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Ignacio Retamal-Farfán1,2, Jorge González-Higueras1,2, Pablo Galaz-Davison1,2

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Metamorphic proteins like RfaH and KaiB can switch between distinct structures. Simplified models reveal their complex refolding pathways, aiding experimental design.

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Area of Science:

  • Protein folding and biophysics
  • Computational biology
  • Structural biology

Background:

  • Metamorphic proteins exhibit multiple stable structures on a single amino acid sequence.
  • These proteins interconvert between states reversibly in response to environmental cues.
  • Studying these large-scale structural rearrangements is computationally and experimentally challenging.

Purpose of the Study:

  • To investigate the refolding landscapes of metamorphic proteins RfaH and KaiB.
  • To utilize simplified dual-basin structure-based models (SBMs) for studying protein fold-switching.
  • To explore the energy landscape theory and minimal frustration principles in protein folding.

Main Methods:

  • Development and application of coarse-grained, dual-basin structure-based models (SBMs).
  • Extraction of native contacts and bonded interactions from experimental structures.
  • Calibration of SBMs for reversible fold-switching simulations using molecular dynamics.
  • Integration of energy landscape theory and minimal frustration principles.

Main Results:

  • Successfully generated and calibrated dual-basin SBMs for RfaH and KaiB.
  • Explored the reversible fold-switch mechanism of these metamorphic proteins.
  • Obtained insights into conformational ensembles and refolding routes.

Conclusions:

  • Simplified SBMs provide a computationally efficient approach to study metamorphic protein dynamics.
  • Simulation insights can guide experimental design and validation.
  • This work advances the understanding of protein folding and structural plasticity.