<scp>PDBsum</scp> extras: <scp>SARS‐CoV</scp>‐2 and <scp>AlphaFold</scp> models

Laskowski, Roman A.; Thornton, Janet M.

doi:10.1002/pro.4238

Cited by 51 publications

(14 citation statements)

References 24 publications

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“…In the present study, we performed the restraint docking between RBD and ACE2 by defining the interaction residues 449:A, 453:A, 455:A, 456:A, 486:A, 487:A, 489:A, 493:A, 496:A, 498:A, 500:A, 501:A, 502:A, 505:A for RBD and 21:B, 24:B, 27:B, 28:B, 30:B, 35:B, 38:B, 79:B, 80:B, 82:B, 83:B, 353:B for ACE2 (A and B represents the chain name) [41]. Afterward, the HADDOCK-generated complexes were submitted to the PDBsum web server ( http://www.ebi.ac.uk/thornton-srv/databases/pdbsum/Generate.html ) ( Laskowski and Thornton, 2022 ) to visualize the bonding interface such as hydrogen bonds, salt bridges, and non-bonded contacts. As the sub-variant XBB has been reported to be involved in immune evasion by escaping the human neutralizing antibodies therefore to verify this statement, we also performed the docking of wild-type and mutant NTD with human mAb.…”

Section: Methodsmentioning

confidence: 99%

The XBB.1.5 slightly increase the binding affinity for host receptor ACE2 and exhibit strongest immune escaping features: molecular modeling and free energy calculation

Suleman¹,

Murtaza²,

Khan³

et al. 2023

Front. Mol. Biosci.

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Introduction: The current XBB variant of SARS-CoV-2 with the strongest immune escaping properties is currently the most dominant variant circulating around the world. With the emergence of XBB global morbidities and mortalities have raised again. In the current scenario, it was highly required to delineate the binding capabilities of NTD of XBB subvariant towards human neutralizing antibodies and to dig out the binding affinity of RBD of XBB subvariant with ACE2 receptor.Materials and Methods: The current study uses molecular interaction and simulation-based approaches to decipher the binding mechanism of RBD with ACE2 and mAb interaction with NTD of the spike protein.Results: Molecular docking of the Wild type NTD with mAb revealed a docking score of −113.2 ± 0.7 kcal/mol while XBB NTD docking with mAb reported −76.2 ± 2.3 kcal/mol. On the other hand, wild-type RBD and XBB RBD with ACE2 receptor demonstrated docking scores of −115.0 ± 1.5 kcal/mol and −120.8 ± 3.4 kcal/mol respectively. Moreover, the interaction network analysis also revealed significant variations in the number of hydrogen bonds, salt-bridges, and non-bonded contacts. These findings were further validated by computing the dissociation constant (KD). Molecular simulation analysis such as RMSD, RMSF, Rg and hydrogen bonding analysis revealed variation in the dynamics features of the RBD and NTD complexes due to the acquired mutations. Furthermore, the total binding energy for the wild-type RBD in complex with ACE2 reported −50.10 kcal/mol while XBB-RBD coupled with ACE2 reported −52.66 kcal/mol respectively. This shows though the binding of XBB is slightly increased but due to the variation in the bonding network and other factors makes the XBB variant to enter into the host cell efficiently than the wild type. On the other hand, the total binding free energy for the wildtype NTD-mAb was calculated to be −65.94 kcal/mol while for XBB NTD-mAb was reported to be −35.06 kcal/mol respectively. The significant difference in the total binding energy factors explains that the XBB variant possess stronger immune evasion properties than the others variants and wild type.Conclusions: The current study provides structural features for the XBB variant binding and immune evasion which can be used to design novel therapeutics.

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Section: Methodsmentioning

confidence: 99%

The XBB.1.5 slightly increase the binding affinity for host receptor ACE2 and exhibit strongest immune escaping features: molecular modeling and free energy calculation

Suleman¹,

Murtaza²,

Khan³

et al. 2023

Front. Mol. Biosci.

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“…Docked complexes obtained in protein–protein docking were visualized using PyMol and Chimera. The protein–protein interactions were analyzed using PDBSum . The 3D chemical structure (.sdf) of 2-bromopalmitate (palmitoyl transferase inhibitor) was retrieved from PubChem database and converted into .pdb format using open BABEL.…”

Section: Materials and Methodsmentioning

confidence: 99%

Identification of a De Novo Peptide against Palmitoyl Acyltransferase 6 to Block Survivability and Infectivity of Leishmania donovani

Srivastava,

Bansal,

Madan

et al. 2024

ACS Infect. Dis.

