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PubMed1986

Guanidine hydrochloride denaturation studies of mutant forms of staphylococcal nuclease.

Several mutant forms of staphylococcal nuclease with one or two defined amino acid substitutions have been purified, and the effects of the altered amino acid sequence on the stability of the folded conformation have been analyzed by guanidine hydrochloride denaturation. Two nuc- mutations, which greatly reduced the level of enzyme activity accumulated in E coli colonies carrying a recombinant plasmid with the mutant nuc gene (ie, a NUC- phenotype), both result in protein unfolding at significantly lower guanidine hydrochloride concentrations than the wild-type protein, whereas three sup mutations isolated on the basis of their ability to suppress partially the NUC- phenotype of the above two mutations result in unfolding at significantly higher guanidine hydrochloride concentrations. Characterization of nuclease molecules with two different amino acid substitutions, either nuc- + sup pairs or sup + sup pairs, suggests that the effect of an amino acid substitution on the stability of the native conformation, as measured by the value of delta delta GD, may not be a constant, but rather a variable that is sensitive to the presence of other substitutions at distant sites in the same molecule. Surprisingly, the slopes of the log Kapp vs guanidine hydrochloride concentration plots vary by as much as 35% among the different proteins.

Amino Acid Sequence↗
PubMed1994

Distribution of globin genes and histone variants in micrococcal nuclease-generated subfractions of chromatin from Friend erythroleukemia cells at different malignant states.

The distribution of the alpha and beta-globin genes and histone variants was examined in micrococcal nuclease-generated chromatin fractions of three Friend murine erythroleukemia cell types differing in malignant potential and inducibility to erythroid differentiation. A preferential concentration of globin gene sequences, as compared to satellite DNA, was noted in a physiological salt-soluble, histone H1-depleted, mononucleosomal chromatin fraction (Sup 120) in all Friend cell types, even those in which the globin gene was not capable of transcriptional activation by chemical induction. The level of globin gene enrichment in the Sup 120 fraction was highest in the most malignant and inducible cell type. The chemical induction of erythroid differentiation in this cell line did not change the distribution of globin genes in the chromatin fractions. The Sup 120 chromatin fraction prepared from mouse brain nuclei was not enriched in globin genes. Besides the previously reported low H2A. 1/H2A.2 ratio [Blankstein and Levy: Nature 260:638-640, 1976], chromatin from the most tumorigenic cell type showed the lowest H2B.2 to H2B.1 ratio, highest levels of histone H4 acetylation, and the most pronounced change in relative amounts of two major electrophoretic bands of histone H1 variants as compared to the less malignant cell types. The histone variant content of the micrococcal nuclease-generated chromatin fractions from the three Friend cell types reflected the core histone variant differences for the respective intact nuclei. However, the electrophoretic separation of mononucleosomes by size revealed several classes with different H2A variant ratios. The results demonstrate the existence of structural differences in globin gene and histone variants in erythroleukemia cell chromatin associated with distinguishable phenotypes during malignant cell progression.

Acetylation↗
PubMed1994

Thermodynamics of staphylococcal nuclease denaturation. II. The A-state.

Staphylococcal nuclease, at low pH and in the presence of high salt concentrations, has previously been proposed to exist in a partially folded or molten globule form called the "A-state" (Fink et al., 1993, Protein Sci 2:1155-1160). We have found that the A-state of nuclease at pH 2.1 in the presence of moderate to high salt concentrations and at low temperature exists in a substantially folded form structurally more similar to a native state. The A-state has the far-UV circular dichroism spectra characteristic of the native protein, which indicates that it has a large degree of secondary structure. Upon heating, the A-state denatures with a sigmoidal change in far-UV ellipticity and an observable peak in a differential scanning calorimeter trace, indicating that it is thermodynamically distinct from the denatured state. Three different mutations in a residue normally buried in the protein's core stabilize or destabilize the A-state in the same way as they affect the denaturation of the native state. The A-state must, therefore, contain at least some tertiary packing of side chains. Unlike the native state, which shows cold denaturation at low temperatures, the A-state is most stable at temperatures below 0 degrees C.

Calorimetry, Differential Scanning↗
PubMed1996

Mobile unnatural amino acid side chains in the core of staphylococcal nuclease.

