Microcalorimetry is an excellent method of determining the thermodynamics of ligand–protein binding in solution, because the signal being measured is the observed binding enthalpy (Db-obsH [Editors’ note: this term can also be written DHobs or DbHobs as seen elsewhere in this book]), which is free of any model assumptions. The affinity (DbG) can be computed from the shape of a binding curve, an...

By means of density functional theory, we systematically investigate the insertion and diffusion of Na and Li in layered Si materials (polysilane and H-passivated silicene), in comparison with bulk Si. It is found that Na binding and mobility can be significantly facilitated in layered Si structures. In contrast to the Si bulk, where Na insertion is energetically unfavorable, Na storage can be ...

An experimental study of the bonding geometry and electronic coupling of cis-bis(isothiocyanato)bis(2,2(')-bipyridyl-4,4(')-dicarboxylato)-ruthenium(II) (N3) adsorbed on rutile TiO(2)(110) is presented, along with supporting theoretical calculations of the bonding geometry. Samples were prepared in situ using ultrahigh vacuum electrospray deposition. Core-level photoemission spectroscopy was us...

Current progress in computational structure-based protein design is reviewed in the areas of methodology and applications. Foundational advances include new potential functions, more efficient ways of computing energetics, flexible treatments of solvent, and useful energy function approximations, as well as ensemble-based approaches to scoring designs for inclusion of entropic effects, improvem...

Recent progress in glycobiology has revealed that cell surface oligosaccharides play an essential role in recognition events. More precisely, these saccharides may be complexed by lectins, carbohydrate-binding proteins other than enzymes and antibodies, able to recognise sugars in a highly specific manner. The ubiquity of lectin-carbohydrate interactions opens enormous potential for their explo...

A dynamic equilibrium between covalent 1:1 hairpin and 2:1 duplex DNA adducts of a pyrrolobenzodiazepine (PBD) minor groove binding agent () has been observed for the first time. The equilibrium, which establishes over 1 hour and must require unfolding of both types of adducts, is surprising given that PBDs normally require DNA minor groove structure for binding and take 24 hours for complete r...

Transcriptional regulation depends upon the binding of transcription factor (TF) proteins to DNA in a sequence-dependent manner. Although many experimental methods address the interaction between DNA and proteins, they generally do not comprehensively and accurately assess the full binding repertoire (the complete set of sequences that might be bound with at least moderate strength). Here, we d...