Hydrolysis of nucleic acids by sepharose-micrococcal endonuclease

Initial reaction rates for the hydrolysis of nucleic acids with micrococcal endonuclease (EC 3.1.31.1) insolubilized on Sepharose are strongly influenced by diffusional limitations. Although the absolute values are low, they can be increased substantially by changing particle and pore size of the support, or enzyme concentration in the insoluble derivative. As a result of steric and diffusional limitations, the course of the reaction and selectivity to hydrolysis products for the insoluble derivatives are different to those of the native enzyme; the former produces mainly large and small fragments but few of intermediate size. Because of these differences in course and selectivity of the reaction, diffusional limitations become less important when high initial reaction rates are not required.     

Design of new immobilized-stabilized carboxypeptidase a derivative for production of aromatic free hydrolysates of proteins

This paper presents stable carboxypeptidase A (CPA)-glyoxyl derivatives, to be used in the controlled hydrolysis of proteins. They were produced after immobilizing-stabilizing CPA on cross-linked 6% agarose beads, activated with low and high concentrations of aldehyde groups, and different immobilization times. The CPA-glyoxyl derivatives were compared to other agarose derivatives, prepared using glutaraldehyde as activation reactant. The most stabilized CPA-glyoxyl derivative was produced using 48 h of immobilization time and high activation grade of the support. This derivative was approximately 260-fold more stable than the soluble enzyme and presented approximately 42% of the activity of the soluble enzyme for the hydrolysis of long-chain peptides (e.g., cheese whey proteins previously hydrolyzed with immobilized trypsin and chymotrypsin) and of the small substrate N-benzoylglycyl-l-phenylalanine (hippuryl-l-Phe). These results were much better than those achieved using the conventional support, glutaraldehyde-agarose. Amino acid analysis of the products of the acid hydrolysis of CPA (both soluble and immobilized) showed that approximately four lysine residues were linked on the glyoxyl agarose beads, suggesting the existence of an intense multipoint covalent attachment between the enzyme and the support. The maximum temperature of hydrolysis was increased from 50 degrees C (soluble enzyme) to 70 degrees C (most stable CPA-glyoxyl derivative). The most stable CPA-glyoxyl derivative could be efficiently used in the hydrolysis of long-chain peptides at high temperature (e.g., 60 degrees C), being able to release 2-fold more aromatic amino acids (Tyr, Phe, and Trp) than the soluble enzyme, under the same operational conditions. This new CPA derivative greatly increased the feasibility of using this protease in the production of protein hydrolysates that must be free of aromatic amino acids.     

Alkylation of nucleic acids by DNA-targeted 4-anilinoquinolinium aniline mustards: kinetic studies

The rate of constant for hydrolysis of a series of 4-substituted aniline mustards Ar-X-pC6H4-N(CH2CH2Cl)2, where Ar is 4-anilinoquinolinium and X = O, CH2, CONH and CO, have been measured in water and 0.02 M imidazole buffer at 37 degrees C and in 50% aqueous acetone at 66 degrees C. The equilibrium binding constants of the compounds and their hydrolysis products to nucleic acids of differing base composition have been determined at varying ionic strengths, and the results are consistent with the compounds binding as expected in the DNA minor groove. The alkylating reactivity of the mustards towards these nucleic acids has been measured in water at 37 degrees C and in 0.01 M HEPES buffer over a range of temperatures from 25 degrees C to 60 degrees C. Evaluation of the thermodynamic parameters for these kinetic and equilibrium studies suggests that the interaction with nucleic acids is via an internal SN2 mechanism involving an aziridinium ion.     

Biotin reagents for antibody pretargeting. 5. Additional studies of biotin conjugate design to provide biotinidase stability.

An investigation was conducted in which the stabilities of four structurally different biotin derivatives were assessed with regard to biotinamide bond hydrolysis by the enzyme biotinidase. The biotin derivatives studied contained an extra methylene in the valeric acid chain of biotin (i.e., homobiotin), or contained conjugated amino acids having hydroxymethylene, carboxylate, or acetate functionalities on a methylene alpha to the biotinamide bond. The biotinidase hydrolysis assay was conducted on biotin derivatives that were radioiodinated at high specific activity, and then subjected to diluted human serum at 37 degrees C for 2 h. After incubation, assessment of biotinamide bond hydrolysis by biotinidase was readily achieved by measuring the percentage of radioactivity that did not bind with avidin. As controls, an unsubstituted biotin derivative which is rapidly cleaved by biotinidase and an N-methyl-substituted biotin derivative which is stable to biotinidase cleavage were included in the study. The results indicate that increasing the distance from the biotin ring structure to the biotinamide bond by one methylene only decreases the rate of biotinidase cleavage, but does not block it. The data obtained also indicate that placing a hydroxymethylene, carboxylate, or acetate alpha to the biotinamide bond is effective in blocking the biotinamide hydrolysis reaction. These data, in combination with data previously obtained, which indicate that biotin derivatives containing hydroxymethylene or carboxylate moieties retain the slow dissociation rate of biotin from avidin and streptavidin [Wilbur, D. S., et al. (2000) Bioconjugate Chem. 11, 569-583], strongly support incorporation of these structural features into biotin derivatives being used for in vivo targeting applications.     

