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

Matching simulation and experiment: a new simplified model for simulating protein folding.

J M Sorenson1, T Head-Gordon

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

Journal of Computational Biology : a Journal of Computational Molecular Cell Biology
|December 7, 2000
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

Predicting cavity formation free energy: how far is the Gaussian approximation valid?

Physical chemistry chemical physics : PCCP·2012
Same author

Hydrogen bond strength and network structure effects on hydration of non-polar molecules.

Physical chemistry chemical physics : PCCP·2010
Same author

Is ambient water inhomogeneous on the nanometer-length scale?

Proceedings of the National Academy of Sciences of the United States of America·2010
Same author

Chemical bonding effects in the determination of protein structures by electron crystallography.

Acta crystallographica. Section A, Foundations of crystallography·2000
Same author

A global optimization strategy for predicting alpha-helical protein tertiary structure.

Computers & chemistry·2000
Same author

Redesigning the hydrophobic core of a model beta-sheet protein: destabilizing traps through a threading approach.

Proteins·2000

This study introduces a new protein folding model that simulates alpha/beta proteins. It reveals cooperative folding with two distinct pathways, offering insights into protein folding dynamics.

Area of Science:

  • Computational Biology
  • Biophysics
  • Protein Dynamics

Background:

  • Simplified protein folding models have advanced understanding of the protein folding problem.
  • Simulations are crucial for investigating complex biological processes like protein folding.

Purpose of the Study:

  • To introduce a novel off-lattice bead model for simulating small protein folding.
  • To characterize the thermodynamics and kinetics of an alpha/beta protein model.
  • To explore folding pathways and their relation to experimental observations.

Main Methods:

  • Utilized constant-temperature Langevin simulations and the multiple multihistogram method.
  • Developed a new off-lattice bead model for simulating protein folding.
  • Analyzed folding free energy landscapes and characterized mean-first passage times.

Related Experiment Videos

Main Results:

  • The model simulates alpha/beta proteins, including sequences resembling IgG-binding proteins L and G.
  • Folding was found to be highly cooperative, with chain collapse closely following folding.
  • Two distinct folding pathways were identified: one with an intermediate and one without.
  • Glasslike kinetics were observed to onset at temperatures significantly lower than the folding temperature.

Conclusions:

  • The proposed model offers a computationally feasible approach to studying protein folding.
  • It can simulate diverse fold classes and provides insights into folding pathways similar to experimental findings for proteins L and G.
  • The model is valuable for future research on interaction roles, mutation effects, and solvation forces in protein folding.