Jove
Visualize
Contact Us
JoVE
x logofacebook logolinkedin logoyoutube logo
ABOUT JoVE
OverviewLeadershipBlogJoVE Help Center
AUTHORS
Publishing ProcessEditorial BoardScope & PoliciesPeer ReviewFAQSubmit
LIBRARIANS
TestimonialsSubscriptionsAccessResourcesLibrary Advisory BoardFAQ
RESEARCH
JoVE JournalMethods CollectionsJoVE Encyclopedia of ExperimentsArchive
EDUCATION
JoVE CoreJoVE BusinessJoVE Science EducationJoVE Lab ManualFaculty Resource CenterFaculty Site
Terms & Conditions of Use
Privacy Policy
Policies

Related Experiment Videos

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

C A Sarisky1, S L Mayo

  • 1Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA, Mail code 147-75, USA.

Journal of Molecular Biology
|April 9, 2001
PubMed
Summary

Computational protein design methods show robustness in creating stable, metal-free protein folds. However, accurately predicting stability requires improved negative design, especially for mutations affecting beta-turns.

Related Concept Videos

You might also read

Related Articles

Articles linked to this work by shared authors, journal, and citation graph.

Sort by
Same author

Systemic immune response of young chickens orally immunized with bovine serum albumin.

In vivo (Athens, Greece)·2003
Same author

De novo backbone and sequence design of an idealized alpha/beta-barrel protein: evidence of stable tertiary structure.

Journal of molecular biology·2002
Same author

Computationally focusing the directed evolution of proteins.

Journal of cellular biochemistry. Supplement·2002
Same author

Enzyme-like proteins by computational design.

Proceedings of the National Academy of Sciences of the United States of America·2001
Same author

Polar residues in the protein core of Escherichia coli thioredoxin are important for fold specificity.

Biochemistry·2001
Same author

Computational method to reduce the search space for directed protein evolution.

Proceedings of the National Academy of Sciences of the United States of America·2001

Area of Science:

  • Protein engineering
  • Computational biology
  • Structural biology

Background:

  • The Zif268 zinc finger protein is a model for studying protein structure and function.
  • Computational methods enable the design of novel protein structures with specific folds.
  • Metal-free protein folds offer advantages in stability and applications.

Purpose of the Study:

  • To investigate the sequence variability tolerance of a computationally designed metal-free betabetaalpha fold.
  • To validate the accuracy of the ORBIT computational protein design process.
  • To identify limitations in predicting peptide stability with sequence mutations.

Main Methods:

  • Synthesis and experimental characterization of six designed peptides.
  • Nuclear Magnetic Resonance (NMR) spectroscopy to determine solution structures.

Related Experiment Videos

  • Comparison of experimental stability data with computational energy calculations.

    • Main Results:

    • Five of six designed peptides exhibited experimental stabilities correlating with ORBIT calculations.
    • A mutation in the beta-turn of peptide FSD-EY disrupted the predicted structure and stability.
    • NMR analysis revealed altered beta-strand register and an unintended turn type in FSD-EY.
    • Two additional peptides with improved turn propensity showed stability comparable to the original design.

    Conclusions:

    • The ORBIT computational design method demonstrates robustness for creating stable protein folds.
    • Accurate prediction of stability is challenged by sequence variations, particularly in beta-turns.
    • Further advancements in negative design are crucial for refining computational protein design.