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Area of Science:

  • Biophysics
  • Computational Chemistry
  • Protein Dynamics

Background:

  • Protein folding is a complex process occurring over multiple timescales.
  • Non-Markovian effects, where past events influence future dynamics, are known in short-timescale protein folding.
  • The influence of memory-dependent friction on long-timescale protein folding kinetics remains unclear.

Purpose of the Study:

  • To investigate the role of memory-dependent friction in long-timescale protein folding kinetics.
  • To determine how changes in pH affect friction and protein folding dynamics.
  • To identify the microscopic origins of non-Markovian friction in protein folding.

Main Methods:

  • Utilized friction memory-kernel extraction techniques.
  • Analyzed extensive all-atom simulations of the α3D protein.
  • Compared folding kinetics under neutral and reduced pH conditions.

Main Results:

  • Reduced pH significantly decreases the friction memory decay time for the α3D protein.
  • This pH-induced change switches folding kinetics from a non-Markovian to a Markovian regime.
  • Elimination of salt-bridge interactions under reduced pH was identified as a key factor causing non-Markovian friction.

Conclusions:

  • Memory effects, particularly friction memory decay time, play a crucial role in protein folding kinetics.
  • pH-dependent friction significantly impacts the transition between non-Markovian and Markovian folding regimes.
  • Salt-bridge interactions are a critical microscopic determinant of non-Markovian friction in protein folding.