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Paris-DÉCOR: A Protocol for the Determination of Fast Protein Backbone Amide Hydrogen Exchange Rates. 2020

Rupashree Dass, and Frans A A Mulder
Department of Chemistry, and Interdisciplinary Nanoscience Center (iNANO), Aarhus University 8000, Aarhus, Denmark.

Determining hydrogen exchange kinetics in proteins can shed light on their structure and dynamics. Nuclear magnetic resonance (NMR) spectroscopy is an important analytical technique to determine exchange rates. In this chapter, we describe a new method (Paris-DÉCOR) to determine fast protein amide backbone hydrogen exchange rates in the range 10 to 104 s-1. Measuring fast exchange rates is particularly important for the study of intrinsically disordered proteins, where there is very little protection from exchange to the solvent by the formation of persistent structure. We provide a protocol to set up the experiment as well as MATLAB scripts for numerical simulation that is needed to determine the exchange rates.

UI MeSH Term Description Entries
D011506 Proteins Linear POLYPEPTIDES that are synthesized on RIBOSOMES and may be further modified, crosslinked, cleaved, or assembled into complex proteins with several subunits. The specific sequence of AMINO ACIDS determines the shape the polypeptide will take, during PROTEIN FOLDING, and the function of the protein. Gene Products, Protein,Gene Proteins,Protein,Protein Gene Products,Proteins, Gene
D006801 Humans Members of the species Homo sapiens. Homo sapiens,Man (Taxonomy),Human,Man, Modern,Modern Man
D006859 Hydrogen The first chemical element in the periodic table with atomic symbol H, and atomic number 1. Protium (atomic weight 1) is by far the most common hydrogen isotope. Hydrogen also exists as the stable isotope DEUTERIUM (atomic weight 2) and the radioactive isotope TRITIUM (atomic weight 3). Hydrogen forms into a diatomic molecule at room temperature and appears as a highly flammable colorless and odorless gas. Protium,Hydrogen-1
D000577 Amides Organic compounds containing the -CO-NH2 radical. Amides are derived from acids by replacement of -OH by -NH2 or from ammonia by the replacement of H by an acyl group. (From Grant & Hackh's Chemical Dictionary, 5th ed) Amide
D012984 Software Sequential operating programs and data which instruct the functioning of a digital computer. Computer Programs,Computer Software,Open Source Software,Software Engineering,Software Tools,Computer Applications Software,Computer Programs and Programming,Computer Software Applications,Application, Computer Software,Applications Software, Computer,Applications Softwares, Computer,Applications, Computer Software,Computer Applications Softwares,Computer Program,Computer Software Application,Engineering, Software,Open Source Softwares,Program, Computer,Programs, Computer,Software Application, Computer,Software Applications, Computer,Software Tool,Software, Computer,Software, Computer Applications,Software, Open Source,Softwares, Computer Applications,Softwares, Open Source,Source Software, Open,Source Softwares, Open,Tool, Software,Tools, Software
D051844 alpha-Synuclein A synuclein that is a major component of LEWY BODIES and plays a role in SYNUCLEINOPATHIES, neurodegeneration and neuroprotection. Non-AB Component of AD Amyloid Protein,Non AB Component of AD Amyloid Protein,alpha Synuclein

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