Effect of compounds of the urea–guanidinium class on renaturation and thermal stability of acid-soluble collagen

The effects of guanidinium salts in decreasing the renaturation rate and lowering the thermal stability of acid-soluble calf-skin collagen have been compared with those of formamide and urea. With the exception of guanidinium sulphate at higher concentrations, no qualitative differences were apparent in the effects of these perturbants, which thus differed only in molar activity. Activity variation in the guanidinium salts reflected a net effect resulting from additivity of cation and anion contributions. As observed in other protein systems, lyotropic activity increased in the series formamide<urea<guanidinium ion, and in the guanidinium salts in the anion order fluoride<sulphate<chloride<bromide<nitrate<iodide. Low activities of guanidinium fluoride and sulphate were attributable to counter-effects of the anions, which acted as structural stabilizers. Changes in renaturation kinetics induced by either temperature or added perturbants appeared to conform with the Flory–Weaver model for the collagen transition. Additivity and non-specificity of the observed effects are discussed with particular reference to a common mechanism involving weak, non-saturated binding of perturbants at protein peptide groups.     

Renaturation of Escherichia coli-derived recombinant human macrophage colony-stimulating factor.

Recombinant human macrophage colony-stimulating factor (rhM-CSF), a homodimeric, disulfide bonded protein, was expressed in Escherichia coli in the form of inclusion bodies. Reduced and denatured rhM-CSF monomers were refolded in the presence of a thiol mixture (reduced and oxidized glutathione) and a low concentration of denaturing agent (urea or guanidinium chloride). Refolding was monitored by nonreducing gel electrophoresis and recovery of bioactivity. The effects of denaturant type and concentration, protein concentration, concentration of thiol/disulfide reagents, temperature, and presence of impurities on the kinetics of rhM-CSF renaturation were investigated. Low denaturant concentrations (<0.5 M urea) and high protein concentrations (>0.4 mg/ml) in the refolding mixture resulted in increased formation of aggregates, although aggregation was never significant even when refolding was carried out at room temperature. Higher protein concentration resulted in higher rates but did not lead to increased yields, due to the formation of unwanted aggregates. Experiments conducted at room temperature resulted in slightly higher rates than those conducted at 4 degrees C. Although the initial renaturation rate for solubilized inclusion body protein without purification was higher than that of the reversed-phase purified reduced denatured rhM-CSF, the final renaturation yield was much higher for the purified material. A maximum refolding yield of 95% was obtained for the purified material at the following refolding conditions: 0.5 M urea, 50 mM Tris, 1.25 mM DTT, 2 mM GSH, 2 mM GSSG, 22 degrees C, pH 8, [protein] = 0.13 mg/ml.     

Effects of microscopic and macroscopic viscosity on the rate of renaturation of DNA

The effect of solvent viscosity on DNA renaturation rates has been investigated as a function of temperature for a number of solvent systems. The results are all consistent with a microscopic viscosity limitation of the rate determining step. Rates of renaturation in perchlorate and quaternary ammonium salt solutions are also discussed. Increasing the macroscopic viscosity with dissolved neutral or anionic polymers increases, rather than decreases, renaturation rates due to the excluded volume of the dissolved polymers.     

DNA conformational kinetics

A model for the time dependence of DNA conformational state probabilities is formulated in the form of first-order differential equations. This model is applied to investigate the renaturation and denaturation rates for T2 and T7 DNA as reported in the series of experiments by Record and Zimm. Qualitative agreement is found in denaturation and for series of renaturation experiments with the same initial condition. However, partial agreement with series of renaturation experiments having the same final condition is obtained only by including an initial bimolecular step with properly matched pairs of strands. Comparison of all experiments with the calculated rates yields 5 × 10⁴ min^?1 as the step rate for melting a single base pair.     

Renaturation and purification of rhGM-CSF with ion-exchange chromatography

The renaturation and purification of recombinant human granulocyte macrophage colony stimulation factor (rhGM-CSF) expressed in Escherichia coli with strong anion-exchange chromatography (SAX) were studied. The effects of pH values, ratios of concentrations of GSH/GSSG, and urea concentrations in the mobile phase on the renaturation and purification of rhGM-CSF with SAX were investigated, respectively. The results show that the above three factors have remarkable influences on the efficiency of renaturation and mass recovery of rhGM-CSF. The addition of GSH/GSSG in the mobile phase can improve the formation of correct disulfide bonds in rhGM-CSF so that its renaturation yield increases. In addition, to enhance the mass recovery of rhGM-CSF with SAX, the low concentration of urea was added in the mobile phase to prevent denatured protein aggregation. Under the optimal conditions, rhGM-CSF was renatured with simultaneous purification on SAX column within 30 min only by one step. After that its specific bioactivity, mass recovery, and purity reached 1.66 x 10(7) IU x mg, 58.8%, and 96.2%, respectively.     

