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

Structural test of the parameterized-backbone method for protein design.

Joseph J Plecs1, Pehr B Harbury, Peter S Kim

  • 1Department of Physics, University of California, Berkeley, 94720, USA.

Journal of Molecular Biology
|August 18, 2004
PubMed
Summary
This summary is machine-generated.

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

The male-biased sex ratio in humans and its role in the transition from promiscuity to pair bonding.

Journal of theoretical biology·2026
Same author

Unification and generalization of models of zygote survival.

Proceedings. Biological sciences·2026
Same author

Optimisation of pembrolizumab therapy for de novo metastatic MSI-H/dMMR colorectal cancer using data-driven delay integro-differential equations.

Journal of theoretical biology·2026
Same author

Targeting of CD28 and CD38 as a potential novel therapeutic strategy for peripheral T-cell lymphomas.

Scientific reports·2026
Same author

Correction to "Oriented Multivalent Display Drives Consistent Serum Immunodominance to the Ebola Virus Glycoprotein".

ACS central science·2026
Same author

Intercellular forces driving stratification in a two-layer corneal epithelium: Insight from a Voronoi cell-based simulation model.

PLoS computational biology·2026

Scientists designed a novel protein fold, RH3, using a parameterized backbone and core packing models. Its crystal structure confirmed the intended fold, revealing insights into protein design and oligomer specificity.

Area of Science:

  • Protein engineering and structural biology.
  • Computational protein design.
  • X-ray crystallography.

Background:

  • Designing de novo protein folds necessitates simultaneous optimization of backbone conformation and side-chain arrangements.
  • Parameterized backbones offer a systematic approach to exploring diverse protein structural families.

Purpose of the Study:

  • To report the crystal structure of a rationally designed protein, RH3, a right-handed, three-helix coiled coil.
  • To validate a protein design methodology employing parameterized backbones and detailed core packing models.
  • To investigate the structural basis of oligomer specificity in designed coiled coils.

Main Methods:

  • Utilized a parameterized backbone approach for protein structure design.
  • Employed detailed modeling of core packing interactions.

Related Experiment Videos

  • Incorporated a metal-binding site for experimental phasing via X-ray crystallography.
  • Determined and analyzed the crystal structure of the designed protein RH3.

    • Main Results:

    • The crystal structure of RH3 confirmed the successful design of the intended novel protein fold.
    • RH3 exhibited unanticipated structural asymmetry within the trimer.
    • Comparison with a related designed tetramer (RH4) highlighted the sensitivity of the design method to single amino acid sequence variations.
    • Analysis revealed that steric overlap and cavity formation are key drivers of oligomer specificity.

    Conclusions:

    • The design methodology is effective in creating novel protein folds not previously observed in nature.
    • Structural asymmetry can arise in designed protein assemblies.
    • The study provides critical insights into the forces governing protein oligomerization and specificity, advancing the field of protein design.