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Analysis of Protein Folding, Transport, and Degradation in Living Cells by Radioactive Pulse Chase
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Analysis of Protein Folding, Transport, and Degradation in Living Cells by Radioactive Pulse Chase

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Nonnative contact effects in protein folding.

Qiang Shao1, Weiliang Zhu

  • 1Drug Discovery and Design Center, CAS Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai, 201203, China. qshao@simm.ac.cn.

Physical Chemistry Chemical Physics : PCCP
|May 29, 2019
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Summary
This summary is machine-generated.

Protein folding mechanisms were explored using molecular dynamics (MD) simulations. Non-native contacts significantly influence protein folding thermodynamics and kinetics by affecting secondary structure formation barriers.

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Area of Science:

  • Biophysics
  • Computational Biology
  • Protein Science

Background:

  • Understanding protein folding is crucial for molecular biology.
  • Experimental and simulation methods face challenges in measuring folding events.
  • Protein folding involves secondary and tertiary structure formation and non-native contacts.

Purpose of the Study:

  • To explore protein folding mechanisms using enhanced sampling MD simulations.
  • To analyze free energy landscapes and identify folding pathways.
  • To investigate the role of non-native contacts in protein folding.

Main Methods:

  • Enhanced sampling molecular dynamics (MD) simulations were performed for three proteins: NTL9, NuG2b, and CspA.
  • Analysis of minimum free energy paths on multi-dimensional free energy landscapes.
  • Quantitative analysis of nucleation-condensation folding mechanism and non-native contacts.

Main Results:

  • Simulations align with existing experimental and computational data.
  • Nucleation-condensation folding mechanism observed, with concurrent secondary and tertiary structure formation.
  • Non-native contacts were prevalent, influencing secondary structure formation free-energy barriers and rate-limiting steps.

Conclusions:

  • Native contacts dictate the protein folding pathway and mechanism.
  • Non-native contacts are critical in determining folding thermodynamics by modulating free energy of secondary structure element formation.
  • The study provides insights into the complex interplay of native and non-native interactions in protein folding.