Temperature dependence of the photosynthetic activities in the thylakoid membranes from the blue-green alga Anacystis nidulans.

The effects of temperature and ethidium bromide on the banding of heat-denatured DNA was studied during equilibrium centrifugation in density gradients of NaI. Centrifugation at 10 degrees C prevents the partial renaturation of Escherichia coli DNA and Clostridium perfringens DNA that occurs at 20 degrees C. A centrifugation temperature of --5 degrees C is required to prevent renaturation of T7 phage DNA. Ethidium bromide decreases renaturation of Escherichia coli DNA during centrifugation at 20 degrees C and causes a small shift in the buoyant density of both denatured and native DNA. Equilibrium centrifugation at lower temperatures prevents DNA renaturation and permits increased utilization of the large buoyant density difference between native and heat-denatured DNA in gradients of NaI.     

Enhanced protein renaturation by temperature-responsive polymers

The application of temperature-sensitive polymer (PNIPAAm) for the renaturation of beta-lactamase from inclusion bodies was investigated. It was observed that PNIPAAm was more effective than PEG in enhancing protein renaturation. At a concentration of 0.1%, PNIPAAm improved the yield of beta-lactamase activity by 41% from 46. 5 to 65.4 IU/mL, compared to 26% with PEG from 46.5 to 58.7 IU/mL. Kinetic study indicated that PNIPAAm did not significantly affect the initial rate of protein renaturation but did increase final activity yield. In the presence of PEG and PNIPAAm, the activity yields increased with temperature, indicating that hydrophobic interactions between denatured protein and polymer molecules contributed to the enhanced protein renaturation with polymers. The sequential addition approach, aiming at enhancing protein renaturation by reducing local protein concentration during renaturation, was also shown effective in enhancing protein renaturation, especially in the presence of polymers. With the sequential addition approach, the activity yield was increased by 60. 5% from 46.5 to 74.6 IU/mL with PNIPAAm. Similar behavior was also observed with PEG. PNIPAAm exhibited similar behavior as PEG on the renaturation of beta-lactamase in terms of temperature effect and concentration effect, indicating that the mechanism for enhanced protein renaturation for the two polymers might be similar. PNIPAAm exhibits a lower critical solution temperature (LCST) of 32 degrees C and can be effectively separated from aqueous solution and recycled. A protein renaturation process employing PNIPAAm, which offers the advantages of enhanced renaturation efficiency, minimum loss of protein aggregates, and ease of polymers recycling, was proposed.     

Renaturation kinetics and thermal stability of DNA in aqueous solutions of formamide and urea.

This paper reports the results of a systematic study of the effects of formamide and urea on the thermal stability and renaturation kinetics of DNA. Increasing concentrations of urea in the range 0 to 8 molar lower the Tm by 2.25 degrees C per molar, and decreases the renaturation rate by approximately 8 percent per molar. Increasing concentrations of formamide in the range from 0 to 50 percent lowers the Tm by 0.60 degrees C per percent formamide for sodium chloride concentrations ranging from 0.035M to 0.88M. At higher salt concentrations the dependence of Tm on percent formamide was found to be slightly greater. Increasing formamide concentration decreases the renaturation rate linearly by 1.1% per percent formamide such that the optimal rate in 50% formamide is 0.45 the optimal rate in an identical solution with no formamide. The effects of urea and formamide on the renaturation rates of DNA are explained by consideration of the viscosities of the solutions at the renaturation temperatures.     

