Structure of ribonuclease A: results of joint neutron and x-ray refinement at 2.0-.ANG. resolution

Wlodawer, Alexander; Sjoelin, Lennart

doi:10.1021/bi00280a021

Cited by 181 publications

(105 citation statements)

References 22 publications

Supporting

Mentioning

101

Contrasting

Order By: Relevance

“…The intramolecular main chain hydrogen-bonding pattern (Fig. 5 ) is very similar to that seen in RNase A (Wlodawer & Sjolin, 1983), in RNase 1-1 18: 11 1-124 (Martin et al, 1987), and in the two Asp 121 analogs (deMel et al, 1992). When comparing the relative location of corresponding atoms in two structures, a change in bond distance was considered significant if it was greater than 0.30A.…”

Section: Data Collection Structure Determination and Refinementsupporting

confidence: 61%

“…A water molecule coincident with WAT 138 is also found in both refined structures of RNase A (Wlodawer & Sjolin, 1983;Borkakoti et al, 1984).…”

Section: Active Site Solvent Moleculesmentioning

confidence: 59%

“…8). In RNase A, a strong hydrogen bond (2.84 A) is seen between NZ of Lys 66 and OD1 of Asp 121 (Wlodawer et al, 1982;Wlodawer & Sjolin, 1983), while in there is a bifurcated hydrogen bond linking NZ of Lys 66 to OD1 of Asp 121 (3.44 A) and to the carbonyl oxygen of Asp 121 (2.79 A) (Fig. 8;Martin et al, 1987).…”

Section: Discussionmentioning

confidence: 99%

See 2 more Smart Citations

Structural investigation of catalytically modified F120L and F120Y semisynthetic ribonucleases

et al. 1994

View full text Add to dashboard Cite

show abstract

Section: Data Collection Structure Determination and Refinementsupporting

confidence: 61%

“…A water molecule coincident with WAT 138 is also found in both refined structures of RNase A (Wlodawer & Sjolin, 1983;Borkakoti et al, 1984).…”

Section: Active Site Solvent Moleculesmentioning

confidence: 59%

See 1 more Smart Citation

Structural investigation of catalytically modified F120L and F120Y semisynthetic ribonucleases

et al. 1994

View full text Add to dashboard Cite

show abstract

“…For ribonuclease the starting model was the joint neutron and X-ray structure of Wlodower and Sjolin (1983) with the PDB designation 5RSA. For DHFR, the starting model was the structure of the methotrexate binary complex with the PDB designation 4DFR Filman et al, 1982).…”

Section: Methodsmentioning

confidence: 99%

The effect of denaturants on protein structure

et al. 1997

View full text Add to dashboard Cite

Virtually all studies of the protein-folding reaction add either heat, acid, or a chemical denaturant to an aqueous protein solution in order to perturb the protein structure. When chemical denaturants are used, very high concentrations are usually necessary to observe any change in protein structure. In a solution with such high denaturant concentrations, both the structure of the protein and the structure of the solvent around the protein can be altered. X-ray crystallography is the obvious experimental technique to probe both types of changes. In this paper, we report the crystal structures of dihydrofolate reductase with urea and of ribonuclease A with guanidinium chloride. These two classic denaturants have similar effects on the native structure of the protein. The most important change that occurs is a reduction in the overall thermal factor. These structures offer a molecular explanation for the reduction in mobility. Although the reduction is observed only with the native enzyme in the crystal, a similar decrease in mobility has also been observed in the unfolded state in solution (Makhatadze G, Privalov PL. 1992. Protein interactions with urea and guanidinium chloride: A calorimetric study. J Mol B i d 226491-505).Keywords: denaturants; dihydrofolate reductase; protein mobility; ribonuclease A Despite our routine use of them, our understanding of the molecular mechanism by which chemical denaturants like urea or guanidinium (Gua) cause a protein to unfold is still rather limited. As has been pointed out by others (Schellman, 1987), part of the problem is that it is difficult to measure binding constants when the protein concentration is M and the denaturant concentration is 4 M. High precision scanning calorimetry has provided one experimental solution to this problem (Makhatadze & Privalov, 1992) but relating the thermodynamic data produced in such an experiment to protein structure can be difficult (Alber, 1989). While it does seem clear that denaturants interact directly with the protein (Simpson & Kauzmann, 1953), it is also clear that at high concentrations these molecules can cause substantial changes to the behavior of the solvent itself (Breslow & Guo, 1990 teins by migrating into the interior of the protein and forming hydrogen bonds to atoms in the backbone (Hedwig et al., 1991). In support of such a model, the exchange rates of some peptide NH protons, which are found on both the surface and the interior of a protein, are decreased in the presence of urea (Kim & Woodward, 1993). In addition, crystallographic studies of diketopiperazine and urea show hydrogen bonding between the amide groups and the urea (Thayer et al., 1993). Other models have suggested that denaturants act by decreasing the hydrophobic effect (Wetlaufer et al., 1964;Roseman & Jencks, 1975), which, in this instance, is usually postulated to be the dominant force stabilizing protein structure. Finally, experiments by Kim and Woodward (1 993) clearly show that, in addition to interacting with peptide bonds, urea alters...

show abstract

“…In RNases such as RNase T1 [27], RNase T2 [28] and RNase A [29], and also in pancreatic DNase I [30] and S1 nuclease [31], histidine has been implicated in the active site of the enzyme. The chemical modification and site-directed mutagenesis used in this study indicated that PRV DNase is a member of the histidine nuclease family and that His$(" is the active-site residue of PRV DNase.…”

Section: Figure 6 Summary Diagram Illustrating Known Functional Featumentioning

confidence: 99%

Identification of a DNA-binding domain and an active-site residue of pseudorabies virus DNase

Hsiang

et al. 2000

Biochemical Journal

View full text Add to dashboard Cite

The pseudorabies virus (PRV) DNase gene has an open reading frame of 1476 nt, capable of coding a 492-residue protein. A previous study showed that PRV DNase is an alkaline exonuclease and endonuclease, exhibiting an Escherichia coli RecBCD-like catalytic function. To analyse its catalytic mechanism further, we constructed a set of clones truncated at the Nterminus or C-terminus of PRV DNase. The deleted mutants were expressed in E. coli with the use of pET expression vectors, then purified to homogeneity. Our results indicate that (1) the region spanning residues 274-492 exhibits a DNA-binding ability 7-fold that of the intact DNase ; (2) the N-terminal 62 residues and the C-terminal 39 residues have important roles in 3h-exonuclease activity, and (3) residues 63-453 are responsible for 5h-and 3h-exonuclease activities. Further chemical modification

show abstract

Structure of ribonuclease A: results of joint neutron and x-ray refinement at 2.0-.ANG. resolution

Cited by 181 publications

References 22 publications

Structural investigation of catalytically modified F120L and F120Y semisynthetic ribonucleases

Structural investigation of catalytically modified F120L and F120Y semisynthetic ribonucleases

The effect of denaturants on protein structure

Identification of a DNA-binding domain and an active-site residue of pseudorabies virus DNase

Contact Info

Product

Resources

About