High-Density Hydration Layer of Lysozymes: Molecular Dynamics Decomposition of Solution Scattering Data

Benchmarking predictive methods for small-angle X-ray scattering from atomic coordinates of proteins using maximum likelihood consensus data

Stimulated by informal conversations at the XVII International Small Angle Scattering (SAS) conference (Traverse City, 2017), an international team of experts undertook a round-robin exercise to produce a large dataset from proteins under standard solution conditions. These data were used to generate consensus SAS profiles for xylose isomerase, urate oxidase, xylanase, lysozyme and ribonuclease A. Here, we apply a new protocol using maximum likelihood with a larger number of the contributed datasets to generate improved consensus profiles. We investigate the fits of these profiles to predicted profiles from atomic coordinates that incorporate different models to account for the contribution to the scattering of water molecules of hydration surrounding proteins in solution. Programs using an implicit, shell-type hydration layer generally optimize fits to experimental data with the aid of two parameters that adjust the volume of the bulk solvent excluded by the protein and the contrast of the hydration layer. For these models, we found the error-weighted residual differences between the model and the experiment generally reflected the subsidiary maxima and minima in the consensus profiles that are determined by the size of the protein plus the hydration layer. By comparison, all-atom solute and solvent molecular dynamics (MD) simulations are without the benefit of adjustable parameters and, nonetheless, they yielded at least equally good fits with residual differences that are less reflective of the structure in the consensus profile. Further, where MD simulations accounted for the precise solvent composition of the experiment, specifically the inclusion of ions, the modelled radius of gyration values were significantly closer to the experiment. The power of adjustable parameters to mask real differences between a model and the structure present in solution is demonstrated by the results for the conformationally dynamic ribonuclease A and calculations with pseudo-experimental data. This study shows that, while methods invoking an implicit hydration layer have the unequivocal advantage of speed, care is needed to understand the influence of the adjustable parameters. All-atom solute and solvent MD simulations are slower but are less susceptible to false positives, and can account for thermal fluctuations in atomic positions, and more accurately represent the water molecules of hydration that contribute to the scattering profile.

Ice formation and solvent nanoconfinement in protein crystals

Ice formation within protein crystals is a major obstacle to the cryocrystallographic study of protein structure, and has limited studies of how the structural ensemble of a protein evolves with temperature in the biophysically interesting range from ∼260 K to the protein-solvent glass transition near 200 K. Using protein crystals with solvent cavities as large as ∼70 Å, time-resolved X-ray diffraction was used to study the response of protein and internal solvent during rapid cooling. Solvent nanoconfinement suppresses freezing temperatures and ice-nucleation rates so that ice-free, low-mosaicity diffraction data can be reliably collected down to 200 K without the use of cryoprotectants. Hexagonal ice (Ih) forms in external solvent, but internal crystal solvent forms stacking-disordered ice (Isd) with a near-random stacking of cubic and hexagonal planes. Analysis of powder diffraction from internal ice and single-crystal diffraction from the host protein structure shows that the maximum crystallizable solvent fraction decreases with decreasing crystal solvent-cavity size, and that an ∼6 Å thick layer of solvent adjacent to the protein surface cannot crystallize. These results establish protein crystals as excellent model systems for the study of nanoconfined solvent. By combining fast cooling, intense X-ray beams and fast X-ray detectors, complete structural data sets for high-value targets, including membrane proteins and large complexes, may be collected at ∼220-240 K that have much lower mosaicities and comparable B factors, and that may allow more confident identification of ligand binding than in current cryocrystallographic practice.

The geometry of protein hydration

Based on molecular dynamics simulations of four globular proteins in dilute aqueous solution, with three different water models, we examine several, essentially geometrical, aspects of the protein-water interface that remain controversial or incompletely understood. First, we compare different hydration shell definitions, based on spatial or topological proximity criteria. We find that the best method for constructing monolayer shells with nearly complete coverage is to use a 5 Šwater-carbon cutoff and a 4 Šwater-water cutoff. Using this method, we determine a mean interfacial water area of 11.1 Ų which appears to be a universal property of the protein-water interface. We then analyze the local coordination and packing density of water molecules in the hydration shells and in subsets of the first shell. The mean polar water coordination number in the first shell remains within 1% of the bulk-water value, and it is 5% lower in the nonpolar part of the first shell. The local packing density is obtained from additively weighted Voronoi tessellation, arguably the most physically realistic method for allocating space between protein and water. We find that water in all parts of the first hydration shell, including the nonpolar part, is more densely packed than in the bulk, with a shell-averaged density excess of 6% for all four proteins. We suggest reasons why this value differs from previous experimental and computational results, emphasizing the importance of a realistic placement of the protein-water dividing surface and the distinction between spatial correlation and packing density. The protein-induced perturbation of water coordination and packing density is found to be short-ranged, with an exponential decay "length" of 0.6 shells. We also compute the protein partial volume, analyze its decomposition, and argue against the relevance of electrostriction.

