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Related Experiment Video

Updated: May 7, 2026

Investigating Protein Sequence-structure-dynamics Relationships with Bio3D-web
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Modeling Structural Flexibility of Proteins with Go-Models.

Ping Jiang1, Ulrich H E Hansmann

  • 1Department of Chemistry and Biochemistry, University of Oklahoma, Norman, OK 73019-5251, USA.

Journal of Chemical Theory and Computation
|September 17, 2013
PubMed
Summary

Flexible protein models reveal subtle dynamics in Menkes disease mutations. New Go-models capture transient unfolding in ATP7A mutants, suggesting disease mechanisms.

Area of Science:

  • Computational Biology
  • Protein Folding Dynamics
  • Structural Bioinformatics

Background:

  • Structure-based protein folding models (Go-models) offer efficiency but often lack structural flexibility due to reliance on single target structures.
  • This limitation can hinder the detection of subtle, mutation-induced changes in protein dynamics, crucial for understanding diseases like Menkes disease.

Purpose of the Study:

  • To develop and implement flexible Go-models that incorporate Nuclear Magnetic Resonance (NMR) ensemble data.
  • To investigate the impact of the A629P mutation on the dynamics and folding pathways of the Menkes protein ATP7A.

Main Methods:

  • Introduced three novel implementations of Go-models that account for protein flexibility using NMR ensembles.
  • Compared the folding behavior of wild-type ATP7A and its A629P mutant using these enhanced Go-models.

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  • Analyzed the resulting conformational distributions and identified differences in folding pathways.

    • Main Results:

    • The flexible Go-models produced broader conformational distributions compared to traditional single-structure Go-models.
    • Detected transient unfolding of a β1β4-sheet in the A629P mutant, a finding consistent with all-atom simulations.
    • Observed differences in folding pathways between wild-type and mutant proteins, not previously accessible with standard methods.

    Conclusions:

    • Flexible Go-models are effective in capturing subtle protein dynamics and uncovering transient structural events.
    • The findings suggest a potential mechanism for Menkes disease caused by the A629P mutation in ATP7A.
    • Enhanced Go-models provide a valuable tool for studying mutation effects on protein folding and dynamics.