Kozielewicz lab - On the need to introduce environmental

Journal article

I. Roterman, A. Sieradzan, K. Stapor, P. Fabian, P. Wesołowski, L. Konieczny
Journal of Molecular Graphics and Modelling, 2022

Semantic Scholar DOI PubMed

Cite

APA Click to copy
Roterman, I., Sieradzan, A., Stapor, K., Fabian, P., Wesołowski, P., & Konieczny, L. (2022). On the need to introduce environmental characteristics in ab initio protein structure prediction using a coarse-grained UNRES force field. Journal of Molecular Graphics and Modelling.

Chicago/Turabian Click to copy
Roterman, I., A. Sieradzan, K. Stapor, P. Fabian, P. Wesołowski, and L. Konieczny. “On the Need to Introduce Environmental Characteristics in Ab Initio Protein Structure Prediction Using a Coarse-Grained UNRES Force Field.” Journal of Molecular Graphics and Modelling (2022).

MLA Click to copy
Roterman, I., et al. “On the Need to Introduce Environmental Characteristics in Ab Initio Protein Structure Prediction Using a Coarse-Grained UNRES Force Field.” Journal of Molecular Graphics and Modelling, 2022.

BibTeX Click to copy

@article{i2022a,
  title = {On the need to introduce environmental characteristics in ab initio protein structure prediction using a coarse-grained UNRES force field.},
  year = {2022},
  journal = {Journal of Molecular Graphics and Modelling},
  author = {Roterman, I. and Sieradzan, A. and Stapor, K. and Fabian, P. and Wesołowski, P. and Konieczny, L.}
}

Abstract

During the protein folding process in computer simulations involving the use of a United RESidue (UNRES) force field, an additional module was introduced to represent directly the presence of a polar solvent in water form. This module implements the fuzzy oil drop model (FOD) where the 3D Gauss function expresses the presence of a polar environment which directs the polypeptide chain folding process towards the generation of a centric hydrophobic core. Sample test polypeptide chains of 8 proteins with chain lengths ranging from 37 to 75 aa were simulated in silico using the UNRES (U) package with an implicit solvent model and a built-in module expressing the FOD model (UNRES-FOD-UNRES (U + F) interleaved simulation). The protein structure obtained by both *** simulation schemes, i.e., accordingly***U and U + F, for all the analyzed protein models shows the presence of a hydrophobic core including where it is absent in the native structure. The proposed FOD-M model (M-modified) explaining the source of this phenomenon reveals the need to modify the external field expressing the role of a folding environment. The modification takes into account the influence of other than polar factors present in the folding environment.