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FollowDependence of Structure and Dynamics of Novel SARS-CoV-2 on Temperature and Humidity in the Atmosphere
Award from the COVID-19 HPC Consortium
Soumya Rath studies proteins in diseases at the National Inst. of Technology Warangal, where she is an Asst. Professor in the Dept. of Biotechnology
Investigators: Soumya Rath, Kishant Kumar
Affiliation: National Institute of Technology Warangal
The havoc caused by the novel SARS-CoV-2 coronavirus has spread across almost all the nations of the world. The pandemic took place due to the highly contagious nature of the virus which can be easily transmitted from humans to humans. Others in the coronavirus family of viruses, such as SARS and MERS, have infected individuals. However, they gradually disappeared in hot and humid conditions. Data obtained from countries with higher temperatures and humidity also indicate a low propensity for infection. This work studies whether the virus undergoes any biophysical changes in response to changes in atmospheric conditions, mainly temperature and humidity. The study uses molecular dynamics (MD) simulations that solve Newton’s law of motion and deterministically determine the position and momentum of atoms in a system. The virus structural proteins will be modeled first in atomistic and later in coarse-grained (CG) methods, and then the difference in dynamics will be analyzed. This study would open a new dimension in the characterization of SARS-CoV-2 and future corona-family class of viruses in prevention, categorization, and drug designing aspects.
Publications
- Rath, Soumya Lipsa; Padhi, Aditya K.; Mandal, Nabanita, "Scanning the RBD-ACE2 molecular interactions in Omicron variant"; Biochemical and Biophysical Research Communications, 592:18-23; 2022 Jan 6, 10.1016/j.bbrc.2022.01.006
- Mandal, Nabanita; Padhi, Aditya K.; Rath, Soumya Lipsa, "Molecular insights into the differential dynamics of SARS-CoV-2 variants of concern"; Journal of Molecular Graphics and Modelling, 114:108194; 2022 Apr 14, 10.1016/j.jmgm.2022.108194
- Bisht, Deepali; Rath, Soumya Lipsa; Roy, Shounak; Jaiswal, Amit, "MoS2 nanosheets effectively bind to the receptor binding domain of the SARS-CoV-2 spike protein and destabilize the spike-human ACE2 receptor interactions"; Soft Matter, 18:8961-8973; 2022 Oct 20, 10.1039/d2sm01181f
- Rath, Soumya Lipsa; Tripathy, Madhusmita; Mandal, Nabanita, "How Does Temperature Affect the Dynamics of SARS-CoV-2 M Proteins? Insights from Molecular Dynamics Simulations"; The Journal of Membrane Biology, 255:341-356; 2022 May 13, 10.1007/s00232-022-00244-y
- Sarkar, Neellohit; Thakur, Abhimanyu; Ghadge, Jigisha; Rath, Soumya Lipsa, "Computational studies reveal Fluorine based quinolines to be potent inhibitors for proteins involved in SARS-CoV-2 assembly"; Journal of Fluorine Chemistry, 250:109865; 2021 Aug 11, 10.1016/j.jfluchem.2021.109865, NERSC repository: m3615
- Rath, Souyma Lipsa; Kumar, Kishant, Investigation of the Effect of Temperature on the Structure of SARS-CoV-2 Spike Protein by Molecular Dynamics Simulations," Frontiers in Molecular Biosciences, 16 October 2020, https://doi.org/10.3389/fmolb.2020.583523
About NERSC and Berkeley Lab
The National Energy Research Scientific Computing Center (NERSC) is a U.S. Department of Energy Office of Science User Facility that serves as the primary high performance computing center for scientific research sponsored by the Office of Science. Located at Lawrence Berkeley National Laboratory, NERSC serves almost 10,000 scientists at national laboratories and universities researching a wide range of problems in climate, fusion energy, materials science, physics, chemistry, computational biology, and other disciplines. Berkeley Lab is a DOE national laboratory located in Berkeley, California. It conducts unclassified scientific research and is managed by the University of California for the U.S. Department of Energy. »Learn more about computing sciences at Berkeley Lab.