Deciphering complex dynamics of water counteraction around secondary structural elements of allosteric protein complex: Case study of SAP-SLAM system in signal transduction cascade

The first hydration shell of a protein exhibits heterogeneous behavior owing to several attributes, majorly local polarity and structural flexibility as revealed by solvation dynamics of secondary structural elements. We attempt to recognize the change in complex water counteraction generated due to substantial alteration in flexibility during protein complex formation. The investigation is carried out with the signaling lymphocytic activation molecule (SLAM) family of receptors, expressed by an array of immune cells, and interacting with SLAM-associated protein (SAP), composed of one SH2 domain. All atom molecular dynamics simulations are employed to the aqueous solutions of free SAP and SLAM-peptide bound SAP. We observed that water dynamics around different secondary structural elements became highly affected as well as nicely correlated with the SLAM-peptide induced change in structural rigidity obtained by thermodynamic quantification. A few instances of contradictory dynamic features of water to the change in structural flexibility are explained by means of occluded polar residues by the peptide. For βD, EFloop, and BGloop, both structural flexibility and solvent accessibility of the residues confirm the obvious contribution. Most importantly, we have quantified enhanced restriction in water dynamics around the second Fyn-binding site of the SAP due to SAP-SLAM complexation, even prior to the presence of Fyn. This observation leads to a novel argument that SLAM induced more restricted water molecules could offer more water entropic contribution during the subsequent Fyn binding and provide enhanced stability to the SAP-Fyn complex in the signaling cascade. Finally, SLAM induced water counteraction around the second binding site of the SAP sheds light on the allosteric property of the SAP, which becomes an integral part of the underlying signal transduction mechanism.

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

The dynamical and structural properties of water at protein interfaces were characterized on the basis of the broadband complex dielectric constant (0.25 to 400 THz) of albumin aqueous solutions. Our analysis of the dielectric responses between 0.25 and 12 THz first revealed hydration water with retarded reorientational dynamics extending ∼8.5 Å (corresponding to three to four layers) out from the albumin surface. Second, the number of nonhydrogen-bonded water was decreased in the presence of the albumin solute, indicating protein inhibits the fragmentation of the water hydrogen-bond network. Finally, water molecules at the albumin interface were found to form a distorted hydrogen-bond structure due to topological and energetic disorder of the protein surface. In addition, the intramolecular O-H stretching vibration of water (∼100 THz), which is sensitive to hydrogen-bond environment, pointed to a trend that hydration water has a larger population of strongly hydrogen-bonded water molecules compared with that of bulk water. From these experimental results, we concluded that the "strengthened" water hydrogen bonds at the protein interface dynamically slow down the reorientational motion of water and form the less-defective hydrogen-bond network by inhibiting the fragmentation of water-water hydrogen bonds. Nevertheless, such a strengthened water hydrogen-bond network is composed of heterogeneous hydrogen-bond distances and angles, and thus characterized as structurally "distorted."

SAXS/SANS on Supercharged Proteins Reveals Residue-Specific Modifications of the Hydration Shell

Water molecules in the immediate vicinity of biomacromolecules, including proteins, constitute a hydration layer characterized by physicochemical properties different from those of bulk water and play a vital role in the activity and stability of these structures, as well as in intermolecular interactions. Previous studies using solution scattering, crystallography, and molecular dynamics simulations have provided valuable information about the properties of these hydration shells, including modifications in density and ionic concentration. Small-angle scattering of x-rays (SAXS) and neutrons (SANS) are particularly useful and complementary techniques to study biomacromolecular hydration shells due to their sensitivity to electronic and nuclear scattering-length density fluctuations, respectively. Although several sophisticated SAXS/SANS programs have been developed recently, the impact of physicochemical surface properties on the hydration layer remains controversial, and systematic experimental data from individual biomacromolecular systems are scarce. Here, we address the impact of physicochemical surface properties on the hydration shell by a systematic SAXS/SANS study using three mutants of a single protein, green fluorescent protein (GFP), with highly variable net charge (+36, -6, and -29). The combined analysis of our data shows that the hydration shell is locally denser in the vicinity of acidic surface residues, whereas basic and hydrophilic/hydrophobic residues only mildly modify its density. Moreover, the data demonstrate that the density modifications result from the combined effect of residue-specific recruitment of ions from the bulk in combination with water structural rearrangements in their vicinity. Finally, we find that the specific surface-charge distributions of the different GFP mutants modulate the conformational space of flexible parts of the protein.

