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New insights into disordered proteins and regions according to the FOD-M model.

ABSTRACT: A collection of intrinsically disordered proteins (IDPs) having regions with the status of intrinsically disordered (IDR) according to the Disprot database was analyzed from the point of view of the structure of hydrophobic core in the structural unit (chain / domain). The analysis includes all the Homo Sapiens as well as Mus Musculus proteins present in the DisProt database for which the structure is available. In the analysis, the fuzzy oil drop modified model (FOD-M) was used, taking into account the external force field, modified by the presence of other factors apart from polar water, influencing protein structuring. The paper presents an alternative to secondary-structure-based classification of intrinsically disordered regions (IDR). The basis of our classification is the ordering of hydrophobic core as calculated by the FOD-M model resulting in FOD-ordered or FOD-unordered IDRs.

SUBMITTER: Roterman I

PROVIDER: S-EPMC9550084 | biostudies-literature | 2022

REPOSITORIES: biostudies-literature

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New insights into disordered proteins and regions according to the FOD-M model.

Roterman Irena I Stapor Katarzyna K Fabian Piotr P Konieczny Leszek L

PloS one 20221010 10

A collection of intrinsically disordered proteins (IDPs) having regions with the status of intrinsically disordered (IDR) according to the Disprot database was analyzed from the point of view of the structure of hydrophobic core in the structural unit (chain / domain). The analysis includes all the Homo Sapiens as well as Mus Musculus proteins present in the DisProt database for which the structure is available. In the analysis, the fuzzy oil drop modified model (FOD-M) was used, taking into acc ...[more]

PMID: 36215254

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Project description:Many disordered proteins function via binding to a structured partner and undergo a disorder-to-order transition. The coupled folding and binding can confer several functional advantages such as the precise control of binding specificity without increased affinity. Additionally, the inherent flexibility allows the binding site to adopt various conformations and to bind to multiple partners. These features explain the prevalence of such binding elements in signaling and regulatory processes. In this work, we report ANCHOR, a method for the prediction of disordered binding regions. ANCHOR relies on the pairwise energy estimation approach that is the basis of IUPred, a previous general disorder prediction method. In order to predict disordered binding regions, we seek to identify segments that are in disordered regions, cannot form enough favorable intrachain interactions to fold on their own, and are likely to gain stabilizing energy by interacting with a globular protein partner. The performance of ANCHOR was found to be largely independent from the amino acid composition and adopted secondary structure. Longer binding sites generally were predicted to be segmented, in agreement with available experimentally characterized examples. Scanning several hundred proteomes showed that the occurrence of disordered binding sites increased with the complexity of the organisms even compared to disordered regions in general. Furthermore, the length distribution of binding sites was different from disordered protein regions in general and was dominated by shorter segments. These results underline the importance of disordered proteins and protein segments in establishing new binding regions. Due to their specific biophysical properties, disordered binding sites generally carry a robust sequence signal, and this signal is efficiently captured by our method. Through its generality, ANCHOR opens new ways to study the essential functional sites of disordered proteins.

Dataset Information

New insights into disordered proteins and regions according to the FOD-M model.

Publications

New insights into disordered proteins and regions according to the FOD-M model.

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