Simultaneous characterization of the reductive unfolding pathways of RNase B isoforms by top-down mass spectrometry

A novel method for characterization of the simultaneous reductive unfolding pathways of five isoforms of bovine pancreatic ribonuclease B (RNase B) is demonstrated. The results indicate that each isoform unfolds reductively through two three-disulfide-containing structured intermediates before proceeding to the fully reduced form, as in the reductive unfolding pathways of the A variant lacking the carbohydrate chain. The rates of reduction of bovine pancreatic ribonuclease A (RNase A) and RNase B and the formation and consumption of their reductive intermediates are identical, indicating that the unfolding events necessary to expose disulfide bonds for reduction are not affected by the oligosaccharide. The method utilizes top-down mass spectrometry and a naturally occurring tag on the protein, viz. the carbohydrate moiety, to obtain unfolding information of an ensemble of protein isoforms and is a generally applicable methodological advance for conducting folding studies on mixtures of different proteins.     

The effect of trimethylamine N-oxide on RNase a stability

The thermal stability of bovine pancreatic ribonuclease (RNase A) has been investigated in the presence of trimethylamine N-oxide (TMAO), a naturally occurring osmolyte, by means of differential scanning calorimetry (DSC) and circular dichroism (CD) measurements at neutral and acid pH conditions. It is well known that compatible osmolytes such as TMAO are effective in stabilizing protein structure and counteracting the denaturing the effect of urea and guanidinium hydrochloride (GuHCl). Calorimetric results show that TMAO stabilizes RNase A at pH 7.0 and does not stabilize the protein at pH 4.0. RNase A thermal denaturation in the presence of TMAO is a reversible two-state N ⇆ D process. We also show that TMAO counteracts the urea and GuHCl denaturing effect at neutral pH, whereas the counteracting ability is lost at acid pH.     

一种核糖核酸酶构象稳定性的研究

Aspergillus niger SA-13-20核糖核酸酶是从突变株A.niger SA-13-20分泌的胞外酶中分离出的一种新的核糖核酸酶。采用紫外光谱、荧光光谱和红外光谱研究了A.niger SA-13-20核糖核酸酶在不同pH值条件下的构象稳定性。紫外光谱和荧光光谱结果均表明该酶蛋白在酸性和弱碱性pH值下构象较稳定,当pH值高于9.6时构象不稳定;红外光谱结合去卷积和曲线拟合技术对蛋白质酰胺Ⅰ带的测定和处理结果表明,在室温下,pH 5.0时该酶蛋白二级结构中α-螺旋、β-折叠、转角和无规结构所占的成分分别为13.28%、42.30%、26.48%和17.95%。测得该酶的热解链温度Tm、解链熵变ΔSm及解链焓变ΔHm分别为70.1℃、644 J.mol-1.K-1及22.1 kJ.mol-1,表明该酶属于耐热能力较强的核糖核酸酶。研究结果有助于揭示该酶结构与功能的关系,推动其在科研和生产等方面的应用。     

A study of the hydration of ribonuclease A using isothermal calorimetry

This work is part of a systematic study undertaken to find the excess thermodynamic functions of binary protein–water systems. Isothermal calorimetry and water sorption measurements were applied to characterize the hydration dependencies of the excess thermodynamic functions. The advantages of our methodology are (i) we are able to simultaneously determine the excess partial quantities of water and proteins; (ii) these thermodynamic quantities can be determined in the entire range of water content. Here, in particular, the excess partial enthalpies of water and bovine pancreatic ribonuclease A (RNase A) have been determined. The excess partial enthalpies for RNase A are compared with the published data for several unrelated globular proteins (lysozyme, chymotrypsinogen A, serum albumin, lactoglobulin). These biomacromolecules represent a series of proteins in which the hydrophobicity of proteins is gradually changed in a wide range. It was found that the excess partial quantities for the studied proteins are determined by the hydration of the hydrophilic and hydrophobic protein groups. The more hydrophilic a protein, the more significant a hydrophilic hydration contribution is and vice versa. RNase A is the most hydrophilic protein under the study. This protein has the most significant hydrophilic hydration contribution. Lactoglobulin is the most hydrophobic protein under the study. This protein has the most significant hydrophobic hydration contribution.     

