HDXrate

Python package for HDX intrinsic exchange rate calculation.

The calculations are based on the following papers:

'Englander xls sheets' papers:

Bai, Y., Milne, J. S., Mayne, L. & Englander, S. W. Primary structure effects on peptide group hydrogen exchange. Proteins Structure, Function, and Bioinformatics 17, 75–86 (1993)

Connelly, G. P., Bai, Y., Jeng, M.-F. & Englander, S. W. Isotope effects in peptide group hydrogen exchange. Proteins 17, 87–92 (1993).

Mori, S., Zijl, P. C. M. van & Shortle, D. Measurement of water–amide proton exchange rates in the denatured state of staphylococcal nuclease by a magnetization transfer technique. Proteins Structure, Function, and Bioinformatics 28, 325–332 (1997)

Nguyen, D., Mayne, L., Phillips, M. C. & Walter Englander, S. Reference Parameters for Protein Hydrogen Exchange Rates. J. Am. Soc. Mass Spectrom. 29, 1936–1939 (2018).

'3ala' reference data:

Stofella, M.; Seetaloo, N.; St John, A. N.; Paci, E.; Phillips, J. J.; Sobott, F. Recalibrating Protection Factors Using Millisecond Hydrogen/Deuterium Exchange Mass Spectrometry. Anal. Chem. 97 (5), 2648–2657 (2025).

pH correction:

Rubinson, K. A. Practical corrections for p(H,D) measurements in mixed H 2 O/D 2 O biological buffers. Anal. Methods 9, 2744–2750 (2017).

See also the excel sheets on the Englander group website: http://hx2.med.upenn.edu/download.html

• Free software: GNU General Public License v3

Features

Calculate intrinsic rate of amide hydrogen exchange in proteins.

Installation

$ pip install hdxrate

or

$ conda install -c conda-forge hdxrate

Usage

>>> from hdxrate import k_int_from_sequence
>>> k_int_from_sequence('HHHHH', 300, 7.)
array([0.00000000e+00, 2.62430718e+03, 6.29527446e+01, 6.29527446e+01,
    9.97734191e-01])

Credits

HDXrate implementation is based on PSX intrinsic rate calculation https://github.com/Niels-Bohr-Institute-XNS-StructBiophys/PSX

Pedersen, M. C. et al. PSX, Protein–Solvent Exchange: software for calculation of deuterium-exchange effects in small-angle neutron scattering measurements from protein coordinates. J Appl Cryst 52, 1427–1436 (2019).

Maintenance

• Jochem Smit <[email protected]> / <[email protected]>