Cargando…

All-Atomic Molecular Dynamic Studies of Human and Drosophila CDK8: Insights into Their Kinase Domains, the LXXLL Motifs, and Drug Binding Site

Cyclin-dependent kinase 8 (CDK8) and its regulatory partner Cyclin C (CycC) play conserved roles in modulating RNA polymerase II (Pol II)-dependent gene expression. To understand the structure and function relations of CDK8, we analyzed the structures of human and Drosophila CDK8 proteins using mole...

Descripción completa

Detalles Bibliográficos
Autores principales: Xu, Wu, Xie, Xiao-Jun, Faust, Ali K., Liu, Mengmeng, Li, Xiao, Chen, Feng, Naquin, Ashlin A., Walton, Avery C., Kishbaugh, Peter W., Ji, Jun-Yuan
Formato: Online Artículo Texto
Lenguaje:English
Publicado: MDPI 2020
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7590003/
https://www.ncbi.nlm.nih.gov/pubmed/33053834
http://dx.doi.org/10.3390/ijms21207511
_version_ 1783600707766583296
author Xu, Wu
Xie, Xiao-Jun
Faust, Ali K.
Liu, Mengmeng
Li, Xiao
Chen, Feng
Naquin, Ashlin A.
Walton, Avery C.
Kishbaugh, Peter W.
Ji, Jun-Yuan
author_facet Xu, Wu
Xie, Xiao-Jun
Faust, Ali K.
Liu, Mengmeng
Li, Xiao
Chen, Feng
Naquin, Ashlin A.
Walton, Avery C.
Kishbaugh, Peter W.
Ji, Jun-Yuan
author_sort Xu, Wu
collection PubMed
description Cyclin-dependent kinase 8 (CDK8) and its regulatory partner Cyclin C (CycC) play conserved roles in modulating RNA polymerase II (Pol II)-dependent gene expression. To understand the structure and function relations of CDK8, we analyzed the structures of human and Drosophila CDK8 proteins using molecular dynamics simulations, combined with functional analyses in Drosophila. Specifically, we evaluated the structural differences between hCDK8 and dCDK8 to predict the effects of the LXXLL motif mutation (AQKAA), the P154L mutations, and drug binding on local structures of the CDK8 proteins. First, we have observed that both the LXXLL motif and the kinase activity of CDK8 are required for the normal larval-to-pupal transition in Drosophila. Second, our molecular dynamic analyses have revealed that hCDK8 has higher hydrogen bond occupation of His149-Asp151 and Asp151-Asn156 than dCDK8. Third, the substructure of Asp282, Phe283, Arg285, Thr287 and Cys291 can distinguish human and Drosophila CDK8 structures. In addition, there are two hydrogen bonds in the LXXLL motif: a lower occupation between L312 and L315, and a relatively higher occupation between L312 and L316. Human CDK8 has higher hydrogen bond occupation between L312 and L316 than dCDK8. Moreover, L312, L315 and L316 in the LXXLL motif of CDK8 have the specific pattern of hydrogen bonds and geometries, which could be crucial for the binding to nuclear receptors. Furthermore, the P154L mutation dramatically decreases the hydrogen bond between L312 and L315 in hCDK8, but not in dCDK8. The mutations of P154L and AQKAA modestly alter the local structures around residues 154. Finally, we identified the inhibitor-induced conformational changes of hCDK8, and our results suggest a structural difference in the drug-binding site between hCDK8 and dCDK8. Taken together, these results provide the structural insights into the roles of the LXXLL motif and the kinase activity of CDK8 in vivo.
format Online
Article
Text
id pubmed-7590003
institution National Center for Biotechnology Information
language English
publishDate 2020
publisher MDPI
record_format MEDLINE/PubMed
spelling pubmed-75900032020-10-29 All-Atomic Molecular Dynamic Studies of Human and Drosophila CDK8: Insights into Their Kinase Domains, the LXXLL Motifs, and Drug Binding Site Xu, Wu Xie, Xiao-Jun Faust, Ali K. Liu, Mengmeng Li, Xiao Chen, Feng Naquin, Ashlin A. Walton, Avery C. Kishbaugh, Peter W. Ji, Jun-Yuan Int J Mol Sci Article Cyclin-dependent kinase 8 (CDK8) and its regulatory partner Cyclin C (CycC) play conserved roles in modulating RNA polymerase II (Pol II)-dependent gene expression. To understand the structure and function relations of CDK8, we analyzed the structures of human and Drosophila CDK8 proteins using molecular dynamics simulations, combined with functional analyses in Drosophila. Specifically, we evaluated the structural differences between hCDK8 and dCDK8 to predict the effects of the LXXLL motif mutation (AQKAA), the P154L mutations, and drug binding on local structures of the CDK8 