Chemical Approaches for Structure and Function of RNA in Postgenomic Era
Table 2
Characteristics of RRM/RNP/RBD domain.
~90–100 amino acids domain and most abundant in vertebrates
Many RNA binding proteins contain more than one RRM
Contain 2 conserved RNP1 (RGQAFVIF in β3) and RNP2 (TIYINNL in β1) in 4 antiparallel β-sheets of βαββαβ-fold
Binds 2–8 nucleotides of RNA (2 in CBP20, nucleolin and 8 in )
A typical RRM containing 4 nucleotide binding sites (UCAC)
(6)
3 conserved aromatic amino acids (Y, F, W, H or P) in central β-strands (2 in RNP1 of β3 and 1 in RNP 2 in β1)
(7)
2 RRMs in a protein are separated by small linker and provide a large RNA binding surface or RNA binding surface point away from each other
(8)
RNA bases are usually spread on the surface of protein domains while the RNA phosphates point away toward the solvent
(9)
Binding surface of the protein is primarily hydrophobic in order to maximize intermolecular contact with the bases of the RNA
(10)
Few intramolecular RNA stacking and many intermolecular stacking mediated by aromatic amino acids
(11)
RNA recognition is a two-step process, in which any RNA is attracted approximately equally well. However, if stacking and hydrogen-bond interactions that “lock” the interaction cannot be properly established, the complex redissociates quickly (large ), which results in overall weak affinity for RNA oligonucleotides of the wrong sequence
(12)
Many ssRNA binding proteins recognize RNA in the loop (stem-loop) better than in ssRNA ( fold & fold, therefore, overall affinity ~2000 fold differences) due to higher entropy loss with ssRNA binding than stem-loop binding and stabilizing interactions of stem
