Ribozymes hammerhead

Hamamelis [84696-19-5] Hamamelis virginiana Ham curing Hammerhead ribozyme Hammer mills Hammett equation Hamposyl 0 Hamposyl C Hamposyl C-30 Hamposyl L Hamposyl L-30 Hand factor Hand lay-up... 

HammerheadRtbozyme. A small RNA molecule that catalyzes cleavage of the phosphodiester backbone of RNA is known as the hammerhead ribozyme. This ribozyme occurs namrally in certain vimses where it facihtates a site-specific self-cleavage at the phosphate and generates a 2 3 -cychc phosphate and a 5 -hydroxyl terminus. The reaction requires a divalent metal ion, such as or, as a cofactor. Whereas the... 

Fig. 10. Three-dimensional stmcmre of the hammerhead ribozyme (shaded cord) bound to a substrate oligonucleotide (nonshaded cord). The uridine mm...

Figure 14-1. Left Relative errors (RELE) in the force as a function of radial distance from the center of the active dynamical region for the VEP-RVM charge-scaling method [80] for the solvated hammerhead ribozyme at different discretization levels [151] of die co surface. Right The projected total electrostatic potential due to the fully solvated hammerhead ribozyme projected onto die YEP surface [80]...

Case Study Role of Divalent Metal Ions in Hammerhead Ribozyme Catalysis... 

Figure 14-8. The 3D density contour maps (yellow) of Na+ ion distributions derived from the activated precursor simulation. The hammerhead ribozyme is shown in blue with the active site in red. Only the high-density contour is shown here to indicate the electrostatic recruiting pocket formed in the active site...

However, there are a number of other miscellaneous biological roles played by this complex. The [Co(NH3)6]3+ ion has been shown to inhibit the hammerhead ribozyme by displacing a Mn2+ ion from the active site.576 However, [Co(NH3)6]3+ does not inhibit ribonuclease H (RNase),577 topoisomerase I,578 or hairpin ribozyme,579 which require activation by Mg2+ ions. The conclusions from these studies were that an outer sphere complex formation between the enzyme and Mgaq2+ is occuring rather than specific coordination of the divalent ion to the protein. These results are in contrast to DNase I inhibition by the same hexaammine complex. Inhibition of glucose-induced insulin secretion from pancreatic cells by [Co(NH3)6]3+ has been found.580 Intracellular injection of [Co(NH3)6]3+ into a neurone has been found to cause characteristic changes to the structure of its mitochondria, and this offers a simple technique to label neuronal profiles for examination of their ultrastructures.581... 

Fortune 500 corporations, as sponsors of research, 24 385 45S5 bioactive glass, 12 611 40-nucleotide hammerhead ribozyme, 17 619... 

The hammerhead ribozyme and leadzyme belong to the second class of ribozymes. The short extra sequences of the ribozymes form the so-called catalytic loop which acts as the enzyme. There are two likely functions for metal ions in the mechanism of action of hammerhead ribozymes formation of metal hydroxide groups or direct coordination to phosphoryl oxygens. 

The hammerhead ribozyme, so named because of its claw hammer shape, is a small catalytic motif conserved in plant viroids. Viroids are infectious agents... 

Many researchers refer to stems 1, 2, and 3 using their Roman numeral equivalents—that is, stems I, II, and III. These motifs are also denoted as helices I, II, and III. It should be noted at the beginning of this hammerhead ribozyme discussion that structure-function relationships, the role of various nucleobases, metal ion participation in catalysis, and other features of the system have not been completely delineated and in some cases remain controversial. Globally, the hammerhead fold appears to be similar in both solution and solid-state studies. In solution, however, the central core of the hammerhead construct appears to be highly dynamic. This may account for different experimental results among the analytical techniques used in solution and certainly explains some distinct differences seen between solution and solid-state (X-ray crystallographic) structures. 

Figure 6.10 Secondary structure of the RNA 6 hammerhead ribozyme as found in the X-ray crystallographic structures PDB IHMH, IMME, 299D, 300D, 301D, 359D, 379D, and 488D. A modified RNA6 was used for crystal structures PDB INYI, and 1Q29.

Figure 6.11 Secondary structure of the HH16 hammerhead ribozyme used for biochemical, spectroscopic, and kinetic studies.

Hammerhead Ribozyme HHal, 17 nt ribozsrme, 27 nt substrate Used in biochemical experiments. 

Figure 6.12 Secondary structure of hammerhead ribozyme constructs used for biochemical, spectroscopic, and kinetic studies. (A) the HHal ribozyme and (B) the HH8 ribozyme. (Reprinted with permission from Figure IB of reference 47.)...

In the following year, Scott and co-workers solved the X-ray crystallographic structure of an all-RNA hammerhead ribozyme with a 2 -OCH3 group incorporated at the active site cytosine (Cn) to prevent cleavage (PDB IMME). This structure differed from that of IHMH in several important ways (1) it was an all-RNA ribozyme rather than an RNA-DNA hybrid (2) the connectivity of the ribozyme backbone strands was different (for instance... 

Herschlag s group continued its study of structure-function relationships in the hammerhead ribozyme using a base-rescue biochemical method. This method substitutes other atoms or molecules for bases at critical catalytic or structural positions and tests whether catalytic activity is lost. If so, the RNA bases (U, A, G, C) or a modified base (for instance, deazaguanine or 2-aminopurine substituted for guanine) is added to the solution to ascertain... 

Figure 6.13 Structure of the hammerhead ribozyme HH16. Dashed boxes surround the 13 substituted positions.

Bold positions are important for transition state hydrogen bonding in hammerhead ribozymes. 

Figure 6 15 Important hydrogen-bonding positions for (A) cytosine and (B) isocytosine in hammerhead ribozymes.

Additional interactions and rearrangements in the transition state with other rescuing bases may take place because it is known from crystal structures that substrate atoms are not in line for nucleophilic attack in the hammerhead ribozyme (at least not in the published crystal structures). Also, a metal ion located -20 A away from the catalytic site was shown to be crucial for catalysis. This same metal ion appeared likely to take on an additional ligand in the transition state, suggesting that conformational changes had to take place before catalysis. ... 

Figure 6.17 Talo-5 C-methyl substituent at the hammerhead ribozyme active site.

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