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

Modeling of protein binary complexes using structural mass spectrometry data.

J K Amisha Kamal1, Mark R Chance

  • 1Center for Proteomics and Mass spectrometry, Case Western Reserve University School of Medicine, Cleveland, Ohio 44106, USA.

Protein Science : a Publication of the Protein Society
|November 29, 2007
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

Recommendations and considerations for hydroxyl radical protein footprinting-mass spectrometry.

Nature methods·2026
Same author

scProfiterole: Clustering of Single-Cell Proteomic Data Using Graph Contrastive Learning via Spectral Filters.

bioRxiv : the preprint server for biology·2026
Same author

What Does Next-Generation Mass Spectrometry Offer for Proteomics? A Comprehensive Platform Comparison.

Journal of proteome research·2026
Same author

Hydroxyl radical footprinting modification reveals an intradomain communication pathway in EFL1 disrupted by a Shwachman-Diamond syndrome-associated mutation.

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

Redox Stoichiometry at the Single-Residue Level Using Mass Spectrometry Reveals Dynamic Methionine Sulfoxide Speciation in Actin and Calmodulin during Brain Aging.

Journal of proteome research·2025
Same author

Structural exposure of different microtubule binding domains determines the propagation and toxicity of pathogenic tau conformers in Alzheimer's disease.

PLoS pathogens·2025
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

This study presents a novel method for modeling protein complex structures using mass spectrometry and molecular docking. Integrating footprinting data guides docking to accurately predict complex structures, even for previously uncharacterized complexes.

Area of Science:

  • Structural Biology
  • Biochemistry
  • Computational Biology

Background:

  • Determining the three-dimensional structure of protein complexes is crucial for understanding biological function.
  • Traditional methods like X-ray crystallography and NMR spectroscopy can be challenging for certain protein complexes.
  • Integrating experimental data with computational modeling offers a complementary approach to structural determination.

Purpose of the Study:

  • To develop and validate a general computational approach for modeling binary protein complex structures.
  • To integrate structural mass spectrometry data, specifically hydroxyl radical mediated oxidative protein footprinting, with molecular docking.
  • To improve the accuracy and reliability of computational models for protein-protein interactions.

Main Methods:

Related Experiment Videos

  • Hydroxyl radical mediated oxidative protein footprinting to identify protein-protein interaction interfaces and conformational changes.
  • Homology modeling to reconstruct individual protein structures when significant conformational changes occur upon binding.
  • Computational modeling using ClusPro, incorporating footprinting data as constraints in docking, energy filtering, and clustering steps.

Main Results:

  • Footprinting data, when used to guide molecular docking, significantly improves the accuracy of predicted protein complex structures.
  • Accurate structural models emerged as top-scoring solutions when docking was constrained by footprinting data, outperforming unguided docking.
  • The method was successfully applied to model known complexes, such as actin/gelsolin segment-1, and to generate a novel model for the actin/cofilin complex.

Conclusions:

  • The combined approach of structural mass spectrometry and guided molecular docking provides a powerful tool for modeling binary protein complexes.
  • This method enhances the accuracy of computational models by leveraging experimental data to refine docking predictions.
  • The approach is particularly valuable for studying complexes lacking high-resolution experimental structures, such as actin/cofilin.