Communication routes in ARID domains between distal residues in helix 5 and the DNA-binding loops.

Gaetano Invernizzi,Matteo Lambrughi,Elena Papaleo,Kresten Lindorff-Larsen,Matteo Tiberti,Bert L De Groot

doi:10.1371/journal.pcbi.1003744

Gaetano Invernizzi, Matteo Lambrughi + Show 4 more

Open Access

https://doi.org/10.1371/journal.pcbi.1003744

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Abstract

ARID is a DNA-binding domain involved in several transcriptional regulatory processes, including cell-cycle regulation and embryonic development. ARID domains are also targets of the Human Cancer Protein Interaction Network. Little is known about the molecular mechanisms related to conformational changes in the family of ARID domains. Thus, we have examined their structural dynamics to enrich the knowledge on this important family of regulatory proteins. In particular, we used an approach that integrates atomistic simulations and methods inspired by graph theory. To relate these properties to protein function we studied both the free and DNA-bound forms. The interaction with DNA not only stabilizes the conformations of the DNA-binding loops, but also strengthens pre-existing paths in the native ARID ensemble for long-range communication to those loops. Residues in helix 5 are identified as critical mediators for intramolecular communication to the DNA-binding regions. In particular, we identified a distal tyrosine that plays a key role in long-range communication to the DNA-binding loops and that is experimentally known to impair DNA-binding. Mutations at this tyrosine and in other residues of helix 5 are also demonstrated, by our approach, to affect the paths of communication to the DNA-binding loops and alter their native dynamics. Overall, our results are in agreement with a scenario in which ARID domains exist as an ensemble of substates, which are shifted by external perturbation, such as the interaction with DNA. Conformational changes at the DNA-binding loops are transmitted long-range by intramolecular paths, which have their heart in helix 5.

Highlights

ARID3A is a member of the ARID (AT-rich interactive domain) family of transcription factors and is known as ‘‘dead ringer-like protein 1’’ (Dril1), ‘‘B-cell regulator of IgH transcription’’ (Bright) and ‘‘E2F-binding protein 1’’ (E2FBP1)
ARID domains are responsible for many of these DNA-protein interactions in proteins involved in important physiological functions, including cell-cycle regulation and embryonic development
Our results show that these mutations perturb wild-type routes of communication, allowing to link their effect on structure and dynamics to function

Summary

Introduction

ARID3A is a member of the ARID (AT-rich interactive domain) family of transcription factors and is known as ‘‘dead ringer-like protein 1’’ (Dril1), ‘‘B-cell regulator of IgH transcription’’ (Bright) and ‘‘E2F-binding protein 1’’ (E2FBP1). The ARID family is a family of DNA-binding proteins with a wide range of cellular functions and participates in different regulatory processes, including embryonic development, gene expression during cell growth, differentiation and development as well as cell cycle control and chromatin remodeling [1,2,3,4]. Human ARID3A is one of the targets of the broad Human Cancer Protein Interaction Network (HCPIN) database, which aims to provide structurefunction annotations of key proteins related to cancer diseases and developmental biology [5]. ARID proteins bind to the major groove in the DNA using a modified helix-turn-helix motif [1,2]. Human ARID3A belongs, together with ARID3B and 3C, to the third mammalian ARID subfamily, which is generally characterized by a core ARID domain with both additional N- and C-terminal extensions [1,2]

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