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

Multipass membrane protein structure prediction using Rosetta.

Vladimir Yarov-Yarovoy1, Jack Schonbrun, David Baker

  • 1Department of Pharmacology, University of Washington, Seattle, Washington 98195, USA.

Proteins
|December 24, 2005
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

CASP11 refinement experiments with ROSETTA.

Proteins·2015
Same author

Structure of a designed tetrahedral protein assembly variant engineered to have improved soluble expression.

Protein science : a publication of the Protein Society·2015
Same author

Unique double-ring structure of the peroxisomal Pex1/Pex6 ATPase complex revealed by cryo-electron microscopy.

Proceedings of the National Academy of Sciences of the United States of America·2015
Same author

Mechanistic Analysis of an Engineered Enzyme that Catalyzes the Formose Reaction.

Chembiochem : a European journal of chemical biology·2015
Same author

Design of ordered two-dimensional arrays mediated by noncovalent protein-protein interfaces.

Science (New York, N.Y.)·2015
Same author

Designing Two-Dimensional Protein Arrays through Fusion of Multimers and Interface Mutations.

Nano letters·2015
Same journal

Engineered HSP90-MP65 Bivalent Fusion Antigen: A Novel Vaccine Candidate Against Invasive Candidiasis.

Proteins·2026
Same journal

Physics-Based Energy Functions for Computational Protein Design.

Proteins·2026
Same journal

Impact of Stabilizing Osmolytes on the Conformational Dynamics of Human and Rat Islet Amyloid Polypeptides.

Proteins·2026
Same journal

Stabilization of Bone Morphogenetic Protein-2 at Physiological pH: Contrasting Roles of CHAPS and Arginine in Aggregation Inhibition.

Proteins·2026
Same journal

Structural Insights Into the Function of Leishmania major Adenylosuccinate Lyase.

Proteins·2026
Same journal

Generalizing the Gaussian Network Model: Spanning-Tree Thermodynamics Shows Entropy-Driven KRAS Activation.

Proteins·2026
See all related articles

Researchers adapted the Rosetta method to predict helical transmembrane protein structures by modeling the membrane environment. This approach accurately predicts protein structures within a simulated membrane.

Area of Science:

  • Biophysics
  • Computational Biology
  • Structural Biology

Background:

  • Transmembrane proteins play crucial roles in cellular functions.
  • Accurate prediction of their structures is essential for understanding their mechanisms.
  • Existing methods often struggle with the complexities of the membrane environment.

Purpose of the Study:

  • To adapt the Rosetta de novo structure prediction method for helical transmembrane proteins.
  • To develop a membrane-specific energy function for improved structure prediction.
  • To evaluate the method's accuracy on known transmembrane protein structures.

Main Methods:

  • Modeling the membrane environment using parallel planes (hydrophobic, interface, polar layers).
  • Optimizing protein embedding by maximizing hydrophobic residue exposure within the membrane.

Related Experiment Videos

  • Utilizing Rosetta fragment assembly and a modified low-resolution energy function accounting for membrane interactions.
  • Sequential addition of helices to mimic protein biogenesis.

    • Main Results:

    • The adapted Rosetta method successfully predicted structures of helical transmembrane proteins.
    • Predictions achieved root-mean-square deviation <4 Å for 51–145 residue segments on 12 known proteins.
    • Sequential helix addition yielded more native-like structures compared to simultaneous folding.

    Conclusions:

    • The adapted Rosetta method provides a robust approach for de novo prediction of helical transmembrane protein structures.
    • The membrane-specific energy function and sequential assembly strategy enhance prediction accuracy.
    • This method aids in understanding protein structure-function relationships in membrane environments.