Protein and Nucleic Acid Metabolism in Germinating Peas

Protease, peptidase, and ribonuclease activities were demonstratedin germinating pea cotyledons and axis tissues. These activitiesindicate that the enzymatic machinery for the hydrolysis ofprotein and nucleic acid reserves are present in the germinatingcotyledon. The fate of hydrolytic products was determined byinjecting leucine-¹⁴C or adenine-8-¹⁴C into the cotyledons.At most, 20 per cent of the leucine-¹⁴C and 10 per cent of theadenine-8-¹⁴C administered were transported from the cotyledonto axis tissues. Both compounds were extensively metabolizedand the labelling patterns suggest that different metabolicpathways are in operation in the two organs. The amounts ofadenine incorporated into nucleic acids and of leucine incorporatedinto protein in the cotyledons suggest that synthesis and turnoverwere occurring at a rapid rate. The adenine transported fromthe cotyledon was not readily available for nucleic acid synthesisin the axis whereas transported leucine was readily incorporatedinto axis protein.     

Monomeric selectively S-alkylated derivatives of seminal ribonuclease: preparation and properties

Procedures are described for preparing monomeric selectively S-carboxamido-methylated and S-aminoethylated derivatives of seminal ribonuclease. The main properties of the derivatives, including their extinction coefficients, have been determined. Their catalytic activities and that of the S-carboxymethyl derivative have been tested. On double-stranded RNA as a substrate the monomeric derivatives are less active than the native dimeric enzyme, but much more active than pancreatic ribonuclease. On yeast RNA as a substrate the amino-ethyl derivative is found to be less active (80%) than the native enzyme, while the other two are over 30 percent more active. The monomers are stable in solution and when lyophilized from acetic acid solution do not associate to the same extent as pancreatic or native seminal ribonucleases.     

Purification and characterization of an extracellular, uracil specific ribonuclease from a Bizionia species isolated from the marine environment of the Sundarbans

The first ribonuclease (RNase) from the Cytophaga-Flavobacterium-Bacteroides phylum, dominant in the marine environment, and also from the first Bizionia species isolated from the tropics was purified and characterized. Extracellular RNase production occurred when the culture medium contained 5-7% (w/v) NaCl. The 53.0 kDa enzyme was purified 29 folds with a recovery of 4% and specific activity of 630unit/mg protein. The pH and temperature optima are 6.5 and 35 degrees C, respectively and the enzyme retains more than half of its activity (relative to optimal assay conditions) after 1h pre-incubation separately with 5% (w/v) NaCl or from pH 5.0 to 8.5 or at 50 degrees C. Dithiothreitol and beta-mercaptoethanol do not inhibit whereas human placental RNase inhibitor protein halves the RNase activity. While Mg(2+), Ba(2+) and Ca(2+) enhanced the enzyme activity, Fe(2+), Cu(2+) and Hg(2+) inactivated it. This RNase degrades uracil containing nucleic acids only. Our isolate could be a novel renewable source of deoxyribonuclease (DNase)--free RNase enzyme.     

A single-sample method for determination of carbohydrate and protein contents glycoprotein bands separated by sodium dodecyl sulfate- polyacrylamide gel electrophoresis.