Hofmeister Effects of Group II Cations as Seen in the Unfolding of Ribonuclease A

This work studies the effects of alkaline-earth cation addition on the unfolding free energy of a model protein, pancreatic Ribonuclease A (RNase A) by differential scanning calorimetry analysis. RNase A was chosen because: a) it does not specifically bind Mg²⁺, Ca²⁺ and Sr²⁺ cations and b) maintains its structural integrity throughout a large pH range. We have measured and compared the effects of NaCl, MgCl₂, CaCl₂ and SrCl₂ addition on the melting point of RNase A. Our results show that even though the addition of group II cations to aqueous solvent reduces the solubility of nonpolar residues (and enhances the hydrophobic effect), their interactions with the amide moieties are strong enough to “salt-them-in” the solvent, thereby causing an overall protein stability reduction. We demonstrate that the amide-cation interactions are a major contributor to the observed “Hofmeister Effects” of group II cations in protein folding. Our analysis suggests that protein folding “Hofmeister Effects” of group II cations, are mostly the aggregate sum of how cation addition simultaneously salts-out hydrophobic moieties by increasing the cavitation free energy, while promoting the salting-in of amide moieties through contact pair formation.     

Separation of rat pancreatic secretory proteins by cation-exchange fast protein liquid chromatography.

Rat pancreatic secretory proteins were separated by an automated liquid chromatography system utilizing a Mono S cation-exchange column. Optimal resolution was obtained with a multistep salt and pH gradient (0.01-2 M LiCl, pH 5.3-63). A total of fourteen well-separated peaks, as well as several minor peaks, were detected by UV absorption. The main pancreatic enzymes were resolved (two amylases, two chymotrypsinogens, two trypsinogens, proelastase, lipase, prophospholipase A2, procarboxypeptidase A, procarboxypeptidase B, and ribonuclease). In addition, proteins without enzymic activity, such as lithostathine and pancreatitis-associated protein, were identified. Activation of proenzymes did not occur during the separation. At a flow-rate of 0.5 ml/min, ca. 250 micrograms to 5 mg of protein could be applied with equal resolution. The reproducibility of retention volumes and peak areas was high (less than 1% or 5% variation, respectively). When radiolabeled proteins were separated, a comparable pattern of peaks was obtained. The technique described is, therefore, not only useful for analytical and preparative separation of pancreatic proteins but can additionally serve for quantitative determination of the pancreatic isoenzyme pattern.     

Protein separation by open tubular capillary electrochromatography employing a capillary coated with phenylalanine functionalized tentacle-type polymer under both cathodic and anodic electroosmotic flows

The use of a phenylalanine (Phe) functionalized tentacle-type polymer coated capillary column for protein separation by open tubular capillary electrochromatography (OTCEC) was demonstrated in this work. The tentacle-type stationary phase was prepared from silanized fused-silica capillaries of 50 microm I.D. by glycidyl methacrylate graft polymerization and subsequent Phe functionalization. Due to the amphoteric functional groups of the Phe bonded on the tentacle-type polymer stationary phase, protein separation in the prepared column can be performed under both cathodic and anodic electroosmotic flow (EOF) by varying the pH values of the mobile phase. Model proteins including ribonuclease A (RNase A), myoglobin, transferrin, insulin were baseline separated under cathodic EOF with a mobile phase of pH 8.8. Comparison between the separation result of the four proteins under conditions of OTCEC and capillary zone electrophoresis indicates that the migration behavior of the four proteins in the prepared column was the result of the interplay of chromatographic retention and electrophoretic migration. Besides, three basic proteins including RNase A, cytochrome c (Cyt-c) and lysozyme (Lys) were fully resolved under anodic EOF with an acidic running buffer (pH 2.5). The elution order was the same as the isoelectric point values of the proteins (RNase A相似文献   

Iceberg Model of the Structure of Globular Protein Adsorption Layers at the Air–Water Interface. Study by the Tritium Planigraphy Technique

The organization of the adsorption layers of insulin, pancreatic inhibitor of trypsin, ribonuclease S, lysozyme, myoglobin, carboxypeptidase A, subtilisin, and thermolysin at the air–water interface was studied by tritium planigraphy technique. The location of globular protein molecules relative to the interface was determined for solution concentrations corresponding to the formation of saturated adsorption layers (10^–4 M, pH 6). It is established that the fraction of solution surface occupied by protein component is equal to 7–62%. Only a small part of globules with the height from 2 to 19% of their effective diameter is above the solution surface, whereas the main part of globules is submerged into water (the iceberg model).     

