Biology subjects

Sottini, A.

Publications and source records attributed to Sottini, A..

3 recordsLinked to original sources

bioRxiv2024

The importance of stereochemistry in the disorder-order continuum of protein-protein interactions

Intrinsically disordered proteins can bind via the formation of highly disordered protein complexes without the formation of 3D-structure. Most naturally occurring proteins are "left-handed" or levorotatory (L), made up only of L-amino acids, imprinting molecular structure and communication with stereochemistry. In contrast, their mirror image "right-handed" or dextrorotatory (D) amino acids are rare in Nature. Whether disordered protein complexes are truly independent of 3D-topology and thus of chiral constraints is not clear. To test the chiral constraints of disordered protein-protein interactions, a set of interacting protein pairs covering the disorder-order continuum was chosen as representative examples. By observing both the natural ligands and their stereochemical mirror images in free and bound states, we discovered that chirality was inconsequential in a fully disordered complex. However, if the interaction relied on the ligand undergoing coupled folding and binding, correct stereochemistry was essential. Between these extremes, binding could be observed for the D-ligand with a strength that correlated with the amount of disorder in the final complex. These findings have important implications for our understanding of protein-protein interactions, the molecular processes leading to complex formation, the use of D-peptides in drug discovery, and the chemistry of protein evolution of the first living entities on Earth.

biophysics↗

bioRxiv2022

Ultrafast molecular dynamics observed within a dense protein condensate

Many biological macromolecules can phase-separate in the cell and form highly concentrated condensates. The mesoscopic dynamics of these assemblies have been widely characterized, but their behavior at the molecular scale has remained more elusive. Here we investigate condensates of two highly charged disordered human proteins as a characteristic example of liquid-liquid phase separation. The dense phase is 1000 times more concentrated and has 300 times higher bulk viscosity than the dilute phase. However, single-molecule spectroscopy in individual droplets reveals that the polypeptide chains are remarkably dynamic, with sub-microsecond reconfiguration times. We rationalize this behavior with large-scale all-atom molecular-dynamics simulations, which reveal an unexpectedly similar short-range molecular environment in the dense and dilute phases, suggesting that local biochemical processes and interactions can remain exceedingly rapid in phase-separated systems.

biophysics↗

bioRxiv2020

Disordered Proteins Enable Histone Chaperoning on the Nucleosome

Proteins with highly charged disordered regions are abundant in the nucleus, where many of them interact with nucleic acids and control key processes such as transcription. The functional advantages conferred by protein disorder, however, have largely remained unclear. Here we show that disorder can facilitate a remarkable regulatory mechanism involving molecular competition. Single-molecule experiments demonstrate that the human linker histone H1 binds to the nucleosome with ultra-high affinity. However, the large-amplitude dynamics of the positively charged disordered regions of H1 persist on the nucleosome and facilitate the interaction with the highly negatively charged and disordered histone chaperone prothymosin . Consequently, prothymosin can efficiently invade the H1-nucleosome complex and displace H1 via competitive substitution. By integrating experiments and simulations, we establish a molecular model that rationalizes this process structurally and kinetically. Given the abundance of charged disordered regions in the nuclear proteome, this mechanism may be widespread in cellular regulation.

biophysics↗