POPPeT: a New Method to Predict the Protection Factor of Backbone Amide Hydrogens

Jürgen Claesen; Argyris Politis

doi:10.1007/s13361-018-2068-x

POPPeT: a New Method to Predict the Protection Factor of Backbone Amide Hydrogens

Jürgen Claesen, Argyris Politis^*

^*Corresponding author for this work

Chemistry

Agoralaan Building C

Research output: Contribution to journal › Article › peer-review

12 Citations (Scopus)

Abstract

Hydrogen exchange (HX) has become an important tool to monitor protein structure and dynamics. The interpretation of HX data with respect to protein structure requires understanding of the factors that influence exchange. Simulated protein structures can be validated by comparing experimental deuteration profiles with the profiles derived from the modeled protein structure. To do this, we propose here a new method, POPPeT, for protection factor prediction based on protein motions that enable HX. By comparing POPPeT with two existing methods, the phenomenological approximation and COREX, we show enhanced predictability measured at both protection factor and deuteration level. This method can be subsequently used by modeling strategies for protein structure prediction.

Original language	English
Pages (from-to)	67-76
Number of pages	10
Journal	Journal of the American Society for Mass Spectrometry
Volume	30
Issue number	1
Early online date	18 Oct 2018
DOIs	https://doi.org/10.1007/s13361-018-2068-x
Publication status	Published - 1 Jan 2019

Keywords

HDX-MS
Protection factor
Protein structure

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10.1007/s13361-018-2068-x

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abstract = "Hydrogen exchange (HX) has become an important tool to monitor protein structure and dynamics. The interpretation of HX data with respect to protein structure requires understanding of the factors that influence exchange. Simulated protein structures can be validated by comparing experimental deuteration profiles with the profiles derived from the modeled protein structure. To do this, we propose here a new method, POPPeT, for protection factor prediction based on protein motions that enable HX. By comparing POPPeT with two existing methods, the phenomenological approximation and COREX, we show enhanced predictability measured at both protection factor and deuteration level. This method can be subsequently used by modeling strategies for protein structure prediction.",

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AU - Claesen, Jürgen

AU - Politis, Argyris

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Y1 - 2019/1/1

N2 - Hydrogen exchange (HX) has become an important tool to monitor protein structure and dynamics. The interpretation of HX data with respect to protein structure requires understanding of the factors that influence exchange. Simulated protein structures can be validated by comparing experimental deuteration profiles with the profiles derived from the modeled protein structure. To do this, we propose here a new method, POPPeT, for protection factor prediction based on protein motions that enable HX. By comparing POPPeT with two existing methods, the phenomenological approximation and COREX, we show enhanced predictability measured at both protection factor and deuteration level. This method can be subsequently used by modeling strategies for protein structure prediction.

AB - Hydrogen exchange (HX) has become an important tool to monitor protein structure and dynamics. The interpretation of HX data with respect to protein structure requires understanding of the factors that influence exchange. Simulated protein structures can be validated by comparing experimental deuteration profiles with the profiles derived from the modeled protein structure. To do this, we propose here a new method, POPPeT, for protection factor prediction based on protein motions that enable HX. By comparing POPPeT with two existing methods, the phenomenological approximation and COREX, we show enhanced predictability measured at both protection factor and deuteration level. This method can be subsequently used by modeling strategies for protein structure prediction.

KW - HDX-MS

KW - Protection factor

KW - Protein structure

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JF - Journal of the American Society for Mass Spectrometry

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POPPeT: a New Method to Predict the Protection Factor of Backbone Amide Hydrogens

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Keywords

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