Model of Early Stage Intermediate in Respect to Its Final Structure.

Piotr Fabian,Katarzyna Stapor,Irena Roterman

doi:10.3390/biom9120866

Piotr Fabian, Katarzyna Stapor + Show 1 more

Open Access

https://doi.org/10.3390/biom9120866

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Abstract

The model, describing a method of determining the structure of an early intermediate in the process of protein folding to analyze nonredundant PDB protein bases, allows determining the relationship between the sequence of tetrapeptides and their structural forms expressed by structural codes. The contingency table expressing such a relationship can be used to predict the structure of polypeptides by proposing a structural form with a precision limited to the structural code. However, by analyzing structural forms in native forms of proteins based on the fuzzy oil drop model, one can also determine the status of polypeptide chain fragments with respect to the assumptions of this model. Whether the probability distributions for both compliant and noncompliant forms were similar or whether the tetrapeptide sequences showed some differences at a level of a set of structural codes was investigated. The analysis presented here indicated that some sequences in both forms revealed differences in probability distributions expressed as a negative statistically significant correlation coefficient. This meant that the identified sections (tetrapeptides) took different forms against the fuzzy oil drop model. It may suggest that the information of the final status with respect to hydrophobic core formation is already carried by the structure of the early-stage intermediate.

Highlights

The protein folding process is seen as a multistage process [1,2,3,4,5,6,7,8]
Positive values of statistically significant correlation coefficients were obtained. This means that specific systems expressed by structural codes occurred in a similar way, both in areas built in protein molecules according to the principle of the spherical micelle and in areas that were recognized as inconsistent with the assumptions
The analysis showed that the synergy that must take place in order to generate a hydrophobic nucleus, of which the structure consisted of relevant chain sections, did not have its mapping in the structure of the early intermediate

Summary

Introduction

For homologous proteins the methods predicting the structure of proteins are based on the so-called comparative modeling (Darwinian model) [9] Using this technique, a starting structure for the energy minimization procedure is constructed based on the similarity of homologous proteins [9,10,11,12]. Other techniques—based on the so-called ab initio model—tend to obtain an initial starting structure for the energy minimization procedure using the so-called coarse-grained model [14,15,16,17]. The introduction of this model dramatically reduces the number of degrees of freedom and makes it easier to search the conformational space in a much shorter computational time. The large number of proposals obtained in this way is subjected to a clustering procedure leading to a reduction in the number of candidates [18,19,20]

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