Unintended consequences? Water molecules at biological and crystallographic protein–protein interfaces

tThe importance of protein–protein interactions (PPIs) is becoming increasingly appreciated, as theseinteractions lie at the core of virtually every biological process. Small molecule modulators that targetPPIs are under exploration as new therapies. One of the greatest obstacles faced in crystallographicallydetermining the 3D structures of proteins is coaxing the proteins to form “artificial” PPIs that lead touniform crystals suitable for X-ray diffraction. This work compares interactions formed naturally, i.e.,“biological”, with those artificially formed under crystallization conditions or “non-biological”. In partic-ular, a detailed analysis of water molecules at the interfaces of high-resolution (≤2.30˚A) X-ray crystalstructures of protein–protein complexes, where 140 are biological protein–protein complex structuresand 112 include non-biological protein–protein interfaces, was carried out using modeling tools basedon the HINT forcefield. Surprisingly few and relatively subtle differences were observed between thetwo types of interfaces: (i) non-biological interfaces are more polar than biological interfaces, yet there isbetter organized hydrogen bonding at the latter; (ii) biological associations rely more on water-mediatedinteractions with backbone atoms compared to non-biological associations; (iii) aromatic/planar residuesplay a larger role in biological associations with respect to water, and (iv) Lys has a particularly large roleat non-biological interfaces. A support vector machines (SVMs) classifier using descriptors from this studywas devised that was able to correctly classify 84% of the two interface types