A non-redundant data set of nanobody-antigen crystal structures is presented. The data set consists of a collection of cleaned pdb files which can be readily used as an input with most automatic analysis software. The accompanying data also include nanobody amino acid sequences with the annotated CDR regions. In the tabular format, we provide data on the interaction properties for each complex such as number of intermolecular interactions, experimental affinity and changes of the solvent accessible area. We also include the data regarding the surface composition of all nanobody and antigen molecules (surface occurrence of each amino acid type and its secondary structure). The data may be used for further structural bioinformatic studies of nanobodies and as the reference data when performing comparisons with the conventional antibodies.
COBISS.SI-ID: 1538192579
Guanine-rich DNA oligonucleotides can adopt G-quadruplex (G4) structures in the presence of specific cations. Folding and unfolding of G4 can be characterized thermodynamically, providing the information on the stability of various G4 conformations. We show how the relevant thermodynamic and sometimes kinetic parameters are obtained by employing differential scanning calorimetry (DSC) and global fitting of an appropriate model to the DSC data. We demonstrate that best-fit values of the thermodynamic parameters can be interpreted in terms of the driving forces accompanying the G4 folding/interconversion and how they are translated into the phase diagrams, which provide an elegant description of the G4 phase space over a wide range of solution conditions.
COBISS.SI-ID: 1538548163
The article explains why a DNA containing AGCGA-rich sequence folds into a specific structure called AGCGA quadruplex. AGCGA repeats are found in many human genes involved in the regulation of normal and disease-related cellular processes (neurological disorders, cancer, abnormalities in bone and cartilage), suggesting the physiological importance of AGCGA-quadruplexes. Thermodynamic analysis of their folding reveals that they are stable enough to regulate gene expression in AGCGA rich regions. The thermodynamic stability “fingerprint” of the AGCGA-quadruplex is different from that for Watson-Crick DNA double-stranded and the non-canonical structure of the G-quadruplex. The differences are mainly due to the specific binding of water molecules and base-stacking, which gives the structure considerable conformational flexibility.
COBISS.SI-ID: 1538129603