Mapping hydration dynamics around a protein surface

Abstract

Protein surface hydration is fundamental to its structure and activity. We report here the direct mapping of global hydration dynamics around a protein in its native and molten globular states, using a tryptophan scan by site-specific mutations. With 16 tryptophan mutants and in 29 different positions and states, we observed two robust, distinct water dynamics in the hydration layer on a few (Ϸ1-8 ps) and tens to hundreds of picoseconds (Ϸ20 -200 ps), representing the initial local relaxation and subsequent collective network restructuring, respectively. Both time scales are strongly correlated with protein's structural and chemical properties. These results reveal the intimate relationship between hydration dynamics and protein fluctuations and such biologically relevant water-protein interactions fluctuate on picosecond time scales.femtosecond dynamics ͉ site-directed mutation ͉ tryptophan scan ͉ water-protein fluctuation W ater motion in the hydration layer is central to protein fluctuation, an essential determinant to its structural stability, dynamics, and function (1-9). Protein surface hydration is a longstanding unresolved problem, but recent extensive studies have merged into a cohesive picture: hydration water molecules are not static but dynamic in nature (1, 2, 10-18). NMR studies (13, 14) have revealed water residence times at protein surfaces within the subnanosecond regime, and molecular dynamics (MD) simulations (15-18) have indicated that water stays in the layer on the time scales from femtoseconds to picoseconds. These processes represent the dynamic exchange of hydration layer water with outside bulk water via thermal fluctuations. Femtosecond-resolved spectroscopic studies of protein solvation (19)(20)(21)(22)(23)(24)(25)(26) recently have shown the dynamics of surface hydration on picosecond time scales with a biphasic distribution. We attributed the first ultrafast solvation to water local relaxation and the second longer-time dynamics to coupled water-protein fluctuations (25,27). To generalize the global heterogeneous hydration dynamics around protein surfaces, correlate the dynamics with protein local structures and chemical identities, and decipher the molecular mechanism of waterprotein fluctuations, we report here our direct mapping of water motions around a globular protein, apomyoglobin (apoMb), in its two states, native and molten globular, using intrinsic tryptophan residue (W) as a local molecular probe to scan the surface by protein engineering.Myoglobin from sperm whale has eight ␣-helices (A-H) with a total of 153 aa (Fig. 1) (28), and all experiments were done with apoMb by removal of the prosthetic heme group. We carefully designed more than 30 mutants and placed tryptophan one at a time along each helix at the protein surface. After we screened all mutant proteins with their structural content, stability, and excited-state lifetime of tryptophan, only 16 mutants are appropriate for mapping global hydration, as shown in Fig. 1. We used a laser wavelength of 290 nm with a pu...

Ultrafast solvation dynamics at binding and active sites of photolyases

“…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).…”

A unified model of protein dynamics

“…The former, however, can be changed in many ways because the hydration shell is not uniform; it is highly structured. Protein surfaces have been designed by evolution and are craggy, contain outcrops and pockets, and have both charged and neutral residues (51,52).…”

Origin of diverse time scales in the protein hydration layer solvation dynamics: A simulation study

“…7, 42 Bhattacharyya et al also obtained timescales in the order of few hundred ps to a few ns. 8,39,40 Much later, Zhong et al employed site directed mutations on sperm whale myoglobin which led to a spectrum of relaxation timescales (1-8 ps and 20-200 ps) 43 that are present at different sites of the same protein. The same group has also studied the effect of charges on the timescales using alanine scan method at different sites.…”