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Updated: Jun 17, 2026
10:50
Assessment of Immunologically Relevant Dynamic Tertiary Structural Features of the HIV-1 V3 Loop Crown R2 Sequence by ab initio Folding
Published on: September 15, 2010
Evolutionary aspect of spike glycoprotein's conformational dynamics
Wentao Xu1, Tianyu Guo1, Haibin Su1
1Department of Chemistry, Laboratory of Theoretical and Computational Chemistry, The Hong Kong University of Science and Technology, Hong Kong, China. haibinsu@ust.hkhaibinsu@ust.hk.
Physical Chemistry Chemical Physics : PCCP
|January 27, 2026
Summary
SARS-CoV-2 Omicron mutations alter the spike protein's receptor binding domain (RBD) motion by affecting glycan dynamics. This molecular mechanism explains viral evolution and adaptability.
Area of Science:
- Virology
- Structural Biology
- Computational Biology
Background:
- The SARS-CoV-2 spike (S) protein's receptor binding domain (RBD) undergoes conformational changes crucial for viral infectivity.
- Understanding how mutations influence RBD dynamics during viral evolution is essential.
Purpose of the Study:
- To investigate the impact of accumulating mutations on the conformational dynamics of the SARS-CoV-2 RBD.
- To elucidate the molecular mechanisms underlying viral evolution and adaptability.
Main Methods:
- All-atomic molecular dynamics simulations were employed to observe RBD motion in wild type and Omicron (BA.2, BA.4&5) variants.
- Analysis of molecular dynamics trajectories revealed differences in RBD motional patterns.
Main Results:
- Significant differences in RBD motion were observed among variants, attributed to specific mutations.
- Omicron variant surface mutations showed a strong coupling effect with glycan dynamics.
- This coupling remodeled the "glycan gate" conformation, regulating RBD motion.
Conclusions:
- Viral surface mutations directly influence glycan dynamics, remodeling the "glycan gate."
- This provides a molecular mechanism for how mutations regulate RBD motion and viral function.
- Findings offer a theoretical basis for understanding SARS-CoV-2 evolutionary adaptability.
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