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Non-Native Cooperative Interactions Modulate Protein Folding Rates.

Fernando Bruno da Silva1, Vinícius G Contessoto2, Vinícius M de Oliveira1

  • 1Department of Physics, Institute of Biosciences, Humanities and Exact Sciences , São Paulo State University (UNESP) , São José do Rio Preto - São Paulo 15054-000 , Brazil.

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Investigating anomalous protein folding rates in alpha-spectrin domains, this study reveals that non-native interactions, not internal friction, likely explain the rapid folding of R15 compared to R16 and R17.

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Area of Science:

  • Biophysics
  • Computational Biology
  • Structural Biology

Background:

  • Protein folding is often described by energy landscape theory.
  • Experimental data, such as alpha-spectrin domain folding rates, present anomalies not fully explained by current models.
  • The rapid folding of alpha-spectrin R15 compared to homologous R16 and R17 is a puzzling observation.

Purpose of the Study:

  • To investigate the underlying mechanisms behind the anomalous folding rates of alpha-spectrin domains.
  • To explore the role of non-native interactions in protein folding dynamics.
  • To provide a more satisfactory explanation for the observed differences in folding speeds.

Main Methods:

  • Utilized molecular dynamics simulations with structure-based Cα models.
  • Separately analyzed hydrophobic and electrostatic contributions to folding.
  • Investigated the effects of mutations in R16 and R17 domains.

Main Results:

  • Simulation folding times qualitatively agreed with experimental data.
  • Simulated folding times for R16 and R17 mutations correlated with experimental observations.
  • Identified a potential link between non-native interactions and internal friction.

Conclusions:

  • Non-native interactions, specifically their cooperativity, may be the primary cause of internal friction affecting protein folding rates.
  • The study offers a new perspective on understanding anomalous protein folding phenomena.
  • Findings challenge the sole reliance on internal friction as an explanation for such discrepancies.