Temperature-induced unfolding of ribonuclease A embedded in spherical polyelectrolyte brushes

We use Fourier Transform infrared spectroscopy (FT-IR) spectroscopy to study the thermal unfolding and refolding behavior of ribonuclease (RNase A) adsorbed to spherical polyelectrolyte brushes (SPB). The SPB consist of a solid poly(styrene) core of ca. 100 nm diameter onto which long chains of poly(styrene sulfonic acid), PSS have been densely attached. The particles bearing the adsorbed protein are dispersed in aqueous buffer solution at a pH close to the isoelectric point (9.6) of the protein. The secondary structure of the protein was analyzed by FT-IR spectroscopy and compared to the structure of the native protein before adsorption. The unfolding of the free RNase A in solution was found to be fully reversible with an unfolding temperature of 65 degrees C, in accordance to previous studies. However, after adsorption to the SPB, the unfolding temperature of the protein molecule is lowered by 10 degrees C and the Van't Hoff enthalpy of the unfolding process is significantly reduced. Moreover the unfolding of the adsorbed protein is irreversible. The phenomenon may be explained by an increase in binding sites due to unfolding of the globular structure. Protein adsorption to a spherical polyelectrolyte brush.     

Polymeric brushes as functional templates for immobilizing ribonuclease A: study of binding kinetics and activity

The ability to immobilize proteins with high binding capacities on surfaces while maintaining their activity is critical for protein microarrays and other biotechnological applications. We employed poly(acrylic acid) (PAA) brushes as templates to immobilize ribonuclease A (RNase A), which is commonly used to remove RNA from plasmid DNA preparations. The brushes are grown by surface-anchored atom-transfer radical polymerization (ATRP) initiators. RNase A was immobilized by both covalent esterification and a high binding capacity metal-ion complexation method to PAA brushes. The polymer brushes immobilized 30 times more enzyme compared to self-assembled monolayers. As the thickness of the brush increases, the surface density of the RNase A increases monotonically. The immobilization was investigated by ellipsometry, X-ray photoelectron spectroscopy (XPS), thermogravimetric analysis (TGA), and near-edge X-ray absorption fine structure spectroscopy (NEXAFS). The activity of the immobilized RNase A was determined using UV absorbance. As much as 11.0 microg/cm(2) of RNase A was bound to PAA brushes by metal-ion complexation compared to 5.8 microg/cm(2) by covalent immobilization which is 30 and 16 times the estimated mass bound in a monolayer. The calculated diffusion coefficient D was 0.63 x 10(-14) cm(2)/s for metal-ion complexation and 0.71 x 10(-14) cm(2)/s for covalent immobilization. Similar values of D indicate that the binding kinetics is similar, but the thermodynamic equilibrium coverage varies with the binding chemistry. Immobilization kinetics and thermodynamics were characterized by ellipsometry for both methods. A maximum relative activity of 0.70-0.80 was reached between five and nine monolayers of the immobilized enzyme. However, the relative activity for covalent immobilization was greater than that of metal-ion complexation. Covalent esterification resulted in similar temperature dependence as free enzyme, whereas metal-ion complexation showed no temperature dependence indicating a significant change in conformation.     

Molecular evolution of B<Subscript>6</Subscript> enzymes: Binding of pyridoxal-5'-phosphate and Lys41Arg substitution turn ribonuclease A into a model B<Subscript>6</Subscript> protoenzyme

Background  

The pyridoxal-5'-phosphate (PLP)-dependent or vitamin B₆-dependent enzymes that catalyze manifold reactions in the metabolism of amino acids belong to no fewer than four evolutionarily independent protein families. The multiple evolutionary origin and the essential mechanistic role of PLP in these enzymes argue for the cofactor having arrived on the evolutionary scene before the emergence of the respective apoenzymes and having played a dominant role in the molecular evolution of the B₆ enzyme families. Here we report on an attempt to re-enact the emergence of a PLP-dependent protoenzyme. The starting protein was pancreatic ribonuclease A (RNase), in which active-site Lys41 or Lys7 readily form a covalent adduct with PLP.     