Roles of curvature and hydrophobic interstice energy in fusion: studies of lipid perturbant effects

We have examined the effects of small amounts (1-4 mol %) of lipids of different molecular shapes, long chain lipids, and hydrocarbon on the kinetics of PEG-mediated fusion of 1,2-dioleoyl-3-sn-phosphatidylcholine/1,2-dioleoyl-3-sn-phosphatidylethanolamine/sphingomyelin/cholesterol (DOPC/DOPE/SM/CH, 35:30:15:30) sonicated vesicles. The effects of these lipid perturbants were different for different steps in the fusion process and varied with the ratio of the cross-sectional areas of headgroup to acyl chain moieties. For lipids with a ratio <1 (negative intrinsic curvature), a decrease in this ratio led to a dramatic increase in the initial rate of vesicle contents mixing but left the initial rate of lipid mixing roughly unchanged. For lipids with ratios >1 (positive intrinsic curvature), the initial rates of both lipid and contents mixing decreased mildly with increasing ratio. In the context of the "stalk model" for fusion, lipid mixing reflects mainly formation of the initial fusion intermediate (stalk), while contents mixing reflects conversion of this intermediate either to a second intermediate or to a fusion pore. Results with positively curved lipids (ganglioside, GM1; lysophosphatidylcholine, LPCs) and negatively curved lipids (dioleoylglycerol, DOG, and 1,2-diphytanoyl-sn-glyvero-3-phosphatidylcholine, DPhPC) can be taken as supportive of the usual interpretation of the stalk model in terms of bending energy, but enhancement of fusion in the presence of long-chain phospholipids, hexadecane, as well as a mixture of GM1 plus hexadecane could not be explained by their curvature alone. We propose that the ability of a lipid perturbant to compensate for lipid packing mismatch, that is, to lower "void" energy, must be taken into account, along with intrinsic curvature, to explain the ability of lipid perturbants to promote pore formation.     

DNA melting temperatures and renaturation rates in concentrated alkylammonium salt solutions

DNA melting temperatures and renaturation rates have been determined for Me₂Et₂NBr and a series of RMe₃NBr and REt₃NBr solvents where R is a linear hydrocarbon chain. The point of independence of DNA melting temperature on base composition has been investigated for each solvent system. Renaturation rates are compared with those found in other concentrated salt solutions. Solvent mixtures which accelerate DNA renaturation have also been investigated.     

Reconstitution of collagen-fold structure with stretching of gelatin film

The gelatin film is stretched more 100% over 75% relative humidity, while the dried gelatin extended only several percent. In this experiment the gelatin film was stretched in a solution of water and ethanol. The sample was extended to 650% of its initial length when ethanol/water was 1.5(w/w) at 30°C. The wide-angle X-ray diffraction photographs of drawn samples showed the three important layer lines with approximate spacing of 10 Å, 4 Å, and 3 Å, which verify the reconstitution of collagen triple helical structure. The sharp spots appeared near 10 Å on the equatirial axis, indicating the high orientation of peptide chains. These patterns become sharp and clear on increasing the extension ratio. The content of the triple helix was investigated by wide-angle X-ray diffraction and differential scanning calorimetry. The maximum renaturation percentage is 25% at the draw ratio of 7.5. Since the formation of a collagen triple helix requires three chains, in which each chain has only three repeatin amino acids, (Gly-Pro-X)_n, and glycoprotein and other impurities interrupt helix formation, the more advanced renaturation will not be expected.     

Kinetic and spectrophotometric studies on the renaturation of deoxyribonucleic acid

The kinetics of the renaturation of Escherichia coli DNA in 0.4-1.0m-sodium chloride at temperatures from 60 degrees to 90 degrees have been studied. The extent of renaturation was a maximum at 65 degrees to 75 degrees and increased with ionic strength, and the rate constant increased with both ionic strength and temperature. The energy and entropy of activation of renaturation were calculated to be 6-7kcal.mole(-1) and -40cal.deg.(-1)mole(-1) respectively. It has been shown that renaturation is a second-order process for 5hr. under most conditions. The results are consistent with a reaction in which the rate-controlling step is the diffusion together of two separated complementary DNA strands and the formation of a nucleus of base pairs between them. The kinetics of the renaturation of T7-phage DNA and Bordetella pertussis DNA have also been studied, and their rates of renaturation related quantitatively to the relative heterogeneity of the DNA samples. By analysis of the spectra of DNA at different stages during renaturation it was shown that initially the renatured DNA was rich in guanine-cytosine base pairs and non-random in base sequence, but that, as equilibrium was approached, the renatured DNA gradually resembled native DNA more closely. The rate constant for the renaturation of guanine-cytosine base pairs was slightly higher than for adenine-thymine base pairs.     

Physical studies of chloroacetaldehyde labelled fluorescent DNA

The reaction of chloroacetaldehyde with denatured DNA produces a fluorescent DNA where both the adenine and cytosine bases are modified. The rate of modification of DNA by chloroacetaldehyde was measured using the absorption spectrum shift. The depolarization and quantum yield of native DNA and denatured DNA were investigated as a function of temperature.The melting points and the renaturation rates of a series of derivative DNA's were investigated. The melting point was decreased by 1.3°C for each base modified per 100 base pairs corresponding to a 2.8 Kcal destabilizing free energy per mismatched base pair. The renaturation rate of the derivative DNA is reduced by a factor 2 when the melting temperature is lowered by 13°C.     

