Role of fast dynamics in the complexation of G-quadruplexes with small molecules

G-quadruplexes (G4s) formed by the human telomeric sequence AG₃ (TTAG₃)₃ (Tel22) play a key role in cancer and aging. We combined elastic incoherent neutron scattering (EINS) and quasielastic incoherent neutron scattering (QENS) to characterize the internal dynamics of Tel22 G4s and to assess how it is affected by complexation with two standard ligands, Berberine and BRACO19. We show that the interaction with the two ligands induces an increase of the overall mobility of Tel22 as quantified by the mean squared displacements (MSD) of hydrogen atoms. At the same time, the complexes display a lower stiffness than G4 alone. Two different types of motion characterize the G4 nanosecond timescale dynamics. Upon complexation, an increasing fraction of G4 atomic groups participate in this fast dynamics, along with an increase in the relevant characteristic length scales. We suggest that the entropic contribution to the conformational free energy of these motions might be crucial for the complexation mechanisms.

A combined spectroscopic and molecular modeling Study on structure-function-dynamics under chemical modification: Alpha-chymotrypsin with formalin preservative

Enzyme function can be altered via modification of its amino acid residues, side chains and large-scale domain modifications. Herein, we have addressed the role of residue modification in catalytic activity and molecular recognition of an enzyme alpha-chymotrypsin (CHT) in presence of a covalent cross-linker formalin. Enzyme assay reveals reduced catalytic activity upon increased formalin concentration. Polarization gated anisotropy studies of a fluorophore 8-Anilino-1-naphthalenesulfonic acid (ANS) in CHT show a dip rise pattern in presence of formalin which is consistent with the generation of multiple ANS binding sites in the enzyme owing to modifications of its local amino acid residues. Molecular docking study on amino acid residue modifications in CHT also indicate towards the formation of multiple ANS binding site. The docking model also predicted no change in binding behavior for the substrate Ala-Ala-Phe-7-amido-4-methylcoumarin (AMC) at the active site upon formalin induced amino acid cross-linking.

Enhancing the enzymatic inhibition performance of Cu-based metal-organic frameworks by shortening the organic ligands

Creating more exposed active sites on the metal-organic framework (MOF) surface is crucial for enhancing the recognition ability of MOF artificial receptors. Here, a copper-based MOF Cu(im)₂ (im = imidazole) was utilized to act as an artificial receptor, inhibiting the activity of α-chymotrypsin. The shortest diazole ligand reduced the distance between regenerative copper sites, creating as many active sites as possible on the MOF unit surface. The amount of copper(ii) centers on the Cu(im)₂ surface was calculated to be 4.96 × 10⁶μm^-2. Thus, Cu(im)₂ showed exceedingly higher inhibition performance than other copper-based MOFs. The ChT activity was almost inhibited (88.8%) after the incubation with only 20 μg mL^-1 Cu(im)₂ for 10 min. The binding between ChT and Cu(im)₂ was very fast with high affinity. Further results proved that Cu(im)₂ inhibited the activity of ChT through electrostatic interactions and coordination interactions via the mixed inhibition mode. This strategy to use short ligands to create more active sites on the MOF surface provides a new direction to enhance the inhibition efficiency.

Dynamics of proteins in solution

The dynamics of proteins in solution includes a variety of processes, such as backbone and side-chain fluctuations, interdomain motions, as well as global rotational and translational (i.e. center of mass) diffusion. Since protein dynamics is related to protein function and essential transport processes, a detailed mechanistic understanding and monitoring of protein dynamics in solution is highly desirable. The hierarchical character of protein dynamics requires experimental tools addressing a broad range of time- and length scales. We discuss how different techniques contribute to a comprehensive picture of protein dynamics, and focus in particular on results from neutron spectroscopy. We outline the underlying principles and review available instrumentation as well as related analysis frameworks.