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Structural, Dynamical, and Entropic Differences between SARS-CoV and SARS-CoV-2 s2m Elements Using Molecular Dynamics

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  • 1Department of Chemistry and Biochemistry and Center for Computational Sciences, Duquesne University, Pittsburgh, Pennsylvania15282, United States.

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PubMed
Summary
This summary is machine-generated.

The SARS-CoV-2 stem-loop II motif (s2m) exhibits increased flexibility and a dynamic "nonaloop," unlike SARS-CoV s2m. These structural differences in the viral RNA motif impact kissing dimer formation and viral lifecycle mechanisms.

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Area of Science:

  • Virology
  • Structural Biology
  • Computational Biology

Background:

  • The stem-loop II motif (s2m) is a conserved RNA element in SARS-CoV and SARS-CoV-2.
  • Its precise function in the viral lifecycle remains unclear, necessitating structural and dynamic studies.

Purpose of the Study:

  • To determine the 3D structure and dynamics of SARS-CoV-2 s2m.
  • To compare the structure and dynamics of SARS-CoV-2 s2m with SARS-CoV s2m.
  • To elucidate how sequence variations affect s2m structure and function.

Main Methods:

  • Construction of 3D coordinates for SARS-CoV and SARS-CoV-2 s2m using NMR data and knowledge-based methods.
  • Extensive molecular dynamics (MD) simulations (3.5 μs) to sample conformational ensembles.
  • Principal Component Analysis (PCA) to identify key conformational substates.

Main Results:

  • SARS-CoV s2m displays a rigid, base-stacked pentaloop, facilitating kissing dimer formation.
  • SARS-CoV-2 s2m exhibits a highly dynamic, expanded
  • nonaloop
  • with increased flexibility and structural disorganization.
  • An entropic penalty explains reduced kissing complex formation in SARS-CoV-2 s2m.
  • Both s2m variants adopt an L-shape due to distinct motif interactions.

Conclusions:

  • Atomistic 3D structures and dynamic differences between SARS-CoV and SARS-CoV-2 s2m were established.
  • Sequence changes lead to significant dynamic variations in the s2m motif.
  • These findings provide a foundation for investigating the biological functions of s2m in viral mechanisms.