Cargando…

Computational analysis of regulatory regions in human protein kinases

Eukaryotic proteins often feature modular domain structures comprising globular domains that are connected by linker regions and intrinsically disordered regions that may contain important functional motifs. The intramolecular interactions of globular domains and nonglobular regions can play critica...

Descripción completa

Detalles Bibliográficos
Autores principales: Pei, Jimin, Cong, Qian
Formato: Online Artículo Texto
Lenguaje:English
Publicado: John Wiley & Sons, Inc. 2023
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10503413/
https://www.ncbi.nlm.nih.gov/pubmed/37632170
http://dx.doi.org/10.1002/pro.4764
_version_ 1785106519929389056
author Pei, Jimin
Cong, Qian
author_facet Pei, Jimin
Cong, Qian
author_sort Pei, Jimin
collection PubMed
description Eukaryotic proteins often feature modular domain structures comprising globular domains that are connected by linker regions and intrinsically disordered regions that may contain important functional motifs. The intramolecular interactions of globular domains and nonglobular regions can play critical roles in different aspects of protein function. However, studying these interactions and their regulatory roles can be challenging due to the flexibility of nonglobular regions, the long insertions separating interacting modules, and the transient nature of some interactions. Obtaining the experimental structures of multiple domains and functional regions is more difficult than determining the structures of individual globular domains. High‐quality structural models generated by AlphaFold offer a unique opportunity to study intramolecular interactions in eukaryotic proteins. In this study, we systematically explored intramolecular interactions between human protein kinase domains (KDs) and potential regulatory regions, including globular domains, N‐ and C‐terminal tails, long insertions, and distal nonglobular regions. Our analysis identified intramolecular interactions between human KDs and 35 different types of globular domains, exhibiting a variety of interaction modes that could contribute to orthosteric or allosteric regulation of kinase activity. We also identified prevalent interactions between human KDs and their flanking regions (N‐ and C‐terminal tails). These interactions exhibit group‐specific characteristics and can vary within each specific kinase group. Although long‐range interactions between KDs and nonglobular regions are relatively rare, structural details of these interactions offer new insights into the regulation mechanisms of several kinases, such as HASPIN, MAPK7, MAPK15, and SIK1B.
format Online
Article
Text
id pubmed-10503413
institution National Center for Biotechnology Information
language English
publishDate 2023
publisher John Wiley & Sons, Inc.
record_format MEDLINE/PubMed
spelling pubmed-105034132023-10-01 Computational analysis of regulatory regions in human protein kinases Pei, Jimin Cong, Qian Protein Sci Research Articles Eukaryotic proteins often feature modular domain structures comprising globular domains that are connected by linker regions and intrinsically disordered regions that may contain important functional motifs. The intramolecular interactions of globular domains and nonglobular regions can play critical roles in different aspects of protein function. However, studying these interactions and their regulatory roles can be challenging due to the flexibility of nonglobular regions, the long insertions separating interacting modules, and the transient nature of some interactions. Obtaining the experimental structures of multiple domains and functional regions is more difficult than determining the structures of individual globular domains. High‐quality structural models generated by AlphaFold offer a unique opportunity to study intramolecular interactions in eukaryotic proteins. In this study, we systematically explored intramolecular interactions between human protein kinase domains (KDs) and potential regulatory regions, including globular domains, N‐ and C‐terminal tails, long insertions, and distal nonglobular regions. Our analysis identified intramolecular interactions between human KDs and 35 different types of globular domains, exhibiting a variety of interaction modes that could contribute to orthosteric or allosteric regulation of kinase activity. We also identified prevalent interactions between human KDs and their flanking regions (N‐ and C‐terminal tails). These interactions exhibit group‐specific characteristics and can vary within each specific kinase group. Although long‐range interactions between KDs and nonglobular regions are relatively rare, structural details of these interactions offer new insights into the regulation mechanisms of several kinases, such as HASPIN, MAPK7, MAPK15, and SIK1B. John Wiley & Sons, Inc. 2023-10-01 /pmc/articles/PMC10503413/ /pubmed/37632170 http://dx.doi.org/10.1002/pro.4764 Text en © 2023 The Authors. Protein Science published by Wiley Periodicals LLC on behalf of The Protein Society. https://creativecommons.org/licenses/by-nc/4.0/This is an open access article under the terms of the http://creativecommons.org/licenses/by-nc/4.0/ (https://creativecommons.org/licenses/by-nc/4.0/) License, which permits use, distribution and reproduction in any medium, provided the original work is properly cited and is not used for commercial purposes.
spellingShingle Research Articles
Pei, Jimin
Cong, Qian
Computational analysis of regulatory regions in human protein kinases
title Computational analysis of regulatory regions in human protein kinases
title_full Computational analysis of regulatory regions in human protein kinases
title_fullStr Computational analysis of regulatory regions in human protein kinases
title_full_unstemmed Computational analysis of regulatory regions in human protein kinases
title_short Computational analysis of regulatory regions in human protein kinases
title_sort computational analysis of regulatory regions in human protein kinases
topic Research Articles
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10503413/
https://www.ncbi.nlm.nih.gov/pubmed/37632170
http://dx.doi.org/10.1002/pro.4764
work_keys_str_mv AT peijimin computationalanalysisofregulatoryregionsinhumanproteinkinases
AT congqian computationalanalysisofregulatoryregionsinhumanproteinkinases