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

Protein clefts in molecular recognition and function

R A Laskowski1, N M Luscombe, M B Swindells

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

Protein Science : a Publication of the Protein Society
|December 1, 1996
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

What is AI? Applications of artificial intelligence to dermatology.

The British journal of dermatology·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 journal

Macromolecular crowding inhibits degradation of alpha-synuclein amyloid fibrils induced by cathepsins and MMP9.

Protein science : a publication of the Protein Society·2026
Same journal

Sequence-encoded differences in the conformational ensembles of CITED transcriptional activation domains impact coactivator binding.

Protein science : a publication of the Protein Society·2026
Same journal

The phospholipid biosynthesis enzyme PlsB contains three distinct domains for membrane association, lysophosphatidic acid synthesis, and dimerization.

Protein science : a publication of the Protein Society·2026
Same journal

Structural basis of ligand selectivity in FAD/NAD(P)H-dependent dehydrogenases: insights from trypanothione reductase and type II NADH dehydrogenase.

Protein science : a publication of the Protein Society·2026
Same journal

Achieving protease substrate-specific inhibition by mAb dual functional selections.

Protein science : a publication of the Protein Society·2026
Same journal

How important are quantum mechanical effects in controlling biological functions: Enzymes, electron transfer and bird navigation.

Protein science : a publication of the Protein Society·2026
See all related articles

Protein cleft size is a key factor in molecular interactions. Large clefts often indicate enzyme active sites or antibody-antigen binding sites, aiding in function prediction.

Area of Science:

  • Structural biology
  • Biophysics
  • Computational biology

Background:

  • Protein surface clefts play a crucial role in molecular interactions.
  • Enzyme active sites and protein-dimer interfaces exhibit distinct cleft characteristics.

Purpose of the Study:

  • To analyze the relationship between protein cleft volumes and their molecular interactions.
  • To investigate the utility of cleft geometry in predicting protein function and interaction sites.

Main Methods:

  • Analysis of three datasets: enzyme-ligand binding, protein-protein dimerization, and antibody-antigen complexes.
  • Geometric analysis of cleft volumes and surface properties.

Main Results:

  • In 83% of single-chain enzymes, ligands bind within the largest cleft, suggesting size is a functional determinant.

Related Experiment Videos

  • Antibody-antigen interactions typically involve large antibody clefts for binding.
  • Protein-protein homodimer interfaces are often planar, though the largest cleft per subunit is frequently involved.

    • Conclusions:

    • Protein cleft size is a strong predictor of functional sites, particularly for enzyme active sites and antibody binding.
    • Geometric analysis can identify potential functional sites, but chemical interactions are sometimes necessary for precise localization.
    • Understanding cleft geometry aids in predicting protein interactions and functions.