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

Exploring structures in protein folding funnels with free energy functionals: the transition state ensemble.

B A Shoemaker1, J Wang, P G Wolynes

  • 1School of Chemical Sciences, University of Illinois Urbana-Champaign, Urbana, IL, 61801, USA.

Journal of Molecular Biology
|March 27, 1999
PubMed
Summary

This study characterizes protein folding free energy surfaces using advanced functionals, revealing how residue ordering influences folding mechanisms from delocalized to classical nuclei. Findings correlate computational models with experimental protein engineering data.

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

Speeding molecular recognition by using the folding funnel: the fly-casting mechanism.

Proceedings of the National Academy of Sciences of the United States of America·2000
Same author

Exploring structures in protein folding funnels with free energy functionals: the denatured ensemble.

Journal of molecular biology·1999
Same author

Structural correlations in protein folding funnels.

Proceedings of the National Academy of Sciences of the United States of America·1997
Same author

Reaction of cytochrome bo3 with oxygen: extra redox center(s) are present in the protein.

Biochemistry·1995
Same author

Regulation of striatal cyclic-3',5'-adenosine monophosphate accumulation and GABA release by glutamate metabotropic and dopamine D1 receptors.

The Journal of pharmacology and experimental therapeutics·1995
Same author

Calculation of relative binding free energies and configurational entropies: a structural and thermodynamic analysis of the nature of non-polar binding of thrombin inhibitors based on hirudin55-65.

Journal of molecular biology·1995

Area of Science:

  • Computational biophysics
  • Protein dynamics
  • Chemical kinetics

Background:

  • Understanding protein folding is crucial for molecular biology and disease research.
  • Fast-folding proteins present unique challenges for characterizing their folding pathways.
  • Transition state ensembles play a key role in determining folding rates and mechanisms.

Purpose of the Study:

  • To characterize free energy surfaces for fast-folding proteins using novel free energy functionals.
  • To investigate the role of residue ordering and cooperativity in protein folding mechanisms.
  • To compare computational predictions with experimental data from protein engineering kinetics.

Main Methods:

  • Utilized free energy functionals incorporating partial residue ordering in the transition state ensemble.

Related Experiment Videos

  • Focused on chymotrypsin inhibitor and lambda-repressor proteins.
  • Compared structural correlations from computational models with experimental extrathermodynamic free energy relations.

    • Main Results:

    • Demonstrated how many-body forces, like side-chain ordering, dictate the transition from delocalized to classical nucleation in protein folding.
    • Showed good agreement between computationally derived transition state ensemble correlations and experimental data.
    • Analyzed barrier sizes and multidimensional free energy profiles to assess reaction coordinates.

    Conclusions:

    • Free energy functionals accounting for residue ordering accurately model fast protein folding.
    • Cooperativity in residue interactions is a key determinant of folding nucleus characteristics.
    • The study provides insights into appropriate reaction coordinates for protein folding.