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

Effective energy function for proteins in solution.

T Lazaridis1, M Karplus

  • 1Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts 02138, USA.

Proteins
|May 1, 1999
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

All-atom empirical potential for molecular modeling and dynamics studies of proteins.

The journal of physical chemistry. B·2014
Same author

A conformational transition in the myosin VI converter contributes to the variable step size.

Biophysical journal·2011
Same author

Calculation of free-energy differences by confinement simulations. Application to peptide conformers.

The journal of physical chemistry. B·2009
Same author

CHARMM: the biomolecular simulation program.

Journal of computational chemistry·2009
Same author

Molecular dynamics studies of NMR relaxation in proteins.

Biophysical journal·2009
Same author

Protein-Protein Interactions in DNA Recognition: H-NMR Studies of Lambda cI Repressors Genetically Altered by Site-Directed Mutagenesis.

Biophysical journal·2009
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

A new Gaussian solvent-exclusion model for protein solvation free energy was developed. This effective energy function (EEF1) accurately simulates protein behavior in solution, aiding in folding studies.

Area of Science:

  • Computational chemistry
  • Biophysics
  • Protein science

Background:

  • Accurate modeling of protein solvation free energy is crucial for understanding protein behavior in solution.
  • Existing models often require significant computational resources or lack sufficient accuracy.
  • Developing efficient and reliable solvation models is an ongoing challenge in computational biology.

Purpose of the Study:

  • To develop a novel Gaussian solvent-exclusion model for calculating protein solvation free energy.
  • To create an effective energy function (EEF1) for simulating proteins in aqueous environments.
  • To validate the accuracy and applicability of the developed model through various computational tests.

Main Methods:

  • Development of a Gaussian solvent-exclusion model based on theoretical considerations and experimental data.

Related Experiment Videos

  • Parameterization using small model compounds for group contributions to solvation free energy.
  • Integration with the CHARMM 19 polar hydrogen energy function to form EEF1.
  • Molecular dynamics simulations of proteins in native conformations and at high temperatures.
  • Calculation of enthalpy of unfolding for a polyalanine helix.

    • Main Results:

    • Stable molecular dynamics trajectories were obtained for proteins in their native conformations.
    • Deviations from experimental structures were comparable to those from explicit water simulations.
    • Calculated enthalpy of unfolding for polyalanine helix showed good agreement with experimental data.
    • EEF1 effectively distinguished correctly from incorrectly folded proteins in static and dynamic simulations.
    • Unfolding pathways from high-temperature simulations aligned with explicit water simulations.

    Conclusions:

    • The developed Gaussian solvent-exclusion model and resulting EEF1 provide a realistic approximation for protein energy landscapes in solution.
    • EEF1 demonstrates accuracy in predicting protein conformations, stability, and unfolding pathways.
    • This model offers a computationally efficient alternative for studying protein behavior in aqueous environments.