Coevolution, Dynamics and Allostery Conspire in Shaping Cooperative Binding and Signal Transmission of the SARS-CoV-2 Spike Protein with Human Angiotensin-Converting Enzyme 2
Abstract
:1. Introduction
2. Results and Discussion
2.1. Sequence Analysis Links Evolutionary Patterns in SARS-CoV Spike Proteins with Shared Conserved Hotspots at the Binding Interface
2.2. Coevolution and Mutual Information Interdependences of the SARS-CoV-RBD and ACE2 Suggest Potential Regulator and Transmitter Sites of Binding and Communication
2.3. Conformational Dynamics of the SARS-CoV and SARS-CoV-2 RBD Proteins: A Comparative Analysis of ACE2-Induced Protein Mobility and Dynamics-Driven Allostery
2.4. Mutational Scanning and Energetic Analysis of the Binding Interfaces: A Cooperative Effect of Multiple Residues Drives SARS-CoV-2 Binding with Host Receptor
3. Materials and Methods
3.1. Sequence Conservation and Coevolutionary Analyses
3.2. Coarse-Grained Molecular Simulations
3.3. Structure Preparation and All-Atom Molecular Dynamics Simulations
3.4. Protein Stability Analysis and Binding Free Energy Calculations
4. Conclusions
Supplementary Materials
Author Contributions
Funding
Acknowledgments
Conflicts of Interest
References
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ConSurf Hotspots | Consurf Score | KL Hotspots | KL Score |
---|---|---|---|
K390 | −0.390 | K390 | 1.12 |
V404 | −0.367 | V404 | 1.07 |
G434 | −0.505 | Y436 | 1.45 |
Y440 | −0.705 | Y440 | 1.19 |
N473 | −0.467 | N473 | 1.51 |
Y475 | −0.705 | Y475 | 1.63 |
Y481 | 473 | Y481 | 0.72 |
SARS-CoV pMI Hotspot Sites | SARS-CoV-2 pMI Hotspot Sites | SARS-CoV cMI Hotspot Sites | SARS-CoV-2 cMI Hotspot Sites |
---|---|---|---|
Y436 | Y449 | L472 | F486 |
Y440 | Y451 | N479 | Q493 |
Y475 | Y489 | T487 | N501 |
W476 | F490 | T433 | G446 |
Y481 | Y495 | T468 | N481 |
Y484 | Q498 | P470 | E484 |
N473 | N487 | Y484 | Q498 |
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Verkhivker, G. Coevolution, Dynamics and Allostery Conspire in Shaping Cooperative Binding and Signal Transmission of the SARS-CoV-2 Spike Protein with Human Angiotensin-Converting Enzyme 2. Int. J. Mol. Sci. 2020, 21, 8268. https://doi.org/10.3390/ijms21218268
Verkhivker G. Coevolution, Dynamics and Allostery Conspire in Shaping Cooperative Binding and Signal Transmission of the SARS-CoV-2 Spike Protein with Human Angiotensin-Converting Enzyme 2. International Journal of Molecular Sciences. 2020; 21(21):8268. https://doi.org/10.3390/ijms21218268
Chicago/Turabian StyleVerkhivker, Gennady. 2020. "Coevolution, Dynamics and Allostery Conspire in Shaping Cooperative Binding and Signal Transmission of the SARS-CoV-2 Spike Protein with Human Angiotensin-Converting Enzyme 2" International Journal of Molecular Sciences 21, no. 21: 8268. https://doi.org/10.3390/ijms21218268