proteins. First, we have observed that both the LXXLL motif and the kinase activity of CDK8 are required for the normal larval-to-pupal transition in Drosophila. Second, our molecular dynamic analyses have revealed that hCDK8 has higher hydrogen bond occupation of His149-Asp151 and Asp151-Asn156 than dCDK8. Third, the substructure of Asp282, Phe283, Arg285, Thr287 and Cys291 can distinguish human and Drosophila CDK8 structures. In addition, there are two hydrogen bonds in the LXXLL motif: a lower occupation between L312 and L315, and a relatively higher occupation between L312 and L316. Human CDK8 has higher hydrogen bond occupation between L312 and L316 than dCDK8. Moreover, L312, L315 and L316 in the LXXLL motif of CDK8 have the specific pattern of hydrogen bonds and geometries, which could be crucial for the binding to nuclear receptors. Furthermore, the P154L mutation dramatically decreases the hydrogen bond between L312 and L315 in hCDK8, but not in dCDK8. The mutations of P154L and AQKAA modestly alter the local structures around residues 154. Finally, we identified the inhibitor-induced conformational changes of hCDK8, and our results suggest a structural difference in the drug-binding site between hCDK8 and dCDK8. Taken together, these results provide the structural insights into the roles of the LXXLL motif and the kinase activity of CDK8 in vivo. MDPI 2020-10-12 /pmc/articles/PMC7590003/ /pubmed/33053834 http://dx.doi.org/10.3390/ijms21207511 Text en © 2020 by the authors. Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (http://creativecommons.org/licenses/by/4.0/).
spellingShingle Article
Xu, Wu
Xie, Xiao-Jun
Faust, Ali K.
Liu, Mengmeng
Li, Xiao
Chen, Feng
Naquin, Ashlin A.
Walton, Avery C.
Kishbaugh, Peter W.
Ji, Jun-Yuan
All-Atomic Molecular Dynamic Studies of Human and Drosophila CDK8: Insights into Their Kinase Domains, the LXXLL Motifs, and Drug Binding Site
title All-Atomic Molecular Dynamic Studies of Human and Drosophila CDK8: Insights into Their Kinase Domains, the LXXLL Motifs, and Drug Binding Site
title_full All-Atomic Molecular Dynamic Studies of Human and Drosophila CDK8: Insights into Their Kinase Domains, the LXXLL Motifs, and Drug Binding Site
title_fullStr All-Atomic Molecular Dynamic Studies of Human and Drosophila CDK8: Insights into Their Kinase Domains, the LXXLL Motifs, and Drug Binding Site
title_full_unstemmed All-Atomic Molecular Dynamic Studies of Human and Drosophila CDK8: Insights into Their Kinase Domains, the LXXLL Motifs, and Drug Binding Site
title_short All-Atomic Molecular Dynamic Studies of Human and Drosophila CDK8: Insights into Their Kinase Domains, the LXXLL Motifs, and Drug Binding Site
title_sort all-atomic molecular dynamic studies of human and drosophila cdk8: insights into their kinase domains, the lxxll motifs, and drug binding site
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7590003/
https://www.ncbi.nlm.nih.gov/pubmed/33053834
http://dx.doi.org/10.3390/ijms21207511
work_keys_str_mv AT xuwu allatomicmoleculardynamicstudiesofhumananddrosophilacdk8insightsintotheirkinasedomainsthelxxllmotifsanddrugbindingsite
AT xiexiaojun allatomicmoleculardynamicstudiesofhumananddrosophilacdk8insightsintotheirkinasedomainsthelxxllmotifsanddrugbindingsite
AT faustalik allatomicmoleculardynamicstudiesofhumananddrosophilacdk8insightsintotheirkinasedomainsthelxxllmotifsanddrugbindingsite
AT liumengmeng allatomicmoleculardynamicstudiesofhumananddrosophilacdk8insightsintotheirkinasedomainsthelxxllmotifsanddrugbindingsite
AT lixiao allatomicmoleculardynamicstudiesofhumananddrosophilacdk8insightsintotheirkinasedomainsthelxxllmotifsanddrugbindingsite
AT chenfeng allatomicmoleculardynamicstudiesofhumananddrosophilacdk8insightsintotheirkinasedomainsthelxxllmotifsanddrugbindingsite
AT naquinashlina allatomicmoleculardynamicstudiesofhumananddrosophilacdk8insightsintotheirkinasedomainsthelxxllmotifsanddrugbindingsite
AT waltonaveryc allatomicmoleculardynamicstudiesofhumananddrosophilacdk8insightsintotheirkinasedomainsthelxxllmotifsanddrugbindingsite
AT kishbaughpeterw allatomicmoleculardynamicstudiesofhumananddrosophilacdk8insightsintotheirkinasedomainsthelxxllmotifsanddrugbindingsite
AT jijunyuan allatomicmoleculardynamicstudiesofhumananddrosophilacdk8insightsintotheirkinasedomainsthelxxllmotifsanddrugbindingsite