Viral protein


Last updated: 2021 Aug 2
Total hit(s): 45
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Molecular interaction studies of SARS-CoV-2 RBD with different variants of hACE2. No major divergence of the interaction interface of SARS-CoV-2 RBD with hACE2
32410735
(Biochem Biophys Res Commun)
PMID
32410735
Date of Publishing: 2020 Jun 30
Title Interaction of the spike protein RBD from SARS-CoV-2 with ACE2: Similarity with SARS -Cov , hot-spot analysis and effect of the receptor polymorphism
Author(s) nameOthman H, Bouslama Z et al.
Journal Biochem Biophys Res Commun
Impact factor
2.73
Citation count: 27
Date of Entry 2021 Aug 2


Heparin binding accelerates the aggregation of pathological amyloid proteins in the brain. Comparative study to the docking score of SARS-CoV-2 S1-heparin complex to amyloid forming proteins shows molecular interaction of the SARS-COV-2 Spike S1 RBD and Heparin shows a high docking score of -282.57. By targeting the binding and aggregation process of the S1 and Heparin, neurodegenration can be prevented.
33789211
(Biochem Biophys Res Commun)
PMID
33789211
Date of Publishing: 2021 May 21
Title SARS-CoV-2 spike protein interactions with amyloidogenic proteins: Potential clues to neurodegeneration
Author(s) name Idrees D, Kumar V.
Journal Biochem Biophys Res Commun
Impact factor
2.73
Citation count: 1
Date of Entry 2021 Aug 12


SARS-CoV-2 S1 RBD binds heparin binding proteins including A, -synuclein, tau, prion, and TDP-43 RRM. The heparin binding site of S1 protein assists the binding to amyloid proteins to the viral surface and initate aggregation of these proteins, leading to neurodegenration in brain. This provides a reasonable explanation for the neurodegenerative distresses caused by a COVID infection. Increase in Kd as the temperature increased from 25 C to 40 C, showed a decrease in binding affinity for SARS-CoV-2 S1 protein complexes.
Increase in temperature usually disrupts the noncovalent interactions between a protein-protein complex, but, the decrease in binding affinity across the temperatures was less apparent for the -Syn complex with S1. This anomaly suggests a stable interaction between -synuclein to SARS-CoV-2 S1 protein.
33789211
(Biochem Biophys Res Commun)
PMID
33789211
Date of Publishing: 2021 May 21
Title SARS-CoV-2 spike protein interactions with amyloidogenic proteins: Potential clues to neurodegeneration
Author(s) name Idrees D, Kumar V.
Journal Biochem Biophys Res Commun
Impact factor
2.73
Citation count: 1
Date of Entry 2021 Aug 12


Based on the intermolecular contact maps (COCOMAPS tool) of ACE2-S complex structure, three short peptides (pep1c, pep1d, pep1e) were designed to block virus-host interaction in the early stages of SARS-CoV-2 infection. New therapeutics for oral administration against SARS-CoV-2 infection can be developed using these peptides, which could be an alternative to traditional drug development.
33918595
(Molecules)
PMID
33918595
Date of Publishing: 2021 Apr 9
Title Native Structure-Based Peptides as Potential ProteinProtein Interaction Inhibitors of SARS-CoV-2 Spike Protein and Human ACE2 Receptor
Author(s) nameOdolczyk N, Marzec E et al.
Journal Molecules
Impact factor
3.01
Citation count: 1
Date of Entry 2021 Aug 12


The study compares the similarities and differences in the structure of heparin sulfate (HS) in human and bat lungs. Also, discusses about the binding capacity of spike protein of SARS-CoV-2 with homosapiens and chiroptera's lung heparin sulfate. The spike glycoprotein of COVID 19 binds 3.5 times stronger to the human lung heparin(HS) sulfate than bat lung heparin sulfate. The molecular weight of the heparin sulfate is more important than the sulfation level for lung HS binding to SARS-CoV-2 virus spike protein.
33712145
(Carbohydr Polym)
PMID
33712145
Date of Publishing: 2021 May 15
Title Heparan sulfates from bat and human lung and their binding to the spike protein of SARS-CoV-2 virus
Author(s) nameYan L, Song Y et al.
Journal Carbohydr Polym
Impact factor
6.23
Citation count: 1
Date of Entry 2021 Aug 11


Molecular interaction studies of SARS-CoV-2 RBD with different variants of hACE2. No major divergence of the interaction interface of SARS-CoV-2 RBD with hACE2
Title Interaction of the spike protein RBD from SARS-CoV-2 with ACE2: Similarity with SARS -Cov , hot-spot analysis and effect of the receptor polymorphism
Date of Entry 2021 Jul 28