A method is described for determination of carbohydrate and protein contents of glycoproteins separated by sodium dodecyl sulfate-polyacrylamide gel electrophoresis and then electroblotted onto polyvinylidene difluoride (PVDF) membranes. Blots were stained, and appropriate pieces of PVDF membranes were excised, destained, and subjected to sequential hydrolysis with 0.2 M trifluoroacetic acid (TFA) for 1 h at 80 degrees C, then with 2 M TFA for 4 h at 100 degrees C, and finally with 6 M HCl at 100 degrees C for 24 h to release sialic acids, neutral sugars with hexosamines, and amino acids, respectively. In some instances preliminary methanolysis was used. Carbohydrates including sialic acids were quantitated by high pH anion exchange chromatography with pulsed amperometric detection. Protein content of the bands was determined as amino acids by the fluorescamine or ninhydrin method. In the calculation of results proper adjustments were made for small amounts of fucose released by hydrolysis with 0.2 M TFA at 80 degrees C, and for partial degradation of protein during hydrolysis with 2 M TFA at 100 degrees C. Recoveries of amino acids from hydrolysates of glycoproteins that had been electroblotted onto PVDF membranes equaled those of carbohydrates. This was possible because of preliminary hydrolysis of glycoproteins with TFA, as well as washing of wet, instead of dried, PVDF membranes after hydrolysis with 6 M HCl. The two modifications increased yields of amino acids by about 30%. The method was successfully applied to the determination of molar and weight percentage composition of human transferrin, band 3 protein, glycophorin A, and alpha(1)-acid glycoprotein. In each case the results obtained for directly hydrolyzed and electrophoresed/electroblotted glycoproteins were practically identical. We also determined the glucosamine content of band 4.1 protein of erythrocytes.     

Digestion of native collagen, denatured collagen, and collagen fragments by extracts of rat liver lysosomes.

Extracts of highly purified lysosomes from rat liver were examined for their ability to degrade native collagen and thermally denatured collagen at pH values between 3.5 and 7.0. After a 24-h digestion at 36 degrees with the lysosomal extract at a pH of 5.5 or lower (collagen/lysosomal protein; 2/1 or 8/1), both native and denatured collagen were degraded to an extent equivalent to 60 to 70% of that observed upon total acid hydrolysis in 6 N HCl as measured by the ninhydrin reaction (570 nm). At a pH of 6.0, native collagen and denatured collagen were degraded by the mixture of lysosomal proteinases to 11% and 40% of total acid hydrolysis, respectively. At pH 6.5 AND 7.0, the corresponding values were 3% versus 33% and 0.3% versus 11%, respectively. Fragments of collagen (TCA and TCB) are produced when mammalian collagenase degrades native collagen at 25 degrees. These fragments were degraded by the lysosomal extract at 36 degrees to an extent equivalent to 28% and 8% of total acid hydrolysis at pH 6.5 and 7.0, respectively. The experiments at pH 6.5 and 7.0 were done using a collagen/lysosomal protein ratio of 2/1. At pH 5.0 (a pH which is found within secondary lysosomes), the lysosomal extracts degraded collagen to a mixture of free amino acids and small peptides. Amino acid analysis established that approximately 30% of the amino acid residues of the collagen appeared in the lysosomal hydrolysate as free amino acids. Hydroxyproline and perhaps hydroxylysine were the only amino acids found in collagen which did not appear at least to some extent as the free amino acid in this hydrolysate.     

Hydrolysis of proteins by immobilized-stabilized alcalase-glyoxyl agarose

This paper presents stable Alcalase-glyoxyl derivatives, to be used in the controlled hydrolysis of proteins. They were produced by immobilizing-stabilizing Alcalase on cross-linked 10% agarose beads, using low and high activation grades of the support and different immobilization times. The Alcalase glyoxyl derivatives were compared to other agarose derivatives, prepared using glutaraldehyde and CNBr as activation reactants. The performance of derivatives in the hydrolysis of casein was also tested. At pH 8.0 and 50 degrees C, Alcalase derivatives produced with 1 h of immobilization time on agarose activated with glutaraldehyde, CNBr, and low and high glyoxyl groups concentration presented half-lives of ca. 10, 29, 60, and 164 h, respectively. More extensive immobilization monotonically led to higher stabilization. The most stabilized Alcalase-glyoxyl derivative was produced using 96 h of immobilization time and high activation grade of the support. It presented half-life of ca. 23 h, at pH 8.0 and 63 degrees C and was ca. 500-fold more stable than the soluble enzyme. Thermal inactivation of all derivatives followed a single-step non-first-order kinetics. The most stable derivative presented ca. 54% of the activity of the soluble enzyme for the hydrolysis of casein and of the small substrate Boc-Ala-ONp. This behavior suggests that the decrease in activity was due to enzyme distortion but not to wrong orientation. The hydrolysis degree of casein at 80 degrees C with the most stabilized enzyme was 2-fold higher than that achieved using soluble enzyme, as a result of the thermal inactivation of the latter. Therefore, the high stability of the new Alcalase-glyoxyl derivative allows the design of continuous processes to hydrolyze proteins at temperatures that avoid microbial growth.     

