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

Rapid protein fold determination using unassigned NMR data.

Jens Meiler1, David Baker

  • 1Department of Biochemistry and Howard Hughes Medical Institute, University of Washington, PO Box 357350, Seattle, WA 98195-7350, USA.

Proceedings of the National Academy of Sciences of the United States of America
|December 12, 2003
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

This study introduces a novel method to generate low-resolution protein structures using unassigned Nuclear Magnetic Resonance (NMR) data and the Rosetta algorithm. This approach accelerates structure determination, aiding in the analysis of rapidly identified protein sequences.

Area of Science:

  • Structural Biology
  • Biophysics
  • Computational Biology

Background:

  • Experimental protein structure determination (X-ray crystallography, NMR) is outpaced by the rate of new sequence identification.
  • Nuclear Magnetic Resonance (NMR) spectroscopy provides valuable structural data (chemical shifts, NOEs, RDCs) but requires time-consuming resonance assignment.
  • Efficient methods are needed to leverage NMR data for rapid protein structure elucidation.

Purpose of the Study:

  • To develop a computational method for generating low-resolution protein structures from unassigned NMR data.
  • To integrate de novo protein structure prediction with a Monte Carlo-based resonance assignment strategy.
  • To assess the utility of the generated structures for subsequent high-resolution refinement.

Main Methods:

Related Experiment Videos

  • Utilized the Rosetta de novo protein structure prediction algorithm to generate an ensemble of candidate structures from sequence information.
  • Employed a Monte Carlo procedure to search for optimal assignments of NMR resonances (CSs, NOEs, RDCs) to atoms for each candidate structure.
  • Ranked candidate structures based on the goodness-of-fit between experimental NMR data and the predicted structure, given the identified assignments.

Main Results:

  • The method successfully generated low-resolution protein models (3-6 Å RMSD) for nine test proteins (56-140 amino acids) using published chemical shift, NOE, and RDC data.
  • In four out of nine cases, the partial assignments derived from the method enabled refinement of structures to high resolution (0.6-1.8 Å).
  • Demonstrated the feasibility of using unassigned NMR data in conjunction with computational prediction for structural analysis.

Conclusions:

  • The developed method provides a viable approach to rapidly generate low-resolution protein structures from unassigned NMR data.
  • This strategy significantly reduces the bottleneck associated with resonance assignment in NMR-based structure determination.
  • The generated models serve as a valuable starting point for high-resolution structure refinement, accelerating the overall structural biology workflow.