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Notch signaling in spermatogenesis and male (in)fertility
Published in Rajender Singh, Molecular Signaling in Spermatogenesis and Male Infertility, 2019
Mahitha Sahadevan, Pradeep G. Kumar
Notch signaling has a simple architecture in all metazoans, consisting of a bipartite protein receptor and ligands, without any amplifier molecules over and above like in other pathways, in between the signal transduction to the nucleus. Four notch receptors – NOTCH1, NOTCH2, NOTCH3 and NOTCH4 and five ligands of the DSL family – JAG1, JAG2, DLL1, DLL3 and DDL4 have been reported in mammals, a single notch receptor in Drosophila and LIN-12 and GLP-1 in C. elegans (10,19–23). Typically, notch receptors consist of an extracellular domain having 36 epidermal growth factor (EGF)-like repeats, a subset of calcium binding sites within EGF-like repeats, three Notch-Lin12 (LN) repeats and a hydrophobic region, which helps in heterodimerization of the receptor. Simple Modular Architectural Research Tool (SMART) analysis of notch receptors in human is shown in Figure 12.1. Notch protein domain (NOD) and NODP represent a region present in many NOTCH proteins and NOTCH homologs in multiple species. The role of the NOD domain remains to be elucidated. DUF3454 also is a domain of unknown function.
Exon globin mutation of β-thalassemia in Indonesian ethnic groups: A bioinformatics approach
Published in Robert Hofstra, Noriyuki Koibuchi, Suthat Fucharoen, Advances in Biomolecular Medicine, 2017
N.I. Sumantri, D. Setiawan, A. Sazali
The mutant residue is smaller than the wild-type residue. The wild-type residue was positively charged, and the mutant residue is neutral. The mutant residue is more hydrophobic than the wild-type residue. The wild-type residue forms a hydrogen bond with glutamic acid at position 122. The difference in hydrophobicity will affect hydrogen bond formation. The wild-type residue forms a salt bridge with glutamic acid at position 122. The difference in charge will disturb the ionic interaction made by the original, wild-type residue. The mutated residue is located on the surface of a domain with unknown function. The residue was not found to be in contact with other domains, the function of which is known within the used structure. However, contact with other molecules or domains is still possible and might be affected by this mutation.
Anisakis
Published in Dongyou Liu, Laboratory Models for Foodborne Infections, 2017
Mauricio Afonso Vericimo, Gerlinde Teixeira, Israel Figueiredo, Janaina Ribeiro, Maria Augusta Moulin Fantezia, Sergio Carmona São Clemente
The abbreviation of the name of the gender (first three letters) and of the species (first letter) followed by a number indicating the chronology of the allergen purification was adopted as the systematic nomenclature of allergens, implemented by the Nomenclature Sub-Committee of the World Health Organization (WHO) and International Union of Immunological Societies. So, the A. simplex allergens are called “Ani s #” (e.g., Ani S1).36A. simplex (ss) has 14 allergens characterized by origin and molecular aspects. The immunoreactivity pattern for these allergens has been studied both with human sera and with experimental animals. A synthesis of the structural classification of Anisakis allergens is presented in Figure 42.3 based mainly on the allergen database AllFam,37 which can be accessed on the web at http://www.meduniwien.ac.at/allergens/allfam. The data was complemented from other published literature. For example, data from the Conserved Domain Database (CDD) and from the domain of unknown function (PF; DUF, Pfam) were used.
