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 conformational switches in proteins.

M Young1, K Kirshenbaum, K A Dill

  • 1Department of Pharmaceutical Chemistry, University of California, San Francisco 94143-0446, USA.

Protein Science : a Publication of the Protein Society
|September 24, 1999
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

Driving forces in the origins of life.

Open biology·2021
Same author

Link between spin fluctuations and electron pairing in copper oxide superconductors.

Nature·2011
Same author

Modeling stochastic dynamics in biochemical systems with feedback using maximum caliber.

The journal of physical chemistry. B·2011
Same author

Superconductivity at 23 K in Pt doped BaFe₂As₂ single crystals.

Journal of physics. Condensed matter : an Institute of Physics journal·2011
Same author

Dynamical fluctuations in biochemical reactions and cycles.

Physical review. E, Statistical, nonlinear, and soft matter physics·2011
Same author

Computer simulations of ionenes, hydrophobic ions with unusual solution thermodynamic properties. The ion-specific effects.

The journal of physical chemistry. B·2009
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

A new computational method, Ambivalent Structure Predictor (ASP), identifies protein conformational switches from amino acid sequences. This tool accurately predicts functionally important regions involved in protein backbone rearrangements.

Area of Science:

  • Computational biology
  • Protein structure prediction
  • Bioinformatics

Background:

  • Protein conformational flexibility is crucial for function.
  • Identifying regions prone to conformational switching is challenging without experimental structural data.

Purpose of the Study:

  • To develop a computational technique for predicting protein conformational switches.
  • To identify regions of conformational ambivalence in protein sequences.

Main Methods:

  • The Ambivalent Structure Predictor (ASP) method was developed.
  • ASP analyzes secondary structure prediction results to find ambivalent regions.
  • The method was tested on 16 protein sequences with known conformational switches and 3 negative controls.

Related Experiment Videos

Main Results:

  • ASP correctly identified all known conformational switch sites in the test set as structurally ambivalent regions.
  • No ambivalent regions were predicted in the negative control sequences.
  • The method demonstrates high accuracy in pinpointing functionally relevant flexible regions.

Conclusions:

  • ASP is a novel computational tool for predicting protein conformational switches from amino acid sequences.
  • The method can guide experimental studies on protein function and dynamics, especially when 3D structural data is limited.