Protocol for Computational Enzymatic Reactivity Based on Geometry Optimisation

• Type: Another Publication in an International Scientific Journal
• Date: 2018

Authors

Nuno M F S A Cerqueira (Author) FCUP; Pedro A Fernandes (Author) FCUP; Ramos, MJ (Author) FCUP

Journal

Title: ChemPhysChem

Vol. 19

Pages: 669-689

ISSN: 1439-4235

Publisher: Wiley-Blackwell

Indexing

ISI Web of Knowledge - 19 Citations

Scopus - 18 Citations

Other information

Authenticus ID: P-00N-TDS

DOI: 10.1002/cphc.201700339

Abstract (EN): Enzymes play a biologically essential role in performing and controlling an important share of the chemical processes occurring in life. However, despite their critical role in nature, attaining a clear understanding of the way an enzyme acts is still cumbersome. Computational enzymology is playing an increasingly important role in this field of research. It allows the elucidation of a complete and detailed mechanism of an enzymatic reaction, including the characterization of reaction intermediates and transition states from both structural and energetic points of view, which is something that no other single experiment can produce alone. In this review, we present a general computational strategy to study enzymatic mechanisms based on adiabatic mapping and free geometry optimization. These methods allow chemical reactions to be studied with high theoretical levels, and allow a more exhaustive exploration of the chemical reactional space than other available methods, albeit being limited to the extent that they explore the enzyme conformational space. Special attention is given to the choice of the theoretical levels, as well as describing the model systems that are currently used to study enzymatic reactions. With this, we aim to provide a good introduction for non-specialised users in this field of research. We also provide a selection of hand-picked examples from our own work that illustrate the power of computational enzymology to study catalytic mechanisms. Some of these studies constitute pioneering work in the field that were later validated by experimental means.

Language: English

Type (Professor's evaluation): Scientific

No. of pages: 21