Secreted Cysteine-Rich Repeat Proteins “SCREPs”: A Novel Multi-Domain Architecture

Abstract

Peptide toxins isolated from animal venom secretions have proven to be useful pharmacological tools for probing the structure and function of a number of molecular receptors. Their molecular structures are stabilized by posttranslational formation of multiple disulfide bonds formed between sidechain thiols of cysteine residues, resulting in high thermal and chemical stability. Many of these peptides have been found to be potent modulators of ion channels, making them particularly influential in this field. Recently, several peptide toxins have been described that have an unusual tandem repeat organization, while also eliciting a unique pharmacological response toward ion channels. Most of these are two-domain peptide toxins from spider venoms, such as the double-knot toxin (DkTx), isolated from the Earth Tiger tarantula (Haplopelma schmidti). The unusual pharmacology of DkTx is its high avidity for its receptor (TRPV1), a property that has been attributed to a bivalent mode-of-action. DkTx has subsequently proven a powerful tool for elucidating the structural basis for the function of the TRPV1 channel. Interestingly, all tandem repeat peptides functionally characterized to date share this high avidity to their respective binding targets, suggesting they comprise an unrecognized structural class of peptides with unique structural features that result in a characteristic set of pharmacological properties. In this article, we explore the prevalence of this emerging class of peptides, which we have named Secreted, Cysteine-rich REpeat Peptides, or “SCREPs.” To achieve this, we have employed data mining techniques to extract SCREP-like sequences from the UniProtKB database, yielding approximately sixty thousand candidates. These results indicate that SCREPs exist within a diverse range of species with greatly varying sizes and predicted fold types, and likely include peptides with novel structures and unique modes of action. We present our approach to mining this database for discovery of novel ion-channel modulators and discuss a number of “hits” as promising leads for further investigation. Our database of SCREPs thus constitutes a novel resource for biodiscovery and highlights the value of a data-driven approach to the identification of new bioactive pharmacological tools and therapeutic lead molecules.

Structure, function, and evolution of Gga -AvBD11, the archetype of the structural avian-double-β-defensin family

“…S31). It is noteworthy that other double-domain disulfide-rich proteins, e.g., double inhibitor cystine knot (ICK) peptides (22), are reported in the literature, yet with differences in the position of Cys residues, the disulfide pairing, and the 3D structure.…”

Structural and functional insights into the inhibition of human voltage-gated sodium channels by μ-conotoxin KIIIA disulfide isomers

“…NaV1.7, 16 NaV1.8, 17 and NaV1.9 3 subtypes are preferentially expressed in the peripheral nervous system. These peripheral sodium channels have been genetically validated to be modulating neuronal excitability associated with different types of pain, including nociception, 17,18 neuropathic pain 3,5,18,19 and acute inflammation. 8,16,20,21 Thus, peripheral NaV subtypes, such as NaV1.7, are potential targets for the development of novel analgesics.…”

ScrepYard: an online resource for disulfide-stabilised tandem repeat peptides

“…The initial dataset is subsequently refined by applying a keyword filter to remove known non-SCREPs based on their annotations. Currently the keyword list consists of 'intracellular' (31), 'disulfide isomerase' (32), 'double CXXCH motif' (33), 'ferredoxin' (34), 'sulphur' (35,36), 'zinc' (37), 'iron' (35), 'cytochrome' (38), 'thioredoxin' (39), and 'dehydrogenase' (37). This heuristic approach allows for continual optimization of the pipeline with the addition of new keywords as these are identified and ongoing updates to the database.…”

“…In the latest update of ScrepYard (Nov 2021), 148,929 sequences were identified as putative SCREPs from the total secreted protein dataset (13,166,720 sequences) -almost three times as many SCREPs as the previous published extraction (May 2018), which comprised 60,935 putative SCREPs from 8,006,061 secreted protein sequences (18). The growth in number of sequences shows the remarkably rapid expansion of available sequences within UniProtKB, further emphasising the need for automated processing tools to extract (which was not certified by peer review) is the author/funder.…”

“…The copyright holder for this preprint this version posted January 20, 2022. ; https://doi.org/10.1101/2022.01.17.476686 doi: bioRxiv preprint domain DRPs contain a tandem repeat (TR) architecture, where the individual domains share high internal sequence homology. Previous bioinformatics studies of these TR-DRPs revealed that they belong to the larger molecular class that we have defined as secreted cysteine-rich repeat proteins (SCREPs) (18).…”