The repetitive structure of DNA clamps: An overlooked protein tandem repeat

Arrías, Paula Nazarena; Monzón, Alexander Miguel; Clementel, Damiano; Mozaffari, Soroush; Piovesan, Damiano; Kajava, Andrey V.; Tosatto, Silvio C. E.

doi:10.1016/j.jsb.2023.108001

Cited by 5 publications

(1 citation statement)

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“…TRPs have been shown to be involved in many biological functions and activities. For example, DNA sliding clamps are TRPs which play an essential role in DNA replication (Arrías et al 2023) while leucine-rich repeats (LRRs) make up the extracellular domains of toll-like receptors (TLRs) involved in host immune responses (Leulier and Lemaitre 2008). In recent years, their significance has garnered increasing attention, owing to their implications in health (de Wit et al 2011;Fournier et al 2013) and their application in protein design (Höcker 2014;Brunette et al 2015;Wu et al 2023).…”

Section: Introductionmentioning

confidence: 99%

STRPsearch: fast detection of structured tandem repeat proteins

Mozaffari,

Arrías,

Clementel

et al. 2024

Preprint

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MotivationState-of-the-art prediction methods are generating millions of publicly available protein structures. Structured Tandem Repeats Proteins (STRPs) constitute a subclass of tandem repeats characterized by repetitive structural motifs. STRPs exhibit distinct propensities for secondary structure and form regular tertiary structures, often comprising large molecular assemblies. They can perform important and diverse biological functions due to their highly degenerated sequences, which maintain a similar structure while displaying a variable number of repeat units. This suggests a disconnection between structural size and protein function. However, automatic detection of STRPs remains challenging with current state-of-the-art tools due to their lack of accuracy and long execution times, hindering their application on large datasets. In most cases, manual curation is the most accurate method for detecting and classifying them, making it impossible to inspect millions of structures.ResultsWe present STRPsearch, a novel computational tool for rapid identification, classification, and mapping of STRPs. Leveraging the manually curated entries in RepeatsDB as the known conformational space of the STRPs, STRPsearch utilizes the latest advancements in structural alignment techniques for a fast and accurate detection of repeated structural motifs in protein structures, followed by an innovative approach to map units and insertions through the generation of TM-score graphs. STRPsearch can serve researchers in structural bioinformatics and protein science as an efficient and practical tool for analysis and detection of STRPs.Availability and implementationSTRPsearch is coded in Python, all the scripts and the associated documentation are available athttps://github.com/BioComputingUP/STRPsearch.Contactalexander.monzon@unipd.it,silvio.tosatto@unipd.itSupplementary informationSupplementary data are available..

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