The kinetics of DNA helix-coil subtransitions

The kinetic analysis of individual helix-coil subtransitions were performed by comparing melting and renaturation profiles obtained at different temperature change rates. The duration of the three transition stages and its dependence on temperature and ionic strength were determined for a T7 phage DNA fragment. The obtained temperature dependence of the melting time for a stretch flanked by melted regions is in quantitative agreement with that predicted by the theory of slow processes (V.V. Anshelevich, A.V. Vologodskii, A.V. Lukashin, M.D. Frank-Kamenetskii, Biopolymers 23, 39 (1984)). The reasons are discussed for the increasing relaxation time of this stretch in the middle of its transition with decreasing ionic strength. The zipping kinetics of a melted region under essentially nonequilibrium conditions was examined for T7 fragment and pAO3 DNAs. The obtained temperature dependence of the zipping time is in quantitative agreement with calculations based on the theory of slow processes. The renaturation times of stretches flanked by helical regions proved fairly small even at a low ionic strength. These times are several orders of magnitude smaller than the renaturation times of the same stretches with one helical boundary. A formal application of the theory of slow processes failed to account for the small renaturation times of stretches that are zipped from both ends. This is probably due to the non-allowance for the changing entropy of the loop linking two helix-coil boundaries migrating towards each other. Slow processes have been revealed in the intramolecular melting of Col E1 DNA at a high ionic strength. The reason for the long relaxation time of one subtransition is the large size of the loop that separates the melting stretch from the helical part of the molecule. This result can be accounted for by the theory of slow processes.     

Thermodynamic identification of stable folding intermediates in the B-subunit of cholera toxin

The structural stability and domain structure of the pentameric B-subunit of cholera toxin have been measured as a function of different perturbants in order to assess the magnitude of the interactions within the B-subunits. For these studies, temperature, guanidine hydrochloride (GuHCl), and pH were used as perturbants, and the effects were measured by high-sensitivity differential scanning calorimetry, isothermal reaction calorimetry, fluorescence spectroscopy, and partial protease digestion. At pH 7.5 and in the absence of any additional perturbants, the thermal unfolding of the B-subunit pentamer is characterized by a single peak in the heat capacity function centered at 77 degrees C and characterized by a delta Hcal of 328 kcal/mol of B-subunit pentamer and delta Hvh/delta Hcal of 0.3. Lowering the pH down to 4 or adding GuHCl up to 2 M results in a decrease of the calorimetric enthalpy with no significant effect on the van't Hoff enthalpy. The transition enthalpy decreases in a sigmoidal fashion with pH, with an inflection point centered at pH 5.3. Isothermal titration calorimetric studies as a function of pH also report a transition centered at pH 5.3 and characterized by an enthalpy change of 27 kcal/mol of B-subunit pentamer at 27 degrees C. Below this pH, the enthalpy change for the unfolding transition is reduced to approximately 100 kcal/mol of B-subunit pentamer. Similar behavior is obtained with GuHCl. In this case, a first transition is observed at 0.5 M GuHCl and a second one at 3 M GuHCl.(ABSTRACT TRUNCATED AT 250 WORDS)     

One hundred-fold acceleration of DNA renaturation rates in solution

Solvents which accelerate DNA renaturation rates have been investigated. Addition of NaCl or LiCl to DNA in 2.4M Et₄NCl initially increases renaturation rates at 45°C and then leads to a loss of second-order behavior. The greatest accelerations are seen with LiCl and dilute DNA. Volume exclusion by dextran sulfate is the most effective method of accelerating DNA renaturation with concentrated DNA. Addition of dextran sulfate beyond 10–12% in 2.4M Et₄NCl fails to increase the acceleration beyond approximately 10-fold. Accelerations of 100-fold may be achieved with 35–40% dextran sulfate in 1M NaCl at 70°C. No other mixed solvent system was found to be more effective, although acceleration may be achieved in solvents containing formamide or other denaturants. The acceleration in 2M NaCl occurs without loss of the normal concentration and temperature dependence of DNA renaturation and is also independent of dextran sulfate concentration if sufficient dextran sulfate is used. Dextran sulfate may be selectively precipitated by use of 1M CsCl.     