Importance of protein conformational motions and electrostatic anchoring sites on the dynamics and hydrogen bond properties of hydration water

The microscopic dynamic properties of water molecules present in the vicinity of a protein are expected to be sensitive to its local conformational motions and the presence of polar and charged groups at the surface capable of anchoring water molecules through hydrogen bonds. In this work, we attempt to understand such sensitivity by performing detailed molecular dynamics simulations of the globular protein barstar solvated in aqueous medium. Our calculations demonstrate that enhanced confinement at the protein surface on freezing its local motions leads to increasingly restricted water mobility with long residence times around the secondary structures. It is found that the inability of the surface water molecules to bind with the protein residues by hydrogen bonds in the absence of protein-water (PW) electrostatic interactions is compensated by enhanced water-water hydrogen bonds around the protein with uniform bulklike behaviors. Importantly, it is further noticed that in contrast to the PW hydrogen bond relaxation time scale, the kinetics of the breaking and formation of such bonds are not affected on freezing the protein's conformational motions.

Hydration potential of lysozyme: protein dehydration using a single microparticle technique

For biological molecules in aqueous solution, the hydration pressure as a function of distance from the molecular surface represents a very short-range repulsive pressure that limits atom-atom contact, opposing the attractive van der Waals pressure. Whereas the separation distance for molecules that easily arrange into ordered arrays (e.g., lipids, DNA, collagen fibers) can be determined from x-ray diffraction, many globular proteins are not as easily structured. Using a new micropipette technique, spherical, glassified protein microbeads can be made that allow determination of protein hydration as a function of the water activity (a(w)) in a surrounding medium (decanol). By adjusting a(w) of the dehydration medium, the final protein concentration of the solid microbead is controlled, and ranges from 700 to 1150 mg/mL. By controlling a(w) (and thus the osmotic pressure) around lysozyme, the repulsive pressure was determined as a function of distance between each globular, ellipsoid protein. For separation distances, d, between 2.5 and 9 A, the repulsive decay length was 1.7 A and the pressure extrapolated to d = 0 was 2.2 x 10(8) N/m(2), indicating that the hydration pressure for lysozyme is similar to other biological interfaces such as phospholipid bilayers.

Thickness of the hydration layer of a protein from molecular dynamics simulation

Water molecules around a protein exhibit slow dynamics with respect to that of pure bulk water. One important issue in protein hydration is the thickness of the hydration layer (i.e., the distance from the protein surface up to which the water dynamics is influenced by the protein). Estimation of thickness is crucial to understand better the properties of "biological water" and the role that it plays in guiding the protein's function. We have performed an atomistic molecular dynamics simulation of an aqueous solution of the protein villin headpiece subdomain or HP-36 to estimate the thickness of its hydration water. In particular, several dynamical properties of water around different segments (three alpha-helices) of the protein have been calculated by varying the thickness of the hydration layers. It is found that in general the influence of the helices on water properties extends beyond the first hydration layer. However, the heterogeneous nature of water among the first hydration layers of the three helices diminishes as the thickness is increased. It indicates that, for a small protein such as HP-36, the thickness of "biological water" is uniform for different segments of the protein.

Temperature dependence of protein-hydration hydrodynamics by molecular dynamics simulations

The dynamics of water molecules near the protein surface are different from those of bulk water and influence the structure and dynamics of the protein itself. To elucidate the temperature dependence hydration dynamics of water molecules, we present results from the molecular dynamic simulation of the water molecules surrounding two proteins (Carboxypeptidase inhibitor and Ovomucoid) at seven different temperatures (T=273 to 303 K, in increments of 5 K). Translational diffusion coefficients of the surface water and bulk water molecules were estimated from 2 ns molecular dynamics simulation trajectories. Temperature dependence of the estimated bulk water diffusion closely reflects the experimental values, while hydration water diffusion is retarded significantly due to the protein. Protein surface induced scaling of translational dynamics of the hydration waters is uniform over the temperature range studied, suggesting the importance protein-water interactions.

Properties of Hydration Shells of Protein Molecules at their Pressure- and Temperature-Induced Native-Denatured Transition

Properties of water at the surface of biomolecules are important for their conformational stability. The behaviour of hydrating water at protein transition (t) pressures P(t) and temperatures T(t) , with the points (P(t),T(t) ) lying in the Native-Denatured (N-D) transition line, is studied. Hydration shells at the hydrophilic regions of protein molecules with surface charge density sigma are investigated with the help of the equation of state of water in an open system. The local values of sigma rather close to each other (sigma(D) approximately 0.3 C m(-2)) are found for six different experimental lines of the N-D transition found in the literature. The values sigma(D) correspond to the crossings of the total pressure (P(t)+Pi) vs sigma isotherms at different T(t) (Pi-electrostriction pressure). The pressures P(t) and temperatures T(t) appear to be related with some selected sites at the surfaces of the protein molecules.