Intrinsic disorder in PRAME and its role in uveal melanoma

Abstract

Introduction The PReferentially expressed Antigen in MElanoma (PRAME) protein has been shown to be an independent biomarker for increased risk of metastasis in Class 1 uveal melanomas (UM). Intrinsically disordered proteins and regions of proteins (IDPs/IDPRs) are proteins that do not have a well-defined three-dimensional structure and have been linked to neoplastic development. Our study aimed to evaluate the presence of intrinsic disorder in PRAME and the role these structureless regions have in PRAME( +) Class 1 UM. Methods A bioinformatics study to characterize PRAME’s propensity for the intrinsic disorder. We first used the AlphaFold tool to qualitatively assess the protein structure of PRAME. Then we used the Compositional Profiler and a set of per-residue intrinsic disorder predictors to quantify the intrinsic disorder. The Database of Disordered Protein Prediction (D2P2) platform, IUPred, FuzDrop, fIDPnn, AUCpred, SPOT-Disorder2, and metapredict V2 allowed us to evaluate the potential functional disorder of PRAME. Additionally, we used the Search Tool for the Retrieval of Interacting Genes (STRING) to analyze PRAME's potential interactions with other proteins. Results Our structural analysis showed that PRAME contains intrinsically disordered protein regions (IDPRs), which are structureless and flexible. We found that PRAME is significantly enriched with serine (p-value < 0.05), a disorder-promoting amino acid. PRAME was found to have an average disorder score of 16.49% (i.e., moderately disordered) across six per-residue intrinsic disorder predictors. Our IUPred analysis revealed the presence of disorder-to-order transition (DOT) regions in PRAME near the C-terminus of the protein (residues 475–509). The D2P2 platform predicted a region from approximately 140 and 175 to be highly concentrated with post-translational modifications (PTMs). FuzDrop predicted the PTM hot spot of PRAME to be a droplet-promoting region and an aggregation hotspot. Finally, our analysis using the STRING tool revealed that PRAME has significantly more interactions with other proteins than expected for randomly selected proteins of the same size, with the ability to interact with 84 different partners (STRING analysis result: p-value < 1.0 × 10–16; model confidence: 0.400). Conclusion Our study revealed that PRAME has IDPRs that are possibly linked to its functionality in the context of Class 1 UM. The regions of functionality (i.e., DOT regions, PTM sites, droplet-promoting regions, and aggregation hotspots) are localized to regions of high levels of disorder. PRAME has a complex protein–protein interaction (PPI) network that may be secondary to the structureless features of the polypeptide. Our findings contribute to our understanding of UM and suggest that IDPRs and DOT regions in PRAME may be targeted in developing new therapies for this aggressive cancer.

A novel nabelschnur protein regulates segregation of the kinetoplast DNA inTrypanosoma brucei

“…4C). Additionally, the coiled coil domain showed the highest confidence (pLDDT 90 >) while the predicted intrinsically disordered region at the C-terminus showed a very low confidence score (pLDDT < 50), a typical score for predicted disordered regions (46).…”

Molecular Genomic Insights into Melanoma Associated Proteins PRAME and BAP1

“…Here we found that for PRAME there is an increase towards moderately flexible residues. Studies have shown that in PRAME, the regions with functionality are located in the Intrinsically Disordered Protein Regions (IDPRs) and are flexible [9]. In BAP1, there was an increase in the disorder promoting residues and a decrease in the order promoting residues and previous studies have also shown that the increase in the intrinsic disorder region helps in the establishment of a complex PPI module [13].…”

“…Preferentially expressed Antigen in Melanoma (PRAME) is a tumor-associated peptide discovered by studying the specificity of tumor-reactive T-cell clones obtained from a patient with metastatic cutaneous melanoma [6]. PRAME was later discovered to be expressed not only in cutaneous melanoma, but also in ocular melanoma and a variety of nonmelanocytic malignant neoplasms such as non-small cell lung cancer, breast carcinoma, renal cell carcinoma, ovarian carcinoma, leukemia, synovial sarcoma, cervical cancer, and myxoid liposarcoma [7,8,9]. Except for the testis, ovary, placenta, adrenals, and endometrium, no normal healthy tissues have been found to express PRAME [10].…”

PRAME Updated: Diagnostic, Prognostic, and Therapeutic Role in Skin Cancer

“…PRAME is an intriguing biomarker and a potential therapeutic target in the field of ocular melanomas, particularly uveal and conjunctival melanomas. 4,5 Understanding its role and implications in these diseases requires a deeper understanding of the molecular biology of melanomas, the specific features of uveal and conjunctival melanomas, and emerging therapeutic strategies targeting PRAME [42,43]. Uveal melanoma originates from melanocytes of the uvea, which includes the iris, ciliary body, and choroid.…”