(214b) Computational Predictions For Sequence Specificity Of Mrna Binding Proteins | AIChE

(214b) Computational Predictions For Sequence Specificity Of Mrna Binding Proteins


Ovacik, M. A. - Presenter, Rutgers University
Jain, A. - Presenter, Rutgers University
Knapinska, A. - Presenter, UMDNJ-Robert Wood Johnson Medical School
Brewer, G. - Presenter, UMDNJ-Robert Wood Johnson Medical School
Androulakis, I. P. - Presenter, Rutgers University

mRNA stability plays a critical role in regulating gene expression and has recently received attention because of its role in protein level determination. mRNA stability is particularly important for immune responses, embryogenesis, and disease development [1]. mRNA stability is determined by molecular interactions between RNA-binding proteins and sequence elements within the mRNAs which mainly based on the secondary and tertiary structure of both the proteins and mRNAs. However there is not much and complete structural information about mRNA-binding protein complexes. One of the most studied families of regulatory mRNA sequences is the A+U-rich element (ARE), located within the 3'-untranslated region of as many as 8% of mRNAs within the human transcriptome. Interaction of an ARE with the protein AUF1 (hnRNP) targets the mRNA for rapid degradation. Numerous studies have examined its RNA-binding mechanism, but it is unknown how AUF1 recognizes AREs. The binding occurs in specific regions of proteins, RNA-recognition motifs (RRMs), via specific amino acids; Phenylalanine(Phe), Arginine(Arg) and Lysine(Lys) [2, 3]. We mutated the DNA structure to ?CCCC- and -GGGG- and ARE (-AUUUA-) performed molecular dynamics simulation. We demonstrated that regardless of the sequence the binding of mRNA to both RRMs of AUF1 with the same mechanism as ARE. Since neither the protein's nor the mRNA's structure are fully solved, in this study we explore salient features in the primary sequence of the protein that lead to the mRNA sequence specificity. For this purpose, we performed multiple alignment analysis between known hnRNPs [4] and attempted to identify distinct patterns that reveal information about mRNA binding. However distinctive patterns were only observed when we clustered hnRNPs using CLUSTALW based on their similarities[5]. Among all hnRNPs, A1,A2,A0, and AUF1 have shown very similar sequences, however A2 selectively binds to -UUAG- whereas the rest of these proteins selectively bind to ARE (?AUUUA-). Finally, we observed that tyrosine, methionine, glycine and histidine predominantly appear in and outside of the mRNA binding sites of hnRNPs, and these aminoacids have been shown to play role in RNA-protein complex [6].

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