Finite Size Effects in Protein Aggregation Simulations
Author Information
Author(s): Amol Pawar, Giorgio Favrin
Primary Institution: Department of Chemistry, University of Cambridge, Cambridge, United Kingdom
Hypothesis
How does the finite number of proteins affect the free energy landscape and stability of protein aggregation?
Conclusion
The study shows that the finite size effect significantly influences the stability of protein aggregates in simulations.
Supporting Evidence
- The study investigates how the number of proteins affects the free energy landscape.
- It highlights the importance of considering finite size effects in protein aggregation simulations.
- The results suggest that larger systems provide more reliable stability estimates.
Takeaway
When simulating proteins, having too few can make it hard to understand how they stick together, like trying to build a tower with only a few blocks.
Methodology
Simulations were performed using the ProFASi model with different numbers of peptides at constant concentration and varying temperatures.
Potential Biases
The finite size effect introduces systematic errors in estimates of stability and rates of formation of aggregates.
Limitations
The estimates of parameters in the finite size scaling analysis are broad and not very reliable due to limited data points.
Digital Object Identifier (DOI)
Want to read the original?
Access the complete publication on the publisher's website