Protein surface water dynamics

The hydration of proteins at subzero temperatures is reviewed. The thermodynamics of the protein-water system and the water molecule dynamics are discussed. The hydration layer around a protein at low temperature is best thought of as being in a glass-like state with the water molecules selectively oriented near ionic and polar groups at the protein surface. Water motions in the nanosecond and microsecond range have been detected. 

Peptides larger than 10 to 20 residues adopt conformations in solution through the interplay of hydrogen bonding, electrostatic and hydrophobic interactions, positioning of polar residues on the solvated surface of the polypeptide, and sequestering of hydrophobic residues in the nonpolar interior. Protein shape is dynamic, changing continuously in response to the solvent environment. The retention process in RPLC is initiated as the protein approaches the stationary-phase surface. Structured water associated at the phase surface and adjacent to hydrophobic contact surfaces on the polypeptide is released into the bulk mobile... 

Bo is the measurement frequency. Rapid exchange between the different fractions is assumed the bulk, water at the protein surface (s) and interior water molecules, buried in the protein and responsible for dispersion (i). In fact, protons from the protein surface exchanging with water lead to dispersion as well and should fall into this category Bulk and s are relevant to extreme narrowing conditions and cannot be separated unless additional data or estimations are available (for instance, an estimation of fg from some knowledge of the protein surface). As far as quadrupolar nuclei are concerned (i.e., and O), dispersion of Rj is relevant of Eqs. (62) and (63) (this evolves according to a Lorentzian function as in Fig. 9) and yield information about the number of water molecules inside the protein and about the protein dynamics (sensed by the buried water molecules). Two important points must be noted about Eqs. (62) and (63). First, the effective correlation time Tc is composed of the protein rotational correlation time and of the residence time iw at the hydration site so that... 

This bimodal dynamics of hydration water is intriguing. A model based on dynamic equilibrium between quasi-bound and free water molecules on the surface of biomolecules (or self-assembly) predicts that the orientational relaxation at a macromolecular surface should indeed be biexponential, with a fast time component (few ps) nearly equal to that of the free water while the long time component is equal to the inverse of the rate of bound to free transition [4], In order to gain an in depth understanding of hydration dynamics, we have carried out detailed atomistic molecular dynamics (MD) simulation studies of water dynamics at the surface of an anionic micelle of cesium perfluorooctanoate (CsPFO), a cationic micelle of cetyl trimethy-lainmonium bromide (CTAB), and also at the surface of a small protein (enterotoxin) using classical, non-polarizable force fields. In particular we have studied the hydrogen bond lifetime dynamics, rotational and dielectric relaxation, translational diffusion and vibrational dynamics of the surface water molecules. In this article we discuss the water dynamics at the surface of CsPFO and of enterotoxin. 

WATER DYNAMICS AT THE SURFACE OF A SMALL PROTEIN, ENTEROTOXIN... 

Smolin, N., and Winter, R. (2004). Molecular dynamics simulations of staphylococcal nuclease Properties of water at the protein surface. J. Phys. Chem. B 108, 15928—19537. 

Molecular dynamics (MD) simulations [29-31], coupled with experimental observations, have played an important role in the understanding of protein hydration. They predicted that the dynamics of ordered water molecules in the surface layer is ultrafast, typically on the picosecond time scales. Most calculated residence times are shorter than experimental measurements reported before, in a range of sub-picosecond to 100 ps. Water molecules at the surface are very mobile and are in constant exchange with bulk water. For example, the trajectory study of myoglobin hydration revealed that among 294 hydration sites, the residence times at 284 sites (96.6% of surface water molecules) are less than lOOps [32]. Furthermore, the population time correlation functions... 

We recently developed a systematic method that uses the intrinsic tryptophan residue (Trp or W) as a local optical probe [49, 50]. Using site-directed mutagenesis, tryptophan can be mutated into different positions one at a time to scan protein surfaces. With femtosecond temporal and single-residue spatial resolution, the fluorescence Stokes shift of the local excited Trp can be followed in real time, and thus, the location, dynamics, and functional roles of protein-water interactions can be studied directly. With MD simulations, the solvation by water and protein (residues) is differentiated carefully to determine the hydration dynamics. Here, we focus our own work and review our recent systematic studies on hydration dynamics and protein-water fluctuations in a series of biological systems using the powerful intrinsic tryptophan as a local optical probe, and thus reveal the dynamic role of hydrating water molecules around proteins, which is a longstanding unresolved problem and a topic central to protein science. 

