Role of salt-bridging interactions in recognition of viral RNA by arginine-rich peptides

Abstract

Interactions between RNA molecules and proteins are critical to many cellular processes and are implicated in various diseases. The RNA-peptide complexes are good model systems to probe the recognition mechanism of RNA by proteins. In this work, we report studies on the binding-unbinding process of a helical peptide from a viral RNA element using nonequilibrium molecular dynamics simulations. We explored the existence of various dissociation pathways with distinct free-energy profiles that reveal metastable states and distinct barriers to peptide dissociation. We also report the free-energy differences for each of the four pathways to be 96.47 5 12.63, 96.1 5 10.95, 91.83 5 9.81, and 92 5 11.32 kcal/mol. Based on the free-energy analysis, we further propose the preferred pathway and the mechanism of peptide dissociation. The preferred pathway is characterized by the formation of sequential hydrogen-bonding and salt-bridging interactions between several key arginine amino acids and the viral RNA nucleotides. Specifically, we identified one arginine amino acid (R8) of the peptide to play a significant role in the recognition mechanism of the peptide by the viral RNA molecule.

Next generation strategy for tuning the thermoresponsive properties of micellar and hydrogel drug delivery vehicles using ionic liquids

“…20,21,23 We produce a series of formulation buffers with different combinations of the traditional excipients, sucrose, trehalose, β-cyclodextrin, L-histidine, L-arginine, tween 20, glycerol, and polyvinylpyrrolidone (PVP). We take into consideration that L-arginine residues can contribute salt bridge interactions, 17,30 and L-histidine and PVP can form a spanning hydrogen bonded network around a protein and with other excipients. 31,32 Additionally, the hydroxyl groups in trehalose, sucrose, cyclodextrin, tween 20 and glycerol could allow for the formation of hydrogen bonds with FITC-IgG surface and OBD.…”

Role of Mutations in Differential Recognition of Viral RNA Molecules by Peptides

“…These structures of unbound and peptide-bound RRE RNA suggest that URA72 changes its conformation on binding of the P1 peptide to RRE. In a previous study of the P2 peptide unbinding from the RRE RNA, we showed that URA72 stacks on URA43 in the unbound and peptide-bound RRE RNA (Figure S10), thereby confirming these mechanistic observations. The structural analyses also revealed that the nucleotide ADE68 is oriented away from the major groove in RRE RNA in unbound states (Figure a,b), while it is oriented away toward the major groove of RRE RNA in the peptide-bound states (Figure c,d).…”

“…Many RNA binding proteins recognize RNA molecules through arginine-rich motifs (ARMs), as they are relatively shorter in length, have little sequence similarity (aside from containing many arginine residues), and adopt diverse conformations (including an α-helix and a β-hairpin) upon association with the viral RNA. − The experimental work using X-ray crystallography and nuclear magnetic resonance (NMR) methods on the peptide–RNA complexes has demonstrated that the RNA backbone interacts with peptides more commonly than the nucleotide bases, suggesting that the majority of peptide–RNA interactions are nonspecific. , Overall, these studies showed that the peptide–RNA interactions occur through dynamic rearrangements in both molecules, which often entail backbone shifts and the flipping of nucleobases and amino acid residues. , Moreover, recent studies have demonstrated that the β-hairpin peptides could be synthesized with ultrahigh affinity toward viral RNA molecules. − However, a de novo design of α-helical peptides that potently and selectively recognize viral RNA molecules is limited due to a poor understanding of the RNA recognition mechanism.…”

“…In this regard, structured RNA elements from the HIV genome ,, serve as good model systems ,, to study the mechanisms of recognition of viral RNA by peptides. The HIV-1 Rev-responsive RNA element (RRE RNA), a 350 nucleotide long RNA found in the env gene, interacts with the arginine-rich motif of the Rev protein to regulate the nuclear export of the unspliced mRNA during the HIV life cycle and is therefore considered to be an important drug target. − …”

Free Energy Landscape of the Adenylation Reaction of the Aminoacylation Process at the Active Site of Aspartyl tRNA Synthetase

“…It has been found through earlier structural, classical simulation, and quantum chemical studies that ATP generally binds at the active site of aaRS in a bent conformation with its α-phosphate pointed toward the adenine base and its β- and γ-phosphate moieties oriented toward the opening of the active site. ,,,, For all class II aminoacyl tRNA synthetases, the adenine ring of ATP gets stacked with the conserved phenylalanine of motif 2 and arginine of motif 3 . Also, the invariant motif 2 arginine binds rather strongly with the α-phosphate of ATP, while one Mg 2+ ion bridges the α- and β-phosphates. ,,− The presence of one or two additional Mg 2+ ions bridging the β- and γ-phosphates of ATP has also been reported in earlier experimental and theoretical studies. ,,,,, Recent simulations have shown that the conserved motif II arginine residue makes contact with both the α-phosphate and attacking oxygen of the carboxylic group of the substrate amino acid and thus helps in anchoring the substrates ATP and amino acid in the reactive conformation. ,, This residue has also been reported to stabilize the transition states of both the activation and transfer steps. ,, Experimental and quantum chemical studies on the effects of mutation of the motif 2 arginine have also shown its important role in catalytic reactions at the active site of class II aminoacyl tRNA synthetases. ,,, The important role of arginine residues has also been reported for biomolecular recognitions involving other proteins and RNA. , …”