The structures of several variants of staphylococcal nuclease with long flexible unnatural amino acid side chains in the hydrophobic core have been determined by X-ray crystallography. The unnatural amino acids are disulfide moieties between the lone cysteine residue in V23C nuclease and methane, ethane, 1-n-propane, 1-n-butane, 1-n-pentane, and 2-hydroxyethyl thiols. We have examined changes in the core packing of these mutants. Side chains as large as the 1-n-propyl cysteine disulfide can be incorporated without perturbation of the structure. This is due, in part, to cavities present in the wild-type protein. The longest side chains are not well defined, even though they remain buried within the protein interior. These results suggest that the enthalpy-entropy balance that governs the rigidity of protein interiors favors tight packing only weakly. Additionally, the tight packing observed normally in protein interiors may reflect, in part, the limited numbers of rotamers available to the natural amino acids.

Amino Acids↗
PubMed1996

A dynamic bundle of four adjacent hydrophobic segments in the denatured state of staphylococcal nuclease.

In an earlier study of the denatured state of staphylococcal nuclease (Wang Y, Shortle D, 1995, Biochemistry 34:15895-15905), we reported evidence of a three-strand antiparallel beta sheet that persists at high urea concentrations and is stabilized by a local "non-native" interaction with four large hydrophobic residues. Because the amide proton resonances for all of the involved residues are severely broadened, this unusual structure is not amenable to conventional NMR analysis and must be studied by indirect methods. In this report, we present data that confirm the important role of interactions involving four hydrophobic residues (Leu 36, Leu 37, Leu 38, and Val 39) in stabilizing the structure formed by the chain segments corresponding to beta 1-beta 2-beta 3-h, interactions that are not present in the native state. Glycine substitutions for each of these large hydrophobic residues destabilizes or disrupts this beta structure, as assessed by HN line sharpening and changes in the CD spectrum. The 13C resonances of the carbonyl carbon for several of the residues in this structure indicate conformational dynamics that respond in a complex way to addition of urea or changes in sequence. Studies of hydrogen exchange kinetics in a closely related variant of staphylococcal nuclease demonstrate the absence of the stable hydrogen bonding between the strands expected for a native-like three-strand beta sheet. Instead, the data are more consistent with the three beta strand segments plus the four adjacent hydrophobic residues forming a dynamic, aligned array or bundle held together by hydrophobic interactions.

Carbon Isotopes↗
PubMed1997

P100, a transcriptional coactivator, is a human homologue of staphylococcal nuclease.

Staphylococcus aureus nuclease (SNase) homologues, previously thought to be restricted to bacteria and archaea, are demonstrated by sequence analysis to be present also in eukaryotes. The human cellular coactivator p100 is shown to contain four repeats, each of which is a SNase homologue. Surprisingly, these repeats are unlikely to possess SNase-like activities as each lacks equivalent SNase catalytic residues, yet they may mediate p100's single-stranded DNA-binding function. Products of Corydalis sempervirens and Saccharomyces cerevisiae open reading frames are predicted to adopt the same fold and possess similar functions as SNase. Five additional hypothetical proteins of bacterial origin are also predicted to be active SNase-like nucleases, including one that appears to be C-terminally truncated in a manner analogous to an engineered active SNase variant. Conservation of Asp-19 and Asp-83 among these homologues suggests a re-evaluation of the roles of these residues in Ca(2+)-binding and/or catalysis.

Amino Acid Sequence↗
PubMed1997

Comparison of straight chain and cyclic unnatural amino acids embedded in the core of staphylococcal nuclease.

We have determined by X-ray crystallography the structures of several variants of staphylococcal nuclease with long flexible straight chain and equivalent length cyclic unnatural amino acid side chains embedded in the protein core. The terminal atoms in the straight side chains are not well defined by the observed electron density even though they remain buried within the protein interior. We have previously observed this behavior and have suggested that it may arise from the addition of side-chain vibrational and oscillational motions with each bond as a side chain grows away from the relatively rigid protein main chain and/or the population of multiple rotamers (Wynn R, Harkins P, Richards FM. Fox RO. 1996. Mobile unnatural amino acid side chains in the core of staphylococcal nuclease. Protein Sci 5:1026-1031). Reduction of the number of degrees of freedom by cyclization of a side chain would be expected to constrain these motions. These side chains are in fact well defined in the structures described here. Over-packing of the protein core results in a 1.0 A shift of helix 1 away from the site of mutation. Additionally, we have determined the structure of a side chain containing a single hydrogen to fluorine atom replacement on a methyl group. A fluorine atom is intermediate in size between methyl group and a hydrogen atom. The fluorine atom is observed in a single position indicating it does not rotate like methyl hydrogen atoms. This change also causes subtle differences in the packing interactions.