Purification and partial characterization of an extracellular ribonuclease from a mutant of Aspergillus niger

A new extracellular ribonuclease (RNase) from a mutant of Aspergillus niger, named A. niger SA-13-20 RNase, was purified to homogeneity by (NH4)2SO4 fractionation (50-85%), DEAE-cellulose anion-exchange chromatography, ultrafiltration and Sephacryl HR-200 chromatography. The enzyme was purified up to 54.4-fold with a final yield of 24.5%. There were differences in the molecular weight, pI value and some physico-chemical properties between A. niger SA-13-20 RNase and that from the parent strain. The enzyme is monomeric and its molecular weight and isoelectric point were 40.1 kDa and 5.3, respectively. The N-terminal amino acid sequence of A. niger SA-13-20 RNase was TIDTYSSDSP. The optimum pH, temperature and buffer concentration for the enzymatic reaction were 3.5, 65 degrees C, and 0.175 M, respectively. Metal ions, such as K+, NH4+, Mg2+, and Ca2+ at the concentration of 1.0 mM had a slight activation effect on the enzyme activity and (NH4)2SO4 activated the enzyme significantly. The enzyme was stable at pH lower than 8.5 and was easy to inactivate in strong alkali solution.     

Simultaneous determination of structural and thermodynamic effects of carbohydrate solutes on the thermal stability of ribonuclease A

This communication describes a new technique for the study of the effects of carbohydrates on the thermal stability of proteins. This approach combines capillary electrophoresis (CE) and protein charge ladders, collections of proteins that differ incrementally in number of chemically modified charged groups, to provide information on both the thermodynamics (i.e., the free energy, DeltaGN-D, of denaturation), and structural changes (i.e., the effective hydrodynamic radius, RH, of proteins in both the native and denatured states) associated with stability. This information, obtained in a single set of electrophoresis experiments, allows a simple microscopic interpretation of the effects of carbohydrate solutes on protein stability. We use this technique to show that the stabilization of ribonuclease A at pH 8.4 by sucrose and fructose can be explained entirely by the contribution these solutes make to the entropy of formation of the protein-solution interface. There is no need, in this case, to refer to quasichemical concepts such as preferential hydration, binding, or exchange of solutes with water at specific sites on the protein to account for the stabilizing effects observed.     

Thermodynamics of thermal denaturation of ribonuclease A and cytochrome c in the presence of 1,1,1,3,3,3-hexafluoro-2-propanol

The thermal denaturation of ribonuclease A and cytochrome c has been studied by differential scanning calorimetry (d.s.c.) and u.v.-visible spectrophotometry in the presence of 1,1,1,3,3,3-hexafluoro-2-propanol (HFIP) at pH  =  5.5 and pH  =  4.0, respectively. The quantitative thermodynamic parameters accompanying the thermal transitions from native to denatured state have been evaluated. The results of the reversible thermal denaturations have been fitted with a two-state native-to-denatured mechanism. A comparison has been made of the relative effect of HFIP on the thermal stability of ribonuclease A and cytochrome c. It has been observed that the denaturation capacity of HFIP tends more towards cytochrome c compared with ribonuclease A. The results have been explained on the basis of a fine balance between the preferential exclusion and binding that take place during the course of the denaturation reaction and the structuring of water around the groups of the protein exposed upon denaturation. Using the thermodynamic data obtained from calorimetric and spectroscopic measurements, we have calculated the changes in preferential solvation of ribonuclease A and cytochrome c upon heat denaturation. It is observed that the preferential solvation of these two proteins is specific, indicating that the solvation mechanism is not the same for them.     

Binary adsorption of globular proteins on ion-exchange media

Adsorption equilibrium of binary pairs of lysozyme (LYS), cytochrome c (CYC) and ribonuclease A (RNase) has been measured on different cation-exchange media at various solution conditions. Adsorption patterns largely follow the intrinsic protein–surface interactions, but can differ significantly for different pairs or even for one pair at different solution conditions. LYS/CYC adsorption shows similar behavior on all the adsorbents examined, with competitive adsorption dominated by LYS and the presence of LYS reducing the adsorption of CYC significantly. Simultaneous and sequential measurements for LYS/CYC show that the order of adsorption does not have a significant effect on the adsorption equilibrium. For LYS/RNase, LYS is consistently more strongly adsorbed. For CYC/RNase, both proteins can display significant adsorption, depending on the pH and salt concentration. A model based on colloidal energetics is developed to calculate the binary adsorption isotherms using parameter values obtained from single-component isotherms. The calculated adsorption is in good agreement with experimental results, with significantly better representation than for other commonly used binary isotherms.     

