Perturbation of the Hierarchical Folding of a Large RNA by the Destabilization of its Scaffold's Tertiary Structure

Journal Article · Sat Jan 01 04:00:00 EST 2005 · J. Mol. Biol.

DOI:https://doi.org/10.1016/j.jmb.2005.09.032· OSTI ID:913910

Shcherbakova, I; Brenowitz, M

The P4-P6 domain serves as a scaffold against which the periphery and catalytic core organize and fold during Mg{sup 2+}-mediated folding of the Tetrahymena thermophila ribozyme. The most prominent structural motif of the P4-P6 domain is the tetraloop-tetraloop receptor interaction which 'clamps' the distal parts of its hairpin-like structure. Destabilization of the tertiary structure of the P4-P6 domain by perturbation of the tetraloop-tetraloop receptor interaction alters the Mg{sup 2+}-mediated folding pathway. The folding hierarchy of P5c{approx}P4-P6>periphery>catalytic core that is a striking attribute of the folding of the wild-type RNA is abolished. The initial steps in folding of the mutant RNA are {ge}50-fold faster than those of the wild-type ribozyme with the earliest observed tertiary contacts forming around regions known to specifically bind Mg{sup 2+}. The interaction between the mutant tetraloop and the tetraloop receptor appears coincidently with slowly forming catalytic core tertiary contacts. Thus, the stability conferred upon the P4-P6 domain by the tetraloop-tetraloop receptor interaction dictates the preferred folding pathway by stabilizing an early intermediate. A sub-denaturing concentration of urea diminishes the early barrier to folding the wild-type ribozyme along with complex effects on the subsequent steps of folding the wild-type and mutant RNA.

• Research Organization: Brookhaven National Laboratory (BNL) National Synchrotron Light Source
• Sponsoring Organization: Doe - Office Of Science
• DOE Contract Number: AC02-98CH10886
• OSTI ID: 913910
• Report Number(s): BNL--78478-2007-JA
• Journal Information: J. Mol. Biol., Journal Name: J. Mol. Biol. Vol. 354; ISSN JMOBAK; ISSN 0022-2836
• Country of Publication: United States
• Language: English

Related Subjects

59 BASIC BIOLOGICAL SCIENCES
MUTANTS
RNA
STABILITY
TETRAHYMENA
UREA
national synchrotron light source