Accelerated Exchange of a Buried Water Molecule in Selectively Disulfide-Reduced Bovine Pancreatic Trypsin Inhibitor

Protein 3D Hydration: A Case of Bovine Pancreatic Trypsin Inhibitor

Characterization of the hydrated state of a protein is crucial for understanding its structural stability and function. In the present study, we have investigated the 3D hydration structure of the protein BPTI (bovine pancreatic trypsin inhibitor) by molecular dynamics (MD) and the integral equation method in the three-dimensional reference interaction site model (3D-RISM) approach. Both methods have found a well-defined hydration layer around the protein and revealed the localization of BPTI buried water molecules corresponding to the X-ray crystallography data. Moreover, under 3D-RISM calculations, the obtained positions of waters bound firmly to the BPTI sites are in reasonable agreement with the experimental results mentioned above for the BPTI crystal form. The analysis of the 3D hydration structure (thickness of hydration shell and hydration numbers) was performed for the entire protein and its polar and non-polar parts using various cut-off distances taken from the literature as well as by a straightforward procedure proposed here for determining the thickness of the hydration layer. Using the thickness of the hydration shell from this procedure allows for calculating the total hydration number of biomolecules properly under both methods. Following this approach, we have obtained the thickness of the BPTI hydration layer of 3.6 Å with 369 water molecules in the case of MD simulation and 3.9 Å with 333 water molecules in the case of the 3D-RISM approach. The above procedure was also applied for a more detailed description of the BPTI hydration structure near the polar charged and uncharged radicals as well as non-polar radicals. The results presented for the BPTI as an example bring new knowledge to the understanding of protein hydration.

How proteins modify water dynamics

Much of biology happens at the protein-water interface, so all dynamical processes in this region are of fundamental importance. Local structural fluctuations in the hydration layer can be probed by ¹⁷O magnetic relaxation dispersion (MRD), which, at high frequencies, measures the integral of a biaxial rotational time correlation function (TCF)-the integral rotational correlation time. Numerous ¹⁷O MRD studies have demonstrated that this correlation time, when averaged over the first hydration shell, is longer than in bulk water by a factor 3-5. This rotational perturbation factor (RPF) has been corroborated by molecular dynamics simulations, which can also reveal the underlying molecular mechanisms. Here, we address several outstanding problems in this area by analyzing an extensive set of molecular dynamics data, including four globular proteins and three water models. The vexed issue of polarity versus topography as the primary determinant of hydration water dynamics is resolved by establishing a protein-invariant exponential dependence of the RPF on a simple confinement index. We conclude that the previously observed correlation of the RPF with surface polarity is a secondary effect of the correlation between polarity and confinement. Water rotation interpolates between a perturbed but bulk-like collective mechanism at low confinement and an exchange-mediated orientational randomization (EMOR) mechanism at high confinement. The EMOR process, which accounts for about half of the RPF, was not recognized in previous simulation studies, where only the early part of the TCF was examined. Based on the analysis of the experimentally relevant TCF over its full time course, we compare simulated and measured RPFs, finding a 30% discrepancy attributable to force field imperfections. We also compute the full ¹⁷O MRD profile, including the low-frequency dispersion produced by buried water molecules. Computing a local RPF for each hydration shell, we find that the perturbation decays exponentially with a decay "length" of 0.3 shells and that the second and higher shells account for a mere 3% of the total perturbation measured by ¹⁷O MRD. The only long-range effect is a weak water alignment in the electric field produced by an electroneutral protein (not screened by counterions), but this effect is negligibly small for ¹⁷O MRD. By contrast, we find that the ¹⁷O TCF is significantly more sensitive to the important short-range perturbations than the other two TCFs examined here.

