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1. Intra- and intermolecular atomic-scale interactions in the receptor binding domain of SARS-CoV-2 spike protein: implication for ACE2 receptor binding

   https://doi.org/10.1039/d0cp03145c  

   Adhikari, Puja ; Li, Neng ; Shin, Matthew ; Steinmetz, Nicole F. ; Twarock, Reidun ; Podgornik, Rudolf ; Ching, Wai-Yim ( September 2020 , Physical Chemistry Chemical Physics)

   null (Ed.)

   The COVID-19 pandemic poses a severe threat to human health with unprecedented social and economic disruption. Spike (S) glycoprotein in the SARS-CoV-2 virus is pivotal in understanding the virus anatomy, since it initiates the early contact with the ACE2 receptor in the human cell. The subunit S1 in chain A of S-protein has four structural domains: the receptor binding domain (RBD), the n-terminal domain (NTD) and two subdomains (SD1, SD2). We report details of the intra- and inter-molecular binding mechanism of RBD using density functional theory, including electronic structure, interatomic bonding and partial charge distribution. We identify five strong hydrogen bonds and analyze their roles in binding. This provides a pathway to a quantum-chemical understanding of the interaction between the S-protein and the ACE2 receptor with insights into the function of conserved features in the ACE2 receptor binding domain that could inform vaccine and drug development. 

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2. Blocking SARS-CoV-2 Delta Variant (B.1.617.2) Spike Protein Receptor-Binding Domain Binding with the ACE2 Receptor of the Host Cell and Inhibiting Virus Infections Using Human Host Defense Peptide-Conjugated Graphene Quantum Dots

   https://doi.org/10.1021/acsomega.2c00113  

   Pramanik, Avijit ; Sharma, Poonam C. ; Patibandla, Shamily ; Gao, Ye ; Ruppa-Kasani, Vinod ; Goli, Jagruti ; Kumar, Animesh ; Chatterjee, Abhirup ; Sinha, Sudarson Sekhar ; Bates, John T. ; et al ( February 2022 , ACS Omega)
3. Identification of Specific Ligand–Receptor Interactions That Govern Binding and Cooperativity of Diverse Modulators to a Common Metabotropic Glutamate Receptor 5 Allosteric Site

   https://doi.org/10.1021/cn400225x  

   Gregory, Karen J. ; Nguyen, Elizabeth D. ; Malosh, Chrysa ; Mendenhall, Jeffrey L. ; Zic, Jessica Z. ; Bates, Brittney S. ; Noetzel, Meredith J. ; Squire, Emma F. ; Turner, Eric M. ; Rook, Jerri M. ; et al ( April 2014 , ACS Chemical Neuroscience)
4. Binding behavior of spike protein and receptor binding domain of the SARS-CoV-2 virus at different environmental conditions

   https://doi.org/10.1038/s41598-021-04673-y  

   Zhang, Meiyi ; Wang, Haoqi ; Foster, Emma R. ; Nikolov, Zivko L. ; Fernando, Sandun D. ; King, Maria D. ( December 2022 , Scientific Reports)

   Abstract A novel coronavirus, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) was identified as the cause of the COVID-19 pandemic that originated in China in December 2019. Although extensive research has been performed on SARS-CoV-2, the binding behavior of spike (S) protein and receptor binding domain (RBD) of SARS-CoV-2 at different environmental conditions have yet to be studied. The objective of this study is to investigate the effect of temperature, fatty acids, ions, and protein concentration on the binding behavior and rates of association and dissociation between the S protein and RBD of SARS-CoV-2 and the hydrophobic aminopropylsilane (APS) biosensors using biolayer interferometry (BLI) validated with molecular dynamics simulation. Our results suggest three conditions—high ionic concentration, presence of hydrophobic fatty acids, and low temperature—favor the attachment of S protein and RBD to hydrophobic surfaces. Increasing the temperature within an hour from 0 to 25 °C results in S protein detachment, suggesting that freezing can cause structural changes in the S protein, affecting its binding kinetics at higher temperature. At all the conditions, RBD exhibits lower dissociation capabilities than the full-length S trimer protein, indicating that the separated RBD formed stronger attachment to hydrophobic surfaces compared to when it was included in the S protein. 

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5. Direct measurements of VEGF–VEGFR2 binding affinities reveal the coupling between ligand binding and receptor dimerization

   https://doi.org/10.1074/jbc.RA119.007737  

   King, Christopher ; Hristova, Kalina ( June 2019 , Journal of Biological Chemistry)