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Sequence of the SARS-CoV-2 Spike Transmembrane Domain Encodes Conformational Dynamics.

Sahil Lall1,2, Padmanabhan Balaram1, M K Mathew1

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The SARS-CoV-2 spike protein

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Area of Science:

  • Structural biology
  • Virology
  • Biophysics

Background:

  • The SARS-CoV-2 spike protein is crucial for viral entry into host cells.
  • The spike protein's transmembrane domain (TMD) anchors it to the viral envelope.
  • The TMD's role in viral fusion, beyond anchoring, is not fully understood.

Purpose of the Study:

  • To computationally investigate the dynamics and self-assembly of the SARS-CoV-2 spike TMD.
  • To determine if the TMD actively promotes viral fusion through conformational changes.
  • To explore the influence of membrane composition on TMD behavior.

Main Methods:

  • Atomistic simulations of spike protein TMD segments in POPC and cholesterol-containing membranes.
  • Coarse-grained multimerization simulations using structures from atomistic simulations.
  • Analysis of TMD dynamics, including bobbing, tilting, and helicity changes.

Main Results:

  • The membrane-embedded TMD segment exhibits dynamic behavior, including local membrane thinning.
  • Trimerization simulations revealed diverse TMD architectures dependent on TM helix structure.
  • Asymmetric TMD conformations were observed, potentially stabilizing fusion intermediates.

Conclusions:

  • The SARS-CoV-2 spike TMD is inherently dynamic due to its sequence and length.
  • Trimerization does not eliminate TMD dynamics, suggesting a functional role.
  • Observed TMD conformations may actively facilitate viral membrane fusion.