tetano
Editor, Senior Moderator
J Biomol Struct Dyn
. 2020 May 25;1-16.
doi: 10.1080/07391102.2020.1773318. Online ahead of print.
Structural and Simulation Analysis of Hot Spot Residues Interactions of SARS-CoV 2 With Human ACE2 Receptor
Ganesh Kumar Veeramachaneni[SUP] 1 [/SUP], V B S C Thunuguntla[SUP] 2 [/SUP], Janaki Ram B[SUP] 3 [/SUP], Jayakumar Singh Bondili[SUP] 1 [/SUP]
Affiliations
Abstract
The novel corona virus disease 2019 (SARS-CoV 2) pandemic outbreak was alarming. The binding of SARS-CoV (CoV) spike protein (S-Protein) Receptor Binding Domain (RBD) to Angiotensin converting enzyme 2 (ACE 2) receptor initiates the entry of corona virus into the host cells leading to the infection. However, considering the mutations reported in the SARS-CoV 2 (nCoV), the structural changes and the binding interactions of the S-protein RBD of nCoV were not clear. The present study was designed to elucidate the structural changes, hot spot binding residues and their interactions between the nCoV S-protein RBD and ACE2 receptor through computational approaches. Based on the sequence alignment, a total of 58 residues were found mutated in nCoV S-protein RBD. These mutations led to the structural changes in the nCoV S-protein RBD 3d structure with 4 helices, 10 sheets and intermittent loops. The nCoV RBD was found binding to ACE2 receptor with 11 hydrogen bonds and 1 salt bridge. The major hot spot amino acids involved in the binding identified by interaction analysis after simulations includes Glu 35, Tyr 83, Asp 38, Lys 31, Glu 37, His 34 amino acid residues of ACE2 receptor and Gln 493, Gln 498, Asn 487, Tyr 505 and Lys 417 residues in nCoV S-protein RBD. Based on the hydrogen bonding, RMSD and RMSF, total and potential energies, the nCoV was found binding to ACE 2 receptor with higher stability and rigidity. Concluding, the hotspots information will be useful in designing blockers for the nCoV spike protein RBD.
Keywords: ACE2 receptor; Novel Coronavirus; Protein interactions; Receptor Binding Domain; Spike protein; hotspots; molecular dynamic simulations.
. 2020 May 25;1-16.
doi: 10.1080/07391102.2020.1773318. Online ahead of print.
Structural and Simulation Analysis of Hot Spot Residues Interactions of SARS-CoV 2 With Human ACE2 Receptor
Ganesh Kumar Veeramachaneni[SUP] 1 [/SUP], V B S C Thunuguntla[SUP] 2 [/SUP], Janaki Ram B[SUP] 3 [/SUP], Jayakumar Singh Bondili[SUP] 1 [/SUP]
Affiliations
- PMID: 32448098
- DOI: 10.1080/07391102.2020.1773318
Abstract
The novel corona virus disease 2019 (SARS-CoV 2) pandemic outbreak was alarming. The binding of SARS-CoV (CoV) spike protein (S-Protein) Receptor Binding Domain (RBD) to Angiotensin converting enzyme 2 (ACE 2) receptor initiates the entry of corona virus into the host cells leading to the infection. However, considering the mutations reported in the SARS-CoV 2 (nCoV), the structural changes and the binding interactions of the S-protein RBD of nCoV were not clear. The present study was designed to elucidate the structural changes, hot spot binding residues and their interactions between the nCoV S-protein RBD and ACE2 receptor through computational approaches. Based on the sequence alignment, a total of 58 residues were found mutated in nCoV S-protein RBD. These mutations led to the structural changes in the nCoV S-protein RBD 3d structure with 4 helices, 10 sheets and intermittent loops. The nCoV RBD was found binding to ACE2 receptor with 11 hydrogen bonds and 1 salt bridge. The major hot spot amino acids involved in the binding identified by interaction analysis after simulations includes Glu 35, Tyr 83, Asp 38, Lys 31, Glu 37, His 34 amino acid residues of ACE2 receptor and Gln 493, Gln 498, Asn 487, Tyr 505 and Lys 417 residues in nCoV S-protein RBD. Based on the hydrogen bonding, RMSD and RMSF, total and potential energies, the nCoV was found binding to ACE 2 receptor with higher stability and rigidity. Concluding, the hotspots information will be useful in designing blockers for the nCoV spike protein RBD.
Keywords: ACE2 receptor; Novel Coronavirus; Protein interactions; Receptor Binding Domain; Spike protein; hotspots; molecular dynamic simulations.