Bound Water at Protein-Protein Interfaces: Partners, Roles and Hydrophobic Bubbles as a Conserved Motif

Abstract

BackgroundThere is a great interest in understanding and exploiting protein-protein associations as new routes for treating human disease. However, these associations are difficult to structurally characterize or model although the number of X-ray structures for protein-protein complexes is expanding. One feature of these complexes that has received little attention is the role of water molecules in the interfacial region.MethodologyA data set of 4741 water molecules abstracted from 179 high-resolution (≤ 2.30 Å) X-ray crystal structures of protein-protein complexes was analyzed with a suite of modeling tools based on the HINT forcefield and hydrogen-bonding geometry. A metric termed Relevance was used to classify the general roles of the water molecules.ResultsThe water molecules were found to be involved in: a) (bridging) interactions with both proteins (21%), b) favorable interactions with only one protein (53%), and c) no interactions with either protein (26%). This trend is shown to be independent of the crystallographic resolution. Interactions with residue backbones are consistent for all classes and account for 21.5% of all interactions. Interactions with polar residues are significantly more common for the first group and interactions with non-polar residues dominate the last group. Waters interacting with both proteins stabilize on average the proteins' interaction (−0.46 kcal mol−1), but the overall average contribution of a single water to the protein-protein interaction energy is unfavorable (+0.03 kcal mol−1). Analysis of the waters without favorable interactions with either protein suggests that this is a conserved phenomenon: 42% of these waters have SASA ≤ 10 Å2 and are thus largely buried, and 69% of these are within predominantly hydrophobic environments or “hydrophobic bubbles”. Such water molecules may have an important biological purpose in mediating protein-protein interactions.

Evidence of Water Molecules—A Statistical Evaluation of Water Molecules Based on Electron Density

“…These water molecules resemble so-called hydrophobic bubbles. 40 In total, only 1438 (0.54%) of all captured water molecules are hydrophobic bubbles sufficiently resolved by electron density (0.06% of the whole data set). They are highly constrained in their position inside the protein, which is probably the reason why they are resolved by electron density; but display a higher thermal motion than PPI, PLI, or other captured water molecules and about the same B-factor as surface water molecules (see Table 7).…”

Open challenges in structure-based virtual screening: Receptor modeling, target flexibility consideration and active site water molecules description

“…<<Place Figure 3 here>> Other examples of the advantage given by water inclusion in pharmacophore [229], docking [230], de novo design [225,226], and many others computational approaches were given and are reported in the literature [21,23,[197][198][199][231][232][233][234][235][236][237][238][239][240][241][242][243]. Unfortunately, there is no general rule to predict whether a water molecule will be retained within a protein-complex formation, or will be removed [22].…”

Applying Computational Scoring Functions to Assess Biomolecular Interactions in Food Science: Applications to the Estrogen Receptors

“…In protein-ligand associations, water molecules in the active site can mediate (i.e., bridge) interactions between the ligand and protein to change unfavorable interactions to favorable by their appropriate use of two hydrogen bond donors and two acceptors. Water can be thought of as a nano-buffer [162]. Water molecules shape the properties of an active site when they present different steric and electrostatic profile than the desolvated biomacromolecule.…”