Biology subjects

Ribeiro, A. J. M.

Publications and source records attributed to Ribeiro, A. J. M..

3 recordsLinked to original sources

bioRxiv2023

The 3D modules of enzyme catalysis: deconstructing active sites into distinct functional entities

Enzyme catalysis is governed by a limited toolkit of residues and organic or inorganic co-factors. Therefore, it is expected that recurring residue arrangements will be found across the enzyme space, which perform a defined catalytic function, are structurally similar and occur in unrelated enzymes. Leveraging the integrated information in the Mechanism and Catalytic Site Atlas (M-CSA) (enzyme structure, sequence, catalytic residue annotations, catalysed reaction, detailed mechanism description), 3D templates were derived to represent compact groups of catalytic residues. A fuzzy template-template search, allowed us to identify those recurring motifs, which are conserved or convergent, that we define as the "modules of enzyme catalysis". We show that a large fraction of these modules facilitate binding of metal ions, co-factors and substrates, and are frequently the result of convergent evolution. A smaller number of convergent modules perform a well-defined catalytic role, such as the variants of the catalytic triad (i.e. Ser-His-Asp/Cys-His-Asp) and the saccharide-cleaving Asp/Glu triad. It is also shown that enzymes whose functions have diverged during evolution preserve regions of their active site unaltered, as shown by modules performing similar or identical steps of the catalytic mechanism. We have compiled a comprehensive library of catalytic modules, that characterise a broad spectrum of enzymes. These modules can be used as templates in enzyme design and for better understanding catalysis in 3D. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=75 SRC="FIGDIR/small/543252v1_ufig1.gif" ALT="Figure 1"> View larger version (28K): org.highwire.dtl.DTLVardef@1ddfb6org.highwire.dtl.DTLVardef@14a5913org.highwire.dtl.DTLVardef@1e2258org.highwire.dtl.DTLVardef@60faf6_HPS_FORMAT_FIGEXP M_FIG C_FIG

bioinformatics↗

bioRxiv2022

EzMechanism: An Automated Tool to Propose Catalytic Mechanisms of Enzyme Reactions

A rich literature dedicated to understanding the reaction mechanisms of hundreds of enzymes has emerged over time from the works of experimental and computational researchers. This body of information can now be the starting point for an entirely novel approach to studying enzyme mechanisms using knowledge-based prediction methods. Here, we present such a method, EzMechanism, (pronounced as "Easy Mechanism") which is able to automatically generate mechanism proposals for a given active site. It works by searching the chemical reaction space available to the enzyme using a set of newly created biocatalytic rules based on knowledge from the literature. EzMechanism aims to complement existing methods for studying enzyme mechanisms by facilitating and improving the hypotheses generating step. We show that EzMechanism works by validating it against 56 enzymes with a known mechanism and identify the limited coverage of the current ruleset as the main target for further improvement.

bioinformatics↗

bioRxiv2021

Conformational variation in enzyme catalysis: A structural study on catalytic residues

Conformational variation in catalytic residues can be captured as alternative snapshots in enzyme crystal structures. Addressing the question of whether active site flexibility is an intrinsic and essential property of enzymes for catalysis, we present a comprehensive study on the 3D variation of active sites of 925 enzyme families, using explicit catalytic residue annotations from the Mechanism and Catalytic Site Atlas and structural data from the Protein Data Bank. Through weighted pairwise superposition of the functional atoms of active sites, we captured structural variability at single-residue level and examined the geometrical changes as ligands bind or as mutations occur. We demonstrate that catalytic centres of enzymes can be inherently rigid or flexible to various degrees according to the function they perform, and structural variability most often involves a subset of the catalytic residues, usually those not directly involved in the formation or cleavage of bonds. Moreover, data suggest that 2/3 of active sites are flexible, and in half of those, flexibility is only observed in the side chain. The goal of this work is to characterise our current knowledge of the extent of flexibility at the heart of catalysis and ultimately place our findings in the context of the evolution of catalysis as enzymes evolve new functions and bind different substrates.

bioinformatics↗