Biomolecular recognition is mediated by water motions, and the dynamics of associated water directly determine local structural fluctuation of interacting partners [4, 9, 91]. The time scales of these interactions reflect their flexibility and adaptability. For water at protein surfaces, the studies of melittin and other proteins [45, 46] show water motions on tens of picoseconds. For trapped water in protein crevices or cavities, the dynamics becomes much slower and could extend to nanoseconds [40, 71, 92], These rigid water molecules are often hydrogen bonded to interior residues and become part of the structural integrity of many enzymes [92]. Here, we study local water motions in various environments, from a buried crevice to an exposed surface using site-selected tryptophan but with different protein conformations, to understand the correlation between hydration dynamics and conformational transitions and then relate them to biological function. 

Figure 39. Dynamic Stokes shifts of all 16 mutants in two states. Circles and squares are the original data, and the black lines are the best fit. The names of mutants are shown on the top, and the ticks correspond to the data points. The inset in the top panel shows the physical meanings of the two Stokes shifts, A i and AE2- The insets in the lower two panels show different contributions of surface water to AEi (big arcs, light arrow) and AE2 (small ellipse, dark arrow) when tryptophan is buried (left) or exposed (right). Water molecules in the big arcs are within - 10 A around tryptophan, and water molecules in the small ellipse are those that directly interact with protein and probed by tryptophan.

The simulation results from both isomer 1 and isomer 2 show that the observed solvation dynamics around the Trp7 site can arise from strongly coupled neighboring water and protein relaxation. Judging by the time dependence of their separate contributions to the total response, the Stokes shift over tens of picoseconds can apparently result from either surface water or protein conformational relaxation for isomers 1 and 2, respectively. To elucidate the origin of these observed time scales, we performed frozen protein and frozen water simulations. 

MD simulations with either protein or water constrained at the instant of photoexcitation were performed for both isomer 1 and isomer 2. For isomer 1, because surface water relaxation dominates the slow component of the total Stokes shift, in Fig. 44a we show the result of simulations of isomer 1 with an ensemble of frozen protein configurations to examine the role of protein fluctuations. Clearly the long component of indole-water interactions disappears when the protein is constrained. This result shows that without protein fluctuations, indole-water relaxation over tens of picoseconds does not occur. Thus, although surface hydrating water molecules seem to drive the global solvation and, from the dynamics of the protein and water contributions, are apparently responsible for the slowest component of the solvation Stokes shift for isomer 1 (Fig. 42), local protein fluctuations are still required to facilitate this rearrangement process. When the protein is frozen, the ultrafast... 

The robust observation of surface hydration dynamics on two time scales and a series of correlations with protein properties provides a molecular picture of water motions and their coupling with protein fluctuations in the layer, as shown in Fig. 46. The dynamic exchange of hydration layer water with outside bulk... 

This section discusses a selection of NMR results with an emphasis on powder studies, on experiments that describe the dynamics of water at the protein surface, and on lysozyme as a model protein. Methods and theory are not discussed. For review discussions see Kuntz and Kauz-mann (1974), Bryant (1978), Koenig (1980), and Fung (1986). A recent review by Bryant (1988) is an elegant summary of the theory and results for NMR measurements of protein hydration, in powders and in solution. 

Measurements of the dynamic properties of the surface water, particularly NMR measurements, have shown that the characteristic time of the water motion is slower than the bulk water value by a factor of less than 100. The motion is anisotropic. There is litde or no irrotadonally bound water. Study of a protein labeled covalently with a nitroxide spin probe (Polnaszek and Bryant, 1984a,b) has shown that the diffusion constant of the surface water is about 5-fold below the bulk water value. The NMR results are in agreement with measurements of dielectric relaxation of water in protein powders (Harvey and Hoekstra, 1972). 

At 0.25 h start of condensation of water onto weakly interacting unfilled patches of protein surface seen in dynamic and thermodynamic properties... 

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