A BETA-BETA-ALPHA FOLD


Experimental Data Snapshot

  • Method: SOLUTION NMR
  • Conformers Calculated: 49 
  • Conformers Submitted: 34 
  • Selection Criteria: structures with the least restraint violations 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

The beta-beta-alpha fold: explorations in sequence space.

Sarisky, C.A.Mayo, S.L.

(2001) J Mol Biol 307: 1411-1418

  • DOI: 10.1006/jmbi.2000.4345
  • Primary Citation of Related Structures:  
    1FME

  • PubMed Abstract: 
  • The computational redesign of the second zinc finger of Zif268 to produce a 28 residue peptide (FSD-1) that assumes a betabetaalpha fold without metal binding was recently reported. In order to explore the tolerance of this metal-free fold towards sequence variability, six additional peptides resulting from the ORBIT computational protein design process were synthesized and characterized ...

    The computational redesign of the second zinc finger of Zif268 to produce a 28 residue peptide (FSD-1) that assumes a betabetaalpha fold without metal binding was recently reported. In order to explore the tolerance of this metal-free fold towards sequence variability, six additional peptides resulting from the ORBIT computational protein design process were synthesized and characterized. The experimental stabilities of five of these peptides are strongly correlated with the energies calculated by ORBIT. However, when a peptide with a mutation in the beta-turn is examined, the calculated stability does not accurately predict the experimentally determined stability. The NMR solution structure of a peptide incorporating this mutation (FSD-EY) reveals that the register between the beta-strands is different from the model structure used to select and score the sequences. FSD-EY has a type I' turn instead of the target EbaaagbE turn (rubredoxin knuckle). Two additional peptides that have improved side-chain to backbone hydrogen bonding and turn propensity for the target turn were characterized. Both are of stability comparable to that of FSD-1. These results demonstrate the robustness of the ORBIT protein design methods and underscore the need for continued improvements in negative design.


    Organizational Affiliation

    Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA, Mail code 147-75, USA.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
FSD-EY PEPTIDEA28N/AMutation(s): 0 
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: SOLUTION NMR
  • Conformers Calculated: 49 
  • Conformers Submitted: 34 
  • Selection Criteria: structures with the least restraint violations 
  • OLDERADO: 1FME Olderado

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2001-04-21
    Type: Initial release
  • Version 1.1: 2008-04-27
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance