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

Electrostatic interactions in a peptide--RNA complex.

Cuauhtémoc García-García1, David E Draper

  • 1Department of Biophysics, Johns Hopkins University, Baltimore, MD 21218, USA.

Journal of Molecular Biology
|July 24, 2003
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

Divalent ion competition reveals reorganization of an RNA ion atmosphere upon folding.

Nucleic acids research·2017
Same author

RNA BIOCHEMISTRY. Factor-dependent processivity in human eIF4A DEAD-box helicase.

Science (New York, N.Y.)·2015
Same author

Reflections on 20 years of RNA.

RNA (New York, N.Y.)·2015
Same author

Comparison of interactions of diamine and Mg²⁺ with RNA tertiary structures: similar versus differential effects on the stabilities of diverse RNA folds.

Biochemistry·2013
Same author

Folding of RNA tertiary structure: Linkages between backbone phosphates, ions, and water.

Biopolymers·2013
Same author

Denaturation of RNA secondary and tertiary structure by urea: simple unfolded state models and free energy parameters account for measured m-values.

Biochemistry·2012
Same journal

Clinical inflammasome biomarkers: Progress and prospects.

Journal of molecular biology·2026
Same journal

Biologically Relevant, Cationic Residues in Human Rhinovirus Stabilize Capsid-Bound RNA Duplexes, and Restrict Capsid Flexibility.

Journal of molecular biology·2026
Same journal

Cryo-EM structures of phage T4 infection intermediate.

Journal of molecular biology·2026
Same journal

A classic fold with a twist: Structural architecture of Dhillonvirus phage Bas18.

Journal of molecular biology·2026
Same journal

Tesorai Search: cloud-based database search engine boosts identifications for mass spectrometry proteomics with a pretrained peptide-spectrum deep-learning model.

Journal of molecular biology·2026
Same journal

Characterization of diverse functions of NRF1 nuclear localization sequence.

Journal of molecular biology·2026
See all related articles

This study quantifies electrostatic interactions between a phage lambda N protein peptide and box B RNA. Experimental and computational methods show excellent agreement, revealing significant charge contributions to binding energetics.

Area of Science:

  • Biophysics
  • Structural Biology
  • Computational Chemistry

Background:

  • Investigating molecular interactions is crucial for understanding biological processes.
  • The N protein of phage lambda interacts with box B RNA, a system relevant to gene regulation.

Purpose of the Study:

  • To quantitatively assess the energetics of electrostatic interactions in the peptide-RNA complex.
  • To compare experimental measurements with theoretical calculations for validation.

Main Methods:

  • Experimental measurement of salt-dependent free energies for peptide folding and RNA binding.
  • Theoretical calculations using the non-linear Poisson-Boltzmann equation.
  • Analysis of variant peptides and RNA to probe specific interactions.

Related Experiment Videos

Main Results:

  • Experimental and calculated salt-dependence of binding free energy showed excellent agreement (5.98 vs. 5.87 kcal/mol).
  • All 12 charged residues of the peptide significantly contribute to electrostatic binding energy.
  • Ion release upon complex formation arises from rearrangements of peptide and RNA ion atmospheres.

Conclusions:

  • Electrostatic interactions play a critical role in the binding of phage lambda N peptide to box B RNA.
  • Theoretical models accurately predict experimental binding energetics.
  • Understanding these interactions provides insights into molecular recognition in biological systems.