Computational Methods for Prediction of Protein-Protein Interaction Sites

Meller, Jarek; Porollo, Aleksey

doi:10.5772/36716

Cited by 10 publications

(5 citation statements)

References 74 publications

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“…V H H (P‐36) protein three‐dimensional (3D) structure was predicted by using the SWISS model (https://swissmodel.expasy.org/) [31] was used to determine the 3D structure of V H H (P‐36) protein by placing the amino acid sequence. The protein data bank (PDB) structures were placed on SPPIDER (http://sppider.cchmc.org/) to anticipate possible active citations [32]. Following receipt of the possible citation, both the receptor/acceptor (Rho1 protein 3D structure of protein, while V H H as donor PDB protein) and the donor PDB protein were submitted to CLUSPro (https://cluspro.org/home.php) [33].…”

Section: Methodsmentioning

confidence: 99%

“…The protein data bank (PDB) structures were placed on SPPIDER (http://sppider. cchmc.org/) to anticipate possible active citations [32]. Following receipt of the possible citation, both the receptor/ acceptor (Rho1 protein 3D structure of protein, while V H H as donor PDB protein) and the donor PDB protein were submitted to CLUSPro (https://cluspro.org/home.php) [33].…”

Section: Rho Binding Domain (Rbd) Dynamics and Structure Studymentioning

confidence: 99%

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A novel cell biological tool to explain mechanics and dynamics in fission yeast

Rasheed,

Mohy‐ud‐Din,

Anwar

et al. 2024

J Basic Microbiol

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The Rho guanosine triphosphatase hydrolase enzyme (GTPase) is required for the control of the actin cytoskeleton, but its activation in vivo condition is unknown. The study's goal was to find a new synthetic nanobody VHH (P‐36 tagged with mNeonGreen) that interacts strongly with the Rho GTPase. We present the first novel synthetic nanobody, VHH (P‐36 tagged with mNeonGreen), tested in fission yeast cells and found to have a particular interaction with Rho1GTPase. Plasmids were constructed by using of certain enzymes to digest the pDUAL‐pef1a vector plasmid to produce a protein that was encoded by cloned genes. A varied VHH library was created synthetically, then transformed into yeast cells, and positive clones were chosen using chemical agents. To investigate protein interactions and cellular reactions, several studies were carried out, such as live cell imaging, growth curve analysis, coimmunoprecipitation, structural analysis, and cell therapies. Prism and RStudio were used for the statistical analysis. The presence of VHH (P‐36) has no effect on the growth pattern making it an appropriate model for studying cytokinesis in vivo. According to a computational biological study, its affinity to interact with Rho1GTPase with all the complementarity‐determining region (CDR) regions found on VHH (P‐36) is extremely strong. We were able to track its subcellular target by localization using a fluorescent confocal microscope, ensuring the maintenance of cell polarity and morphology. Spheroplast analysis revealed a circular‐shaped cell with an even distribution of Rho1 tagged VHH (P‐36), indicating that the interaction occurs near the plasma membrane. The introduction of latrunculin‐A (Lat‐A) disrupted Rho GTPase localization, demonstrating the control over actin production, and the cell did not show evidence of mitotic phase commencement while Lat‐A was present. Finally, this important biological tool can aid in our understanding of the mechanics and dynamics of cytokinesis in relation to Rho1GTPase.

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Section: Methodsmentioning

confidence: 99%

Section: Rho Binding Domain (Rbd) Dynamics and Structure Studymentioning

confidence: 99%

A novel cell biological tool to explain mechanics and dynamics in fission yeast

Rasheed,

Mohy‐ud‐Din,

Anwar

et al. 2024

J Basic Microbiol

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“…The molecular docking was performed between the selected DNA-directed RNA polymerases of SPPV, GTPV, and LSDV and bee peptides. The SPPIDER (an online server) was used to predict the active site residues of each viral protein [35]. The molecular docking was carried out by the HADDOCK server [36] to explore specific protein-peptide interactions between selected peptides and the DNA-directed RNA polymerase of three viral variants.…”

Section: Protein-peptide Dockingmentioning

confidence: 99%

In Silico Analysis of Honey Bee Peptides as Potential Inhibitors of Capripoxvirus DNA-Directed RNA Polymerase

