Abstract
BAF250a and BAF250b are subunits of the SWI/SNF chromatin-remodeling complex that recruit the complex to chromatin allowing transcriptional activation of several genes. Despite being the central subunits of the SWI/SNF complex, the structural and functional annotation of BAF250a/b remains poorly understood. BAF250a (nearly 2200 residues protein) harbors an N-terminal DNA binding ARID (~110 residues) and a C-terminal folded region (~250 residues) of unknown structure and function, recently annotated as BAF250_C. Using hydrophobic core analysis, fold prediction and comparative modeling, here we have defined a domain boundary and associate a β-catenin like ARM-repeat fold to the C-terminus of BAF250a that encompass BAF250_C. The N-terminal DNA-binding ARID is found in diverse domain combinations in proteins imparting unique functions. We used a comparative sequence analysis based approach to study the ARIDs from diverse domain contexts and identified conserved residue positions that are important to preserve its core structure. Supporting this, mutation of one such conserved residue valine, at position 1067, to glycine, resulted in destabilization, loss of structural integrity and DNA binding affinity of ARID. Additionally, we identified a set of conserved and surface-exposed residues unique to the ARID when it co-occurs with the ARM repeat containing BAF250_C in BAF250a. Several of these residues are found mutated in somatic cancers. We predict that these residues in BAF250a may play important roles in mediating protein-DNA and protein-protein interactions in the BAF complex.
Publication types
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Research Support, Non-U.S. Gov't
MeSH terms
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Cell Differentiation
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Chromatin Assembly and Disassembly / genetics*
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Computational Biology
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DNA-Binding Proteins
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Datasets as Topic
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Glycine / genetics
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Molecular Dynamics Simulation
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Multienzyme Complexes / chemistry
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Multienzyme Complexes / genetics*
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Mutagenesis, Site-Directed
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Mutation
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Nuclear Magnetic Resonance, Biomolecular
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Nuclear Proteins / chemistry
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Nuclear Proteins / genetics*
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Nuclear Proteins / isolation & purification
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Protein Binding / genetics
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Protein Domains / genetics*
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Recombinant Proteins / chemistry
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Recombinant Proteins / genetics
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Recombinant Proteins / isolation & purification
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Sequence Alignment
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Transcription Factors / chemistry
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Transcription Factors / genetics*
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Transcription Factors / isolation & purification
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Valine / genetics
Substances
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ARID1A protein, human
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DNA-Binding Proteins
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Multienzyme Complexes
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Nuclear Proteins
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Recombinant Proteins
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Transcription Factors
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Valine
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Glycine
Grants and funding
This work is supported by Indian Institute of Science (M.S), IISc-DBT Partnership program (M.S.), Ramalingaswami Fellowship (BT/RLF/Re-entry/23/2013) (M.S.) from Department of Biotechnology (DBT), India, and Early Career Award (ECR/2015/000023) (M.S.) from Department of Science and Technology (DST), India. A.M would like to acknowledge DBT, India for the Research Associateship and India Alliance for current Early Career Fellowship (IA/E/15/1/502321). M.G. would like to acknowledge DST, India for INSPIRE fellowship. Authors acknowledge DST and DBT, India for the NMR facilities at the Indian Institute of Science, Bengaluru. Authors acknowledge ITC facility at National Centre for Biological Sciences, Bengaluru. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.