Selected article for: "domain structural arrangement and structural flexibility"
Author: Serena H. Chen; M. Todd Young; John Gounley; Christopher Stanley; Debsindhu Bhowmik
Title: Distinct Structural Flexibility within SARS-CoV-2 Spike Protein Reveals Potential Therapeutic Targets
  • Document date: 2020_4_18
    • ID: klb8oe9q_8
    Snippet: The NTD and RBD are within the S1 subunit and are responsible for binding to host receptors, while the S2 domain is in the S2 subunit which mediates fusion of the viral and host membranes [14] , [15] . Fig. 1 A-D shows the initial protomer structures of the four S proteins, each highlighted by the three domains. To determine the dynamic change of the domain organization in the protomer structures, we measured the distribution of the interdomain d.....
    Document: The NTD and RBD are within the S1 subunit and are responsible for binding to host receptors, while the S2 domain is in the S2 subunit which mediates fusion of the viral and host membranes [14] , [15] . Fig. 1 A-D shows the initial protomer structures of the four S proteins, each highlighted by the three domains. To determine the dynamic change of the domain organization in the protomer structures, we measured the distribution of the interdomain distances from 5,000 structures of each system taken from 25 independent 200 ns MD simulations (Fig. 1 E-G) . Given the limited timescale, we made no attempt to reproduce the thermodynamics but focused on computing the structural features of the systems [17] . The overall distributions of the three interdomain distances are broad, ranging from 40Ã… to 110Ã… between S2 and NTD/RBD domains and 30Ã… to 100Ã… between NTD and RBD domains. These wide distributions indicate enhanced structural flexibility in the domain arrangement of the four protomer systems compared to the cryo-EM structures.

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