Combination of HDX-MS and in silico modeling to study enzymatic reactivity and stereo-selectivity at different solvent conditions

被引：6

作者：

Makarov, Alexey A. ^{[1
]}

Iacob, Roxana E. ^{[3
]}

Pirrone, Gregory F. ^{[1
]}

Rodriguez-Granillo, Agustina ^{[2
]}

Joyce, Leo ^{[1
]}

Mangion, Ian ^{[1
]}

Moore, Jeffrey C. ^{[1
]}

Sherer, Edward C. ^{[2
]}

Engen, John R. ^{[3
]}

机构：

[1] Merck & Co Inc, Proc Res & Dev, Rahway, NJ 07065 USA

[2] Merck & Co Inc, Computat & Struct Chem, Rahway, NJ 07065 USA

[3] Northeastern Univ, Dept Chem & Chem Biol, Boston, MA 02115 USA

来源：

JOURNAL OF PHARMACEUTICAL AND BIOMEDICAL ANALYSIS | 2020年 / 182卷

关键词：

Transaminase; Protein conformational structure; Protein molecular dynamics simulations; Enzyme directed evolution; SIZE-EXCLUSION CHROMATOGRAPHY; HYDROGEN-EXCHANGE; ASYMMETRIC-SYNTHESIS; PROTEIN;

D O I：

10.1016/j.jpba.2020.113141

中图分类号：

O65 [分析化学];

学科分类号：

070302 ; 081704 ;

摘要：

The higher-order structure of a protein defines its function, and protein structural dynamics are often essential for protein binding and enzyme catalysis. Methods for protein characterization in solution are continuously being developed to understand and explore protein conformational changes with regards to function and activity. The goal of this study was to survey the use of combining HDX-MS global conformational screening with in silica modeling and continuous labeling peptide-level HDX-MS as an approach to highlight regions of interest within an enzyme required for biocatalytic processes. We surveyed in silico modeling correlated with peptide level HDX-MS experiments to characterize and localize transaminase enzyme structural dynamics at different conditions. This approach was orthogonally correlated with a global Size-Exclusion-HDX (SEC-HDX) screen for global conformational comparison and global alpha-helical content measurements by circular dichroism. Enzymatic activity and stereo-selectivity of transaminases were compared at different reaction-solution conditions that forced protein conformational changes by increasing acetonitrile concentration. The experimental peptide-level HDX-MS results demonstrated similar trends to the modeling data showing that certain regions remained folded in transaminases ATA-036 and ATA-303 with increasing acetonitrile concentration, which is also associated with shifting stereoselectivity. HDX modeling, SEC-HDX and CD experimental data showed that transaminase ATA-234 had the highest level of global unfolding with increasing acetonitrile concentration compared to the other two enzymes, which correlated with drastically reduced product conversion in transamination reaction. The combined HDX modeling/experimental workflow, based on enzymatic reactions studied at different conditions to induce changes in enzyme conformation, could be used as a tool to guide directed evolution efforts by identifying and focusing on the regions of an enzyme required for reaction product conversion and stereoselectivity. (C) 2020 Elsevier B.V. All rights reserved.

引用

页数：10

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