Amino Acids↗
PubMed2005

Elucidation of information encoded in tryptophan 140 of staphylococcal nuclease.

We investigated the role of W140 in the folding of Staphylococcal nuclease. For this purpose, we constructed the 19 possible substitution mutations at residue 140. Only three mutants, W140F, W140H, and W140Y, adopted native-like structures under physiological conditions and showed native-like enzymatic activities. In contrast, the other 16 mutants took on compact unfolded structures under physiological conditions and the enzymatic activities of these mutants were decreased to approximately 70% of wild-type levels. These 16 mutants maintained substrate-induced foldability. These results strongly indicate that the side-chain information encoded by residue 140 is essential to maintain a stable native structure, and that this residue must be an aromatic side chain. The order of thermal stability was wild type > W140H > W140F = W140Y. Therefore, the five-membered nitrogen-containing ring of the indole is thought to bear the essential information. In the crystal structure of staphylococcal nuclease, the five-membered ring is at the local center of the C-terminal cluster through hydrophobic interactions. This cluster plays a key role in the interaction connecting the C-terminal region and the N-terminal beta-core. Mutants other than W140H, W140F, and W140Y lost the ability to form the local core, which caused the loss of the long-range interactions between the C-terminal and N-terminal regions. Inhibitor or substrate binding to these mutants compensates for the lack of long-range interactions generated by W140.

Circular Dichroism↗
PubMed2006

Characterization of the residual structure in the unfolded state of the Delta131Delta fragment of staphylococcal nuclease.

The determination of the conformational preferences in unfolded states of proteins constitutes an important challenge in structural biology. We use inter-residue distances estimated from site-directed spin-labeling NMR experimental measurements as ensemble-averaged restraints in all-atom molecular dynamics simulations to characterise the residual structure of the Delta131Delta fragment of staphylococcal nuclease under physiological conditions. Our findings indicate that Delta131Delta under these conditions shows a tendency to form transiently hydrophobic clusters similar to those present in the native state of wild-type staphylococcal nuclease. Only rarely, however, all these interactions are simultaneously realized to generate conformations with an overall native topology.

Computer Simulation↗
PubMed1992

Structural and energetic differences between insertions and substitutions in staphylococcal nuclease.

In a previous study, the small protein staphylococcal nuclease was shown to readily accommodate single alanine and glycine insertions, with average losses in stability comparable to substitutions at the same sites (PROT. 7:299-305, 1990). To more fully explore this unexpected adaptability to changes in residue spacing, 2 double amino acid insertions (alanyl-glycine, glycyl-glycine) and 3 additional single amino acid insertions with dissimilar side chains (proline, leucine, and glutamine) were constructed at 10 of the sites previously studied. At 8 of these sites, the type of amino acid side chain on the inserted residue significantly influenced the stability of the mutant protein. However, at 9 of the 10 sites, the double insertions were found to be no more destabilizing than the single alanine or glycine insertions. In contrast, double substitution mutations of staphylococcal nuclease, which replace two adjacent residues with alanine, do not show this striking degree of non-additivity. A comparison of the effects of single glutamine and single glycine insertions with alanyl-glycine insertions indicates that insertion of alanine into the peptide backbone is, on average, less destabilizing than appending the equivalent atoms onto the side chain of a glycine insertion. To explain their very different energetic effects, we propose that, unlike most substitutions, the inserted residue(s) must induce lateral displacements of the polypeptide chain, forcing the folded conformation away from that of wild type. The resulting obligatory shifts in the positioning of residues flanking the insertion generate a large number of degrees of freedom around which the mutant structure can relax.(ABSTRACT TRUNCATED AT 250 WORDS)

Alanine↗
PubMed1994

Residual structure in a staphylococcal nuclease fragment. Is it a molten globule and is its unfolding a first-order phase transition?

Temperature-induced unfolding of staphylococcal nuclease and its large fragment, which lacks 13 C-terminal amino acid residues, was studied calorimetrically, and by CD and fluorescence spectroscopy. It was shown that, in contrast to the full length protein which includes two domains and unfolds in two distinct stages under some conditions, the fragment unfolds in one stage. Unfolding of the fragment proceeds in the same temperature range in which the N-terminal beta-barrel domain unfolds in the full length staphylococcal nuclease. Therefore, the fragment is initially partly unfolded. It retains a stable N-terminal domain which unfolds co-operatively with significant heat absorption. Unfolding of the fragment can be regarded as a first-order phase transition, but its initial state certainly does not represent a molten globule, as it was believed.

