Roles of the Stereochemical Code and the Entropic Index q in the Protein Folding Process: How to Map Out Folding Intermediate Conformations

Abstract

Background: Here, the inverse protein folding problem is approached from the viewpoint of the entropic index q. We present a brief overview of the problem. Further, we provide general information about the three-dimensional structure of proteins and the universal characteristics of the folding process. Methods: We explain how the stereochemical model was conceived. Our main objective is to change how Monte Carlo (MC) simulations are performed. We replace the Boltzmann weight with the Tsallis weight in order to achieve better sampling. This change leads to the q Monte Carlo method (MCq). There are two main ways to employ the index q: one is to set it as a fixed parameter (MCq*), and the other is to set it as an autonomous variable associated with the instantaneous molecular radius of gyration, a feature that is allowed by the Beck-Cohen superstatistics. In addition, we propose a meaningful physical interpretation for the index q. Furthermore, we explain how to assemble amino acid sequences for the inverse problem. Results: We present several results and discuss the implications associated with the MC and MCq methods. The latter method is an efficient approach to tracking down folding intermediate conformations, which can enable us to better find and define folding pathways for successive configurations of a polymeric chain kept in solution at the same macroscale temperature, T. Conclusion: We have explained how and why protein kinetics becomes significantly more advantageous when we employ q ≠ 1. However, this is only possible if we set the correct upper value of qmax.