Molecular interaction studies of RBD from SARS-CoV-2 and SARS-CoV with different ACE2 orthologues Q493 might be responsible forhigher affinity due to a better satisfaction of the Van der Waals by the longer polar side chain of asparagine.
32410735
(Biochem Biophys Res Commun)
PMID
32410735
Date of Publishing: 2020 Jun 30
Title Interaction of the spike protein RBD from SARS-CoV-2 with ACE2: Similarity with SARS -Cov , hot-spot analysis and effect of the receptor polymorphism
Author(s) nameOthman H, Bouslama Z et al.
Journal Biochem Biophys Res Commun
Impact factor
2.73
Citation count: 27
Date of Entry 2021 Jul 28


Molecular interaction studies of RBD from SARS-CoV-2 and SARS-CoV with different ACE2 orthologues Q493 might be responsible forhigher affinity due to a better satisfaction of the Van der Waals by the longer polar side chain of asparagine.
32410735
(Biochem Biophys Res Commun)
PMID
32410735
Date of Publishing: 2020 Jun 30
Title Interaction of the spike protein RBD from SARS-CoV-2 with ACE2: Similarity with SARS -Cov , hot-spot analysis and effect of the receptor polymorphism
Author(s) nameOthman H, Bouslama Z et al.
Journal Biochem Biophys Res Commun
Impact factor
2.73
Citation count: 27
Date of Entry 2021 Jul 28


Molecular interaction studies of SARS-CoV-2 RBD with different variants of hACE2. No major divergence of the interaction interface of SARS-CoV-2 RBD with hACE2
Title Interaction of the spike protein RBD from SARS-CoV-2 with ACE2: Similarity with SARS -Cov , hot-spot analysis and effect of the receptor polymorphism
Date of Entry 2021 Jul 28


Molecular interaction study between polymorphic spike protein and human ACE2 The variants in the spike protein of SARS-CoV-2 and hACE2 would provide a database for tracking the adaptive mutation of SARS-CoV-2 and potential recombination events across different species.
33542420
(Sci Rep)
PMID
33542420
Date of Publishing: 2021 Feb 4
Title Dynamics of binding ability prediction between spike protein and human ACE2 reveals the adaptive strategy of SARS-CoV-2 in humans
Author(s) nameXue X, Shi J et al.
Journal Sci Rep
Impact factor
4.12
Citation count: 1
Date of Entry 2021 Jul 28


Molecular interaction of B6 (monoclonal antibody) and spike protein of SARS-CoV-2. B6 binding sterically interferes with S fusogenic conformational changes and blocks viral entry through inhibition of membrane fusion
33981021
(Nat Struct Mol Biol)
PMID
33981021
Date of Publishing: 2021 May 12
Title Structural basis for broad coronavirus neutralization
Author(s) nameSauer MM, Tortorici MA et al.
Journal Nat Struct Mol Biol
Impact factor
9.8
Citation count: 5
Date of Entry 2021 Jul 28


Host protein arginine methyltransferases (PRMTs) methylates SARS-CoV-2 N protein at residues R95 and R177 within RGG/RG motifs.Type I PRMT inhibitor (MS023) or substitution of R95 or R177 with lysine inhibits interaction of N protein with the 5-UTR of SARS-CoV-2 genomic RNA, a property required for viral packaging. Type I PRMT inhibitors (MS023), cancer drug canditates, have found to reduce SARS-CoV-2 production by inhibiting the methylation of arginine in the N protein of SARS-CoV-2 and hence are promising antivirals.
34029587
(J Biol Chem)
PMID
34029587
Date of Publishing: 2021 May 23
Title Arginine methylation of SARS-Cov-2 nucleocapsid protein regulates RNA binding, its ability to suppress stress granule formation, and viral replication
Author(s) nameCai T, Yu Z et al.
Journal J Biol Chem
Impact factor
3.96
Citation count: 1
Date of Entry 2021 Jul 28


Surface plasmon resonance (SPR) was used to compare the kinetics of SARS-CoV-2 S protein both D614 and D614G binding to human ACE2. D614G decreases the affinity for ACE2 by increasing the rate of dissociation. The increased infectivity of D614G is not explained by greater ACE2 binding strength.
32991842
(Cell)
PMID
32991842
Date of Publishing: 2020 Oct 29
Title Structural and Functional Analysis of the D614G SARS-CoV-2 Spike Protein Variant
Author(s) nameYurkovetskiy L, Wang X et al.
Journal Cell
Impact factor
27.35
Citation count: 52
Date of Entry 2021 Jun 15


