On the need to introduce environmental characteristics in ab initio protein structure prediction using a coarse-grained UNRES force field

Roterman, Irena; Sieradzan, Adam K.; Stąpor, Katarzyna; Fabian, Piotr; Wesołowski, Patryk; Konieczny, Leszek

doi:10.1016/j.jmgm.2022.108166

Cited by 16 publications

(20 citation statements)

References 52 publications

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“…Bipolar amino acids reproduce the structure of micelles to a limited extent, depending on the ability of the amino acid sequence to achieve such an order. These conditions are changed by factors such as the amphipathic membrane or the specificity of the periplasmic environment . The diversity resulting from the variability of amino acid sequences is complemented not only by the diversity of the environment in the form of an external force field provided by the changed water characteristics (pH, ionic strength) but also by the presence of other molecules affecting the folding processprefoldin, chaperones, or chaperonins. , These molecules act periodically to support the folding process at a specific stage.…”

Section: Discussionmentioning

confidence: 99%

Hydrophobicity-Based Force Field In Enzymes

Roterman,

Konieczny,

Stapor

et al. 2024

ACS Omega

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The biocatalysis process takes place with the participation of enzymes, which, depending on the reaction carried out, require, apart from the appropriate arrangement of catalytic residues, an appropriate external force field. It is generated by the protein body. The relatively small size of the part directly involved in the process itself is supported by the presence of an often complex structure of the protein body, the purpose of which is to provide an appropriate local force field, eliminating the influence of water. Very often, the large size of the enzyme is an expression of the complex form of this field. In this paper, a comparative analysis of arbitrarily selected enzymes, representatives of different enzyme classes, was carried out, focusing on the measurement of the diversity of the force field provided by a given protein. This analysis was based on the fuzzy oil drop model (FOD) and its modified version (FOD-M), which takes into account the participation of nonaqueous external factors in shaping the structure and thus the force field within the protein. The degree and type of ordering of the hydrophobicity distribution in the protein molecule is the result of the influence of the environment but also the supplier of the local environment for a given process, including the catalysis process in particular. Determining the share of a nonaqueous environment is important due to the ubiquity of polar water, whose participation in processes with high specificity requires control. It can be assumed that some enzymes in their composition have a permanently built-in part, the role of which is reduced to that of a permanent chaperone. It provides a specific external force field needed for the process. The proposed model, generalized to other types of proteins, may also provide a form of recording the environment model for the simulation of the in silico protein folding process, taking into account the impact of its differentiation.

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Section: Discussionmentioning

confidence: 99%

Hydrophobicity-Based Force Field In Enzymes

Roterman,

Konieczny,

Stapor

et al. 2024

ACS Omega

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“…The FOD model and its modified version (FOD‐M—taking into account the external conditions) can be applied to any protein under consideration. This statement is based on the analysis of the large number of proteins, structures of which were also interpreted with respect to their biological activity, namely the down‐hill, fast‐folding, ultra‐fast‐folding and antifreeze proteins, 21,22 intrinsically disordered proteins, 90 membrane 91–94 and amyloid proteins, 95–97 as well as when studying for example the influence of mutation, 8 complexation 98 or simulation of protein forlding process 99 . FOD model can help to answer many questions depending on the aim of the research.…”

Section: Discussionmentioning

confidence: 99%

New insights on the catalytic center of proteins from peptidylprolyl isomerase group based on the FOD‐M model

Roterman

Stąpor

Konieczny

2023

J of Cellular Biochemistry

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Generating the structure of the hydrophobic core is based on the orientation of hydrophobic residues towards the central part of the protein molecule with the simultaneous exposure of polar residues. Such a course of the protein folding process takes place with the active participation of the polar water environment. While the self‐assembly process leading to the formation of micelles concerns freely moving bi‐polar molecules, bipolar amino acids in polypeptide chain have limited mobility due to the covalent bonds. Therefore, proteins form a more or less perfect micelle‐like structure. The criterion is the hydrophobicity distribution, which to a greater or lesser extent reproduces the distribution expressed by the 3D Gaussian function on the protein body. The vast majority of proteins must ensure solubility, so a certain part of it—as it is expected—should reproduce the structuring of micelles. The biological activity of proteins is encoded in the part that does not reproduce the micelle‐like system. The location and quantitative assessment of the contribution of orderliness to disorder is of critical importance for the determination of biological activity. The form of maladjustment to the 3D Gauss function may be varied—hence the obtained high diversity of specific interactions with strictly defined molecules: ligands or substrates. The correctness of this interpretation was verified on the basis of the group of enzymes Peptidylprolyl isomerase—E.C.5.2.1.8. In proteins representing this class of enzymes, zones responsible for solubility—micelle‐like hydrophobicity system—the location and specificity of the incompatible part in which the specific activity of the enzyme is located and coded were identified. The present study showed that the enzymes of the discussed group show two different schemes of the structure of catalytic center (taking into account the status as defined by the fuzzy oil drop model).

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“…The values of 0.4 > K > 0.0 in globular proteins prove a different degree of influence on the structuring of proteins of external factors. The identification of specificity identified in a periplasmic protein expressed by K = 0.6 also suggests the possibility of the universal character of the FOD-M model [ 70 ].…”

Section: Discussionmentioning

confidence: 99%

Connexins and Pannexins—Similarities and Differences According to the FOD-M Model

et al. 2022

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Connexins and pannexins are the transmembrane proteins of highly distinguished biological activity in the form of transport of molecules and electrical signals. Their common role is to connect the external environment with the cytoplasm of the cell, while connexin is also able to link two cells together allowing the transport from one to another. The analysis presented here aims to identify the similarities and differences between connexin and pannexin. As a comparative criterion, the hydrophobicity distribution in the structure of the discussed proteins was used. The comparative analysis is carried out with the use of a mathematical model, the FOD-M model (fuzzy oil drop model in its Modified version) expressing the specificity of the membrane’s external field, which in the case of the discussed proteins is significantly different from the external field for globular proteins in the polar environment of water. The characteristics of the external force field influence the structure of protein allowing the activity in a different environment.

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On the need to introduce environmental characteristics in ab initio protein structure prediction using a coarse-grained UNRES force field

Cited by 16 publications

References 52 publications

Hydrophobicity-Based Force Field In Enzymes

Hydrophobicity-Based Force Field In Enzymes

New insights on the catalytic center of proteins from peptidylprolyl isomerase group based on the FOD‐M model

Connexins and Pannexins—Similarities and Differences According to the FOD-M Model

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