Determinants of neuroglobin plasticity highlighted by joint coarse-grained simulations and high pressure crystallography

Abstract

Investigating the effect of pressure sheds light on the dynamics and plasticity of proteins, intrinsically correlated to functional efficiency. Here we detail the structural response to pressure of neuroglobin (Ngb), a hexacoordinate globin likely to be involved in neuroprotection. In murine Ngb, reversible coordination is achieved by repositioning the heme more deeply into a large internal cavity, the “heme sliding mechanism”. Combining high pressure crystallography and coarse-grain simulations on wild type Ngb as well as two mutants, one (V101F) with unaffected and another (F106W) with decreased affinity for CO, we show that Ngb hinges around a rigid mechanical nucleus of five hydrophobic residues (V68, I72, V109, L113, Y137) during its conformational transition induced by gaseous ligand, that the intrinsic flexibility of the F-G loop appears essential to drive the heme sliding mechanism, and that residue Val 101 may act as a sensor of the interaction disruption between the heme and the distal histidine.

Ligand pathways in neuroglobin revealed by low-temperature photodissociation and docking experiments

“…This hypothesis was supported by molecular-dynamics (MD) simulations, showing the similarity between the cavity system in Ngb and the xenon sites in Mb (Anselmi et al, 2007), since during MD trajectories they both host ligands and constitute a preferential pathway for migration within the protein. High hydrostatic pressure also reinforces this hypothesis, showing that Ngb would hinge around a mechanical nucleus of five hydrophobic residues (Val68, Ile72, Val109, Leu113 and Tyr137) lining the cavity just behind the heme (Colloc'h, Sacquin-Mora et al, 2017). Mutation studies have indeed highlighted the possibility that these residues could be involved in ligand migration (Astudillo et al, 2012;Tejero et al, 2015).…”

“…5(c) and 5(d)]. This cavity corresponds to the Xe-III site (Abraini et al, 2014;Colloc'h, Carpentier et al, 2017;Colloc'h, Sacquin-Mora et al, 2017;Moschetti et al, 2009), which is devoid of electron density in all Ngb structures determined so far in the absence of pressurized gases [Figs. 5(a) Table 4 shows a list of the atoms lining the Xe-III niche and their distances from docked O 2 , within a radius of 5 Å .…”

“…From this analysis, the hydrophobic nature of the Xe-III site surface is evident, since only two atoms out of 12 reported are polar. An analysis of the internal network of cavities in Ngb, carried out using coarse-grained Brownian dynamic simulations, highpressure crystallography and mapping of noble-gas and nitrous oxide docking sites by XRD, led to the hypothesis that the Xe-III site acts as a storage site for small gaseous ligands (Abraini et al, 2014;Colloc'h, Carpentier et al, 2017;Colloc'h, Sacquin-Mora et al, 2017;Moschetti et al, 2009). This would be relevant for radical scavenging and, more generally, would support a catalytic role for Ngb.…”

Coarse-grain simulations on NMR conformational ensembles highlight functional residues in proteins

“…Similar to what has been observed in previous studies 28,39 , the analogous aspects of the profiles reflect the common globin fold, with α-helices appearing as grouped rigidity and in human Hb, gating movements of the leucine residue in G12 governs the hopping of gaseous ligand from and to different binding sites 51 . In neuroglobin, the mechanical properties for all four MN residues have also been shown to be particularly sensitive to pressure changes in high-pressure crystallography 52 .…”

Coarse-grain simulations on NMR conformational ensembles highlight functional residues in proteins

“…In neuroglobin, the mechanical properties for all four MN residues have also been shown to be particularly sensitive to pressure changes in high-pressure crystallography [60].…”