The in silico interaction analysis of CARMIL1 protein-containing leucine-rich repeat (LRR) regions with interleukin-1 receptor-associated kinase 1 (IRAK1) protein and LLR peptide

Year 2022, Volume: 8 Issue: 6, 810 - 820, 04.11.2022

Nail Beşli , Güven Yenmiş

https://doi.org/10.18621/eurj.1011372

Abstract

Objectives: Capping protein Arp2/3 and myosin-I linker protein 1 (CARMIL1) encoded by the CARMIL, is a major, multidomain, membrane-linked protein regulating actin assembly; however, its function in inflammatory signaling is not fully elucidated. The leucine-rich repeat (LRR) region of CARMIL1 has been associated with interleukin (IL)-1 receptor-associated kinase (IRAK) in fibroblasts by many methods including tandem mass tag mass spectrometry, immunoprecipitation, and CRISPR-Cas9. This study, therefore, set out to assess the interaction of CARMIL1 with each IRAK1 protein and a novel LRR peptide.

Methods: The molecular docking techniques were employed to compare the binding modes and affinities of the 3D structure of CARMIL1 each of LRR peptides and IRAK1 protein. 3D structure model of CARMIL1 protein and LRR peptide was predicted through Robetta tool considering the structures and function of these proteins.

Results: As an overall conclusion of docking, the LRR peptide was observed to contact the residues in the LRR 1-2 of the human CARMIL1, whereas the IRAK1 protein was to interact with the residues in the LRR 1, 2, and 10 regions of the human CARMIL1.

Conclusions: Our computational results suggest that LRRs in CARMIL1 are involved in the formation of protein-peptide binding interfaces with its structural conformation.

Keywords

CARMIL1, IRAK1, LRR peptide, molecular docking simulation

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