title: Thermal activation of 'allosteric-like' large-scale motions in a eukaryotic Lactate Dehydrogenase.
abstract: Conformational changes occurring during the enzymatic turnover are essential for the regulation of protein functionality. Individuating the protein regions involved in these changes and the associated mechanical modes is still a challenge at both experimental and theoretical levels. We present here a detailed investigation of the thermal activation of the functional modes and conformational changes in a eukaryotic Lactate Dehydrogenase enzyme (LDH). Neutron Spin Echo spectroscopy and Molecular Dynamics simulations were used to uncover the characteristic length- and timescales of the LDH nanoscale motions in the apo state. The modes involving the catalytic loop and the mobile region around the binding site are activated at room temperature, and match the allosteric reorganisation of bacterial LDHs. In a temperature window of about 15 degrees, these modes render the protein flexible enough and capable of reorganising the active site toward reactive configurations. On the other hand an excess of thermal excitation leads to the distortion of the protein matrix with a possible anti-catalytic effect. Thus, the temperature activates eukaryotic LDHs via the same conformational changes observed in the allosteric bacterial LDHs. Our investigation provides an extended molecular picture of eukaryotic LDH's conformational landscape that enriches the static view based on crystallographic studies alone.
authors.affiliation: Laboratoire de Biochimie Théorique, IBPC, CNRS UPR9080, Univ. Paris Diderot, Sorbonne Paris Cité, 13 rue Pierre et Marie Curie, 75005, Paris, France.
authors.forename: Marina
authors.initials: M
authors.lastname: Katava
authors.affiliation: Univ. Grenoble Alpes - Laboratoire TIMC/IMAG UMR CNRS 5525, Grenoble Pavillon Taillefer Domaine de la merci, 38700 La Tronche, France.
authors.forename: Marco
authors.initials: M
authors.lastname: Maccarini
authors.affiliation: Laboratoire de Biochimie Théorique, IBPC, CNRS UPR9080, Univ. Paris Diderot, Sorbonne Paris Cité, 13 rue Pierre et Marie Curie, 75005, Paris, France.
authors.forename: Guillaume
authors.initials: G
authors.lastname: Villain
authors.affiliation: Dipartimento di Fisica e Geologia, Universitá di Perugia, via A. Pascoli, 06123 Perugia, Italy.
authors.forename: Alessandro
authors.initials: A
authors.lastname: Paciaroni
authors.affiliation: European Syncrotron Radiation Facility, 6, rue Jules Horowitz, 38042, Grenoble, France.
authors.forename: Michael
authors.initials: M
authors.lastname: Sztucki
authors.affiliation: Jülich Centre for Neutron Science (JCNS) at Heinz Maier-Leibnitz Zentrum (MLZ), Forschungszentrum Jülich GmbH, Garching, Germany.
authors.forename: Oxana
authors.initials: O
authors.lastname: Ivanova
authors.affiliation: Institut de Biologie Structurale (IBS), Univ. Grenoble Alpes, CEA, CNRS, 38044 Grenoble, France.
authors.forename: Dominique
authors.initials: D
authors.lastname: Madern
authors.affiliation: Laboratoire de Biochimie Théorique, IBPC, CNRS UPR9080, Univ. Paris Diderot, Sorbonne Paris Cité, 13 rue Pierre et Marie Curie, 75005, Paris, France.
authors.forename: Fabio
authors.initials: F
authors.lastname: Sterpone
mesh_terms: D000494:Allosteric Regulation / Q000235:genetics*; D001426:Bacterial Proteins / Q000737:chemistry / Q000235:genetics / Q000378:metabolism*; D001665:Binding Sites; D020134:Catalytic Domain; D056890:Eukaryota / Q000201:enzymology* / Q000235:genetics; D007770:L-Lactate Dehydrogenase / Q000737:chemistry / Q000235:genetics / Q000378:metabolism*; D008279:Magnetic Resonance Imaging; D056004:Molecular Dynamics Simulation; D011485:Protein Binding; D011487:Protein Conformation; D013696:Temperature
chemical_list: D001426:Bacterial Proteins; D007770:L-Lactate Dehydrogenase