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Intermediate heterogeneity modulates coupling between chain compaction and structure formation during protein

Anushka Kaushik1, Jayant B Udgaonkar1

  • 1Department of Biology, Indian Institute of Science Education and Research, Pune, India.

Protein Science : a Publication of the Protein Society
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Summary

Protein folding involves chain compaction and structure formation. This study shows that intermediate-state heterogeneity, influenced by backbone rigidity, allows independent control over compaction and structure formation during protein folding.

Keywords:
backbone rigiditychain compactionfolding intermediatesmaximum entropy methodprotein foldingstructural heterogeneitytime‐resolved FRET

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Area of Science:

  • Biochemistry
  • Structural Biology
  • Protein Dynamics

Background:

  • Polypeptide chains fold through compaction and structure formation.
  • The mechanistic coupling between these processes during protein folding is not fully understood.
  • Sequence-encoded constraints may regulate chain collapse and later folding stages.

Purpose of the Study:

  • To investigate the coupling between chain compaction and structure formation during protein folding.
  • To determine if sequence-encoded structural constraints regulate this coupling.
  • To examine the role of intermediate-state heterogeneity in protein folding.

Main Methods:

  • Studied the folding of the small protein monellin.
  • Utilized time-resolved fluorescence resonance energy transfer (TR-FRET).
  • Analyzed data with the maximum entropy method to resolve molecular sub-populations.

Main Results:

  • Mutations relieving backbone rigidity (Pro41Ala, Pro93Ala) stabilized minor conformations.
  • These minor conformations were more compact than major ones.
  • Stabilization of minor conformations increased chain contraction without affecting structure formation, decoupling the processes.

Conclusions:

  • Intermediate-state heterogeneity in protein folding is modifiable by backbone rigidity.
  • This heterogeneity provides a basis for tunable coupling between chain compaction and structure formation.
  • Sub-populations can undergo chain contraction independently of structure formation.