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

Long-range electrostatic interactions in molecular dynamics: an endothelin-1 case study.

Eva Fadrná1, Klára Hladecková, Jaroslav Koca

  • 1National Centre for Biomolecular Research, Department of Organic Chemistry, Faculty of Science, Masaryk University, Kotlárská 2, 611 37 Brno, Czech Republic. evaf@chemi.muni.cz

Journal of Biomolecular Structure & Dynamics
|August 3, 2005
PubMed
Summary

Comparing electrostatic treatments in molecular dynamics (MD) simulations of endothelin-1 revealed that the cutoff method, particularly with NMR structures, offered more reliable results than Particle Mesh Ewald (PME). Careful selection of electrostatics is recommended over automatic PME use.

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

The catalytic reaction mechanism of tyrosylprotein sulfotransferase-1.

Physical chemistry chemical physics : PCCP·2021
Same author

NAChRDB: A Web Resource of Structure-Function Annotations to Unravel the Allostery of Nicotinic Acetylcholine Receptors.

ACS omega·2021
Same author

Correction to: Optimized SQE atomic charges for peptides accessible via a web application.

Journal of cheminformatics·2021
Same author

Optimized SQE atomic charges for peptides accessible via a web application.

Journal of cheminformatics·2021
Same author

Uncovering of cytochrome P450 anatomy by SecStrAnnotator.

Scientific reports·2021
Same author

Mol* Viewer: modern web app for 3D visualization and analysis of large biomolecular structures.

Nucleic acids research·2021

Area of Science:

  • Computational chemistry
  • Molecular modeling

Background:

  • Accurate simulation of biomolecular systems requires precise treatment of electrostatic interactions.
  • Long-range electrostatic interactions significantly influence molecular dynamics (MD) simulations.
  • Particle Mesh Ewald (PME) is a common but computationally intensive method for handling long-range electrostatics.

Purpose of the Study:

  • To compare the impact of different long-range electrostatic treatments on MD simulations.
  • To evaluate the performance of residue-based cutoff versus PME methods.
  • To determine the most reliable electrostatic treatment for simulating the peptide endothelin-1.

Main Methods:

  • Conformational search in explicit solvent using MD simulations.
  • Comparison of residue-based cutoff and PME for electrostatic interactions.

Related Experiment Videos

  • Analysis of free energy (MM-PBSA), secondary structure, and hydrogen bonds.
  • Simulations initiated from both X-ray and NMR-derived structures.

    • Main Results:

    • No single electrostatic treatment method (cutoff vs. PME) provided unambiguously superior results for all analyses.
    • Molecular dynamics simulations using the cutoff method with an NMR-derived starting structure yielded the most reliable data.
    • Differences in secondary structure elements and hydrogen bond patterns were observed between the two electrostatic treatments.

    Conclusions:

    • The choice of long-range electrostatic treatment in MD simulations should be carefully considered and not automatically defaulted to PME.
    • Starting structure (X-ray vs. NMR) can influence the outcome of MD simulations with different electrostatic treatments.
    • The cutoff method may offer a viable and reliable alternative to PME for specific systems like endothelin-1.