Ribonucleases structural analysis

Nolan JM, Pace NR (1996) Structural analysis of bacterial ribonuclease P RNA, p 109-128. In Eckstein F, Lilley DMJ (ed) Catalytic RNA, vol. 10. Springer, Berlin Heidelberg New York... 

Ijeucine aminopeptidase has been applied in many ways to particular problems in structural analysis of peptides and proteins. Sequences in the amino-terminal portion of a peptide can often be established by measurement of the order of appearance of amino acids that are released during hydrolysis. The procedure has been used with a variety of proteins and peptides, including ribonuclease (Hirs et al., 1960), hemoglobin (Konigsberg and Hill, 1962, 1963 Schroeder et al., 1963), cytochrome c (Margoliash, 1962 Matsubara and Smith, 1963), and lysozyme (Canfield, 1963). 

The purpose of an RNA footprinting experiment is to predict the structure of the RNA and/or to identify the binding site(s) for proteins or ligands. The experimental approach for the structural analysis of RNA, or RNA-protein to complexes, utilises a number of different chemicals and ribonucleases which react with nucleotides in certain structural conformations of the RNA. The properties required of the chemicals and ribonucleases used for probing of the RNA structure are not necessarily the same as the properties required for probing of an RNA-protein complex (Fig. 4.6). 

A. D. MacKerell, Jr., L. Nilsson, R. Rigler, and W. Saenger, Biochemistry, 27,4547 (1988). Molecular Dynamics Simulations of Ribonuclease Tl Analysis of the Effect of Solvent on the Structure, Fluctuations, and Active Site of the Free Enzyme. 

Woodward, J.R. D. Craik, A. Dell, K.H. Khoo, S.L.A Munro, A.E. Clarke, and A. Bade Structural analysis of the V-linked glycan chains from a stylar glycoprotein associated with expression of self-incompatibility in Nicotiana alata Glycobiology 2 (1992) 241-250. Wray, J.L., R.E. Brick, and L. Fowden Development of aminoacyl tRNA synthetases in cultured Nicotiana tabacum cells Phytochemistry 13 (1974) 697-701. Wyen, N.V., J. Udvardy, S. Erdei, and C.L. Farkas Level of a relatively purine-specific ribonuclease increases in virus-infected hypersensitive of mechanically injured tobacco leaves Virology 48 (1972) 337-341. 

For each entry, a table summarizes information regarding (1) the X-ray diffraction data upon which the analysis is based, (2) the methods employed in structure analysis and refinement and their main results, and (3) some structural characteristics. In a separate table, the ribonuclease amino acid sequence is... 

William Howard Stein fl 911-1980) was born in New York City and received his Ph.D. in 1938 from the Columbia College of Physicians and Surgeons. He immediately joined the faculty of the Rockefeller Institute, where he remained until his death. In 1972, he shared the Nobel Prize in chemistry for his work with Stanford Moore on developing methods of amino acid analysis and for determining the structure of ribonuclease. 

Fig. 11. Amide F thermal denaturation spectra for ribonuclease A as followed by FTIR (left) and VCD (right), which show the IR peak shifting from the dominant /3-sheet frequency (skewed with a maximum at 1635 cm-1) to the random coil frequency ( 1645-1650 cm-1) and the VCD shape changing from the W-pattern characteristic of an a + p structure to a broadened negative couplet typical of a more disordered coil form. The process clearly indicates loss of one form and gain of another while encompassing recognition of an intermediate form. (This is seen here most easily as the decay and growth back of the 1630 cm-1 VCD feature, but is more obvious after factor analysis of the data set, Fig. 15).

Fig. 12. Thermal denaturation for ribonuclease Tj as followed by VCD, from 20° to 65°C. The matrix descriptors determined for the native state and the unfolded high-temperature data are indicated. The values indicate a loss of the helix segment but maintenance of sheet segments. Also listed are the spectrally determined fractional contributions (FC) to the secondary structure. When combined with the segment analysis, this implies that the residual sheet segments must be very short. Reprinted with permission from Pancoska, P., et al. (1996). Biochemistry 35(40), 13094-13106, the American Chemical Society.

Chattopadhyay D, Finzel BC, Munson SH, Evans B, Sharma SK, Strakalattis NA, et al. Crystallographic analysis of an active HIV-1 ribonuclease H domain show structural features that distinguish it from the inactive form. Acta Crystallogr 1993 D49 423-427. 

Yang W, Hendrickson WA, Crouch RJ, Satow Y. Structure of ribonuclease H phased at 2 A resolution by MAD analysis of the selenomethionyl protein. Science 1990 249 1398-1405. 

Reported applications of DMA include the cross-linking of bovine pancreatic ribonuclease A (Hartman and Wold, 1967), treatment of erythrocyte membranes to reduce the effects of sickle cell anemia (Waterman et al., 1975), conjugation and analysis of the outer membrane proteins of Neisseria gonorrhoeae (Newhall et al., 1980), protein structural studies of bovine a-crystalline (Siezen et al., 1980), cross-linking of hemoglobin S (Pennathur-Das et al., 1982), and forming S-carbomethoxy-valeramidine during hydrolysis of DMA (Mentzer et al., 1982). 

Many of these features are evident in the three-dimensional structures of ribonuclease and myoglobin shown in Figure II-3. To understand the common and distinguishing features of the secondary and tertiary structure of various proteins as determined by x-ray crystallographic analysis, the student should study several examples in standard textbooks of biochemistry. 

Discontinuous SARs. Consistent with the results of our qualitative SAR analysis presented above, SARI scoring indicates that ribonuclease A inhibitors are a prototypic example of discontinuous SARs. The potency among these highly similar nucleotide analogs differs by up to three orders of magnitude (Figure 4.7b). As already mentioned above, these features clearly indicate the presence of discontinuous SARs. The low SARI score of 0.16 mirrors these findings. It results from the combination of a very low continuity score of nearly zero (0.004) that reflects the lack of structural diversity within the... 

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