Pisum sativum endonuclease. Studies on substrate specificity and possible use as a biochemical tool

An endonuclease purified from germinating pea (Pisum sativum) seeds has been shown to catalyze the hydrolysis of heat-denatured single-stranded DNA. Since P. sativum endonuclease shows appreciable activity in the presence of DNA destabilizing agents and, unlike many similar endonucleases, significant activity at neutral pH, it is a potentially valuable tool for studies of the secondary structure of nucleic acids. The residual hydrolysis of duplex DNA is directed towards partially denatured, A,T-rich areas in native DNA. The rate of hydrolysis of deoxypolynucleotides was in the order poly(dT) greater than denatured DNA greater than poly(dA) greater than poly(dA-dT) = native DNA. Neither poly(dC), poly(dG) nor poly(dC).poly(dG) were attacked by the enzyme. Supercoiled, covalently closed circular phage PM2 form I DNA is converted to singly hit nicked circular form II and doubly hit linear from III duplexes. Prolonged treatment with enzyme does not further cleave the linear form III DNA. Addition of increasing concentrations of NaCl in the incubation mixture suppresses the conversion of form I to form II, but not the conversion of form II to form III, which is enhanced with the increasing ionic strength. The enzymatically relaxed circular form, I degree, obtained by unwinding of supercoiled DNA with a DNA-relaxing protein, is resistant to the action of the enzyme. Molecules with intermediate superhelix densities do not serve as substrates. The sites of cleavage of P. sativum endonuclease in PM2 DNA occur within regions that are readily denaturable in a topologically constrained superhelical molecule.     

Characterization of chemically treated bacterial (Acetobacter xylinum) biopolymer: some thermo-mechanical properties

Bacterial cellulose prepared from pellicles of Acetobacter xylinum (Gluconacetobacter xylinus) is a unique biopolymer in terms of its molecular structure, mechanical strength and chemical stability. The biochemical analysis revealed that various alkali treatment methods were effective in removing proteins and nucleic acids from native membrane resulting in pure cellulose membrane. The effect of various treatment regimens on thermo-mechanical properties of the material was investigated. The cellulose in the form of purified cellulose membranes was characterized by differential scanning calorimetry (DSC), thermo-gravimetric analysis (TGA) and dynamic mechanical thermal analysis (DMTA). The glass transition temperature (T(g)) of the native cellulose (untreated, compressed and dried pellicle) was found to be 13.94 degrees C, in contrast, the chemically treated cellulose membranes has higher T(g) values, ranging from 41.41 degrees C to 48.82 degrees C. Investigations on isothermal crystallization were carried out to study the bulk crystallization kinetics. Thermal decomposition pattern of the native as well as alkali treated cellulose was determined by obtaining thermo-gravimetric curves. At higher temperatures (>300 degrees C), the biopolymer was found to degrade. Nevertheless, the alkaline treated cellulose membrane was more stable (between 343.27 degrees C and 370.05 degrees C) in comparison to the native cellulose (298.07 degrees C). Further, the percentage weight loss in case of native cellulose was found to be 26.57%, in comparison to 6.45% for the treated material, at 300 degrees C. The DMTA revealed complex dynamic modulus of the material, at different temperatures and fixed shear stress, applied at a frequency of 5 Hz. The study delineated the effect of alkali treatment regimens, on the thermo-mechanical properties of bacterial cellulose for its application over a wide range of temperatures.     

Temperature dependence of the preferential interactions of ribonuclease A in aqueous co-solvent systems: thermodynamic analysis.

The temperature dependence of preferential solvent interactions with ribonuclease A in aqueous solutions of 30% sorbitol, 0.6 M MgCl2, and 0.6 M MgSO4 at low pH (1.5 and 2.0) and high pH (5.5) has been investigated. This protein was stabilized by all three co-solvents, more so at low pH than high pH (expect 0.6 M MgCl2 at pH 5.5). The preferential hydration of protein in all three co-solvents was high at temperatures below 30 degrees C and decreased with a further increase in temperature (for 0.6 M MgCl2 at pH 5.5, this was not significant), indicating a greater thermodynamic instability at low temperature than at high temperature. The preferential hydration of denatured protein (low pH, high temperature) was always greater than that of native protein (high pH, high temperature). In 30% sorbitol, the interaction passed to preferential binding at 45% for native ribonuclease A and at 55 degrees C for the denatured protein. Availability of the temperature dependence of the variation with sorbitol concentration of the chemical potential of the protein, (delta mu(2)/delta m3)T,p,m2, permitted calculation of the corresponding enthalpy and entropy parameters. Combination with available data on sorbitol concentration dependence of this interaction parameter gave (approximate) values of the transfer enthalpy, delta H2,tr, and transfer entropy delta S2,tr. Transfer of ribonuclease A from water into 30% sorbitol is characterized by positive values of the transfer free energy, transfer enthalpy, transfer entropy, and transfer heat capacity. On denaturation, the transfer enthalpy becomes more positive. This increment, however, is small relative to both the enthalpy of unfolding in water and to the transfer enthalpy of the native protein from water a 30% sorbitol solution.     

