Mapping Residual Structure in Intrinsically Disordered Proteins at Residue Resolution Using Millisecond Hydrogen/Deuterium Exchange and Residue Averaging

Measurement of residual structure in intrinsically disordered proteins can provide insights into the mechanisms by which such proteins undergo coupled binding and folding. The present work describes an approach to measure residual structure in disordered proteins using millisecond hydrogen/deuterium...

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Bibliographic Details
Published in:Journal of the American Society for Mass Spectrometry 2015-04, Vol.26 (4), p.547-554
Main Authors: Keppel, Theodore R., Weis, David D.
Format: Article
Language:English
Subjects:
Analytical Chemistry
Binding
Bioinformatics
Biotechnology
Chemistry
Chemistry and Materials Science
Computer simulation
Deuteration
Deuterium
Deuterium Exchange Measurement - methods
Exchanging
Focus: Emerging Investigators: Research Article
Intrinsically Disordered Proteins - analysis
Intrinsically Disordered Proteins - chemistry
Mass spectrometry
Mass Spectrometry - methods
NMR
Nuclear magnetic resonance
Organic Chemistry
Peptide Mapping - methods
Protein Structure, Secondary
Proteins
Proteomics
Spatial resolution
Workflow
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Summary:Measurement of residual structure in intrinsically disordered proteins can provide insights into the mechanisms by which such proteins undergo coupled binding and folding. The present work describes an approach to measure residual structure in disordered proteins using millisecond hydrogen/deuterium (H/D) exchange in a conventional bottom-up peptide-based workflow. We used the exchange mid-point, relative to a totally deuterated control, to quantify the rate of H/D exchange in each peptide. A weighted residue-by-residue average of these midpoints was used to map the extent of residual structure at near single-residue resolution. We validated this approach both by simulating a disordered protein and experimentally using the p300 binding domain of ACTR, a model disordered protein already well-characterized by other approaches. Secondary structure elements mapped in the present work are in good agreement with prior nuclear magnetic resonance measurements. The new approach was somewhat limited by a loss of spatial resolution and subject to artifacts because of heterogeneities in intrinsic exchange. Approaches to correct these limitations are discussed. Graphical Abstract ᅟ
ISSN:1044-0305
1879-1123
DOI:10.1007/s13361-014-1033-6