Calorimetry↗
PubMed1996

The M32L substitution of staphylococcal nuclease: disagreement between theoretical prediction and experimental protein stability.

The M32L substitution mutation of staphylococcal nuclease was made to test the theoretical prediction by Yamaotsu, Moriguchi and Hirono that it would be approximately 1.6 kcal/mol more stable than the wild-type protein. Instead M32L and the closely related M32I mutant were 0.8 and 0.6 kcal/mol less stable than the wild-type protein, respectively. The theoretical treatment had successfully predicted the stability effects of other mutations in staphylococcal nuclease. The discrepancy found here may be due to a general problem of the theoretical treatment, such as inadequate molecular dynamics simulation time, or possibly due to more specific difficulty in assessing the strength of the sulfur-aromatic interaction that is present in the wild-type.

Enzyme Stability↗
PubMed1996

Accretion of structure in staphylococcal nuclease: an 15N NMR relaxation study.

15N main-chain dynamics are compared in four forms of staphylococcal nuclease with different stabilities to unfolding: (1) SN-T, the ternary complex of the protein, Ca2+, and the inhibitor thymidine 3', 5'-bisphosphate; (2) SN, the protein in the absence of added ligands; (3) SN-OB, a folded fragment that corresponds to an "OB-fold" subdomain; (4) delta 131 delta, a denatured 131-residue fragment. SN-T exhibits very little internal motion on the nanosecond timescale. In SN, a moderate increase in flexibility is observed for the first three strands of the five-stranded beta-sheet, and for a loop between strands 4 and 5. In SN-OB, the loops between strands 3 and 4, and between strands 4 and 5, are extremely flexible on the nanosecond timescale. While the beta-sheets of SN-OB and SN have comparable dynamics on the nanosecond timescale, the beta-sheet in SN-OB experiences additional motion on a slower timescale of 330(+/-170) microseconds. We attribute the latter to interconversion between a major folded (> or = 98%) and a minor unfolded (> or = 2%) conformation. In delta 131 delta, the first three strands of beta-sheet experience conformational averaging on the millisecond timescale. Most of the remainder of the polypeptide chain is highly flexible on the nanosecond timescale. When all four forms of nuclease are considered, there is an increase in the proportion of residues with large amplitude internal motions (low order parameters) as the stability of the folded state is decreased. Residues with low order parameters cluster to distinct regions of the chain, and have H alpha chemical shifts and 3JHN-H alpha coupling constants that tend towards "random coil" values. Conversely, a trend towards uniformly high order parameters suggests a consolidation of structure with increasing stability to denaturation.

Magnetic Resonance Spectroscopy↗
PubMed1997

Characterization of long-range structure in the denatured state of staphylococcal nuclease. II. Distance restraints from paramagnetic relaxation and calculation of an ensemble of structures.

Structural analysis of delta131delta, a fragment model of the denatured state of staphylococcal nuclease, has been extended by obtaining long-range distance restraints between chain segments by paramagnetic relaxation enhancement. Fourteen unique PROXYL spin labels were introduced at sites that are solvent-exposed in the native state, and the resulting enhancements of T2 for the amide protons were measured by NMR spectroscopy. When these data were combined with either measured or estimated correlation times tau(c), the r(-6)-weighted, time and ensemble-averaged distance between the spin label and 30 to 60 amide protons could be calculated for each spin-labeled protein. On the basis of approximately 700 such loose distance restraints, ensembles of compatible structures were generated by a combined distance geometry/molecular dynamics approach. Because of the large uncertainty in the physical basis of these distance restraints, a number of calculations were carried out to establish the sensitivity of the calculated structures to systematic errors in these restraints. Overall, the structural features reflected in the paramagnetic relaxation data were robust; large variations in tau(c), in the bounds window of allowed distances, or in the number of restraint distances used had small effects on the general features common to all calculated structures. The global topology of this denatured form of staphylococcal nuclease, as described by an ensemble of conformations consistent with the data, is strikingly similar to that of the native state, the major difference being the segregation of two hydrophobic segments that form a beta hairpin in the native state. These findings suggest that the topology of a protein's fold is established in the denatured state in the absence of cooperative interactions involving tight packing or stable hydrogen bonding. Hydrophobic interactions alone may encode global topology.

