Modeling Protein–Protein or Protein–DNA/RNA Complexes Using the HDOCK Webserver

Yan, Yumeng; Huang, Sheng‐You

doi:10.1007/978-1-0716-0708-4_12

Cited by 22 publications

(15 citation statements)

References 33 publications

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“…Protein–protein interactions are a crucial prerequisite for many biological interactions involved in cellular signaling, immunity, and cellular transport [ 21 ]. Potential interactions between the SARS-CoV-2 proteins and α-Syn were examined by the HDOCK server.…”

Section: Resultsmentioning

confidence: 99%

SARS-CoV-2 Proteins Interact with Alpha Synuclein and Induce Lewy Body-like Pathology In Vitro

Zhang

Huang

et al. 2022

IJMS

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Growing cases of patients reported have shown a potential relationship between (severe acute respiratory syndrome coronavirus 2) SARS-CoV-2 infection and Parkinson’s disease (PD). However, it is unclear whether there is a molecular link between these two diseases. Alpha-synuclein (α-Syn), an aggregation-prone protein, is considered a crucial factor in PD pathology. In this study, bioinformatics analysis confirmed favorable binding affinity between α-Syn and SARS-CoV-2 spike (S) protein and nucleocapsid (N) protein, and direct interactions were further verified in HEK293 cells. The expression of α-Syn was upregulated and its aggregation was accelerated by S protein and N protein. It was noticed that SARS-CoV-2 proteins caused Lewy-like pathology in the presence of α-Syn overexpression. By confirming that SARS-CoV-2 proteins directly interact with α-Syn, our study offered new insights into the mechanism underlying the development of PD on the background of COVID-19.

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Section: Resultsmentioning

confidence: 99%

SARS-CoV-2 Proteins Interact with Alpha Synuclein and Induce Lewy Body-like Pathology In Vitro

Zhang

Huang

et al. 2022

IJMS

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“…The sequence identity was of 5.3% while the secondary structure similarity was of 65.8% between amino acids 367-410 of RTAM-PAP1 2 nd and 154-191 of Uracil-DNA-Glycosylase (UDG). A hybrid algorithm of template-based and template-free docking was performed for the three compounds, RTA-PAPS1, RTAM-PAP1 and RTAM-PAP1 2 nd , against SARS-CoV-2 FSE (Protein-RNA docking) using the HDOCK webserver [7]. The results (table 1) clearly show the gain of function on binding energies for the three chimeras in comparison with the moieties alone.…”

Section: Resultsmentioning

confidence: 99%

“…RTAM-PAP1 2 nd was compared by superimposition on the available crystallography in RCSB using MATRAS pairwise 3D alignment (http://strcomp.protein.osaka-u.ac.jp/matras/matras_pair.html). The structures of the Protein-RNA bound complexes were generated by a hybrid algorithm of template-based and template-free docking using HDOCK webserver [7]. Additional models of the RTA-PAPS1, RTAM-PAP1, RTAM-PAP1 2 nd , RTA-PAPS1-FSE, RTAM-PAP1-FSE and RTAM-PAP1 2nd-FSE complexes were generated using ZDOCK [23] without inputting the active residues.…”

Section: Methodsmentioning

confidence: 99%

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Post-Infection Entry Mechanism of Ricin A Chain-Pokeweed Antiviral Proteins (RTA-PAPs) Chimeras is Mediated by Viroporins

Hassan¹

2021

Preprint

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The limitations of virus-specific antiviral drugs became apparent during the current COVID-19 pandemic. The search for broad range antiviral proteins of a new kind to answer current and future pandemics has become an even more pressing matter. Here, the author further describes the expected anti-SARS-CoV-2 mechanisms of a novel broad range antiviral chimeric protein constructed between ricin A chain and pokeweed antiviral proteins. The latest in protein-ligand docking software were used to determine binding affinity of RTA-PAPs to SARS-CoV-2 frameshift stimulation element and elucidate the preferential post-infection entry mechanisms of RTA-PAPs into virus infected cells over non-infected ones, by doing a comparative analysis between in vitro and in silico results on numerous viruses. The results obtained strongly suggest that the post-infection preferential entry of RTA-PAPs into infected cells is mediated by the presence of viroporins integrated into the host cell membrane. The discovery of this mechanism revealed RTA-PAPs, and proteins like them, to be a new class of broad range antivirals that target with high specificity viroporin producing viruses, and with gain of functions in antiviral activities, post-infection.

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“…We demonstrated the efficacy of JEDII using PDNA-285 dataset and validated it using the different benchmark datasets. We compared the performance of JEDII with GraphBind (74) and HDock (108,109) on the PDNA-285 dataset. We used the GraphBind standalone version to make predictions on proteins from the PDNA-285 dataset.…”

Section: Prediction Algorithmmentioning

confidence: 99%

JEDII: Juxtaposition Enabled DNA-binding Interface Identifier

Nair

Madhusudhan

2022

Preprint

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The specific recognition of small stretches of the genomic sequence by their cognate binding protein partners is crucial for various biological processes. Traditionally the prediction of DNA-protein interactions has been treated as two separate problems - one where we predict the most probable DNA sequence that a given protein would bind to and another where we determine the amino acids constituting the DNA binding pocket on a protein. In this study, we introduce JEDII, a template-based method that combines these two aspects of DNA-protein interactions and predicts the residues, nucleotides and amino acids, that would mediate the interaction. Our computational method utilises known structures of DNA-protein complexes in a protocol that superimposes amino acid-nucleotide hydrogen-bonding donor and acceptors atoms on one another to identify the protein-DNA interface. The corner stone of the method is that specificity bestowing hydrogen-bonding interactions are structurally conserved. We validated the accuracy of our procedure on a dataset of 285 DNA-protein complexes where JEDII predicted the cognate DNA sequence with a 62% accuracy. It predicted the DNA-binding amino acids on the protein with 94 % accuracy and an MCC of 0.70. JEDII was also separately compared to other popular methods that predict the cognate DNA sequence and to methods that predict the DNA binding residues. The comparisons were done over four different datasets and JEDII outperformed most methods over all these data sets. JEDII is a robust method following a simple replicable algorithm to determine the molecular basis of DNA-protein specificity and could be instrumental in predicting DNA-protein complexes that are central to key biological phenomena.

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Modeling Protein–Protein or Protein–DNA/RNA Complexes Using the HDOCK Webserver

Cited by 22 publications

References 33 publications

SARS-CoV-2 Proteins Interact with Alpha Synuclein and Induce Lewy Body-like Pathology In Vitro

SARS-CoV-2 Proteins Interact with Alpha Synuclein and Induce Lewy Body-like Pathology In Vitro

Post-Infection Entry Mechanism of Ricin A Chain-Pokeweed Antiviral Proteins (RTA-PAPs) Chimeras is Mediated by Viroporins

JEDII: Juxtaposition Enabled DNA-binding Interface Identifier

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