Conformational dynamics of the Beta and Kappa SARS-CoV-2 spike proteins and their complexes with ACE2 receptor revealed by cryo-EM

The emergence of SARS-CoV-2 Kappa and Beta variants with enhanced transmissibility and resistance to neutralizing antibodies has created new challenges for the control of the ongoing COVID-19 pandemic. Understanding the structural nature of Kappa and Beta spike (S) proteins and their association with ACE2 is of significant importance. Here we present two cryo-EM structures for each of the Kappa and Beta spikes in the open and open-prone transition states. Compared with wild-type (WT) or G614 spikes, the two variant spikes appear more untwisted/open especially for Beta, and display a considerable population shift towards the open state as well as more pronounced conformational dynamics. Moreover, we capture four conformational states of the S-trimer/ACE2 complex for each of the two variants, revealing an enlarged conformational landscape for the Kappa and Beta S-ACE2 complexes and pronounced population shift towards the three RBDs up conformation. These results implicate that the mutations in Kappa and Beta may modify the kinetics of receptor binding and viral fusion to improve virus fitness. Combined with biochemical analysis, our structural study shows that the two variants are enabled to efficiently interact with ACE2 receptor despite their sensitive ACE2 binding surface is modified to escape recognition by some potent neutralizing MAbs. Our findings shed new light on the pathogenicity and immune evasion mechanism of the Beta and Kappa variants.

Thermodynamic analysis of cooperative ligand binding by the ATP-binding DNA aptamer indicates a population-shift binding mechanism

The ATP-binding DNA aptamer is often used as a model system for developing new aptamer-based biosensor methods. This aptamer follows a structure-switching binding mechanism and is unusual in that it binds two copies of its ligand. We have used isothermal titration calorimetry methods to study the binding of ATP, ADP, AMP and adenosine to the ATP-binding aptamer. Using both individual and global fitting methods, we show that this aptamer follows a positive cooperative binding mechanism. We have determined the binding affinity and thermodynamics for both ligand-binding sites. By separating the ligand-binding sites by an additional four base pairs, we engineered a variant of this aptamer that binds two adenosine ligands in an independent manner. Together with NMR and thermal stability experiments, these data indicate that the ATP-binding DNA aptamer follows a population-shift binding mechanism that is the source of the positive binding cooperativity by the aptamer.

The Fading of Distinctiveness

The 1970s were marked by dramatic changes in government policies during the governorship of Sir Murray MacLehose. The New Territories became the locus of a planned population shift away from crowded Hong Kong and Kowloon, and the idea of ‘New Towns’, based on Tsuen Wan’s developments, was central. It went hand-in-hand with infrastructural developments, which revolutionized transportation and ended the relative isolation of Tsuen Wan through the MTR. The administration of Tsuen Wan fundamentally changed and the creation of District Boards (later Councils), beginning first in Tsuen Wan, altered the system of political consultation throughout Hong Kong. The 1980s were marked by dramatic changes in economic policies within China, not least in the areas of China adjacent to Hong Kong, which saw industrialization through the Pearl River delta region and de-industrialization in Tsuen Wan. Emergence of a distinctive Hong Kong identity, and a new political culture, emerged as sovereignty over Hong Kong was resumed by China in 1997. Tsuen Wan changed from the working class town that it has been into one dominated by middle class housing developments, much like the rest of Hong Kong, although the villages of the original inhabitants remained.