QM/MM study of N501 involved intermolecular interaction between SARS-CoV-2 receptor binding domain and antibody of human origin.

Intermolecular interaction between key residue N501 of the epitope on SARS-CoV-2 RBD and screening antibody B38 was studied using the QM/MM and QM approach. The QM/MM optimized geometry shows that angle X-H---Y is 165° for O-H---O between mAb light chain S30 and RBD N501. High level MP2 calculations indicated the interaction between RBD N501 and S30 of B38 Fab light chain provide a relatively strong attractive force of - 3.32 kcal/mol, whereas the hydrogen bond between RBD Q498 and S30 was quantified as 0.10 kcal/mol. The decrease in ESP partial charge on hydrogen atom of hydroxyl group on S30 drops from 0.38 a.u. to 0.31 a.u., exhibiting the sharing of 0.07 a.u. from the lone pair electron oxygen of N501 due to hydrogen bond formation. The NBO occupancy of hydrogen atom also decreases from 25.79 % to 22.93 % in the hydroxyl H-O NBO bond of S30. However, the minor change of NBO hybridization of hydroxyl oxygen of S30 from sp3.00 to sp3.05 implies the rigidity of hydrogen bond tetrahedral geometry in the relative dynamic protein complex. The O-H---O angle is 165° which is close but not exactly linear. The structural requirement for sp3 hybridization of oxygen for hydroxyl group on S30 and dimension of protein likely prevent O-H---O from adopting linear geometry. The hydrogen bond strengths were also calculated using a variety of DFT methods, and the result of - 3.33 kcal/mol from the M06L method is the closest to that of the MP2 calculation. Results of this work may aid in the COVID-19 vaccine and drug screening.

Travel changes and equitable access to urban parks in the post COVID-19 pandemic period: Evidence from Wuhan, China.

COVID-19 has spread worldwide, leading to a significant impact on daily life. Numerous studies have confirmed that people have changed their travel to urban green spaces during the COVID-19 pandemic. However, in China, where COVID-19 has been effectively controlled, how the travel behavior of visitors to urban parks has changed under different risk levels (RLs) of COVID-19 is unclear. Faced with these gaps, we took a highly developed city, Wuhan, as a case study and a questionnaire survey was conducted with 3276 respondents to analyze the changes in park visitors' travel behaviors under different COVID-19 RLs. Using a stated preference (SP) survey method, four RLs were assigned: new cases in other provinces (RL1), Hubei province (RL2), Wuhan (RL3), and in the district of the park (RL4). The results indicated that visitors reduced their willingness to visit urban parks, with 78.39%, 37.97%, and 13.34% of visitors remaining under RL2, RL3, and RL4, respectively. Furthermore, the service radius of urban parks also shrank from 4230 m under no new cases of COVID-19 to approximately 3000 m under RL3. A higher impact was found for visitors using public transport, those with a higher income and higher education, and female visitors. Based on the modified travel behaviors, the Gaussian-based two-step floating catchment area (2SFCA) method was used to evaluate the accessibility and the Gini coefficient was calculated to represent the equality of the urban parks. A higher RL led to lower accessibility and greater inequitable access. The results should help the government guide residents' travel behaviors after COVID-19.