Search PubMed⌕ Search

Biomedical subjects

C N Pace

Publications and source records attributed to C N Pace.

At least 55 records · Page 3Linked to original sources
PubMed1992

Contribution of hydrogen bonding to the conformational stability of ribonuclease T1.

For 30 years, the prevailing view has been that the hydrophobic effect contributes considerably more than hydrogen bonding to the conformational stability of globular proteins. The results and reasoning presented here suggest that hydrogen bonding and the hydrophobic effect make comparable contributions to the conformational stability of ribonuclease T1 (RNase T1). When RNase T1 folds, 86 intramolecular hydrogen bonds with an average length of 2.95 A are formed. Twelve mutants of RNase T1 [Tyr----Phe (5), Ser----Ala (3), and Asn----Ala (4)] have been prepared that remove 17 of the hydrogen bonds with an average length of 2.93 A. On the basis of urea and thermal unfolding studies of these mutants, the average decrease in conformational stability due to hydrogen bonding is 1.3 kcal/mol per hydrogen bond. This estimate is in good agreement with results from several related systems. Thus, we estimate that hydrogen bonding contributes about 110 kcal/mol to the conformational stability of RNase T1 and that this is comparable to the contribution of the hydrophobic effect. Accepting the idea that intramolecular hydrogen bonds contribute 1.3 +/- 0.6 kcal/mol to the stability of systems in an aqueous environment makes it easier to understand the stability of the "molten globule" states of proteins, and the alpha-helical conformations of small peptides.

Amino Acid Sequence↗
PubMed1990

Contribution of histidine residues to the conformational stability of ribonuclease T1 and mutant Glu-58----Ala.

The pK values of the histidine residues in ribonuclease T1 (RNase T1) are unusually high: 7.8 (His-92), 7.9 (His-40), and 7.3 (His-27) [Inagaki et al. (1981) J. Biochem. 89, 1185-1195]. In the RNase T1 mutant Glu-58----Ala, the first two pK values are reduced to 7.4 (His-92) and 7.1 (His-40). These lower pKs were expected since His-92 (5.5 A) and His-40 (3.7 A) are in close proximity to Glu-58 at the active site. The conformational stability of RNase T1 increases by over 4 kcal/mol between pH 9 and 5, and this can be entirely accounted for by the greater affinity for protons by the His residues in the folded protein (average pK = 7.6) than in the unfolded protein (pk approximately 6.6). Thus, almost half of the net conformational stability of RNase T1 results from a difference between the pK values of the histidine residues in the folded and unfolded conformations. In the Glu-58----Ala mutant, the increase in stability between pH 9 and 5 is halved (approximately 2 kcal/mol), as expected on the basis of the lower pK values for the His residues in the folded protein (average pK = 7.1). As a consequence, RNase T1 is more stable than the mutant below pH 7.5, and less stable above pH 7.5. These results emphasize the importance of measuring the conformational stability as a function of pH when comparing proteins differing in structure.

Alanine↗
PubMed1990

pH dependence of the urea and guanidine hydrochloride denaturation of ribonuclease A and ribonuclease T1.

To investigate the pH dependence of the conformational stability of ribonucleases A and T1, urea and guanidine hydrochloride denaturation curves have been determined over the pH range 2-10. The maximum conformational stability of both proteins is about 9 kcal/mol and occurs near pH 4.5 for ribonuclease T1 and between pH 7 and 9 for ribonuclease A. The pH dependence suggests that electrostatic interactions among the charged groups make a relatively small contribution to the conformational stability of these proteins. The dependence of delta G on urea concentration increases from about 1200 cal mol-1 M-1 at high pH to about 2400 cal mol-1 M-1 at low pH for ribonuclease A. This suggests that the unfolded conformations of RNase A become more accessible to urea as the net charge on the molecule increases. For RNase T1, the dependence of delta G on urea concentration is minimal near pH 6 and increases at both higher and lower pH. An analysis of information of this type for several proteins in terms of a model developed by Tanford [Tanford, C. (1964) J. Am. Chem. Soc. 86, 2050-2059] suggests that the unfolded states of proteins in urea and GdnHCl solutions may differ significantly in the extent of their interaction with denaturants. Thus, the conformations assumed by unfolded proteins may depend to at least some extent on the amino acid sequence of the protein.