精氨酸、精氨酸盐酸、半胱氨酸、胱氨酸对重组人tPA蛋白复性的影响

以重组人tPA蛋白为材料研究了精氨酸、精氨酸盐酸盐、半胱氨酸、胱氨酸对蛋白质复性效果的影响,重组tPA蛋白包涵体经尿素变性溶解后,在精氨酸、精氨酸盐酸盐、半胱氨酸、胱氨酸存在的条件下进行复性,结果表明,碱性的精氨酸在质量分数0.2%时可减少蛋白质凝聚,显著提高复性效果,tPA复性后的活性可提高50%以上,半胱氨酸单独使用具有类似β-巯基乙醇的作用,精氨酸盐酸盐和胱氨酸单独使用对复性无影响,而半胱氨酸和胱氨酸联合使用,有类似氧化-还原系统作用。可提高活性20%。     

Independence of length and temperature effects on the rate of helix formation between complementary ribopolymers

The rate of double helix formation by single stranded Poly A plus Poly U, Poly I plus Poly C, Poly G plus Poly C, and T2 DNA has been investigated as a function of both the length of the reacting strands and temperature. The length dependence of the rate is found to be independent of temperature. All of the reactions studied show a rate approximately proportional to the square root of the length of the shorter of the complementary strands. At or about 30°C below the melting temperature the ribopolymers react with about the same rate. This rate is four to five times slower than DNA renaturation rates. The effect of temperature on ribopolymer reaction rates is interpreted in terms of a steady-state model for helix propagation.     

The Kinetics of DNA Helix-Coil Subtransitions

Abstract

The kinetic analysis of individual helix-coil subtransitions was performed by comparing melting and renaturation profiles obtained at different temperature change rates. The duration of the three transition stages and its dependence on temperature and ionic strength were determined for a T7 phage DNA fragment. The obtained temperature dependence of the melting time for a stretch flanked by melted regions is in quantitative agreement with that predicted by the theory of slow processes (V.V. Anshelevich, A.V. Vologodskii, A.V. Lukashin, M.D. Frank-Kamenetskii, Biopolymers 23, 39 (1984)). The reasons are discussed for the increasing relaxation time of this stretch in the middle of its transition with decreasing ionic strength.

The zipping kinetics of a melted region under essentially nonequilibrium conditions was examined for T7 fragment and pAO3 DNAs. The obtained temperature dependence of the zipping time is in quantitative agreement with calculations based on the theory of slow processes.

The renaturation times of stretches flanked by helical regions proved fairly small even at a low ionic strength. These times are several orders of magnitude smaller than the renaturation times of the same stretches with one helical boundary. A formal application of the theory of slow processes failed to account for the small renaturation times of stretches that are zipped from both ends. This is probably due to the non-allowance for the changing entropy of the loop linking two helix-coil boundaries migrating towards each other.

Slow processes have been revealed in the intramolecular melting of Col E1 DNA at a high ionic strength. The reason for the long relaxation time of one subtransition is the large size of the loop that separates the melting stretch from the helical part of the molecule. This result can be accounted for by the theory of slow processes.     

Important parameters affecting efficiency of protein refolding by reversed micelles

Refolding of denatured RNase A as a model of inclusion bodies was performed by reversed micelles formulated with sodium di-2-ethylhexyl sulfosuccinate (AOT) in isooctane. In the novel refolding process, a solid-liquid extraction was utilized as an alternative to the ordinary protein extraction by reversed micelles based on a liquid-liquid extraction. First, the effects of operational parameters such as concentration of AOT, W(o) (= [H(2)O]/[AOT]), and pH were examined on the solubilization of solid denatured proteins into a reversed micellar solution. The solubilization was facilitated by a high AOT concentration, a high W(o) value, and a high pH in water pools. These conditions are favorable for the dispersion of the solid protein aggregates in an organic solvent. Second, the renaturation of the denatured RNase A solubilized into the reversed micellar solution was conducted by addition of glutathione as a redox reagent. A complete renaturation of RNase A was accomplished by adjusting the composition of the redox reagent even at a high protein concentration in which protein aggregation would usually occur in aqueous media. In addition, the renaturation rates were improved by optimizing water content (W(o)) and the pH of water pools in reversed micelles. Finally, the recovery of renatured RNase A from the reversed micellar solution was performed by adding a polar organic solvent such as acetone into the reversed micellar solution. This precipitation method was effective for recovering proteins from reversed micellar media without any significant reduction in enzymatic activity.