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Dramatic Shape Changes Occur as Cytochrome c Folds.

Serdal Kirmizialtin1, Felicia Pitici2, Alfredo E Cardenas3

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|August 26, 2020
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Summary
This summary is machine-generated.

Simulations reveal cytochrome c folding intermediates and sequential mechanisms. This protein folding involves dramatic shape changes, aligning with experimental data and suggesting universal characteristics for globular proteins.

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Area of Science:

  • Biophysics
  • Computational Biology
  • Protein Folding

Background:

  • Cytochrome c (Cyt c) is a well-studied small protein ideal for atomic simulations.
  • Understanding protein folding pathways and timescales is crucial for molecular biology.
  • Previous experimental studies provide a basis for computational validation.

Purpose of the Study:

  • To quantitatively characterize structural transitions and folding timescales of Cyt c using atomic simulations.
  • To identify folding intermediates and mechanisms by analyzing folding trajectories.
  • To compare simulation results with time-resolved small-angle X-ray scattering (SAXS) experiments.

Main Methods:

  • Atomically detailed folding trajectories generated using stochastic difference equations.
  • Calculation of time-dependent small-angle X-ray scattering (SAXS) profiles from simulation data.
  • Analysis of structural changes, including compaction and sphericity, during folding.

Main Results:

  • Excellent agreement between simulated and experimental time-dependent SAXS spectra.
  • Identification of folding intermediates, supporting a sequential folding mechanism for Cyt c.
  • Demonstration of dramatic changes in shape from a prolate ellipsoid to a sphere during folding.
  • Coincidence of hydrophobic collapse and amide group protection around 100 microseconds.

Conclusions:

  • Simulations accurately reproduce experimental SAXS data, validating the folding pathway.
  • Cyt c folding proceeds via a sequential mechanism involving significant structural rearrangement.
  • Protein compaction and shape change are proposed as universal features of globular protein folding.