Substrate induced dynamical remodeling of the binding pocket generates GTPase specificity in DOCK family of guanine nucleotide exchange factors

TitleSubstrate induced dynamical remodeling of the binding pocket generates GTPase specificity in DOCK family of guanine nucleotide exchange factors
Publication TypeJournal Article
Year of Publication2022
AuthorsRoy, D, Sengupta, D, Kulkarni, K
JournalBiochemical and Biophysical Research Communications
Date PublishedNOV
Type of ArticleArticle
KeywordsDedicator of cytokinesis, GTPase specificity, Guanine exchange factors, Molecular dynamics simulations, Mutual information, Rho GTPases

Dedicator of cytokinesis (DOCK) family of guanine nucleotide exchange factors (GEFs) activate two members of Rho family GTPases, Rac1/Cdc42, to exert diverse cellular processes, including cell migration. As DOCK GEFs have been critically implicated in tumour cell migration, understanding their function and specificity is imperative for designing anti-metastatic drugs. Based on their GTPase specificity they have been classified as Rac, Cdc42 and dual specific GEFs. Despite extensive structural studies, the factors that determine GTPase specificity of DOCK GEFs have remained elusive. Here, we show that subtle dynamical coupling between GEF and GTPase structures modulate the binding interface to generate mutual spec-ificity. To cluster the dynamically coupled residues in GEF-GTPase complexes a novel intra-residue backbone-torsion-angles based mutual information (TMI) technique was employed. TMI was calcu-lated from 4500 trajectories obtained from a total of 4.5ms molecular dynamics simulations performed on members of all the three clades of DOCK GEFs. The obtained clusters suggest a specificity generation mechanism that involves optimization of the binding pocket for the crucial divergent residue at the 56th position of Rac/Cdc42 (FCdc42/WRac1). These clusters encompass five residues from the structural segment lobe C -a10 helix of the DOCK proteins and functional SWI region of GTPase, which induce orchestrated structural modulations to generate the specificity. Even the conserved residues from SWI region are seen to augment the specificity defining dynamical rearrangements. Furthermore, the pro-posed dynamical GTPase-DOCK GEF specificity model was verified using mutagenesis studies on Rac1 and dual GTPase specific Dock2 and Dock6, respectively. Thus the current study provides the generic substrate specificity determinants of DOCK GEFs, which are not apparent from the conventional struc-tural analysis.(c) 2022 Elsevier Inc. All rights reserved.

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Divison category: 
Biochemical Sciences
Physical and Materials Chemistry
Web of Science (WoS)

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