Aspergillus oryzae↗
PubMed1990

Measuring and increasing protein stability.

Recently, it has become possible to construct proteins to order and this has promoted interest in learning how to increase their stability. This article describes recent developments in the methods used to measure the conformational stability of globular proteins, and discusses the approaches being used to increase their stability.

Globulins↗
PubMed1990

Conformational stability of globular proteins.

The conformational stability of ribonuclease T1 has been measured as a function of the variables of most interest to biochemists: temperature, pH, salt concentration, disulfide-bond content and amino acid sequence. The results provide insight into the forces that stabilize globular proteins.

Amino Acid Sequence↗
PubMed1989

Conformational stability and activity of ribonuclease T1 and mutants. Gln25----Lys, Glu58----Ala, and the double mutant.

Ribonuclease T1 (RNase T1) and mutants Gln25----Lys, Glu58----Ala, and the double mutant were prepared from a chemically synthesized gene, cloned and expressed in Escherichia coli. The wild-type RNase T1 prepared from the cloned gene was identical in every functional and physical property examined to RNase T1 prepared from Aspergillus oryzae. Urea and thermal unfolding experiments show that Gln25----Lys is 0.9 kcal/mol more stable and Glu58----Ala is 0.8 kcal/mol less stable than wild-type RNase T1. In the double mutant, these contributions cancel and the stability does not differ significantly from that of wild-type RNase T1. For the double mutant, the dependence of delta G on urea concentration is significantly greater than for wild-type RNase T1 or the single mutants. This suggests that the double mutant unfolds more completely in urea than the other proteins. The activity of Gln25----Lys is identical with that of wild-type RNase T1. The activities of Glu58----Ala and the double mutant are 7% of wild-type when GpC hydrolysis is measured (due to a 35-fold decrease in kcat), and 37% of wild-type when RNA hydrolysis is measured. Thus, Glu58 is important, but not essential to the activity of RNase T1.

Aspergillus oryzae↗
PubMed1989

Conformational stability and mechanism of folding of ribonuclease T1.

Urea and thermal unfolding curves for ribonuclease T1 (RNase T1) were determined by measuring several different physical properties. In all cases, steep, single-step unfolding curves were observed. When these results were analyzed by assuming a two-state folding mechanism, the plots of fraction unfolded protein versus denaturant were coincident. The dependence of the free energy of unfolding, delta G (in kcal/mol), on urea concentration is given by delta G = 5.6 - 1.21 (urea). The parameters characterizing the thermodynamics of unfolding are: midpoint of the thermal unfolding curve, Tm = 48.1 degrees C, enthalpy change at Tm, delta Hm = 97 kcal/mol, and heat capacity change, delta Cp = 1650 cal/mol deg. A single kinetic phase was observed for both the folding and unfolding of RNase T1 in the transition and post-transition regions. However, two slow kinetic phases were observed during folding in the pre-transition region. These two slow phases account for about 90% of the observed amplitude, indicating that a faster kinetic phase is also present. The slow phases probably result from cis-trans isomerization at the 2 proline residues that have a cis configuration in folded RNase T1. These results suggest that RNase T1 folds by a highly cooperative mechanism with no structural intermediates once the proline residues have assumed their correct isomeric configuration. At 25 degrees C, the folded conformation is more stable than the unfolded conformations by 5.6 kcal/mol at pH 7 and by 8.9 kcal/mol at pH 5, which is the pH of maximum stability. At pH 7, the thermodynamic data indicate that the maximum conformational stability of 8.3 kcal/mol will occur at -6 degrees C.

