RNAse modell

The RNAse model compound of Hamilton was constructed in a few steps (Scheme 15) [30]. Benzoyl isothiocyanate was allowed to react with diamine 59 to yield bis(thiourea) 61 after deprotection. S-methylation activated the urea moieties for guanidine formation with Af,A -dimethyl-ethy-lenediamine 62 to reach the desired compound 53. 

The squaraine probe 9g was tested for its sensitivity to trace the formation of protein-lipid complexes [57]. The binding of dye 9g to model membranes composed of zwitter-ionic lipid phosphatidylcholine (PC) and its mixtures with anionic lipid cardiolipin (CL) in different molar ratios was found to be controlled mainly by hydrophobic interactions. Lysozyme (Lz) and ribonuclease A (RNase) influenced the association of 9g with lipid vesicles. The magnitude of this effect was much higher... 

Rait VK, Xu L, O Leary TJ, et al. Modeling formalin fixation and antigen retrieval with bovine pancreatic RNase A II. Interrelationship of cross-linking, immunore-activity, and heat treatment. Lab. Invest. 2004 84 300-306. 

The catalytic groups in the reactive center of ribonuclease A, a further polynueleotide-cleaving enzyme, are an imidazole (acting as a general base) and an imidazolinium eation (acting as a general acid). In a series of papers starting as early as 1978, Breslow and coworkers describe the use of -cyclodextrinyl-bis(imidazoles) 62 as model compounds for RNase A [94], In the course of the... 

Fio. 2. Stereoscopic view of a skeletal model of RNase-S deduced from the 3.5-A resolution map and chemical sequence data. The small balls locate sulfur atoms. Die large ball hanging from the top support plate shows the van der Waals size of a paraffinic hydrogen atom. 

Wyckoff et al. (62) have provided a preliminary coordinate list of all nonhydrogen atoms in RNase-S. Along with the list is a series of notations on the quality of the map and the fit of the atomic model to the electron density contours. The following comments concerning group accessibilities are based on this coordinate list, but detailed interpretations must be made with caution in view of the uncertainties in many parts of the structure. 

Hybrid dimers have been prepared from alkylated monomer fractions (382) and the native enzyme in various permutations. The products gave the predicted activities. In particular a dimer prepared from CM-His-12-RNase (inactive) and CM-His-119-RNase (inactive) had 50% of the specific activity of RNase-A. This activity was lost on dissociation of the dimer. All of these experiments together strongly confirm the proposed model. This also fits nicely into the observed behavior of the RNase-S system as outlined in Fig. 7. 

Liu, F. and Altman, S. (1996) Requirements for cleavage by a modified RNase P of a small model substrate. Nucleic Acids Res., 24,2690-2696. 

Potentiometry was used to investigate the speciation of La(ni) in methanolic methox-ide solutions, with and without diphenyl phosphate or methyl 4-nitrophenyl phosphate (98), substrates which are very efficiently methanolysed by such solutions.2 La(III)-catalysed methanolysis is thus regarded as a good model for the metal-containing RNAses and DNases which cleave phosphate diester linkages. In the high [La(III)] domain, the data fitted, as one possibility among several, a spontaneous decomposition... 

The apparent usefulness of the modeling approach suggested that possible active site interactions important in understanding the mode of action of the well-characterized enzymes, ribonuclease (16) and staphylococcal nuclease (17). may be revealed. Both have been the subject of extensive crystallographic studies (18,19) with suitable inactive substrates in place. We considered the first step of hydrolytic action of ribonuclease (RNase) on the dinucleotide substrate uridylyl-(3 -5 )-adenosine(UpA). Our results (20) on the enzyme mechanism were consistent with the main features summarized by Roberts et al (21). The first step is a transphosphorylation leading to cleavage "oT the phosphodiester... 

Figure 2.3 Proposed model for the semisynthetic RNAse-S complex incorporating a pyridoxal-based amino acid residue. The S-peptide fragment is highlighted, illustrating the location ofpyridoxal (Palg) and the general acid-base pair. (Reprinted with permission from Ref. 28.

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