Salamanders and caecilians, neglected from the chemical point of view
Published in Toxin Reviews, 2022
Isadora Alves de Vasconcelos, Jéssica Oliveira de Souza, Jessica Schneider de Castro, Carlos José Correia de Santana, Ana Carolina Martins Magalhães, Mariana de Souza Castro, Osmindo Rodrigues Pires Júnior
A multi-tissue transcriptome study of five caecilian species of multiple families (Caecilia tentaculata, Microcaecilia dermatophaga, Microcaecilia unicolor, Rhinatrema bivittatum, and Typhlonectes compressicauda) was made with RNA-seq using a range of tissues indicated, including skin (Torres-Sánchez et al.2019). For most of the skin tissue-specific gene expression, there were no matches in any gene family already known. There were 108 uncharacterized clusters in skin. From those, 91 different protein domains were found, 16 of them exclusive occurring in this skin. These results demonstrate the lack of characterization of molecular components from the skin of caecilians. A few of the protein domains found in the caecilian skin-specific novel gene families were toxins and protease-like molecules, such as Asp_protease_2, Toxin_TOLIP, UPAR_LY6, and gag-asp_protease, which suggested activities associated with defense mechanisms. The domain for the amino acid storage receptor PhaP_Bmeg was also found in the skin-specific gene families. This protein is possibly related to the parental care of the caecilians when providing nutrition. There was also the presence of skin-specific gene families that have domains of unknown function might be related to the scales present in some caecilian, such as DUF.
How can we turn the PI3K/AKT/mTOR pathway down? Insights into inhibition and treatment of cancer
Published in Expert Review of Anticancer Therapy, 2021
Said M. Afify, Aung Ko Ko Oo, Ghmkin Hassan, Akimasa Seno, Masaharu Seno
Class IA PI3Ks are heterodimers consisting of a p85 regulatory subunit and p110 catalytic subunits (p110 α/β/δ). The kinase moiety consists of an adaptor-binding domain in the N-terminal region, that can bind to the inter-SH2 domain in the regulatory subunit, a Ras-binding domain, a C2 domain that binds phosphatidylserine on the membrane, a helical domain of unknown function, and a catalytic subunit with a kinase catalyzing phosphatidyl inositol phosphorylation (Figure 1). Upon stimulation by a growth factor, the regulatory p85 subunit binds to an activated receptor through phosphotyrosine residues with SH2 domains, recruiting p110, having an affinity for the inter-SH2 domain in its adaptor-binding domain, on the membrane through both Ras-binding and C2 domains, to activate PI3K. Activated PI3K catalyzes the phosphorylation of phosphatidylinositol-4,5-bisphosphate, PI(4,5)P2, to produce phosphatidylinositol-3,4,5-trisphosphate, PI(3,4,5)P3, which leads to the activation of multiple signaling pathways [19,20] (Figure 2).
The complex barnacle perfume: identification of waterborne pheromone homologues in Balanus improvisus and their differential expression during settlement
Published in Biofouling, 2019
Anna Abramova, Ulrika Lind, Anders Blomberg, Magnus Alm Rosenblad
Except for the relatively high sequence identity to WSP from B. amphitrite, the WSP homologues in B. improvisus did not have any reliable matches to other proteins in the databases. However, all B. improvisus WSP homologues contained a region with weak resemblance to the cupin_5 domain (PF06172) (Table S2). Cupin_5 is a domain of unknown function, and proteins containing this domain belong to the cupin superfamily (http://www.ebi.ac.uk/interpro/entry/IPR009327). In the Pfam database, for metazoans there are currently only 17 sequences from 10 species indicated to have a cupin_5 domain. Among these sequences, the scores for the predicted cupin_5 domain varied from 41.3 to 139.2 with the only two crustacean representatives having scores of 70.5 or 78.7, both coming from Daphnia (see Table S3 in Supplemental material). The Pfam cupin_5 domain scores for the B. improvisus WSP homologues varied between 19.8 and 36.3, with some of them thus being below the Pfam cupin_5 profile threshold score of 25.0 (Table S2). However, proteins with higher cupin_5 Pfam scores in both B. improvisus and B. amphitrite (with scores 45.4 and 46.0) were found, and these were named Bi_cupin and Ba_cupin, respectively. The Bi_cupin sequence was only 15% identical to Bi_WSP. Even if some of the WSP homologues in B. improvisus have a domain with weak similarity (slightly above the threshold score) to cupin_5, for the ease of the following discussion only proteins with high domain scores, ie Bi_cupin, Ba_cupin and Daphnia cupin_5, will be referred to as ‘cupin_5 proteins’ further in the text.