Quantitative Assessment of Protein Structural Models by Comparison of H/D Exchange MS Data with Exchange Behavior Accurately Predicted by DXCOREX

Abstract

Peptide amide hydrogen/deuterium exchange mass spectrometry (DXMS) data are often used to qualitatively support models for protein structure. We have developed and validated a method (DXCOREX) by which exchange data can be used to quantitatively assess the accuracy of 3-D models of protein structure. The method utilizes the COREX algorithm to predict a protein’s amide hydrogen exchange rates by reference to a hypothesized structure, and these values are used to generate a virtual data set (deuteron incorporation per peptide) that can be quantitatively compared to the deuteration level of the peptide probes measured by hydrogen exchange experimentation. The accuracy of DXCOREX was established in studies performed with thirteen proteins for which both high-resolution structures and experimental data were available. The DXCOREX-calculated and experimental data for each protein was highly correlated. We then employed correlation analysis of DXCOREX-calculated vs. DXMS experimental data to assess the accuracy of a recently proposed structural model for the catalytic domain of a Ca2+- independent phospholipase A2. The model’s calculated exchange behavior was highly correlated with the experimental exchange results available for the protein, supporting the accuracy of the proposed model. This method of analysis will substantially increase the precision with which experimental hydrogen exchange data can help decipher challenging questions regarding protein structure and dynamics.

Using Hydrogen/Deuterium Exchange Mass Spectrometry to Define the Specific Interactions of the Phospholipase A2 Superfamily with Lipid Substrates, Inhibitors, and Membranes

“…GVIA-2 iPLA 2 H/D data provided a good fit with the homology model (19). This homology model also showed a high correlation when validated by a recently developed program, DXCOREX, by which H/D exchange results were used to quantitatively assess the accuracy of tertiary protein structure models (52). The membrane interaction site was determined in an iPLA 2 /1-palmitoyl-2-arachidonoyl-sn-phosphatidylcholine lipid vesicle DXMS experiment in the presence of the inhibitor MAFP.…”

“…It is also hard to understand changes in the exchange rates without the availability of a three-dimensional structure. However, homology models coupled with DXMS data and computational modeling may be very useful to allow interpretation of H/D dynamic information (52). DXMS has to be used as a tool alongside other methods such as x-ray, NMR, mutagenesis, fluorescence, and molecular modeling.…”

Estimation of Hydrogen-Exchange Protection Factors from MD Simulation Based on Amide Hydrogen Bonding Analysis

“…Liu et al 11 published the DXCOREX algorithm using an empirical energy function based on the parameterization of energy and entropy terms as a function of SASA of polar and nonpolar atoms as derived from a limited base set of globular proteins. Their algorithm uses a statistical thermodynamics formulation enumerating an ensemble of native-like states by sequence-partitioning.…”

Characterizing monoclonal antibody structure by carboxyl group footprinting

“…6,25 Reversible CL of protein backbone using hydrogen-deuterium exchange (HDX) MS has been increasingly used to characterize biopharmaceuticals such as mAbs. 26,27,28 The advantages of HDX include its non-invasive nature and the potential of providing structural information across the length of the protein sequence. In particular, HDX is a very powerful technique for assessing secondary structure of proteins.…”