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

Predicting Ca(2+)-binding sites in proteins

M Nayal1, E Di Cera

  • 1Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, MO 63110.

Proceedings of the National Academy of Sciences of the United States of America
|January 18, 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

Dual effect of histone H4 on prothrombin activation.

Journal of thrombosis and haemostasis : JTH·2016
Same author

WEDGE: an anticoagulant thrombin mutant produced by autoactivation.

Journal of thrombosis and haemostasis : JTH·2014
Same author

Na+ binding to meizothrombin desF1.

Cellular and molecular life sciences : CMLS·2008
Same author

Role of the A chain in thrombin function.

Cellular and molecular life sciences : CMLS·2008
Same author

Thrombostatin FM compounds: direct thrombin inhibitors - mechanism of action in vitro and in vivo.

Journal of thrombosis and haemostasis : JTH·2008
Same author

Serine peptidases: classification, structure and function.

Cellular and molecular life sciences : CMLS·2008

A new algorithm accurately predicts calcium (Ca2+) ion binding sites in proteins by calculating a "valence" score for potential binding points. This method precisely locates cation-binding sites, aiding protein engineering and understanding metal ion interactions.

Area of Science:

  • Biochemistry
  • Structural Biology
  • Computational Biology

Background:

  • Cation binding sites in proteins are crucial for numerous biological functions.
  • The coordination shell of Ca2+ ions typically involves oxygen and carbon atoms.
  • Accurate prediction of cation binding sites remains a challenge in structural biology.

Purpose of the Study:

  • To develop and validate a computational method for precisely locating cation-binding sites in proteins.
  • To assess the utility of a calculated valence score for identifying Ca2+, Mg2+, and Na+ binding locations.
  • To explore the potential of this method for protein engineering and understanding molecular recognition.

Main Methods:

  • An empirical expression was used to evaluate the bond-strength contribution of ligating oxygen atoms.

Related Experiment Videos

  • A grid-based algorithm calculated the valence of potential Ca2+-binding sites within protein structures.
  • The distribution of valence values was analyzed, and predictions were validated against known Ca2+-binding sites.

    • Main Results:

    • A valence score distribution peaked around 0.4 was obtained for potential Ca2+-binding sites.
    • A small fraction of points (0.06%) exhibited a valence > or = 1.4, clustering around known Ca2+ ions.
    • A valence > or = 1.4 was found to be both necessary and sufficient for predicting Ca2+ binding site locations with high accuracy (87%).
    • The algorithm successfully predicted Mg2+ and Na+ binding sites in various proteins.

    Conclusions:

    • The calculated valence is a highly accurate tool for pinpointing cation-binding sites in proteins.
    • This method can be applied to various cations beyond Ca2+, including Mg2+ and Na+.
    • The valence calculation offers potential for engineering high-affinity binding sites and characterizing protein-metal ion interactions.