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Palmitoylation is an essential post-translational modification in Leishmania donovani, catalyzed by enzymes called palmitoyl acyl transferases (PATs) and has an essential role in virulence. Due to the toxicity and promiscuity of known PAT inhibitors, identification of new molecules is needed. Herein, we identified a specific novel de novo peptide inhibitor, PS1, against the PAT6 Leishmania donovani palmitoyl acyl transferase (LdPAT6). To demonstrate specific inhibition of LdPAT6 by PS1, we employed a bacterial orthologue system and metabolic labeling-coupled click chemistry where both LdPAT6 and PS1 were coexpressed and displayed palmitoylation suppression. Furthermore, strong binding of the LdPAT6-DHHC domain with PS1 was observed through analysis using microscale thermophoresis, ELISA, and dot blot assay. PS1 specific to LdPAT6 showed significant growth inhibition in promastigotes and amastigotes by expressing low cytokines levels and invasion. This study reveals discovery of a novel de novo peptide against LdPAT6-DHHC which has potential to block survivability and infectivity of L. donovani.

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“…The 3D structure was validated with ProSA‐web, which exploits interactive web‐based applications to display energy and values plots that highlight possible errors in the protein structures (Wiederstein & Sippl, 2007). PDBSum was used to further validate the structure by generating a Ramachandran plot, which shows the phi( φ )–psi( ψ ) torsion angles for all amino acid residues (Laskowski & Thornton, 2021).…”

Section: Methodsmentioning

confidence: 99%

Immunoinformatics aided design of a peptide‐based kit for detecting Escherichia coliO157:H7 from food sources

Oladipo,

Oluwasegun,

Oladunni

et al. 2023

Journal of Food Safety

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Food and water‐borne enterohemorrhagic Escherichia coli (EHEC) serotype O157:H7 is a zoonotic bacterium that causes gastroenteritis and other human diseases. It has also been linked to chronic foodborne diseases with high mortality rates worldwide, particularly in children. Hence, this study was carried out to designed a peptide base kit for quick detection of E. coli in food. A peptide‐based rapid detection kit was designed using an immunoinformatic technique and some antigenic target genes (stx1A, stx2B, escC, fliC, and eae). The antigenic gene sequences retrieved were screened for antigenicity, transmembrane topology, B‐cells and helper T‐cells. Selected epitopes were joined with appropriate linkers to form a chimeric protein which consists of five B‐cell epitopes, five interleukin‐4 (IL‐4) inducer epitopes and five interleukin‐10 (IL‐10) inducer epitopes. The improved and optimized chimeric protein sequence was cloned in‐silico in a suitable expression host, E. coli‐strain K12. The designed peptide refined and validated tertiary structure was molecularly docked with the tertiary structures of each antigenic target gene. The physicochemical properties of the chimeric protein showed that the construct has an amino acid length of 295 amino acids, a molecular weight of 29.876 kiloDalton (kDa), an aliphatic index of 75.05 and an instability index of 14.82 which confers stability. The construct was hydrophilic with a GRAVY value of −0.261 and had a considerable half‐life of 4.4 h (mammalian reticulocytes, in vitro), >20 h (yeast, in vivo) and >10 h (E. coli, in vivo). Conclusively, the final construct has successfully met the design requirements for the development of a lateral flow kit, which has the potential to provide fast and efficient detection of E. coli O157:H7. However, it is the additional validation through the vitro and in vivo techniques needed to confirm that this designed peptide based test kit.

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PDBsum extras: SARS‐CoV‐2 and AlphaFold models

Cited by 51 publications

References 24 publications

The XBB.1.5 slightly increase the binding affinity for host receptor ACE2 and exhibit strongest immune escaping features: molecular modeling and free energy calculation

The XBB.1.5 slightly increase the binding affinity for host receptor ACE2 and exhibit strongest immune escaping features: molecular modeling and free energy calculation

Identification of a De Novo Peptide against Palmitoyl Acyltransferase 6 to Block Survivability and Infectivity of Leishmania donovani

Immunoinformatics aided design of a peptide‐based kit for detecting Escherichia coliO157:H7 from food sources

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