Protein Hydration Dynamics and Molecular Mechanism of Coupled Water−Protein Fluctuations

Abstract

Protein surface hydration is fundamental to its structural stability and flexibility, and water-protein fluctuations are essential to biological function. Here, we report a systematic global mapping of water motions in the hydration layer around a model protein of apomyoglobin in both native and molten globule states. With site-directed mutagenesis, we use intrinsic tryptophan as a local optical probe to scan the protein surface one at a time with single-site specificity. With femtosecond resolution, we examined 16 mutants in two states and observed two types of water-network relaxation with distinct energy and time distributions. The first water motion results from the local collective hydrogen-bond network relaxation and occurs in a few picoseconds. The initial hindered motions, observed in bulk water in femtoseconds, are highly suppressed and drastically slow down due to structured water-network collectivity in the layer. The second water-network relaxation unambiguously results from the lateral cooperative rearrangements in the inner hydration shell and occurs in tens to hundreds of picoseconds. Significantly, this longtime dynamics is the coupled interfacial water-protein motions and is the direct measurement of such cooperative fluctuations. These local protein motions, although highly constrained, are necessary to assist the longtime water-network relaxation. A series of correlations of hydrating water dynamics and coupled fluctuations with local protein's chemical and structural properties were observed. These results are significant and reveal various water behaviors in the hydration layer with wide heterogeneity. We defined a solvation speed and an angular speed to quantify the water-network rigidity and local protein flexibility, respectively. We also observed that the dynamic hydration layer extends to more than 10 A. Finally, from native to molten globule states, the hydration water networks loosen up, and the protein locally becomes more flexible with larger global plasticity and partial unfolding.

Hydrogen Bond Network of Water around Protein Investigated with Terahertz and Infrared Spectroscopy

“…5) in albumin aqueous solution masks the variation of the ''aggregated'' g S , but we can assert the damping constant of hydration water is qualitatively larger than that of bulk water. Since the damping constant g S represents the degree of heterogeneity of the HB environment, large g S of hydration water compared with that of bulk claims that hydration water has a heterogeneous HB network structure, which consists of various HB distances and angles, in good accordance with previous experiments (26,35,37) and simulations (12,14,21,96,97). Such heterogeneous HBs are associated with the distortion of the water HB network, since they involve the distortion of the O...O...O angles from the ideal tetrahedral value.…”

“…Molecular dynamics (MD) simulations (12)(13)(14)(15)(16)(17)(18)(19)(20)(21)(22) and other experimental approaches (23)(24)(25)(26)(27)(28)(29)(30)(31)(32)(33)(34)(35)(36)(37) have revealed the protein is surrounded by dynamically retarded hydration water, with the innermost shell having a density higher than that of bulk water. However, even today, experimentally characterizing the dynamics and the structure of the water HB network in this hydration shell is challenging, because the water-water HB lifetime is very short (typically 1 ps) (38).…”

Ultrafast solvation dynamics at binding and active sites of photolyases

“…To further evaluate the local flexibility, we define an average solvation speed (or an average environment reorganization rate) to express how much energy drop (in cm −1 ) per picosecond by local relaxation (20):…”

“…Thus, the comparable time scale, stabilization energy, and solvation speed indicate that both sites have the similar polar environment and initial ultrafast response. The second relaxation in tens of picoseconds reflects the coupled water-protein motions, a collective rearrangement of the local configuration (19,20,39). Although both sites have a similar time scale of approximately 20 ps, the At(6-4)-Wt has a stabilization energy of 471 cm −1 , about ten times larger than that of EcPhr-Wt, leading to a significantly larger solvation speed.…”

“…Typically, extrinsic dye molecules or synthetic amino acids were used as local optical probes to label function sites, and the local relaxations were observed, ranging from femtoseconds to nanoseconds (5,(12)(13)(14). Such labeling of bulky dye molecules usually induces significant local perturbations, and direct characterization with intrinsic chromophores in proteins eliminates those interferences and reveals intact environment responses (4,7,(15)(16)(17)(18)(19)(20)(21), as recently examined in green fluorescence proteins (21). We have recently studied a series of flavoproteins using intrinsic flavin molecule as the optical probe (10,22,23) and especially found the important functional role of local solvation in photolyase (10).…”