Effects of tryptophan residue fluorination on streptavidin stability and biotin-streptavidin interactions via molecular dynamics simulations

Due to its highly specific and very strong binding, the (strept)avidin-biotin system forms the basis for numerous applications in the life sciences: immunoassays, DNA detection systems, affinity chromatog., etc. Fine-tuning of the ligand binding abilities of this system might provide new technologies with relevance to nanoscale research. Here, we report our computational investigations on wild type (WT) and modified streptavidin (SAV), assessing the impact of fluorination of tryptophan residues on biotin binding ability. Complexes of biotin with four SAV protein variants (WT-SAV, 4fW-SAV, 5fW-SAV and 6fW-SAV) were studied. We found that protein stability and folding are predicted to be weakly affected by fluorination. The host protein binding pocket decreases its ability to form numerous hydrogen bonds to biotin in the case of the 4fW-SAV variant. Conversely, the 5fW-SAV mutant is predicted to have an even more stable ligand-host hydrogen bonding network than WT-SAV. Thermodn. perturbation investigations predict a decrease in biotin binding free energy from 3.0 to 6.5 kcal/mol per tetrameric host, with the 5fW-SAV mutant being least affected. Overall, the computational findings indicate that 6fW-SAV and, esp., 5fW-SAV to be promising variants of streptavidin for potential modifiable picomolar binding of the biotin ligand family

Influence of Environmental Humidity on Organization and Molecular Dynamics of Heteromacrocyclic Assemblies

1D and 2D NMR study, Car–Parrinello molecular dynamics, as well as classical molecular dynamics were employed to investigate <i>three derivatives of</i> benzodiazacoronands (achiral compounds which are able to form single crystals with a planar chirality) with intention to explain all subtle effects important during their preorganization, the step anticipating formation of crystals. The experimental study was carried out in two solvents: chloroform and DMSO either containing traces of water (commercial samples) or carefully dried over molecular sieves. Both methods revealed that environmental humidity has a dramatic influence on topology of solute–solvent interactions. Damping of the macrocycle dynamics by its diverse types of interactions with water molecules was shown by computational means. In the most spectacular experiment, we have proved that in chloroform-<i>d</i> during the low temperature measurements traces of water dramatically change the spectral pattern, leading to isochronous NMR signals of the AB spin system of benzodiazacoronand. The temperature of isochronous point (TIP) strongly depends on the benzodiazacoronand/water (BW) ratio. This observation opens a pathway to a new strategy based on variable temperature crystallizations and fitting of BW ratio with hope to optimize conditions for formation of chiral crystals