The Role of Bridging Water and Hydrogen Bonding as Key Determinants of Noncovalent Protein-Carbohydrate Recognition.

Mechanisms of protein-carbohydrate recognition attract a lot of interest due to their roles in various cellular processes and metabolism disorders. We have performed a large-scale analysis of protein structures solved in complex with glucose, galactose and their substituted analogues. We found that, on average, sugar molecules establish five hydrogen bonds (HBs) in the binding site, including one to three HBs with bridging water molecules. The free energy contribution of bridging and direct HBs was estimated using the free energy perturbation (FEP+) methodology for mono- and disaccharides that bind to l-ABP, ttGBP, TrmB, hGalectin-1 and hGalectin-3. We show that removing hydroxy groups that are engaged in direct HBs with the charged groups of Asp, Arg and Glu residues, protein backbone amide or buried water dramatically decreases binding affinity. In contrast, all solvent-exposed hydroxy groups and hydroxy groups engaged in HBs with the solvent-exposed bridging water molecules contribute weakly to binding affinity and so can be replaced to optimize ligand potency. Finally, we rationalize an effect of binding site water replacement on the binding affinity to l-ABP.

Developmental hearing loss impedes auditory task learning and performance in gerbils.

The consequences of developmental hearing loss have been reported to include both sensory and cognitive deficits. To investigate these issues in a non-human model, auditory learning and asymptotic psychometric performance were compared between normal hearing (NH) adult gerbils and those reared with conductive hearing loss (CHL). At postnatal day 10, before ear canal opening, gerbil pups underwent bilateral malleus removal to induce a permanent CHL. Both CHL and control animals were trained to approach a water spout upon presentation of a target (Go stimuli), and withhold for foils (Nogo stimuli). To assess the rate of task acquisition and asymptotic performance, animals were tested on an amplitude modulation (AM) rate discrimination task. Behavioral performance was calculated using a signal detection theory framework. Animals reared with developmental CHL displayed a slower rate of task acquisition for AM discrimination task. Slower acquisition was explained by an impaired ability to generalize to newly introduced stimuli, as compared to controls. Measurement of discrimination thresholds across consecutive testing blocks revealed that CHL animals required a greater number of testing sessions to reach asymptotic threshold values, as compared to controls. However, with sufficient training, CHL animals approached control performance. These results indicate that a sensory impediment can delay auditory learning, and increase the risk of poor performance on a temporal task.