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

Dynamic structure of subtilisin-eglin c complex studied by normal mode analysis

H Ishida1, Y Jochi, A Kidera

  • 1Department of Chemistry, Graduate School of Science, Kyoto University, Japan.

Proteins
|August 26, 1998
PubMed
Summary

Normal mode analysis reveals how subtilisin-eglin c complex dynamics facilitate binding. The enzyme and inhibitor exhibit correlated motions that maximize flexibility and minimize entropy loss, explaining experimental binding observations.

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

[Knowing similarity in protein 3D structure].

Tanpakushitsu kakusan koso. Protein, nucleic acid, enzyme·2002
Same author

Dynamical transition of myoglobin in a crystal: comparative studies of X-ray crystallography and Mössbauer spectroscopy.

European biophysics journal : EBJ·2001
Same author

Environmental influence on electron scattering from a molecule.

Acta crystallographica. Section A, Foundations of crystallography·2001
Same author

Physicochemical evaluation of protein folds predicted by threading.

European biophysics journal : EBJ·2001
Same author

Human ABCA1 contains a large amino-terminal extracellular domain homologous to an epitope of Sjögren's Syndrome.

Biochemical and biophysical research communications·2001
Same author

Vibrational energy transfer in a protein molecule.

Physical review letters·2000

Area of Science:

  • Biophysics
  • Computational Biology
  • Enzymology

Background:

  • Protein-protein interactions are crucial in biological systems.
  • Understanding the dynamics of enzyme-inhibitor complexes is key to drug design.
  • Subtilisin-eglin c complex serves as a model system for studying binding interfaces.

Purpose of the Study:

  • To investigate the dynamic mechanisms at the interface of the subtilisin-eglin c complex.
  • To analyze the interplay between internal molecular motions and external rigid-body movements.
  • To correlate dynamic properties with observed thermodynamic changes upon binding.

Main Methods:

  • Normal Mode Analysis (NMA) was employed to calculate the vibrational modes of the complex.
  • The calculated normal modes were decomposed into internal molecular deformations and external rigid-body motions.

Related Experiment Videos

  • Correlations between different types of motions were analyzed at the interface regions.

    • Main Results:

    • A negative correlation was observed between internal and external motions within each molecule, reducing interfacial motion amplitudes.
    • A positive correlation was found between the external motions of the enzyme and inhibitor, minimizing interference.
    • These coupled dynamics allow for greater motional freedom at the binding interface.

    Conclusions:

    • The dynamic structure of the subtilisin-eglin c complex contributes significantly to the binding process.
    • The observed motional correlations explain the large entropy gain upon binding, beyond hydrophobic interactions.
    • This study highlights the importance of considering molecular dynamics in understanding protein complex formation and stability.