Conformation and dynamics of human urotensin II and urotensin related peptide in aqueous solution

Conformation and dynamics of the vasoconstrictive peptides human urotensin II (UII) and urotensin related peptide (URP) have been investigated by both unrestrained and enhanced-sampling molecular-dynamics (MD) simulations and NMR spectroscopy. These peptides are natural ligands of the G-protein coupled urotensin II receptor (UTR) and have been linked to mammalian pathophysiology. UII and URP cannot be characterized by a single structure but exist as an equilibrium of two main classes of ring conformations, <i>open</i> and <i>folded</i>, with rapidly interchanging subtypes. The <i>open</i> states are characterized by turns of various types centered at K⁸Y⁹ or F⁶W⁷ predominantly with no or only sparsely populated transannular hydrogen bonds. The <i>folded</i> conformations show multiple turns stabilized by highly populated transannular hydrogen bonds comprising centers F⁶W⁷K⁸ or W⁷K⁸Y⁹. Some of these conformations have not been characterized previously. The equilibrium populations that are experimentally difficult to access were estimated by replica-exchange MD simulations and validated by comparison of experimental NMR data with chemical shifts calculated with density-functional theory. UII exhibits approximately 72% <i>open</i>:28% <i>folded</i> conformations in aqueous solution. URP shows very similar ring conformations as UII but differs in an <i>open:folded</i> equilibrium shifted further toward <i>open</i> conformations (86:14) possibly arising from the absence of folded N-terminal tail-ring interaction. The results suggest that the different biological effects of UII and URP are not caused by differences in ring conformations but rather by different interactions with UTR

Theoretical study of structural and dynamic properties of FtsZ

FtsZ est une protéine indispensable à la multiplication bactérienne. Elle est une cible thérapeutique intéressante dans la recherche de nouvelles molécules antibiotiques. FtsZ se polymérise en filaments qui s'assemblent en une structure : le "Z-ring". FtsZ est une GTPase qui lie et hydrolyse le GTP, pour donner un GDP. L'objectif de cette thèse est d'étudier par dynamique moléculaire l'influence du nucléotide GTP/GDPet de l'ion Mg2+ sur les changements conformationnels ainsi que sur la dynamique de FtsZ. Une première approche a consisté à étudier le monomère de FtsZ. Ces simulations n'ont révélé que peu d'influence de la nature du nucléotide sur la structure. Cependant, la présence de l'ion Mg2+ dans la poche du nucléotide provoque des changements conformationnels de FtsZ-GDP ainsi qu'un mouvement du GDP au sein du site actif. Dans la deuxième partie, l'étude du dimère de FtsZ a permis d'explorer en plus de l'influence du nucléotide, celle de l'état de protonation des chaînes latérales de trois acides aspartiques (Asp72A, Asp235B et Asp238B) présents à l'interface. Les résultats ont démontré que les chaînes latérales des Asp235B et 238B doivent être protonées pour que le dimère FtsZ-GTP-Mg soit stable. D'autre part, dans le dimère FtsZ-GDP-Mg en solution, la protonation des Asp 235B et 238B provoque une courbure du dimère avec un éloignement des monomères et un déplacement du GDP à l'interface. Cette séparation ressemble à un début de dépolymérisation. le GDP et l'ion Mg2+ provoquent des déformations du monomère et du dimère de FtsZ. Une étude approfondie de la protonation des résidus de l'interface permettrait de mieux comprendre la polymérisation et l'hydrolyse du GTP.Most bacteria use a prokaryotic protein, FtsZ to divide. FtsZ polymerizes and assembles into the "Z-ring". FtsZ is a GTPase that can bind and hydrolyze GTP. The aim of this study is to explore FtsZ structure and dynamics as a function of GTP/GDP. First, we performed molecular dynamics simulations of FtsZ monomer to study the influence of GTP/GDP and Mg2+ ion on its structure and dynamics. These simulations revealed that the nature of the nucleotide doesn't affect the structure of FtsZ. However, the presence of the magnesium ion in the nucleotide-binding pocket causes conformational changes of FtsZ monomer when bound to GDP. The Mg2+ ion induces a dynamical motion of the GDP within the nucleotide-binding site. In the second part, we studied the influence of the nucleotide on FtsZ dimer by molecular dynamics. These simulations also allowed to investigate the influence of the protonation state of three aspartic acids sidechains (Asp72A, Asp235B and Asp238B). These Asp are present at the dimer interface. We demonstrated that the sidechains of two aspartic acids Asp235B and Asp238B have to be protonated during polymerization of FtsZ-GTP-Mg dimer. On the other hand, when the sidechains of Asp235B and Asp238B are protonated, FtsZ-GDP-Mg dimer gets curved and the two monomers are separated. We also observed a GDP motion at the dimer interface. This separation looks like the beginning of depolymerization. The association of GDP with the Mg2+ ion causes important conformational changes of FtsZ monomer and dimer. An in-depth study of the protonation state of residues at the interface would allow a better understanding of polymerization of FtsZ and GTP hydrolysis

Conformation and dynamics of human urotensin II and urotensin related peptide in aqueous solution

Conformation and dynamics of the vasoconstrictive peptides human urotensin II (UII) and urotensin related peptide (URP) have been investigated by both unrestrained and enhanced-sampling molecular-dynamics (MD) simulations and NMR spectroscopy. These peptides are natural ligands of the G-protein coupled urotensin II receptor (UTR) and have been linked to mammalian pathophysiology. UII and URP cannot be characterized by a single structure but exist as an equilibrium of two main classes of ring conformations, open and folded, with rapidly interchanging subtypes . The open states are characterized by turns of various types centered at K8Y9 or F6W7 predominantly with no or only sparsely populated transannular hydrogen bonds. The folded conformations show multiple turns stabilized by highly populated transannular hydrogen bonds comprising centers F6W7K8 or W7K8Y9. Some of these conformations have not been characterized previously. The equilibrium populations that are experimentally difficult to access were estimated by replica-exchange MD simulations and validated by comparison of experimental NMR data with chemical shifts calculated with density-functional theory. UII exhibits approximately 72% open : 28% folded conformations in aqueous solution. URP shows very similar ring conformations as UII but differs in an open:folded equilibrium shifted further toward open conformations (86:14) possibly arising from the absence of folded N-terminal tail - ring interaction. The results suggest that the different biological effects of UII and URP are not caused by differences in ring conformations but rather by different interactions with UTR