Exoribonucleases↗
PubMed1989

A new method for determining the heat capacity change for protein folding.

In order to use results from calorimetry or thermal unfolding curves to estimate the free energy change for protein unfolding at 25 degrees C, it is necessary to know the change in heat capacity for unfolding, delta Cp. We describe a new method for measuring delta Cp which is based on results from urea and thermal unfolding curves but does not require a calorimeter. We find that delta Cp = 1650 +/- 200 cal/(deg.mol) for the unfolding of ribonuclease T1 and that delta Cp = 2200 +/- 300 cal/(deg.mol) for the unfolding of ribonuclease A.

Calorimetry↗
PubMed1988

Conformational stability and activity of ribonuclease T1 with zero, one, and two intact disulfide bonds.

Ribonuclease T1 has two disulfide bonds linking cysteine residues 2-10 and 6-103. We have prepared a derivative of ribonuclease T1 in which one disulfide bond is broken and the cysteine residues carboxymethylated, (2-10)-RCM-T1, and three derivatives in which both disulfides are broken and the cysteine residues reduced, R-T1, carboxamidomethylated, RCAM-T1, or carboxymethylated, RCM-T1. The RNA hydrolyzing activity of these proteins has been measured, and urea and thermal denaturation studies have been used to determine conformational stability. The activity, melting temperature, and conformational stability of the proteins are: ribonuclease T1 (100%, 59.3 degrees C, 10.2 kcal/mol), (2-10)-RCM-T1 (86%, 53.3 degrees C, 6.8 kcal/mol), R-T1 (53%, 27.2 degrees C, 3.0 kcal/mol), RCAM-T1 (43%, 21.2 degrees C, 1.5 kcal/mol), and RCM-T1 (35%, 16.6 degrees C, 0.9 kcal/mol). Thus, the conformational stability is decreased by 3.4 kcal/mol when one disulfide bond is broken and by 7.2-9.3 kcal/mol when both disulfide bonds are broken. It is quite remarkable that RNase T1 can fold and function with both disulfide bonds broken and the cysteine residues carboxymethylated. The large decrease in the stability is due mainly to an increase in the conformational entropy of the unfolded protein which results when the constraints of the disulfide bonds on the flexibility are removed. We propose a new equation for predicting the effect of a cross-link on the conformational entropy of a protein: delta Sconf = -2.1 - (3/2)R 1n n, where n is the number of residues between the side chains which are cross-linked. This equation gives much better agreement with experimental results than other forms of this equation which have been used previously.

Aspergillus↗
PubMed1988

Ribonuclease T1 is stabilized by cation and anion binding.

The stability of the folded conformation of ribonuclease T1 is increased by 0.8, 1.8, and 3.3 kcal/mol in the presence of 0.1 M NaCl, MgCl2, and Na2HPO4, respectively. This remarkable increase in the conformational stability results primarily from the preferential binding to the native protein of one Mg2+ or two Na+ ions at cation-binding sites and by the binding of one HPO4(2-) ion at an anion-binding site. Only modest binding constants, 6.2 (Na+), 155 (Mg2+), and 282 M-1 (HPO4(2-)), are required to account for the enhanced stability. One important goal of the modification of proteins through genetic engineering is to increase their stability. Our results suggest that the creation of specific cation- and anion-binding sites on the surface of a protein through amino acid substitutions might be a generally useful way of achieving this goal. The design of these sites will be aided by the recent availability of detailed structural information on cation- and anion-binding sites.

Anions↗
PubMed1987

Purification of ribonuclease T1.

An improved method for purifying ribonuclease T1 from Aspergillus oryzae is described. The method uses gradient elution from DEAE-cellulose and sulfopropyl-Sephadex columns followed by gel filtration on Sephadex G-50 to give almost 100 mg (50% yield) of ribonuclease T1 from 100 g of starting material in less than 5 days.

