A common binding motif in the ET domain of BRD3 forms polymorphic structural interfaces with host and viral proteins

Abstract

SummaryThe extra-terminal (ET) domain of BRD3 is conserved among BET proteins (BRD2, BRD3, BRD4), interacting with multiple host and viral protein-protein networks. Solution NMR structures of complexes formed between BRD3-ET domain with either the 79-residue murine leukemia virus integrase (IN) C-terminal domain (IN329-408), or its 22-residue IN tail peptide (TP) (IN386-407) alone, reveal similar intermolecular three-stranded β-sheet formation. 15N relaxation studies reveal a 10-residue linker region (IN379-388) tethering the SH3 domain (IN329-378) to the ET-binding motif (IN389-405)-ET complex. This linker has restricted flexibility, impacting its potential range of orientations in the IN - nucleosome complex. The complex of the ET-binding peptide of host NSD3 protein (NSD3148-184) and BRD3-ET domain includes a similar three-stranded β-sheet interaction, but the orientation of the β−hairpin is flipped compared to the two IN : ET complexes. These studies expand our understanding of molecular recognition polymorphism in complexes of ET-binding motifs with viral and host proteins.HighlightsThe BRD3 ET domain binds to key peptide motifs of diverse host and viral proteins.These complexes reveal conformational plasticity in molecular recognition.NMR studies demonstrate restricted interdomain motion in the IN CTD / ET complex.A cost-effective approach is described for producing isotopically-labeled peptides.Etoc BlurbWe address structurally how the MLV Integrase (IN) usurps the host function of the BET protein through comparative studies of the IN : Brd3 ET complex with that of the host NSD3. MLV integration and thus its pathogenesis is driven through protein interactions of the IN : BET family.

Computational Modeling as a Tool to Investigate PPI: From Drug Design to Tissue Engineering

“…Knowing the bound conformation of a protein-peptide system does not imply that other peptide sequences can adopt the same bound conformation. This binding plasticity is best exemplified by: 1) receptors that bind different peptide sequences in different conformations ( Aiyer et al, 2021 ) and 2) peptide sequences that can adopt different structures when binding different receptors ( Huart and Hupp, 2013 ). This amount of binding plasticity is a challenge for predicting peptide-protein interactions and for computing binding affinities.…”

“…Approaches to model protein flexibility include the use of soft potentials ( Fernández et al, 2002 ; Ferrari et al, 2004 ), explore rotameric states ( Leach, 1994 ), using different protein receptor structures ( Amaro et al, 2018 ; Falcon et al, 2019 ) or refining with molecular dynamics ( Alonso et al, 2006 ). The challenges in modeling peptides arises from: 1) peptides can have different conformations in their free/bound states; 2) the same peptide sequence might bind different proteins in different conformations ( Huart and Hupp, 2013 ), and 3) different peptide sequences can bind the same receptor in different conformations ( Aiyer et al, 2021 ). Most docking methods use a flexible strategy for the peptide conformation.…”

“…This includes the conformational changes of the protein receptor as well as the ability to accommodate multiple binding conformations. This is especially characteristic of protein interaction hubs such as those involved in gene regulation ( Aiyer et al, 2021 ). Many peptides are intrinsically disordered and fold upon binding, hence optimization of peptide design will often try to maximize interactions in the complex as well as the propensity of the peptide to adopt bound structures (e.g.…”

Structure determination of protein-peptide complexes from NMR chemical shift data using MELD

“…Here we describe an integrative approach to structure determination for peptide-protein complexes combining NMR chemical shift data and molecular simulations. High information-content NMR studies rely on extracting many distance and orientation restraints to solve the structure of the peptide-protein complex 7 . At the other extreme, lower information-content NMR studies, such as backbone chemical shift data which is prerequisite to more extensive studies, provide valuable information about the binding epitope and (in some cases) the bound-state conformation of the peptide, but do not usually provide enough data to reliably characterize the binding mode and structure of the resulting complex.…”

“…This pipeline allows more rapid structure determination of complexes than conventional NMR approaches, and can provide structures of complexes even for systems for which extensive NMR data cannot be obtained. We focus on the binding of polypeptides to the extra-terminal domain (ET) of bromo and extra-terminal domain (BET) proteins, which exhibit disorder to order transitions of the polypeptide upon binding, allosteric changes in the receptor, and accommodate peptides binding in different conformations 7 . This biologically-important system exhibits a large degree of plasticity in binding modes and peptide conformations 7,17–19 ,, as well as a large range in binding affinities, and poses challenges to current computational and experimental approaches.…”