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

Improved continuum electrostatic modelling in proteins, with comparison to experiment

J Warwicker1

  • 1Protein Engineering Department, AFRC Institute of Food Research Reading Laboratory, U.K.

Journal of Molecular Biology
|February 25, 1994
PubMed
Summary

Continuum electrostatics calculations for macromolecules are improved by including realistic solvent and counterion properties. Adjusting dielectric models and counterion behavior enhances accuracy for electrostatic interactions at various ionic strengths.

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

Polyunsaturated fatty acids inhibit Kv1.4 by interacting with positively charged extracellular pore residues.

American journal of physiology. Cell physiology·2016
Same author

Specific ion and buffer effects on protein-protein interactions of a monoclonal antibody.

Molecular pharmaceutics·2014
Same author

The role of electrostatics in protein-protein interactions of a monoclonal antibody.

Molecular pharmaceutics·2014
Same author

Freezing and folding behavior in simple off-lattice heteropolymers.

The Journal of chemical physics·2004
Same author

Biochemical and genetic evidence for a family of heterotrimeric G-proteins in Trichomonas vaginalis.

Molecular and biochemical parasitology·2003
Same author

A second eIF4E protein in Schizosaccharomyces pombe has distinct eIF4G-binding properties.

Nucleic acids research·2001

Area of Science:

  • Computational biology
  • Biophysics
  • Molecular modeling

Background:

  • Continuum models are used to calculate electrostatic interactions in macromolecules.
  • Previous models often oversimplified solvent and counterion effects, impacting accuracy.

Purpose of the Study:

  • To assess and improve continuum electrostatics calculations for macromolecules.
  • To investigate the impact of dielectric and counterion modeling on interaction accuracy.

Main Methods:

  • Finite difference method applied to a continuum model.
  • Comparison with experimental data across various ionic strengths.
  • Adjustment of model parameters including dielectric constants and counterion accessibility.

Main Results:

Related Experiment Videos

  • Overestimation of dielectric effects occurs with a uniform dielectric constant of 80.
  • Including Kirkwood correlation sphere and dielectric saturation improves agreement.
  • Counterion modeling requires balancing solvent layer restrictions and accessibility for accurate damping.

Conclusions:

  • Physically realistic solvent and counterion properties are crucial for accurate continuum electrostatics.
  • Improvements in dielectric and counterion modeling enhance the computation of ionic strength effects.
  • This study highlights potential for advancing continuum electrostatics calculations.