scholarly journals Non-local effects of point mutations on the stability of a protein module

2017 ◽  
Vol 147 (10) ◽  
pp. 105101 ◽  
Author(s):  
Mateusz Chwastyk ◽  
Andrés M. Vera ◽  
Albert Galera-Prat ◽  
Melissabye Gunnoo ◽  
Damien Thompson ◽  
...  
Atmosphere ◽  
2021 ◽  
Vol 12 (2) ◽  
pp. 284
Author(s):  
Evan A. Kalina ◽  
Mrinal K. Biswas ◽  
Jun A. Zhang ◽  
Kathryn M. Newman

The intensity and structure of simulated tropical cyclones (TCs) are known to be sensitive to the planetary boundary layer (PBL) parameterization in numerical weather prediction models. In this paper, we use an idealized version of the Hurricane Weather Research and Forecast system (HWRF) with constant sea-surface temperature (SST) to examine how the configuration of the PBL scheme used in the operational HWRF affects TC intensity change (including rapid intensification) and structure. The configuration changes explored in this study include disabling non-local vertical mixing, changing the coefficients in the stability functions for momentum and heat, and directly modifying the Prandtl number (Pr), which controls the ratio of momentum to heat and moisture exchange in the PBL. Relative to the control simulation, disabling non-local mixing produced a ~15% larger storm that intensified more gradually, while changing the coefficient values used in the stability functions had little effect. Varying Pr within the PBL had the greatest impact, with the largest Pr (~1.6 versus ~0.8) associated with more rapid intensification (~38 versus 29 m s−1 per day) but a 5–10 m s−1 weaker intensity after the initial period of strengthening. This seemingly paradoxical result is likely due to a decrease in the radius of maximum wind (~15 versus 20 km), but smaller enthalpy fluxes, in simulated storms with larger Pr. These results underscore the importance of measuring the vertical eddy diffusivities of momentum, heat, and moisture under high-wind, open-ocean conditions to reduce uncertainty in Pr in the TC PBL.


2015 ◽  
Vol 23 (20) ◽  
pp. 26064 ◽  
Author(s):  
Rahul Trivedi ◽  
Yashna Sharma ◽  
Anuj Dhawan

2017 ◽  
Author(s):  
Juan José Mompó ◽  
Haritz Iribas ◽  
Javier Urricelqui ◽  
Alayn Loayssa
Keyword(s):  

2020 ◽  
Author(s):  
Mohamed Raef Smaoui ◽  
Hamdi Yahyaoui

Abstract The interaction between the receptor-binding domain of the SARS-CoV-2 spike glycoprotein and the ACE2 enzyme is believed to be the entry point of the virus into various cells in the body, including the lungs, heart, liver, and kidneys. The current focus of several therapeutic design efforts explore attempts at affecting the binding interaction between the two proteins to limit the activity of the virus and disease progression. In this work, we analyze the stability of the spike protein under all possible single-point mutations in the receptor-binding domain and computationally explore mutations that can affect the binding with the ACE2 enzyme. We unravel the mutation landscape of the receptor region and assess the toxicity potential of single and multi-point mutations, generating insights for future vaccine efforts on potential mutations that might further stabilize the spike protein and increase its infectivity. We developed a tool, called SpikeMutator, to construct full atomic protein structures of the mutant spike proteins and shared a database of 3,800 single-point mutant structures. We analyzed the recent 65,000 reported spike sequences across the globe and observed the emergence of stable multi-point mutant structures. Using the landscape, we searched through 7.5 million possible 2-point mutation combinations and report that the (R355D K424E) mutation produces one of the strongest spike proteins that therapeutic efforts should investigate for the sake of developing an effective vaccine.


2004 ◽  
Vol 98 (4) ◽  
pp. 345-363 ◽  
Author(s):  
Ashley P. Willis ◽  
Anvar Shukurov ◽  
Andrew M. Soward ◽  
Dmitry Sokoloff

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