Effect of protein disulfide isomerase on the regeneration of bovine ribonuclease A with dithiothreitol.

The role of protein disulfide isomerase (PDI) in the regeneration of ribonuclease A with dithiothreitol (DTT) was investigated at three different temperatures. The rates of formation of the native protein were markedly increased in the presence of PDI, 9-fold at 15 degrees C, 6-fold at 25 degrees C and 62-fold at 37 degrees C, respectively. In the presence of PDI, major changes were found in the distribution of intermediates in the three-disulfide region at 25 and 15 degrees C and also in the one-disulfide region at 15 degrees C, with the fast accumulation of the two native-like species des-[65-72] and des-[40-95]. The present results indicate that PDI does not alter the two major parallel pathways involving des-[65-72] and des-[40-95] in the regeneration of ribonuclease A with DTT.     

Ribonuclease structure and catalysis: effects of crystalline enzyme, alcohol cryosolvents, low temperatures, and product inhibition

In order to determine the necessary conditions to stabilize intermediates in ribonuclease A catalysis at subzero temperatures for structural studies, we have examined the suitability of alcohol-based cryosolvents. On the basis of thermal denaturation transition curves, the enzyme is in the native conformation in high concentrations of ethanol and methanol, provided the temperature is suitably low. The effects of methanol on the catalytic properties for the hydrolysis for mono- and dinucleotide substrates also are consistent with the absence of adverse effects of the cosolvent. Significant methanolysis occurs in the presence of methanol as cosolvent. The kinetics of 2',3'-CMP hydrolysis are complicated by severe competitive product inhibition, both in aqueous and in methanolic solvents, accounting for the previously observed effect of substrate concentration on the observed Km. Computer-aided analysis allowed the determination of the inhibition constant as a function of experimental parameters. The reaction of ribonuclease A with 2',3'-CMP was investigated at subzero temperatures. The turnover reaction could be made negligible at temperatures below -60 degrees C at pH 3-6 in 70% methanol and below -35 degrees C at pH 2.1. The rate of the catalytic reaction with crystalline enzyme was compared to that of enzyme in solution for both 2',3'-CMP and the dinucleotide CpC. The rates were 50- and 200-fold slower, respectively, in the crystal. These investigations allowed calculation of the necessary conditions for NMR and X-ray diffraction experiments on the trapped enzyme--substrate intermediate.     

Production of xylo-oligosaccharides by immobilized-stabilized derivatives of endo-xylanase from Streptomyces halstedii

An endoxylanase from Streptomyces halstedii was stabilized by multipoint covalent immobilization on glyoxyl-agarose supports. The immobilized enzyme derivatives preserved 65% of the catalytic activity corresponding to the one of soluble enzyme that had been immobilized. These immobilized derivatives were 200 times more stable 200 times more stable than the one-point covalently immobilized derivative in experiments involving thermal inactivation at 60 °C. The activity and stability of the immobilized enzyme was higher at pH 5.0 than at pH 7.0. The optimal temperature for xylan hydrolysis was 10 °C higher for the stabilized derivative than for the non-stabilized derivative. On the other hand, the highest loading capacity of activated 10% agarose gels was 75 mg of enzyme per mL of support. To prevent diffusional limitations, low loaded derivatives (containing 0.2 mg of enzyme per mL of support) were used to study the hydrolysis of xylan at high concentration (close to 1% (w/v)). 80% of the reducing sugars were released after 3 h at 55 °C. After 80% of enzymatic hydrolysis, a mixture of small xylo-oligosaccharides was obtained (from xylobiose to xylohexose) with a high percentage of xylobiose and minimal amounts of xylose. The immobilized-stabilized derivatives were used for 10 reaction cycles with no loss of catalytic activity.     

Expression, purification and characterization of the recombinant ribonuclease P protein component from Bacillus subtilis.

