Short Peptides as Predictors for the Structure of Polyarginine Sequences in Disordered Proteins,Biophysical Journal

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Short Peptides as Predictors for the Structure of Polyarginine Sequences in Disordered Proteins
Biophysical Journal ( IF 3.2 ) Pub Date : 2021-01-01 , DOI: 10.1016/j.bpj.2020.12.026
Bridget Milorey ₁ , Reinhard Schweitzer-Stenner ₁ , Brian Andrews ₂ , Harald Schwalbe ₃ , Brigita Urbanc ₂

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Intrinsically disordered proteins (IDPs) and regions (IDRs) are frequently enriched in charged amino acids. IDRs are regularly involved in important biological processes, where one or more charged residues is the driving force behind a protein-biomolecule interaction. Several lines of experimental and computational evidence suggest that polypeptides and proteins that carry high net charges have a high preference for extended conformations with average end to end distances exceeding expectations for self-avoiding random coils. Here, we show that charged arginine (R) residues in even short glycine (G) capped model peptides (GRRG and GRRRG) significantly affect the conformational propensities of each other when compared to the intrinsic propensities of a mostly unperturbed arginine in the tripeptide GRG. A conformational analysis based on experimentally determined J-coupling constants from heteronuclear NMR spectroscopy and amide I' band profiles from vibrational spectroscopy reveals that nearest neighbor interactions stabilize extended β-strand conformations at the expense of polyproline II and turn conformations. The results from MD simulations with an CHARMM36m force field and TIP3P water reproduce our results only to a limited extent. The use of the Ramachandran distribution of the central residue of GRRRG in a calculation of end-to-end distances of polyarginines of different length yielded the expected power law behavior. The scaling coefficient of 0.66 suggests that such peptides would be more extended than predicted by a self-avoiding random walk. Our findings thus support in principle theoretical predictions of Mao et al. (Proc. Natl. Acad. Sci. USA, 107, 8183-8188, 2010).

更新日期：2021-01-01

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