Statistical survey of the buried waters in the Protein Data Bank

The structures of buried water molecules were studied in an ensemble of high-quality and non-redundant protein crystal structures. Buried water molecules were clustered and classified in lake-like clusters, which are completely isolated from the bulk solvent, and bay-like clusters, which are in contact with the bulk solvent through a surface water molecule. Buried water molecules are extremely common: lake-like clusters are found in 89 % of the protein crystal structures and bay-like clusters in 93 %. Clusters with only one water molecule are much more common than larger clusters. Both cluster types incline to be surrounded by loop residues, and to a minor extent by residues in extended secondary structure. Helical residues on the contrary do not tend to surround clusters of buried water molecules. One buried water molecule is found every 30-50 amino acid residues, depending on the secondary structures that are more abundant in the protein. Both main- and side-chain atoms are in contact with buried waters; they form four hydrogen bonds with the first water and 1-1.5 additional hydrogen bond for each additional water in the cluster. Consequently, buried water molecules appear to be firmly packed and rigid like the protein atoms. In this regard, it is remarkable to observe that prolines often surround water molecules buried in the protein interior. Interestingly, clusters of buried water molecules tend to be just beneath the protein surface. Moreover, water molecules tend to form a one-dimensional wire rather than more compact arrangements. This agrees with recent evidence of the mechanisms of solvent exchange between internal cavities and bulk solvent.

Transient access to the protein interior: simulation versus NMR

Many proteins rely on rare structural fluctuations for their function, whereby solvent and other small molecules gain transient access to internal cavities. In magnetic relaxation dispersion (MRD) experiments, water molecules buried in such cavities are used as intrinsic probes of the intermittent protein motions that govern their exchange with external solvent. While this has allowed a detailed characterization of exchange kinetics for several proteins, little is known about the exchange mechanism. Here, we use a millisecond all-atom MD trajectory produced by Shaw et al. (Science2010, 330, 341) to characterize water exchange from the four internal hydration sites in the protein bovine pancreatic trypsin inhibitor. Using a recently developed stochastic point process approach, we compute the survival correlation function probed by MRD experiments as well as other quantities designed to validate the exchange-mediated orientational randomization (EMOR) model used to interpret the MRD data. The EMOR model is found to be quantitatively accurate, and the simulation reproduces the experimental mean survival times for all four sites with activation energy discrepancies in the range 0-3 kBT. On the other hand, the simulated hydration sites are somewhat too flexible, and the water flip barrier is underestimated by up to 6 kBT. The simulation reveals that water molecules gain access to the internal sites by a transient aqueduct mechanism, migrating as single-file water chains through transient (<5 ns) tunnels or pores. The present study illustrates the power of state-of-the-art molecular dynamics simulations in validating and extending experimental results.

Molecular dynamics free energy calculations to assess the possibility of water existence in protein nonpolar cavities

Are protein nonpolar cavities filled with water molecules? Although many experimental and theoretical investigations have been done, particularly for the nonpolar cavity of IL-1 beta, the results are still conflicting. To study this problem from the thermodynamic point of view, we calculated hydration free energies of four protein nonpolar cavities by means of the molecular dynamics thermodynamic integration method. In addition to the IL-1 beta cavity (69 A(3)), we selected the three largest nonpolar cavities of AvrPphB (81 A(3)), Trp repressor (87 A(3)), and hemoglobin (108 A(3)) from the structural database, in view of the simulation result from another study that showed larger nonpolar cavities are more likely to be hydrated. The calculations were performed with flexible and rigid protein models. The calculated free energy changes were all positive; hydration of the nonpolar cavities was energetically unfavorable for all four cases. Because hydration of smaller cavities should happen more rarely, we conclude that existing protein nonpolar cavities are not likely to be hydrated. Although a possibility remains for much larger nonpolar cavities, such cases are not found experimentally. We present a hypothesis to explain this: hydrated nonpolar cavities are quite unstable and the conformation could not be maintained.

SIMPLE estimate of the free energy change due to aliphatic mutations: Superior predictions based on first principles

The bioinformatics revolution of the last decade has been instrumental in the development of empirical potentials to quantitatively estimate protein interactions for modeling and design. Although computationally efficient, these potentials hide most of the relevant thermodynamics in 5-to-40 parameters that are fitted against a large experimental database. Here, we revisit this longstanding problem and show that a careful consideration of the change in hydrophobicity, electrostatics, and configurational entropy between the folded and unfolded state of aliphatic point mutations predicts 20-30% less false positives and yields more accurate predictions than any published empirical energy function. This significant improvement is achieved with essentially no free parameters, validating past theoretical and experimental efforts to understand the thermodynamics of protein folding. Our first principle analysis strongly suggests that both the solute-solute van der Waals interactions in the folded state and the electrostatics free energy change of exposed aliphatic mutations are almost completely compensated by similar interactions operating in the unfolded ensemble. Not surprisingly, the problem of properly accounting for the solvent contribution to the free energy of polar and charged group mutations, as well as of mutations that disrupt the protein backbone remains open.