Protein packing defects "heat up" interfacial water.

Ligands must displace water molecules from their corresponding protein surface binding site during association. Thus, protein binding sites are expected to be surrounded by non-tightly-bound, easily removable water molecules. In turn, the existence of packing defects at protein binding sites has been also established. At such structural motifs, named dehydrons, the protein backbone is exposed to the solvent since the intramolecular interactions are incompletely wrapped by non-polar groups. Hence, dehydrons are sticky since they depend on additional intermolecular wrapping in order to properly protect the structure from water attack. Thus, a picture of protein binding is emerging wherein binding sites should be both dehydrons rich and surrounded by easily removable water. In this work we shall indeed confirm such a link between structure and dynamics by showing the existence of a firm correlation between the degree of underwrapping of the protein chain and the mobility of the corresponding hydration water molecules. In other words, we shall show that protein packing defects promote their local dehydration, thus producing a region of "hot" interfacial water which might be easily removed by a ligand upon association.

Wrapping mimicking in drug-like small molecules disruptive of protein-protein interfaces.

The discovery of small-molecule drugs aimed at disrupting protein-protein associations is expected to lead to promising therapeutic strategies. The small molecule binds to the target protein thus replacing its natural protein partner. Noteworthy, structural analysis of complexes between successful disruptive small molecules and their target proteins has suggested the possibility that such ligands might somehow mimic the binding behavior of the protein they replace. In these cases, the molecules show a spatial and "chemical" (i.e., hydrophobicity) similarity with the residues of the partner protein involved in the protein-protein complex interface. However, other disruptive small molecules do not seem to show such spatial and chemical correspondence with the replaced protein. In turn, recent progress in the understanding of protein-protein interactions and binding hot spots has revealed the main role of intermolecular wrapping interactions: three-body cooperative correlations in which nonpolar groups in the partner protein promote dehydration of a two-body electrostatic interaction of the other protein. Hence, in the present work, we study some successful complexes between already discovered small disruptive drug-like molecules and their target proteins already reported in the literature and we compare them with the complexes between such proteins and their natural protein partners. Our results show that the small molecules do in fact mimic to a great extent the wrapping behavior of the protein they replace. Thus, by revealing the replacement the small molecule performs of relevant wrapping interactions, we convey precise physical meaning to the mimicking concept, a knowledge that might be exploited in future drug-design endeavors.

Explanation of experimental results of mixed micelles of homologous surfactants through a MM2 bidimensional modeling.

A computational modeling (in gas phase) to study the disposition of the homologous surfactants in a bidimensional simple model of mixed and homogeneous micelles was performed for the case of R-trimethylammonium bromide surfactants with different linear R lengths from R = C(5) to C(17). First, the bidimensional homogeneous (one component) micelle was modeled, and as a second step, heterogeneous (two components) bidimensional micelles were modeled. The difference in the number of carbon atoms between hydrocarbon chains of the surfactants in the heterogeneous micelles, Δn(C), ranged from 2 to 8. Results were contrasted with experimental data obtained at our own laboratory. The exothermic values of the steric energy changes showed strong attraction between components of homologous surfactants mixture, especially when one of the surfactants has a long chain. It may be argued that the inclusion of a shorter surfactant in the mixture and the twisting of the longer surfactant makes the bidimensional arrangement formation more exothermic. All predictions were in agreement with previous experimental results.