Aspergillus oryzae↗
PubMed1986

The disulphide folding pathway of ribonuclease T1.

The pathway of unfolding and refolding that accompanies, respectively, the breakage and formation of the two disulphide bonds of ribonuclease T1 has been determined kinetically and compared with those of other proteins.

Amino Acid Sequence↗
PubMed1984

Kinetics of tryptic hydrolysis of the arginine-valine bond in folded and unfolded ribonuclease T1.

We have used ribonuclease T1 and its chemically modified derivatives as substrates, and trypsin as proteinase, to investigate the kinetics of proteolysis of a specific peptide bond in the folded and unfolded conformations of a protein. Steady-state kinetic studies showed that Km = 0.27 mM and Kcat. = 2.45 s-1 for the tryptic hydrolysis of the Arg(77)-Val(78) peptide bond in unfolded ribonuclease T1. This Km is somewhat lower than, and the kcat. value similar to, values found for the tryptic hydrolysis of comparable bonds in small peptides. Our data for the initial velocity of hydrolysis of the Arg(77)-Val(78) bond in a solution of the folded protein indicate that the bond is at least 1700 times less rapidly hydrolysed in the folded than in the unfolded conformation of ribonuclease T1, and do not exclude the possibility that the bond is completely resistant to hydrolysis in the folded protein.

Arginine↗
PubMed1981

Globular protein stability: aspects of interest in protein turnover.

The conformational stability of globular proteins is remarkably low. Under physiological conditions, the native globular conformation is only from 5 to 15 kcal/mole more stable than unfolded conformations. In addition, small changes in the structure of a protein such as removing one terminal residue or cleaving a single peptide bond frequently lead to a substantial decrease in the stability. Likewise, single substitutions in the amino acid sequence can increase or decrease the stability by several kilocalories per mole. The low conformational stability of globular proteins and the sensitivity to small changes in structure suggest a possible role for conformational stability in the intracellular degradation of proteins. Several lines of evidence from in vivo studies of protein degradation are consistent with this idea.

Cytochrome c Group↗
PubMed1980

Substrate stabilization of lysozyme to thermal and guanidine hydrochloride denaturation.

The thermal and guanidine hydrochloride (GdnHCl) denaturation of lysozyme has been investigated at various concentrations of tri-N-acetylglucosamine ((GlcNAc)3), a trisaccharide which binds specifically at the active site of native lysozyme. The presence of (GlcNAc)3 leads to a readily observable stabilization of the protein to thermal and GdnHCl denaturation. An analysis of guanidine hydrochloride denaturation curves shows that the stability of lysozyme is increased by 495 cal/mol by the presence of 3 x 10(-4) M (GlcNAc)3. The midpoint of the thermal denaturation curve, T 1/2, is increased 1.6 and 5.3 degrees C by 2.02 x 10(-4) M and 1.38 x 10(-3) M (GlcNAc)3, respectively. This corresponds to an increase in the stability of lysozyme of 385 and 1275 cal/mol. These results are in excellent agreement with predictions based on an equation derived by Schellman ((1975) Biopolymers 14, 999-1018) to take into account the effect of ligand binding on the melting temperature of a protein. delta T 1/2 = TT0R divided by delta HD ln (1 + KB[S]) where T and T0 are T1/2 values in the presence and absence of (GlcNAc)3, delta HD is the enthalpy of denaturation in the presence of (GlcNAc)3, KB in the equilibrium constant for the binding of (GlcNAc)3 to lysozyme, and [S] is the free concentration of (GlcNAc)3. Thus, the increased stability of an enzyme in the presence of its substrate, coenzyme, or any small molecule that it binds specifically results because binding to the native state shifts the unfolding equilibrium and decreases the concentration of unfolded states of the enzyme. It is suggested that this may be a more important factor than substrate-induced conformational changes in acccounting for the decreased rates of protein catabolism frequently observed in vivo at elevated substrate concentrations.

Acetylglucosamine↗