Complex of ACE2 receptor and N501Y spike protein ectodomains shows Y501 inserted into a cavity at the binding interface near Y41 of ACE2 providing a structural explanation for the increased ACE2 affinity of the N501Y mutant, and its increased infectivity, but the mutation does note cause large structural changes. Structural studies establish the molecular basis showing the increase in ACE2 binding efficiency conferred by the N501Y mutation. Despite the higher infectivity of SARS-CoV-2 viruses carrying the N501Y mutation, the availability of the extended epitope surface on the RBD enables effective neutralization by VH ab8 and Fab ab1.
33914735
(PLoS Biol)
PMID
33914735
Date of Publishing: 2021 Apr 29
Title Cryo-electron microscopy structures of the N501Y SARS-CoV-2 spike protein in complex with ACE2 and 2 potent neutralizing antibodies
Author(s) nameZhu X, Mannar D et al.
Journal PLoS Biol
Impact factor
7.62
Citation count: 2


SARS-CoV-2 receptor-binding domain (RBD) binds to human ACE2 receptor (hACE2) more strongly than that of bat ACE2 2 from Rhinolophus macrotis (bACE2-Rm). Glycosylation modification in bACE2-Rm doesn't influence the binding of SARS-CoV-2 RBD with bACE2-Rm.ns.
Patch 2 interaction in bACE2-Rm and hACE2 was highly conserved compared to Patch 1 interaction which showed significant differences in both.
In bACE2-Rm, residues Y41 and E42 are significant within the interface of SARS-CoV-2 RBD, whereas the residues in human include Y41 and Q42.
Most of the residues involved in ACE2 homodimer formation were conserved in both human and bats, indicating possible conservation of ACE2 dimer attributes during evolution.
33335073
(Proc Natl Acad Sci U S A)
PMID
33335073
Date of Publishing: 2021 Jan 5
Title Cross-species recognition of SARS-CoV-2 to bat ACE2
Author(s) nameLiu K, Tan S et al.
Journal Proc Natl Acad Sci U S A
Impact factor
9.35
Citation count: 1


Molecular docking study to determine the potential binding interfaces of SARS-CoV-2 ORF7a with leukocyte marker - LFA-1 (lymphocyte function-associated antigen) and Mac-1 ( Macrophage-1 antigen ) ORF7a-mediated effects on immune cells such as T lymphocytes and macrophages (leukocytes) could help understand the disease further and develop effective treatments.
33305306
(Biosci Rep)
PMID
33305306
Date of Publishing: 2020 Dec 11
Title Structural assessment of SARS-CoV2 accessory protein ORF7a predicts LFA-1 and Mac-1 binding potential
Author(s) nameNizamudeen ZA, Xu ER et al.
Journal Biosci Rep
Impact factor
2.51
Citation count: 1


Nsp13-1 stabilizes SARS-CoV-2 replication and transcription (RTC) complex by contacting with nsp13-2, which anchors the 5'-extension of RNA template, and interacting with nsp7-nsp8-nsp12-RNA. Different orientations of nsp13-1 results in different interactions with the two forms of mini RTC. Mini RTC with an nsp12R365A mutation has greater helicase activity compared to individual apsnsp13. Nsp13-1T216A mutation has a decreased helicase activity.
33208736
(Nat Commun)
PMID
33208736
Date of Publishing: 2020 Nov 18
Title Architecture of a SARS-CoV-2 mini replication and transcription complex
Author(s) nameYan L, Zhang Y et al.
Journal Nat Commun
Impact factor
11.8
Citation count: 4


Reporting strong interaction between S2 subunit of SARS-nCoV-2 with tumor suppressor protein p53 Further experimental research is required to unveil the impact of COVID-19 in cancer patients and to explore the functional role of these interactions.
32619819
(Transl Oncol)
PMID
32619819
Date of Publishing: 2020 Oct
Title S2 Subunit of SARS-nCoV-2 Interacts with Tumor Suppressor Protein p53 and BRCA: an In Silico Study
Author(s) name Singh N, Bharara Singh A.
Journal Transl Oncol
Impact factor
3.3
Citation count: 4


