Free enthalpies of replacing water molecules in protein binding pockets

Water molecules in the binding pocket of a protein and their role in ligand binding have increasingly raised interest in recent years. Displacement of such water molecules by ligand atoms can be either favourable or unfavourable for ligand binding depending on the change in free enthalpy. In this study, we investigate the displacement of water molecules by an apolar probe in the binding pocket of two proteins, cyclin-dependent kinase 2 and tRNA-guanine transglycosylase, using the method of enveloping distribution sampling (EDS) to obtain free enthalpy differences. In both cases, a ligand core is placed inside the respective pocket and the remaining water molecules are converted to apolar probes, both individually and in pairs. The free enthalpy difference between a water molecule and a CH₃ group at the same location in the pocket in comparison to their presence in bulk solution calculated from EDS molecular dynamics simulations corresponds to the binding free enthalpy of CH₃ at this location. From the free enthalpy difference and the enthalpy difference, the entropic contribution of the displacement can be obtained too. The overlay of the resulting occupancy volumes of the water molecules with crystal structures of analogous ligands shows qualitative correlation between experimentally measured inhibition constants and the calculated free enthalpy differences. Thus, such an EDS analysis of the water molecules in the binding pocket may give valuable insight for potency optimization in drug design.     

Morphology of pentacene films deposited on Cu(1 1 9) vicinal surface

We investigate the morphology of a pentacene (C₂₂H₁₄) film adsorbed on the Cu(1 1 9) vicinal surface by scanning tunnelling microscopy (STM). Thermal treatment of a thick film of molecules generates a long-range ordered structure. Series of molecular rows are alternated with areas where the molecules assume two equivalent orientations. STM data analysis suggests that the ordered structure can be described by a rippled morphology. The behaviour of the film at different annealing temperatures suggests a possible explanation of the film structure as due to an adsorbate-induced modification of the substrate.     

Geometric aspects of p-capacitary potentials

We provide monotonicity formulas for solutions to the p-Laplace equation defined in the exterior of a convex domain. A number of analytic and geometric consequences are derived, including the classical Minkowski inequality as well as new characterizations of rotationally symmetric solutions and domains. The proofs rely on the conformal splitting technique introduced by the second author in collaboration with V. Agostiniani.     

Effect of nature and location of defects on bandgap narrowing in black TiO2 nanoparticles

The increasing need for new materials capable of solar fuel generation is central in the development of a green energy economy. In this contribution, we demonstrate that black TiO(2) nanoparticles obtained through a one-step reduction/crystallization process exhibit a bandgap of only 1.85 eV, which matches well with visible light absorption. The electronic structure of black TiO(2) nanoparticles is determined by the unique crystalline and defective core/disordered shell morphology. We introduce new insights that will be useful for the design of nanostructured photocatalysts for energy applications.     

From lin-benzoguanines to lin-benzohypoxanthines as ligands for Zymomonas mobilis tRNA-guanine transglycosylase: replacement of protein-ligand hydrogen bonding by importing water clusters

The foodborne illness shigellosis is caused by Shigella bacteria that secrete the highly cytotoxic Shiga toxin, which is also formed by the closely related enterohemorrhagic Escherichia coli (EHEC). It has been shown that tRNA-guanine transglycosylase (TGT) is essential for the pathogenicity of Shigella flexneri. Herein, the molecular recognition properties of a guanine binding pocket in Zymomonas mobilis TGT are investigated with a series of lin-benzohypoxanthine- and lin-benzoguanine-based inhibitors that bear substituents to occupy either the ribose-33 or the ribose-34 pocket. The three inhibitor scaffolds differ by the substituent at C(6) being H, NH(2), or NH-alkyl. These differences lead to major changes in the inhibition constants, pK(a) values, and binding modes. Compared to the lin-benzoguanines, with an exocyclic NH(2) at C(6), the lin-benzohypoxanthines without an exocyclic NH(2) group have a weaker affinity as several ionic protein-ligand hydrogen bonds are lost. X-ray cocrystal structure analysis reveals that a new water cluster is imported into the space vacated by the lacking NH(2) group and by a conformational shift of the side chain of catalytic Asp102. In the presence of an N-alkyl group at C(6) in lin-benzoguanine ligands, this water cluster is largely maintained but replacement of one of the water molecules in the cluster leads to a substantial loss in binding affinity. This study provides new insight into the role of water clusters at enzyme active sites and their challenging substitution by ligand parts, a topic of general interest in contemporary structure-based drug design.     

Selective O-acylation of unprotected N-benzylserine methyl ester and O,N-acyl transfer in the formation of cyclo[Asp-Ser] diketopiperazines

The synthesis of two diastereomeric cyclo[Asp-N-Bn-Ser] diketopiperazines (2a and 2b) was investigated. Initial formation of the Boc-aspartyl-N-benzyl serine isopeptide methyl esters (4a and 4b) was observed, which derive from the selective O-acylation of unprotected (S)- or (R)-N-benzylserine. This unexpected O-acylation is preferred over the formation of the tertiary amide and the resulting ester bond is stable in solution to O,N-acyl transfer. The O,N-acyl migration is then triggered by cleavage of the Boc protecting group and treatment with base, which also promotes immediate cyclization to the diketopiperazines.     

Community structure in large-scale cortical networks during motor acts

The purpose of the present work is to evaluate the community structure of the cortical network subserving the neurophysiologic processes in simple motor acts.To this end, we studied the topological properties of the functional brain connectivity in the frequency domain. The functional networks were estimated by means of the imaginary coherence from a dataset of high-resolution EEG recordings (4094 cortical sources) in a group of healthy subjects (n = 10) during a finger extension task. The analysis of the community structure was addressed through a particular detection algorithm that optimizes the modularity, a function related to the level of internal clustering inside the communities in the network. The principal results indicate that the cortical network changes its structural organization during the motor execution with respect to a baseline condition. Notably in the Beta band (12.5–30 Hz), the level of intra-module connectivity decreases, while inter-module connectivity increases reflecting the need for a neural integration of distant regions. Notably, this distributed interaction involves anatomical regions belonging to both the hemispheres including pre-motor and primary motor areas in the frontal and central part of the cortex as well as parietal associative regions, which are related to the planning, selection and execution of actions.