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Origin of subdiffusions in proteins: Insight from peptide systems
Chenliang Xia1, Xuefeng He1, Jun Wang1
1School of Physics, Nanjing University, Nanjing 210093, People's Republic of China and National Laboratory of Solid State Microstructure, and Collaborative Innovation Center of Advanced Microstructures, Nanjing University, Nanjing 210093, People's Republic of China.
Physical Review. E
|January 20, 2021
Summary
Subdiffusion in peptides arises from distinct mechanisms. Flexible peptides show subdiffusion due to energy landscape traps, while helical peptides exhibit it via fractal topology, highlighting diverse kinetic scenarios.
Area of Science:
- Biophysics
- Computational Chemistry
- Protein Dynamics
Background:
- Subdiffusive kinetics are commonly observed in protein and peptide systems.
- Understanding the underlying mechanisms of subdiffusion is crucial for diverse protein interactions.
Purpose of the Study:
- To investigate the mechanisms of subdiffusion in two model peptides.
- To explore the relationship between peptide interactions and subdiffusive behavior.
- To differentiate the kinetic scenarios leading to similar subdiffusion patterns.
Main Methods:
- Simulating long trajectories of two model peptides.
- Analyzing free-energy profiles and subdiffusive kinetics.
- Employing hierarchical plateau analysis on mean square displacement.
- Generating transition networks between peptide conformations.
Main Results:
- Identified distinct subdiffusion mechanisms for flexible and helical peptides.
- Flexible peptide subdiffusion is linked to energy landscape trap depth distribution.
- Helical peptide subdiffusion is attributed to fractal topology of local minima.
- Transition network analysis confirmed distinct kinetic scenarios.
Conclusions:
- Peptide subdiffusion mechanisms are diverse and depend on energy landscape characteristics.
- Energy landscape topology and trap distribution significantly influence protein kinetics.
- Disordered peptides' subdiffusion is affected by trap depth, while structural proteins' kinetics depend on landscape topology.
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