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Polysaccharide-Degrading Biocatalysts
2023, 75-107

State-of-the-art experimental and computational approaches to investigate structure, substrate recognition, and catalytic mechanism of enzymes

Camila Ramos Santosa, Clelton Aparecido dos Santosa, Evandro Ares de Araujob

Brazilian Biorenewables National Laboratory (LNBR), Brazilian Center for Research in Energy and Materials (CNPEM), Campinas, São Paulo, Brazil.

Abstract

The elucidation of the molecular mechanisms underpinning the specificity, substrate binding, and catalytic reaction of enzymes is central to the development of enhanced biocatalysts for industrial purposes and to shed light on the biological roles exerted by them in nature. This chapter aims to provide a roadmap for the most employed experimental and computational approaches to elucidate the structure and molecular mechanisms underlying the functioning of enzymes including (i) the preparation of a “structural biology-grade” sample, (ii) techniques to assess protein oligomerization and conformation in solution, (iii) classical and serial X-ray crystallography, (iv) high-resolution single-particle cryogenic electron microscopy, (v) structural mass spectrometry, and (vi) computational methods to analyze substrate interactions and to determine catalytic itineraries. Together, these approaches summarize the state of the art of both experimental and computational approaches for structural and mechanistic dissection of enzymatic systems.

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