Internal Water and Microsecond Dynamics in Myoglobin

Abstract

Myoglobin (Mb) binds diatomic ligands, like O2, CO, and NO, in a cavity that is only transiently accessible. Crystallography and molecular simulations show that the ligands can migrate through an extensive network of transiently connected cavities but disagree on the locations and occupancy of internal hydration sites. Here, we use water 2H and 17O magnetic relaxation dispersion (MRD) to characterize the internal water molecules in Mb under physiological conditions. We find that equine carbonmonoxy Mb contains 4.5 ± 1.0 ordered internal water molecules with a mean survival time of 5.6 ± 0.5 μs at 25 °C. The likely locations of these water molecules are the four polar hydration sites, including one of the xenon-binding cavities, that are fully occupied in all high-resolution crystal structures of equine Mb. The finding that water escapes from these sites, located 17–31 Å apart in the protein, on the same μs time scale suggests a global exchange mechanism. We propose that this mechanism involves transient penetration of the protein by H-bonded water chains. Such a mechanism could play a functional role by eliminating trapped ligands. In addition, the MRD results indicate that 2 or 3 of the 11 histidine residues of equine Mb undergo intramolecular hydrogen exchange on a μs time scale.

Time Scales of Conformational Gating in a Lipid-Binding Protein

“…In the joint fit, the three parameters describing components 0 and 1, which are both associated with the external hydration shell, were assumed , is invariably found for cross-linked proteins but not for proteins in solution. 34,35 The parameter values obtained for rIFABP are similar to those found for other proteins: τ S,1 = 6.8 ± 0.8 ns and = ± N 2.4 0.2 1 1 2 for BPTI 34,44 and τ S,1 = 6 ± 1 ns and = ± N 3.6 0.6 1 1 2 for myoglobin. 35 As before, 34,35 we attribute component 1 chiefly to interfacially confined water molecules in the dense protein clusters of the spatially heterogeneous gel.…”

“…34,35 The parameter values obtained for rIFABP are similar to those found for other proteins: τ S,1 = 6.8 ± 0.8 ns and = ± N 2.4 0.2 1 1 2 for BPTI 34,44 and τ S,1 = 6 ± 1 ns and = ± N 3.6 0.6 1 1 2 for myoglobin. 35 As before, 34,35 we attribute component 1 chiefly to interfacially confined water molecules in the dense protein clusters of the spatially heterogeneous gel. 39 From component 0 we obtain the dynamic perturbation factor ξ H = 7.6 ± 0.2, not significantly different from BPTI (7.8 ± 0.3) 34,44 or myoglobin (7.3 ± 0.5).…”

The Multiple Roles of Waters in Protein Solvation

“…Water molecules showing long residence times on the surface of the protein are uncommon for any protein fold, and water molecules continuously bound to a single residue are extremely rare (see Figure 5), as was in fact anticipated from static measures (see above). In summary, the concept of structural waters as defined from X-Ray crystallography does not fit well with the dynamic picture of solvation derived from our simulations where, as discussed by others (for example 7,9,[17][18][19] ), fast exchange of protein-interacting water is a universal trend.…”

A rapid, non-invasive and non-destructive method for studying swelling behavior and microstructure variations of hydrogels

“…In swollen hydrogel, the lifetime of bound water on the polymer surface is of the order of nanosecond if there is no rigid water residing in phase-separated regions (Kaieda & Halle, 2013). This means that on the timescale of T2, covering many tens of ms (even s), bound water exchanges rapidly with the intermediate water, so the intermediate water carries the bound-water information in an indirect way via the diffusive average (Shapiro, 2011).…”