Colorimetric quantification of linking in thermoreversible nanocrystal gel assemblies

Nanocrystal gel networks can be responsive, tunable materials, but deliberately designing their structure and controlling their properties have been challenging. By employing reversibly bonded molecular linkers, gelation can be realized under conditions predicted by thermodynamics. But, simulations have offered the only microscopic insights, with no experimental means to monitor linking leading to gelation. Here, we introduce a metal coordination linkage with a distinct optical signature allowing us to quantify linking in situ and establish the structural and thermodynamic basis for assembly. Due to coupling between linked indium tin oxide nanocrystals, their infrared absorption shifts abruptly at a chemically tunable gelation temperature. We quantify bonding spectroscopically and use molecular dynamics simulations to understand bonding motifs as a function of temperature, revealing that gel formation is governed by reaching a critical number of effective links that extend the nanocrystal network. Microscopic insights from our colorimetric linking chemistry enable switchable gels based on equilibrium thermodynamic principles, opening the door to rational design of programmable nanocrystal net-work assemblies.

Kinetic Constraints in the Specific Interaction between Phosphorylated Ubiquitin and Proteasomal Shuttle Factors

Ubiquitin (Ub) specifically interacts with the Ub-associating domain (UBA) in a proteasomal shuttle factor, while the latter is involved in either proteasomal targeting or self-assembly coacervation. PINK1 phosphorylates Ub at S65 and makes Ub alternate between C-terminally relaxed (pUbRL) and retracted conformations (pUbRT). Using NMR spectroscopy, we show that pUbRL but not pUbRT preferentially interacts with the UBA from two proteasomal shuttle factors Ubqln2 and Rad23A. Yet discriminatorily, Ubqln2-UBA binds to pUb more tightly than Rad23A does and selectively enriches pUbRL upon complex formation. Further, we determine the solution structure of the complex between Ubqln2-UBA and pUbRL and uncover the thermodynamic basis for the stronger interaction. NMR kinetics analysis at different timescales further suggests an indued-fit binding mechanism for pUb-UBA interaction. Notably, at a relatively low saturation level, the dissociation rate of the UBA-pUbRL complex is comparable with the exchange rate between pUbRL and pUbRT. Thus, a kinetic constraint would dictate the interaction between Ub and UBA, thus fine-tuning the functional state of the proteasomal shuttle factors.

Relative Humidity: A Control Valve of the Steam Engine Climate

In the words of Heinrich Hertz in 1885, the Earth is a “gigantic steam engine”. On average, of the planet’s cross section exposed to sunlight, 72 % belong to the global ocean. With a delay of only 2-3 months, most of the heat absorbed there is released by evaporation rather than by thermal radiation. Water vapour is the dominating “greenhouse gas” of the marine troposphere with a typical relative humidity (RH) of 80 % at the surface. Observing the heat transport across the ocean surface permits insight in the powerhouse of the “steam engine”, controlled by the RH at the surface, a quantity that is often considered the “Cinderella” among the climate data. RH of the troposphere also controls cloud formation that is equally fundamental as challenging for climate research. As a precise and perfectly consistent thermodynamic basis for the description of such processes, the new oceanographic standard TEOS-10 was introduced by UNESCO/IOC in 2010 and IUGG in 2011. Its equations cover all thermodynamic properties of liquid water, seawater, ice and humid air, as well as their mutual equilibria and phase transitions. For harmonisation of the inconsistent RH definitions of humid air between meteorology and climatology, the relative fugacity has been defined as a physically more reasonable RH substitute that does not rely on the approximation of ideal gases. Doi: 10.28991/HEF-2021-02-02-06 Full Text: PDF

Thermodynamic basis of the α-helix and DNA duplex

Analysis of calorimetric and crystallographic information shows that the α-helix is maintained not only by the hydrogen bonds between its polar peptide groups, as originally supposed, but also by van der Waals interactions between tightly packed apolar groups in the interior of the helix. These apolar contacts are responsible for about 60% of the forces stabilizing the folded conformation of the α-helix and their exposure to water on unfolding results in the observed heat capacity increment, i.e. the temperature dependence of the melting enthalpy. The folding process is also favoured by an entropy increase resulting from the release of water from the peptide groups. A similar situation holds for the DNA double helix: calorimetry shows that the hydrogen bonding between conjugate base pairs provides a purely entropic contribution of about 40% to the Gibbs energy while the enthalpic van der Waals interactions between the tightly packed apolar parts of the base pairs provide the remaining 60%. Despite very different structures, the thermodynamic basis of α-helix and B-form duplex stability are strikingly similar. The general conclusion follows that the stability of protein folds is primarily dependent on internal atomic close contacts rather than the hydrogen bonds they contain.