Algorithms↗
PubMed1998

Isolation and physical characterization of random insertions in Staphylococcal nuclease.

Using genetic engineering techniques we generated randomly located internal tandem duplications of random size within Staphylococcal nuclease. Those insertions, possessing greater than 0.1% of normal activity, were sequenced and characterized physically. Insertions were found to begin and end in regions possessing secondary structure as well as in regions without secondary structure. All proteins remained folded and monomeric, although one mutant appeared, by both circular dichroism and size exclusion chromatography, to be partially unfolded. The stability of the insertions as assayed by guanidine hydrochloride denaturation ranged from nearly normal to destabilized by almost 4 kcal per mol. The activities of the insertion mutants ranged from 1/30 to 1/2000 of the parental nuclease.

Chromatography, Gel↗
PubMed2000

Increasing the thermostability of staphylococcal nuclease: implications for the origin of protein thermostability.

Seven hyper-stable multiple mutants have been constructed in staphylococcal nuclease by various combinations of eight different stabilizing single mutants. The stabilities of these multiple mutants determined by guanidine hydrochloride denaturation were 3.4 to 5.6 kcal/mol higher than that of the wild-type. Their thermal denaturation midpoint temperatures were 12.6 to 22.9 deg. C higher than that of the wild-type. These are among the greatest increases in protein stability and thermal denaturation midpoint temperature relative to the wild-type yet attained. There has been great interest in understanding how proteins found in thermophilic organisms are stabilized. One frequently cited theory is that the packing of hydrophobic side-chains is improved in the cores of proteins isolated from thermophiles when compared to proteins from mesophiles. The crystal structures of four single and five multiple stabilizing mutants of staphylococcal nuclease were solved to high resolution. No large overall structural change was found, with most changes localized around the sites of mutation. Rearrangements were observed in the packing of side-chains in the major hydrophobic core, although none of the mutations was in the core. It is surprising that detailed structural analysis showed that packing had improved, with the volume of the mutant protein's hydrophobic cores decreasing as protein stability increased. Further, the number of van der Waals interactions in the entire protein showed an experimentally significant increase correlated with increasing stability. These results indicate that optimization of packing follows as a natural consequence of increased protein thermostability and that good packing is not necessarily the proximate cause of high stability. Another popular theory is that thermostable proteins have more electrostatic and hydrogen bonding interactions and these are responsible for the high stabilities. The mutants here show that increased numbers of electrostatic and hydrogen bonding interactions are not obligatory for large increases in protein stability.

Crystallography, X-Ray↗
PubMed1993

Measurement of two- and three-bond 13C-1H J couplings to the C delta carbons of leucine residues in staphylococcal nuclease.

A new 1H-detected 3D NMR experiment is described that permits quantitative measurement of two- and three-bond 13C-1H couplings in proteins with selectively 13C-enriched methyl sites. The method is demonstrated for staphylococcal nuclease selectively [5,5 13C]-labeled in all 11 leucine positions and ligated with thymidine 3',5'-biphosphate and Ca2+. Two- and three-bond 13C methyl-proton couplings are reported and, together with the measured three-bond JC alpha C delta in uniformly 13C-enriched staphylococcal nuclease, the chi 2-angles and the stereospecific assignments of the C delta methyl group with respect to the prochiral beta-protons were determined. The same residues that were previously found to have high degrees of internal mobility on the basis of 13C relaxation times have measured coupling constants that are indicative of motional averaging.

Amino Acid Sequence↗
PubMed1979

Staphylococcal nuclease reviewed: a prototypic study in contemporary enzymology. II. Solution studies of the nucleotide binding site and the effects of nucleotide binding.

This is the second of a series of four articles in which the chemical, enzymological and crystallographic work on Ribonucleate (deoxyribonucleate)-3'-nucleotidohydrolase, EC 3.1.4.4. (staphylococcal nuclease, micrococcal nuclease) will be reviewed and correlated. This article discusses studies in solution delineating the extent of the binding site of the enzyme and identifying some of the particular amino acid residues that form this site. In addition, the effects of the very potent inhibitory combination of thymidine-3',5'-diphosphate and Ca2+ on the conformation of the enzyme and its physical, chemical and enzymological properties will be reviewed.

Binding Sites↗