Active-site protein dynamics and solvent accessibility in nativeAchromobacter cycloclastescopper nitrite reductase

Abstract

Microbial nitrite reductases are denitrifying enzymes that are a major component of the global nitrogen cycle. Multiple structures measured from one crystal (MSOX data) of copper nitrite reductase at 240 K, together with molecular-dynamics simulations, have revealed protein dynamics at the type 2 copper site that are significant for its catalytic properties and for the entry and exit of solvent or ligands to and from the active site. Molecular-dynamics simulations were performed using different protonation states of the key catalytic residues (Asp CAT and His CAT ) involved in the nitrite-reduction mechanism of this enzyme. Taken together, the crystal structures and simulations show that the Asp CAT protonation state strongly influences the active-site solvent accessibility, while the dynamics of the active-site 'capping residue' (Ile CAT ), a determinant of ligand binding, are influenced both by temperature and by the protonation state of Asp CAT . A previously unobserved conformation of Ile CAT is seen in the elevated temperature series compared with 100 K structures. DFT calculations also show that the loss of a bound water ligand at the active site during the MSOX series is consistent with reduction of the type 2 Cu atom.

Insight into Compounds with Cu(H2O)62+ Units: New Ideas for Understanding Cu2+ in Tutton Salts

“…22 Furthermore, at the present time there is a growing interest in copper-doped Tutton salts because of their potential application to the study of a number of copper-containing enzymes whose substrates are proposed to displace water in the active site. 22,23 The Cu(H 2 O) 6 2+ complex has also been studied 24−27 in Zn(H 2 O) 6 SiF 6 , a lattice with higher symmetry than a Tutton salt. 28 It should be remarked that the trigonal lattice Zn(H 2 O) 6 SiF 6 doped with Cu 2+ was the first system providing indisputable evidence 29,12,14,26 on the occurrence of the socalled static Jahn−Teller effect (JTE) 30−32 at low temperatures, where the geometry of the Cu(H 2 O) 6 2+ complex is clearly elongated.…”

Resolving polymorphs and radiation-driven effects in microcrystals using fixed-target serial synchrotron crystallography

“…As structural differences in the loop region around Asp188 were observed between polymorphs, further comparison was undertaken to seek to understand the mechanism behind the switching between populations. Multiple single-crystal structures are available for resting-state AcNiR, primarily measured at 100 K but also at elevated cryogenic temperatures (Sen et al, 2017). Superposition of this loop region in AcNiR structures determined at different temperatures ( Supplementary Fig.…”

The Effect of Cofactor Binding on the Conformational Plasticity of the Biological Receptors in Artificial Metalloenzymes: The Case Study of LmrR

“…Molecular Modeling has been widely used to decode the nature of the dynamical events involved in structure-function relationship of naturally-occurring biological macromolecules. From short to large scale motions, theoretical (e.g., Molecular Dynamics (MD) simulations and Normal Modes Analysis) studies constantly provide evidence on how the dynamics of the protein host is influenced by the presence or absence of substrates and/or inhibitors as well as the tight relationship between these changes and the accessibility to catalytically efficient configurations (Dutta and Mishra, 2017; Sen et al, 2017; Sharma et al, 2017; Wilson and Wetmore, 2017; Wilson et al, 2017; Kamariah et al, 2018; Luirink et al, 2018; Rout et al, 2018; Schlee et al, 2018). It is therefore a legitimate question to use computation to assess to what extent bridging chemical and biological entities disturb the natural conformational space of the biomolecules and how damaging/beneficial this can be for catalysis.…”