Reporting strong interaction between S2 subunit of SARS-nCoV-2 with tumor suppressor protein BRCA-1 Further experimental research is required to unveil the impact of COVID-19 in cancer patients and to explore the functional role of these interactions.
32619819
(Transl Oncol)
PMID
32619819
Date of Publishing: 2020 Oct
Title S2 Subunit of SARS-nCoV-2 Interacts with Tumor Suppressor Protein p53 and BRCA: an In Silico Study
Author(s) name Singh N, Bharara Singh A.
Journal Transl Oncol
Impact factor
3.3
Citation count: 4


Structural characterization of SARS-CoV-2 spike glycoprotein (subdomain 1 to S2 quadruple mutant (u1S2q 2 Up RBD state)) construct and determing its binding with the antibody CR3022 human cell receptor ACE2 The spike glycoprotein mutant construct (u1S2q) with mutation A570L,T572I, F855Y, N856I were developed. The u1S2q 2 Up RBD Spike Protein Trimer were docked with the CR3022 Fab - RBD complex (PDB 6YLA) and potential clashes were observed in between.
32699321
(Nat Struct Mol Biol)
PMID
32699321
Date of Publishing: 2020 Oct
Title Controlling the SARS-CoV-2 spike glycoprotein conformation
Author(s) nameHenderson R, Edwards RJ et al.
Journal Nat Struct Mol Biol
Impact factor
9.8
Citation count: 43


Structural characterization of SARS-CoV-2 spike glycoprotein (subdomain 1 to S2 quadruple mutant (u1S2q 1 Up RBD)) construct. And determing its binding with the antibody CR3022 and human cell receptor ACE2. The spike glycoprotein mutant construct (u1S2q) with mutation A570L,T572I, F855Y, N856I were developed. The u1S2q 1 Up RBD Spike Protein Trimer were docked with the CR3022 Fab - RBD complex (PDB 6YLA) and potential clashes were observed in between.
32699321
(Nat Struct Mol Biol)
PMID
32699321
Date of Publishing: 2020 Oct
Title Controlling the SARS-CoV-2 spike glycoprotein conformation
Author(s) nameHenderson R, Edwards RJ et al.
Journal Nat Struct Mol Biol
Impact factor
9.8
Citation count: 43


Structural characterization of SARS-CoV-2 spike glycoprotein (RBD to S2 double mutant (rS2d)) constructs. And determing its binding with the antibody CR3022 and human cell receptor ACE2. The spike glycoprotein mutant constructs (rS2d) with double mutation S383C, D985C were developed. The RBD in the rS2d construct is locked in the 'down ' state conformation.
32699321
(Nat Struct Mol Biol)
PMID
32699321
Date of Publishing: 2020 Oct
Title Controlling the SARS-CoV-2 spike glycoprotein conformation
Author(s) nameHenderson R, Edwards RJ et al.
Journal Nat Struct Mol Biol
Impact factor
9.8
Citation count: 43


Reporting strong interaction between S2 subunit of SARS-nCoV-2 with tumor suppressor protein BRCA-2 Further experimental research is required to unveil the impact of COVID-19 in cancer patients and to explore the functional role of these interactions.
32619819
(Transl Oncol)
PMID
32619819
Date of Publishing: 2020 Oct
Title S2 Subunit of SARS-nCoV-2 Interacts with Tumor Suppressor Protein p53 and BRCA: an In Silico Study
Author(s) name Singh N, Bharara Singh A.
Journal Transl Oncol
Impact factor
3.3
Citation count: 4


Structural characterisation of the SARS-CoV-2 receptor binding domain in complex with CR3022 Fab (crystal form 1) The binding of ACE2 to the RBD is perturbed by the presence of CR3022.
32585135
(Cell Host Microbe)
PMID
32585135
Date of Publishing: 2020 Sep 9
Title Neutralization of SARS-CoV-2 by destruction of the Prefusion Spike
Author(s) nameHuo J, Zhao Y et al.
Journal Cell Host Microbe
Impact factor
10.45
Citation count: 39


Crystal structure of the SARS-CoV-2 receptor binding domain in complex with CR3022 Fab The spike protein is an attractive candidate for both vaccine development and immunotherapy. As monoclonal antibodies are recognised as potential antivirals,the results in this study suggest that CR3022 could be of immediate utility because the mechanism of neutralization will be unusually resistant to virus escape.
32585135
(Cell Host Microbe)
PMID
32585135
Date of Publishing: 2020 Sep 9
Title Neutralization of SARS-CoV-2 by destruction of the Prefusion Spike
Author(s) nameHuo J, Zhao Y et al.
Journal Cell Host Microbe
Impact factor
10.45
Citation count: 39