Hydration dynamics as an intrinsic ruler for refining protein structure at lipid membrane interfaces

Abstract

Knowing the topology and location of protein segments at watermembrane interfaces is critical for rationalizing their functions, but their characterization is challenging under physiological conditions. Here, we debut a unique spectroscopic approach by using the hydration dynamics gradient found across the phospholipid bilayer as an intrinsic ruler for determining the topology, immersion depth, and orientation of protein segments in lipid membranes, particularly at water-membrane interfaces. This is achieved through the sitespecific quantification of translational diffusion of hydration water using an emerging tool, 1 H Overhauser dynamic nuclear polarization (ODNP)-enhanced NMR relaxometry. ODNP confirms that the membrane-bound region of α-synuclein (αS), an amyloid protein known to insert an amphipathic α-helix into negatively charged phospholipid membranes, forms an extended α-helix parallel to the membrane surface. We extend the current knowledge by showing that residues 90-96 of bound αS, which is a transition segment that links the α-helix and the C terminus, adopt a larger loop than an idealized α-helix. The unstructured C terminus gradually threads through the surface hydration layers of lipid membranes, with the beginning portion residing within 5-15 Å above the phosphate level, and only the very end of C terminus surveying bulk water. Remarkably, the intrinsic hydration dynamics gradient along the bilayer normal extends to 20-30 Å above the phosphate level, as demonstrated with a peripheral membrane protein, annexin B12. ODNP offers the opportunity to reveal previously unresolvable structure and location of protein segments well above the lipid phosphate, whose structure and dynamics critically contribute to the understanding of functional versatility of membrane proteins.electron paramagnetic resonance | site-directed spin labeling | protein-lipid interaction | liposomes | Parkinson disease

Probing Water Density and Dynamics in the Chaperonin GroEL Cavity

“…Interestingly, we find that the water dynamics at the GroES surface are minimally retarded relative to bulk water, unlike the significantly slowed water dynamics observed in cases of hydrophilic lipid membrane surfaces 32 or representative protein surfaces. 12 This implies that the GroES surface is not attracting water significantly and that the GroES surface-water vs bulk water–water interaction is balanced, so that the interaction of other biomolecular constituents (e.g., protein substrates) with the GroES surface is relatively unhindered.…”

Cholesterol enhances surface water diffusion of phospholipid bilayers

“…In order to compare water diffusivity in different local environments, we introduce the retardation factor, τ /τ bulk , which is the ratio of the τ value of hydration water to that of bulk water, τ bulk . The retardation factor is typically 2-5 for hydration water on water-exposed surfaces of protein or lipid membrane, 6,57,68,75,76 whereas it is around 5-11 in the bilayer interior of lipid assemblies. 72,77,78 However, the relatively modest retardation factor for water within the lipid bilayer only reports on the relatively fast diffusion dynamics of the highly sparse water molecules across the bilayer, but does not provide any information about water content.…”

“…4 Consequently, faster (slower) diffusivity of hydration water reflects on lower (higher) energy barrier for the formation and breaking of hydrogen bonds between water molecules in close proximity to the biomolecular surfaces, encompassing up to at least 2-3 hydration layers off the surface. [5][6][7] Rapid hydrogen-bond rearrangements and fast water diffusivity near the protein-water interface are suggested to a) Chi-Yuan Cheng and Luuk L. C. Olijve contributed equally to this work. b) Present address: Schlumberger Doll research, Cambridge, Massachusetts 02139, USA.…”

Membrane remodeling and mechanics: Experiments and simulations of α-Synuclein

“…In Section 3, we focus on proteins that alter the mechanical properties of both flat and vesicular membranes. First, we highlight EPR spectroscopy and NMR relaxometry as techniques that have been used, specifically in the context of αSyn, to determine the protein's insertion depth in the bilayer [36–38]. Complimentary continuum theory and molecular simulation approaches are introduced next.…”