Question

Can the side-chain of glutamine make a bidentate interaction in the major groove at a G-U wobble base-pair in RNA? Explain your answer.

Answer 1

Ans. -

The double stranded RNA binding domain (dsRBD) is a small protein domain of 65–70 amino acids adopting an αβββα fold, whose central property is to bind to double stranded RNA (dsRNA). This domain is present in proteins implicated in many aspects of cellular life, including antiviral response, RNA editing, RNA processing, RNA transport and last but not least RNA silencing. Even though proteins containing dsRBDs can bind to very specific dsRNA targets in vivo , the binding of dsRBDs to dsRNA is commonly believed to be shape-dependent rather than sequence-specific.

The dsRBD is one of the most abundant RNA binding domain after the RNA recognition motif which is a well characterized single-stranded RNA binding domain and zinc fingers which are best known for their ability to bind to DNA but which may also interact with dsRNA. Geometry of an A-form RNA helix and the nature of the chemical groups accessible to proteins in dsRNA, binding of dsRBDs to their dsRNA targets is commonly believed to be shape-dependent rather than sequence-specific.

It is exposed at the surface of the dsRBD and does not make any significant interaction with other part of the domain. The conserved alanine of the motif is packed against the β-sheet surface. A likely explanation for the conservation of this alanine is that a bulky side-chain at this position would cause steric clashes that would destabilize the β-sheet. In the third dsRBD of Staufen this alanine is replaced by a serine without causing any major rearrangements.