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

Satisfying hydrogen bonding potential in proteins

I K McDonald1, J M Thornton

  • 1Department of Biochemistry and Molecular Biology, University College London, U.K.

Journal of Molecular Biology
|May 20, 1994
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

Large-scale annotation of biochemically relevant pockets and tunnels in cognate enzyme-ligand complexes.

Journal of cheminformatics·2024
Same author

Resolvin D2 promotes host defense in a 2 - hit model of sepsis with secondary lung infection.

Prostaglandins & other lipid mediators·2022
Same author

Lipoxin A4 promotes reduction and antibiotic efficacy against Pseudomonas aeruginosa biofilm.

Prostaglandins & other lipid mediators·2020
Same author

Clinical management of Brucella suis infection in dogs and implications for public health.

Australian veterinary journal·2017
Same author

Modeling birds on wires.

Journal of theoretical biology·2016
Same author

HydroCoils, occlusion rates, and outcomes: a large single-center study.

AJNR. American journal of neuroradiology·2010

Protein structures contain unsatisfied hydrogen bond donors and acceptors. Lower resolution data shows more unsatisfied atoms, but some remain even with relaxed criteria, suggesting complex interactions in protein folding.

Area of Science:

  • Structural Biology
  • Biophysics
  • Computational Chemistry

Background:

  • Hydrogen bonds are crucial for protein structure and function.
  • Understanding the satisfaction of hydrogen bond potential in proteins is key to accurate structural analysis.

Purpose of the Study:

  • To analyze the frequency of satisfied hydrogen bond donors and acceptors in protein molecules.
  • To investigate the impact of resolution on hydrogen bond satisfaction.
  • To identify instances of unsatisfied hydrogen bonds and explore potential explanations.

Main Methods:

  • Analysis of protein structures using standard hydrogen bond criteria.
  • Examination of main-chain nitrogen and oxygen atoms.
  • Comparison of results based on varying resolution of crystallographic data.

Related Experiment Videos

Main Results:

  • A small percentage of buried main-chain nitrogen (9.5%) and oxygen (5.1%) atoms fail to form hydrogen bonds under standard criteria.
  • These percentages decrease with improved data resolution.
  • Relaxing criteria reveals weak hydrogen bonds for many unsatisfied atoms, but some remain unbonded without clear compensating interactions (1.3% NH, 1.8% CO).

Conclusions:

  • Standard criteria reveal a non-negligible fraction of unsatisfied hydrogen bond potential in proteins.
  • Data resolution significantly influences the observed satisfaction of hydrogen bonds.
  • Some unsatisfied buried atoms suggest the presence of uncharacterized stabilizing interactions in protein structures.