Affiliation:
1. Jagiellonian University - Medical College
2. Silesian University of Technology
Abstract
Abstract
Background
Recently, significant progress has been made in the field of protein structure prediction by application of artificial intelligence techniques, as shown by the results of the CASP13 and CASP14 (Critical Assessment of Structure Prediction) competition. However, the question of the mechanism behind the protein folding process itself remains unanswered. Correctly predicting the structure also does not solve the problem of, for example, amyloid proteins, where a polypeptide chain with an unaltered sequence adopts a different 3D structure.
Results
This work was an attempt at explaining structural variation by considering the contribution of the environment to protein structuring. The application of the fuzzy oil drop (FOD) model to assess the validity of the selected models provided in the CASP13, CASP14 and CASP15 projects reveals the need for an environmental factor to determine the 3D structure of proteins. Consideration of the external force field in the form of polar water (FOD) and a version modified by the presence of the hydrophobic factor, FOD-M reveals that the protein folding process is environmentally dependent. An analysis of selected models from the CASP competitions indicates the need for structure prediction as dependent on consideration of the protein folding environment.
Conclusions
The conditions governed by the environment direct the protein folding process occurring in the certain environment. Therefore, the variation of the external force field should be taken into account in the models used in protein structure prediction.
Publisher
Research Square Platform LLC