Comparative In Silico Analysis and Functional Characterization of TANK-Binding Kinase 1–Binding Protein 1

Abstract

Protein modelling plays a vital role in the drug discovery process. TANK-binding kinase 1–binding protein 1 is also called an adapter protein, which is encoded by gene TBK1 present in Homo sapiens. It is found in lungs, small intestine, leukocytes, heart, placenta, muscle, kidney, lower level of thymus, and brain. It has a number of protein-binding sites, to which TBK1 and IKBKE bind and perform different functions as immunomodulatory, antiproliferative, and antiviral innate immunity which release different types of interferons. Our study predicts the comparative model of 3-dimensional (3D) structure through different bioinformatics tools that will be helpful for further studies in future. The reactivity and stability of these proteins were evaluated physicochemically and through domain determination and prediction of secondary structure using bioinformatics methods such as ProtParam, Pfam, and SOPMA, respectively. Robetta, an ab initio approach, I-TASSER, and AlphaFold was used for 3D structure prediction, and the models were validated using the SAVESv6.0 (PROCHECK) server. Conclusively, the best 3D structure of TBK1-binding protein 1 was predicted using Robetta software. After unveiling the 3D structure of the novel protein, we concluded that this structure will help us to find out its role other than in antiviral innate immunity and by producing torsion in its 3D structure researchers will be able to detect either this protein is involved in any disease or not because according to previous studies it was not associated with any disease.

Assessing the efficacy of cinnamon compounds against H. pylori through molecular docking, MD Simulations and ADMET analyses

“…In the current study, the predicted structures of virB4 , virB8 and virB9 proteins were then subjected to molecular docking analysis after structure quality assessment by their respective Ramachandran plots. In a comparative analysis of structural and functional characterization of TANK-Binding Kinase 1-Binding Protein by Sawal et al ., the same method was opted to assess the stereochemical quality of the predicted protein structures [ 51 ].…”

Comparative genomics profiling revealed multi-stress responsive roles of the CC-NBS-LRR genes in three mango cultivars

“…Alphafold2 ( https://rb.gy/dlamz ) was used for this purpose ( Jumper et al., 2021 ). Further, the predicted structures were validated using SAVES ( https://saves.mbi.ucla.edu/ ) ( Sawal et al., 2023 ) and MolProbity ( http://molprobity.biochem.duke.edu/ ) ( Davis et al., 2007 ). PyMOL was used to visualize these structures ( Alexander et al., 2011 ).…”

Global Analysis of the WOX Transcription Factor Family in Akebia trifoliata

“…The ExPASy's Prot-Param online tool (http://www.ExPASy.org/tools/protparam.html/, 25 August 2022) was used to predict the physical and chemical properties of the AktWOX transcription factors [21]. We used SOPMA (https://npsa-prabi.ibcp.fr/cgi-bin/, 1 September 2022) [22] to predict the secondary structure of the WOX gene in A. trifoliata. DataProt-Comp9.0 (http://linux1.softberry.com/berry.phtml?topic=protcomppl&group=Programs& subgroup=proloc, 9 September 2022) and SignalIP5.0 (https://services.healthtech.dtu.dk/ service/SignalP-5.0, 15 September 2022) were used for subcellular localization and signal peptide prediction [23].…”

“…There were three cis-acting elements related to stress resistance: defense and stress response elements (13), low-temperature induction response elements (8), light responsiveness elements (131), anaerobic induction elements (22), zein metabolism regulation elements (9), elements involved in endosperm expression (9) and elements involved in flavonoid biosynthesis genes (2). Cis-acting elements related to hormone regulation mainly included auxin (7), gibberellin (11), abscisic acid (33), MeJA responsiveness elements (42) and salicylic acid response elements (8).…”