Mustafa

Mahrosh

Salman

et al. 2023

Animals

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The genus Capripoxvirus belongs to the Poxviridae family. The sheeppox, goatpox, and lumpy skin disease viruses are three species of this genus with 96% identity in their genomes. These are financially devastating viral infections among cattle, which cause a reduction in animal products and lead to a loss in livestock industries. In the current study, the phylogenetic analysis was carried out to reveal the evolutionary relationships of Capripoxvirus species (i.e., sheeppox virus (SPPV), goatpox virus (GTPV), and lumpy skin disease virus (LSDV)) with other viruses from the Poxviridae family with >96% query coverage to find the similarity index among all members. The three viruses (i.e., SPPV, GTPV, and LSDV) joined the clade of Capripoxvirus of the Poxviridae family in the phylogenetic tree and exhibited close evolutionary relationships. The multiple sequence alignment using ClustalOmega revealed significant variations in the protein sequences of the DNA-dependent RNA polymerase of SPPV, GTPV, and LSDV. The three-dimensional structures of five selected bee peptides and DNA-directed RNA polymerase of SPPV, GTPV, and LSDV were predicted using trRosetta and I-TASSER and used for molecular docking and simulation studies. The protein–protein docking was carried out using HADDOCK server to explore the antiviral activity of peptides as honey bee proteins against SPPV, GTPV, and LSDV. In total, five peptides were docked to DNA-directed RNA polymerase of these viruses. The peptides mellitin and secapin-1 displayed the lowest binding scores (−106.9 +/− 7.2 kcal/mol and −101.4 +/− 11.3 kcal/mol, respectively) and the best patterns with stable complexes. The molecular dynamics simulation indicated that the complex of protein DNA-dependent RNA polymerase and the peptide melittin stayed firmly connected and the peptide binding to the receptor protein was stable. The findings of this study provide the evidence of bee peptides as potent antimicrobial agents against sheeppox, goatpox, and lumpy skin disease viruses with no complexity.

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“…These algorithms have been applied to create computational tools and web servers to predict RNA/protein interaction partners. A detailed description of these tools is beyond the scope of this review but those readers who seek more insights will find it useful to read the manuscript from the Dobbs' lab (Muppirala et al, 2013 ) and book chapters (Chang, 2012 ; Meller and Porollo, 2012 ). More recently, an innovative large-scale pipeline has been developed by Ribeiro and colleagues to identify candidate lncRNAs acting as scaffolding molecules for protein complexes (Ribeiro et al, 2017 ).…”

Section: New Technologies For the Study Of Lncrnas/protein Interactiomentioning

confidence: 99%

The Ever-Evolving Concept of the Gene: The Use of RNA/Protein Experimental Techniques to Understand Genome Functions

Cipriano

Ballarino

2018

Front. Mol. Biosci.

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The completion of the human genome sequence together with advances in sequencing technologies have shifted the paradigm of the genome, as composed of discrete and hereditable coding entities, and have shown the abundance of functional noncoding DNA. This part of the genome, previously dismissed as “junk” DNA, increases proportionally with organismal complexity and contributes to gene regulation beyond the boundaries of known protein-coding genes. Different classes of functionally relevant nonprotein-coding RNAs are transcribed from noncoding DNA sequences. Among them are the long noncoding RNAs (lncRNAs), which are thought to participate in the basal regulation of protein-coding genes at both transcriptional and post-transcriptional levels. Although knowledge of this field is still limited, the ability of lncRNAs to localize in different cellular compartments, to fold into specific secondary structures and to interact with different molecules (RNA or proteins) endows them with multiple regulatory mechanisms. It is becoming evident that lncRNAs may play a crucial role in most biological processes such as the control of development, differentiation and cell growth. This review places the evolution of the concept of the gene in its historical context, from Darwin's hypothetical mechanism of heredity to the post-genomic era. We discuss how the original idea of protein-coding genes as unique determinants of phenotypic traits has been reconsidered in light of the existence of noncoding RNAs. We summarize the technological developments which have been made in the genome-wide identification and study of lncRNAs and emphasize the methodologies that have aided our understanding of the complexity of lncRNA-protein interactions in recent years.

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Computational Methods for Prediction of Protein-Protein Interaction Sites

Cited by 10 publications

References 74 publications

A novel cell biological tool to explain mechanics and dynamics in fission yeast

A novel cell biological tool to explain mechanics and dynamics in fission yeast

In Silico Analysis of Honey Bee Peptides as Potential Inhibitors of Capripoxvirus DNA-Directed RNA Polymerase

The Ever-Evolving Concept of the Gene: The Use of RNA/Protein Experimental Techniques to Understand Genome Functions

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