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Role of Histone Methyltransferase in Breast Cancer
Published in Meenu Gupta, Rachna Jain, Arun Solanki, Fadi Al-Turjman, Cancer Prediction for Industrial IoT 4.0: A Machine Learning Perspective, 2021
Surekha Manhas, Zaved Ahmed Khan
Further, this above idea is preferably supported by means of work, which shows that promoters due to lack of H3K36me2/3 highlighted mark, and also KDM2A/B, H3K36me2-dependent demethylases co-localize with H3 residue, H3K4me3 at the specific CpGI promoters, which ensure the active H3K36me2 removal from TSS [62,63]. Recognition of H3K36me2/3 is accompanied by PWWP domain, a protein motif, mostly found in various nuclear-based chromatin-dependent binding proteins [64–67]. Interestingly, all three members linked with H3K36-dependent methyltransferases belong to the NSD family, which catalyses H3K36me1/2, each having 2-PWWP domains and preferentially bind with H3 peptides, which contain H3K36me3 [66,67]. This indicates that recognition of H3K36me2/3 by means of its writers could be highly important for H3K36me1 propagation. Mono-/dimethylation of protein residue, H3K36, is specifically highly pervasive compared to the H3K36me3 and is not restricted to a region’s euchromatic domain or active transcription [68,69]. The recognizable biological functional role displayed by mono-/dimethylation has been unknown until now, though an H3K36me2 increase due to mutational changes in NSD2 has been directly associated with the upregulation mechanism of gene-dependent expression profiles in the case of tumors [70,71]. H3K36me2 may have crucial biological activity in its own right or may be necessary to serve the required substrate for successive SETD2-mediated trimethylation of H3K36. H3K36me3 and H3K36me2 distribution over active gene chromatin could also delay spreading and prevent silencing marks accumulation like H3K27me3 by directly inhibiting the PRC2, polycomb complex [72,73]. Histone methyltransferase, G9a, that controls in vivo functional activity of H3K9me2 predominantly represses the activity of genes at euchromatic regions [4].
Identification and validation of Sertoli cell homing peptides as molecular steering for testis targeted drug delivery
Published in Journal of Drug Targeting, 2023
Yugandhara Jirwankar, Vikas Dighe
Motif discovery analysis of common 1551 peptide sequences using STREME (Sensitive, Thorough, Rapid, Enriched Motif Elicitation) [39] (https://doi.org/10.1093/bioinformatics/btab203) resulted in six enriched ungapped motifs with p-value <0.05. GSAK motif is enriched in 203 (13.1%) sequences followed by FRAQPTI, YSLRLT, SVTAPT, RDTH, and MKA (Figure 5 A–F), a summary of their p-values, E-values, and sites are shown in Supplementary Table 2. Further, these motifs were submitted to Tomtom, a motif comparison tool (https://doi.org/10.1186/gb-2007-8-2-r24) [40] which compared the submitted protein motif with motifs on the prosite database. Out of six enriched motifs, only GSAK and YSLRLT resulted in one hit each with E value <0.1. The motif similarity of GSAK and YSLRLT was found with Eukaryotic initiation factor 5 A hypusine signature (PS00302) and Stress-induced proteins SRP1/TIP1 family signature (PS00724), respectively (Supplementary Figure 3). Though the E-value for these two alignments is <0.1, these motifs are not 100% similar to their hits, indicating the novelty of the discovered motifs. Seqlogo analysis of common 1551 peptides with TBtool (Figure 5G) revealed GSWNTFRAQ and PTI as enriched domains, which is the actual sequence of the SCHP1 peptide.
Plant-Derived Natural Non-Nucleoside Analog Inhibitors (NNAIs) against RNA-Dependent RNA Polymerase Complex (nsp7/nsp8/nsp12) of SARS-CoV-2
Published in Journal of Dietary Supplements, 2023
Sreus A. G. Naidu, Ghulam Mustafa, Roger A. Clemens, A. Satyanarayan Naidu
Hydrogen (H)-bonds are responsible for secondary and tertiary structural protein motifs. In protein environments, redox (H+ proton transfer) reactions occur along polar or charged residues and isolated water molecules. These compounds consist of H-bond networks that serve as redox sensors; therefore, an in-depth understanding of redox mechanism(s) is essential to elucidate H-bond energetics in protein-ligand interactions (61). Since, protons (H+) are redox sensors, the formation of H-bonds between a ligand and a protein motif explains the binding affinity of an inhibitor toward the RdRp protein target in molecular dynamic simulations; accordingly, more number of H-bonds reflect a stronger interaction (62). The active site of the SARS-CoV-2 RdRp is formed by conserved polymerase motifs (A-G), where the motifs A and C have the divalent-cation-binding amino acid Asp618, and the catalytic residues Ser759-Asp760-Asp761, respectively (23). The cellular redox state governs the van der Waals and π-Sulfur interactions with amino acid residues of the catalytic center and the NTP entry channel of the SARS-CoV-2 RdRp-RNA complex (59, 63).
TMT-Based proteomics analysis of LPS-induced acute lung injury
Published in Experimental Lung Research, 2021
Shengsong Chen, Yi Zhang, Qingyuan Zhan
First, all protein sequences were aligned to the Linux server database downloaded from NCBI (ncbi-blast-2.2.28+-win32.exe), and only the sequences in the top 10 with an E-value< =1e-3 were retained. Second, the GO term (database version: go_201504.obo) for the sequence with the top bit score by Blast2GO was selected. Then, protein annotation based on the GO terms was completed with Blast2GO Command Line. After elementary annotation, InterProScan was used to search the EBI database by motif, and functional protein motif information was then added to improve the annotation. Then, annotations and connections between GO terms were further improved with ANNEX. Fisher’s exact test was used to assess GO term enrichment by comparing the number of DEPs and total proteins correlated with the GO terms.