Effect of Molecular Crowding on the Temperature–Pressure Stability Diagram of Ribonuclease A

FT‐IR spectroscopic and thermodynamic measurements were designed to explore the effect of a macromolecular crowder, dextran, on the temperature and pressure‐dependent phase diagram of the protein Ribonuclease A (RNase A), and we compare the experimental data with approximate theoretical predictions based on configuration entropy. Exploring the crowding effect on the pressure‐induced unfolding of proteins provides insight in protein stability and folding under cell‐like dense conditions, since pressure is a fundamental thermodynamic variable linked to molecular volume. Moreover, these studies are of relevance for understanding protein stability in deep‐sea organisms, which have to cope with pressures in the kbar range. We found that not only temperature‐induced equilibrium unfolding of RNase A, but also unfolding induced by pressure is markedly prohibited in the crowded dextran solutions, suggesting that crowded environments such as those found intracellularly, will also oppress high‐pressure protein unfolding. The FT‐IR spectroscopic measurements revealed a marked increase in unfolding pressure of 2 kbar in the presence of 30 wt % dextran. Whereas the structural changes upon thermal unfolding of the protein are not significantly influenced in the presence of the crowding agent, through stabilization by dextran the pressure‐unfolded state of the protein retains more ordered secondary structure elements, which seems to be a manifestation of the entropic destabilization of the unfolded state by crowding.     

伴刀豆球蛋白亲和色谱柱的制备及其在糖蛋白核糖核酸酶B结构分析中的应用

通过对硅胶基质进行化学改性键合伴刀豆球蛋白(Con A),制备了对糖蛋白具有特异亲和作用的亲和色谱固定相;该固定相非特异性吸附弱,对于糖蛋白和糖肽的分离效果良好。对亲和色谱的分离条件进行了优化,以标准糖蛋白核糖核酸酶B(RNase B)为模型,对其进行了纯化;用糖苷酶切除糖链,并对切除糖链前后的RNase B用胰蛋白酶酶解;用基质辅助激光解吸电离飞行时间质谱(MALDI-TOF MS)对亲和色谱分离得到的糖蛋白、糖链及糖肽进行了分析,确定了RNase B的一级结构、糖含量、糖基化位点及糖连接方式。该方法快速准确,适于糖蛋白和糖肽的分离表征。将其应用于血清中糖蛋白及酶解后血清中糖肽的分离富集,取得了很好的效果。     

Reactivity of Singlet Oxygen Toward Proteins: The Effect of Structure in Basic Pancreatic Trypsin Inhibitor and in Ribonuclease A

The reactions of singlet oxygen, ¹O₂, with large peptides have been described previously. It was found that even in these systems, which in their native form are generally not supposed to possess a stable structure in solution, the polypeptide does impede the access of ¹O₂ to the amino acids that react readily with ¹O₂. Here we describe the ¹0₂ reaction with two proteins of well-defined structure. The quenching of ¹O₂ by bovine pancreatic trypsin inhibitor (BPTI) and by ribonuclease A (RNase A) was compared to that of a solution at the same concentration as those of its constituent amino acids that react readily with ¹O₂. The proteins were studied in their native form, when partly denatured by splitting their S-S bonds and when fully denatured. It was found that while in the native form the quenching rate constant was seven times lower in BPTI (2.2 vs 15.2 times 10⁷WM^-1 s^-1) and three times lower in RNase A (11.0 vs 32 times 10⁷M^-l s^-1) than in a mixture of its constituent amino acid residues, it increased upon denaturation reaching in the fully denatured state the value of the corresponding amino acid mixture. More striking is the effect of the protein structure when comparing the fraction of the encounters between ¹O₂ and protein, which cause damage to the protein, as reflected in the decrease of its biological activity. This decrease is assumed to be due to the chemical (oxidative) reactions of ¹O₂ in the protein. In the exceptionally stable BPTI the fraction of such encounters was 0.05 and in RNase A it was 0.2, whereas for the amino acid tryptophan in solution, 0.7 of the collisions with ¹O₂ led to a chemical reaction.