Ribonuclease P is a ribonucleoprotein complex that catalyzes the essential 5' maturation of all precursor tRNA molecules. The protein component both alters the conformation of the RNA component and enhances the substrate affinity and specificity. To facilitate biochemical and biophysical studies, the protein component of Bacillus subtilis ribonuclease P (RNase P) was overproduced in Escherichia coli using the native amino acid sequence with the initial 20 codons optimized for expression in E.coli . A simple purification procedure using consecutive cation exchange chromatography steps in the presence and absence of urea was developed to purify large quantities of P protein without contaminating nucleic acids. The identity of the recombinant protein as a cofactor of RNase P was established by its ability to stimulate the activity of the RNA component in low ionic strength buffer in a 1:1 stoichiometry. Circular dichroism studies indicate that P protein is a combination of alpha-helix and beta-sheet secondary structures and is quite stable, with a T m of 67 degrees C. The described methods facilitated the large scale purification of homogeneous, RNA-free P protein required for high resolution crystallographic analyses and may be useful for the preparation of other RNA binding proteins.     

HISTONES AND ALKALINE FAST GREEN STAINING OF ONION ROOTS

Onion root tips were freeze killed or fixed in 12 different chemical fixatives to determine the possible effects of such treatments on subsequent staining with alkaline Fast green (pH 8.0-8.1) to reveal the presence of histones. Ethanol, methanol, neutral formalin, and a mixture of methanolchloroform-acetic acid produced nearly comparable results. Subsequent to fixation or freeze drying the sections were treated with hot 5% trichloroacetic acid (TCA) to remove nucleic acids prior to Fast green staining. Staining of histones does not occur in chemically fixed material if TCA hydrolysis is omitted. Nuclei, chromosomes during mitosis, and cytoplasm (to varying degrees) were stainable after TCA treatment. Positive staining occurs in nuclei, nucleoli, and cytoplasm in freeze-dried material with or without prior TCA treatment. Comparisons are made with chemical fixations. The use of ribonuclease instead of TCA permits staining of the cytoplasm and of chromosomes during mitosis. Discussions are included on the stainability of nucleoli and the possibility that native histone is associated with ribonucleic acid (RNA).     

Involvement of thiol enzymes in the lysosomal breakdown of native and denatured proteins

We have investigated the effect of thiols on the breakdown of some proteins by extracts from highly purified Triton WR-1339-filled rat liver lysosomes at pH 5 and 38°C.The rate as well as the final degree of hydrolysis of serum albumin, a protein which remains presumably native at pH 5, was stimulated by thiols like dithiothreitol and strongly inhibited by monoiodoacetic acid. These effects were also found with native and performic acid-oxidized ribonuclease, with cytochrome c and with horse radish peroxidase. The digestion of hemoglobin was not stimulated by dithiothreitol, but partly inhibited by monoiodoacetic acid; yeast invertase was not hydrolysed at all.Our results indicate (a) that thiol-cathepsins are essential for the breakdown of many proteins by lysosomes; (b) that apparently native proteins like albumin and ribonuclease can be degraded extensively by lysosomal cathepsins; (c) that this degradation is, to a large extent, an all-or-none reaction.     

The thermal denaturation of ribonuclease A in aqueous-methanol solvents.

Circular dichroism was used to monitor the thermal unfolding of ribonuclease A in 50% aqueous methanol. The spectrum of the protein at temperatures below -10 degrees C (pH* 3.0) was essentially identical to that of native ribonuclease A in aqueous solution. The spectrum of the thermally denatured material above 70 degrees C revealed some residual secondary structure in comparison to protein unfolded by 5 M Gdn.HCl at 70 degrees C in the presence or absence of methanol. The spectra as a function of temperature were deconvoluted to determine the contributions of different types of secondary structure. The position of the thermal unfolding transition as monitored by alpha-helix, with a midpoint at 38 degrees C, was at a much higher temperature than that monitored by beta-sheet, 26 degrees C, which also corresponded to that observed by delta A286, tyrosine fluorescence and hydrodynamic radius (from light scattering measurements). Thus, the loss of beta-sheet structure is decoupled from that of alpha-helix, suggesting a step-wise unfolding of the protein. The transition observed for loss of alpha-helix coincides with the previously measured transition for His-12 by NMR from a partially folded state to the unfolded state, suggesting that the unfolding of the N-terminal helix in RNase A is lost after unfolding of the core beta-sheet during thermal denaturation. The thermally denatured protein was relatively compact, as measured by dynamic light scattering.