Protein–RNA interactions: exploring binding patterns with a three-dimensional superposition analysis of high resolution structures

Abstract

The program ENTANGLE is available from http://www.bioc.rice.edu/~shamoo

RNA pentaloop structures as effective targets of regulators belonging to the RsmA/CsrA protein family

“…4). 35 In pltA RNA, the G9 interaction with RsmE additionally strengthens the contacts of the neighboring residues with RsmE ( Table 3). Indeed, the SELEX consensus sequence RUA CAR GGA UGU (28) reflects a preference for G or A (= R) over U or C at position 9, albeit in a hexaloop configuration.…”

“…10 We ran molecular dynamics simulations of the complexes and analyzed the RNA-protein interactions found in the resulting conformations with the Entangle program. 35 We also estimated the theoretical binding free energy (ΔG) using the structures obtained by molecular dynamics simulations with the Molecular Mechanics -Generalized Born Surface Area (MM-GBSA) method. This method allows decomposing the binding free energy into residue contributions and provides insight into the origin of binding ( Table 3).…”

“…The structures extracted from the MD simulations were analyzed with the program to explore the RNA-protein interactions, Entangle; van der Waals contacts and hydrogen bond were analyzed. 35 The free energy of binding, ΔG, between each RNA molecule and the RsmE dimer was calculated with the MM-GBSA method. 50 The ΔG values were obtained for each system and, subsequently, decomposed into per-residue contributions.…”

A new affinity approach to isolate Escherichia coli 6S RNA with histidine‐chromatography

“…Furthermore, atomic studies performed on protein-RNA complex structures have shown that histidine has a strong tendency to interact with nucleotides (Jeong et al, 2003). As for the exact type of interactions, these may include (i) hydrogen-bonding between H-donor (NtH) and H-acceptor (Np) atoms in the non-protonated histidine with base edges; (ii) ring stacking/hydrophobic interactions and (iii) water-mediated hydrogen bonds (Hoffman et al, 2004;Morozova et al, 2006). Thus, and considering the fact that at the working pH (7.0), histidine (pK a ¼ 6.5) is not significantly protonated (Ö zkara et al, 2002;Pitiot and Vijayalakshmi, 2002) the elution of sRNA when salt concentration is decreased suggests that ring stacking/ hydrophobic interactions and histidine-RNA direct hydrogenbonding are the dominant effects.…”

Structure determination and dynamics of protein–RNA complexes by NMR spectroscopy

“…Intermolecular contacts present in protein-RNA complexes can be assessed by specific programs such as NUCPLOT [350] or ENTANGLE [351]. Both programs read a coordinate file of a protein-nucleic acid complex in PDB format and identify intermolecular interactions, such as hydrogen-bonding and stacking interactions.…”