An Evolutionary Molecular Journey Through the Structural and Dynamical Landscape of Allosteric enzymes
Group members associated: Sandrine Coquille, Sylvain Engilberge, Julien Martel, Eric Girard, Bruno Franzetti, Giuseppe Zaccai
How does nature generate new enzyme function, catalytic regulation and appropriate stabilization mechanism to fold properly is a central issue in biology. To address this question, we use a multidisciplinary approach combining bioinformatics, biochemistry, biophysical characterization, NMR, molecular dynamics simulations, and X-ray time-resolved crystallography. For these time-resolved experiments, a new in situ mixing method was employed to obtain precise snapshots of the catalysis from hundreds of milliseconds to minutes after reaction initiation. Our favourite model enzymes belong to the large family of malate and lactate dehydrogenases. By using resurrected ancestral enzymes, we can study how the evolutionary trajectories have shaped the various properties of contemporary enzymes. At the final stage of our investigation, we describe the molecular motions of ancestral enzymes and modern’s orthologs, a strategy allowing us to reveal how transient conformers that populate the conformational landscape of enzymes are enriched by key amino acids replacements acting on dynamics. We also describe at the atomic level the networks of interactions that favour or prevent signal propagation in a series of representative non-allosteric, allosteric and pre-allosteric enzymes.
From left to right: Phylogenetic tree of the LDH/MalDH family. Cations and anions associated to the surface of a modern halophilic malate dehydrogenase. Electrostatic surface representation of a modern halophilic malate dehydrogenase. Ribbon drawing of an ancestral halophilic malate dehydrogenase.
Funding
ANR AlloAnc (2017-2020), AlloSpace (2022-2026)
Collaborations
The bioinformatics is done by Pr Céline Brochier-Armanet, (LBBE, Lyon 1 University). The dynamics is studied by Fabio Sterpone (LBT, Paris), by Paul Schanda (IST-Austria) and Roman Lichtenecker (University of Vienna). The effect of irradiation on activity and conformational stability of extremophilic lactate dehydrogenases is studied in collaboration with Dr Frédéric Halgand and Pr Chantal Houée Levin (LCP, Orsay University).
Diffraction data are collected at the French beam line for investigation of proteins.
Publications
- Pereira CS, Coquille S, Brochier-Armanet C, Sterpone F, Madern D
Unraveling the Link Between Thermal Adaptation and Latent Allostery in Malate Dehydrogenase from Methanococcales. J Mol Biol. 2025 Nov 20:169552.
- Coquille S, Pereira CS, Roche J, Santoni G, Engilberge S, Brochier-Armanet C, Girard E, Sterpone F, Madern D
Allostery and Evolution: A Molecular Journey Through the Structural and Dynamical Landscape of an Enzyme Super Family. Mol Biol Evol. 2025 Jan 6;42(1):msae265.
- Madern D, Halgand F, Houée-Levin C, Dufour AB, Coquille S, Ansanay-Alex S, Sacquin-Mora S, Brochier-Armanet C
The Characterization of Ancient Methanococcales Malate Dehydrogenases Reveals That Strong Thermal Stability Prevents Unfolding Under Intense γ-Irradiation. Mol Biol Evol. 2024 Dec 6;41(12):msae231.
- Bertrand Q, Coquille S, Iorio A, Sterpone F, Madern D
Biochemical, structural and dynamical characterizations of the lactate dehydrogenase from Selenomonas ruminantium provide information about an intermediate evolutionary step prior to complete allosteric regulation acquisition in the super family of lactate and malate dehydrogenases. J Struct Biol. (2023) 215(4):108039
- Robin AY, Brochier-Armanet C, Bertrand Q, Barette C, Girard E, Madern D
Deciphering Evolutionary Trajectories of Lactate Dehydrogenases Provides New Insights into Allostery. Mol Biol Evol. (2023) 40(10):msad223
- Iorio A, Roche J, Engilberge S, Coquelle N, Girard E, Sterpone F, Madern D
Biochemical, structural and dynamical studies reveal strong differences in the thermal-dependent allosteric behavior of two extremophilic lactate dehydrogenases. J Struct Biol. (2021), 213(3), pp.107769
- Brochier-Armanet C, Madern D
Phylogenetics and biochemistry elucidate the evolutionary link between l-malate and l-lactate dehydrogenases and disclose an intermediate group of sequences with mix functional properties. Biochimie. (2021) 191, pp.140-153
- Blanquart S, Groussin M, Le Roy A, Szöllosi GJ, Girard E, Franzetti B, Gouy M, Madern D
Resurrection of Ancestral Malate Dehydrogenases Reveals the Evolutionary History of Halobacterial Proteins: Deciphering Gene Trajectories and Changes in Biochemical Properties. Mol Biol Evol. (2021) 38(9), pp.3754-3774
- Marina Katava, Marco Maccarini, Guillaume Villain, Alessandro Paciaroni, Michael Sztucki et al.
Thermal activation of ’allosteric-like’ large-scale motions in a eukaryotic Lactate Dehydrogenase. Scientific Reports (2017), 7, pp.41092
- Maria Kalimeri, Eric Girard, Dominique Madern, Fabio Sterpone
Interface matters: the stiffness route to stability of a thermophilic tetrameric malate dehydrogenase. PLoS ONE (2014), 9 (12), pp.e113895
- Jacques Philippe Colletier, Alexei aleksandrov, Nicolas Coquelle, Sonia Mraihi, Elena Mendoza-Barbera et al.
Sampling the conformational ernergy landscape of a hyperthermophilic protein by engineering key substitutions. Mol Biol Evol (2012) 29(6), pp1683-1194