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Sedimentation Equilibrium of a Small Oligomer-forming Membrane Protein: Effect of Histidine Protonation on Pentameric Stability
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A pH-Dependent Coarse-Grained Model for Disordered Proteins: Histidine Interactions Modulate Conformational

Rivka Calinsky1, Yaakov Levy1

  • 1Department of Chemical and Structural Biology, Weizmann Institute of Science, Rehovot 76100, Israel.

The Journal of Physical Chemistry Letters
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Modeling histidine (His) in disordered proteins is challenging due to its neutral (His0) and charged (His+) states. Our new model accurately captures these states, revealing critical His0 interactions for protein compaction at high pH.

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Area of Science:

  • Biophysics
  • Computational Biology
  • Protein Science

Background:

  • Histidine's dual charge states (neutral His0 and charged His+) complicate modeling of intrinsically disordered proteins (IDPs).
  • Existing coarse-grained (CG) models often use an averaged histidine charge, neglecting crucial short-range interactions.
  • These interactions, including cation-π, π-π, and charge-charge, are vital for understanding protein structure and function.

Purpose of the Study:

  • To develop an improved coarse-grained model for intrinsically disordered proteins that explicitly accounts for both histidine charge states.
  • To investigate the impact of neutral histidine (His0) interactions on the conformational properties of histidine-rich IDPs.

Main Methods:

  • Development of the IDPH model, a 21-amino acid coarse-grained model incorporating both His0 and His+ states.
  • Simulations of histidine-rich IDPs (Histatin-5, CPEB4) using the IDPH model at varying pH conditions.

Main Results:

  • The IDPH model demonstrates that His0 interactions significantly influence the compaction of histidine-rich IDPs, particularly at high pH.
  • His0-His0 and His0-Arg interactions were identified as key contributors to structural stabilization.
  • These findings highlight the importance of including the neutral histidine state in protein modeling.

Conclusions:

  • Accurate modeling of intrinsically disordered proteins requires explicit consideration of both histidine charge states.
  • The IDPH model provides a more refined approach to simulating histidine-containing IDPs, improving predictions of their conformational behavior.
  • Neglecting His0 interactions leads to inaccuracies, especially in understanding protein behavior at physiological or high pH conditions.