On the need to introduce environmental characteristics in ab initio protein structure prediction using a coarse-grained UNRES force field.
J Mol Graph Model
; 114: 108166, 2022 07.
Article
em En
| MEDLINE
| ID: mdl-35325843
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.
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Base de dados:
MEDLINE
Assunto principal:
Proteínas
/
Dobramento de Proteína
Idioma:
En
Ano de publicação:
2022
Tipo de documento:
Article