What is it about?
When dealing with the protein folding process, degrees of freedom matters. We see the entropic index q as a dial; it allows us to tune physical degrees of freedom and statistical degrees of freedom. When we perform q Monte Carlo simulations (MCq), the index q allows us to map out folding intermediate conformations. We believe such aspect can help us to shed light upon folding pathways. In other words, such aspect can elucidate how a small globular protein folds and how it finds its native structure within finite intervals of time.
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Why is it important?
From Beck-Cohen superstatistics viewpoint, we exchanged the thermal fluctuation in the solvent medium (macroscale) with the hypothesis of local thermal fluctuations happening in the molecule in contact with the solvent (microscale). This choice allows us to propose a plausible physical interpretation to the entropic index q, and it enables us to get more precision to our data. In addition, we believe MCq approach can be extended to other finite chain-solvent systems like, for instance, DNA-solvent and RNA-solvent systems and then map out their behavior. In short, MCq allows us to better understand the behavior of polymers in solution.
Perspectives
I wrote this review article as a way to present a convincing discussion about MCq method. In short, I show what MCq can do for the inverse protein folding problem, how and why. In addition, I explained results presented earlier in other publications. I believe the presented discussion can be useful for other researchers/students working in the same field and correlated fields of research.
João Paulo Dal Molin
Read the Original
This page is a summary of: Roles of the Stereochemical Code and the Entropic Index q in the
Protein Folding Process: How to Map Out Folding Intermediate
Conformations, Current Physical Chemistry, July 2023, Bentham Science Publishers,
DOI: 10.2174/1877946813666230220115356.
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