Circular dichroism study on the early folding events of beta-lactoglobulin entrapped in wet silica gels

beta-Lactoglobulin is a predominantly beta-sheet protein that folds by forming excess alpha-helices within milliseconds. In this study, the refolding of beta-lactoglobulin was dramatically decelerated by entrapping in wet nanoporous silica gel matrices, and monitored on a time scale of minutes or hours by far-UV circular dichroism spectroscopy. Analysis of kinetics and transient spectra allowed to define the sequence of folding events that consist of alpha-helical formation, beta-sheet core formation, and alpha-to-beta transition. The results suggest that the initially formed alpha-helices, presumably including the native alpha-helix, help to guide the formation of the adjacent beta-sheet core.     

Interpretations of the effects of pH on the spectra of purple membrane.

The absorption and circular dichroism of the purple membrane in solution and the linear and circular dichroism of the purple membrane oriented in a film were used to detect changes in the membrane protein structure and membrane organization in the pH range of 2.4 to 12.6. Main findings are (a) the membrane protein structure is stable at every level of organization to pH changes over the range of 5.0 to 8.5. (b) Tertiary structural changes occur in the membrane protein structure in the pH range of 2.4 to 5.0 and 8.5 to 11.8 without any secondary structural involvement. (c) An irreversible change occurs in the membrane organization in the pH range of 11.8 to 12.6 involving large tertiary and secondary structural changes in the membrane protein. (d) The retinyl chromophore is influenced by a nearby ionizable group. (e) The membrane crystalline structure is highly stable to pH perturbation except at the high pH range of 11.0 to 11.8.     

Control by bacteriophage T4 of two sequential phosphorylations of the alpha subunit of Escherichia coli RNA polymerase

The effect of 2′-O-methylation upon the base-stacking properties of dinucleoside monophosphates has been studied by circular dichroism measurements over the temperature range from ?20 °C to +80 °C at high and at low salt concentration of 13 2′-O-methyl derivatives in neutral aqueous solution. It is found that 2′-O methylation generally enhances the stacking propensity of dinucleoside monophosphates except for the dimers with adenine in the 3′-linked nucleoside, where the converse trend is observed. The influence of 2′-O-methylation upon the base-stacking property of a dimer correlates in part with the effect of a reduction in salt concentration, suggesting that the 2′-O-methyl group effects the stacking by displacing ions from the immediate environment of the dimer as well as by intramolecular steric effects. The dimers which exhibit an enhanced stacking due to the 2′-O-methylation are found in a larger than statistical abundance in yeast transfer RNA, whereas those showing a reduced stacking occur in minor abundance. These observations are discussed in relation to some current views on the role of modified nucleosides in the conformation of ribonucleic acids.     

Circular dichroism of double-helical oligoribonucleotides

The ultraviolet circular dichroism and absorption of 15 double-stranded helical oligoribonucleotides have been measured. These molecules of chain-length 6 to 12 contain all 10 possible nearest neighbors of Watson-Crick base pairs. They are thus good models for short double-stranded regions in RNA molecules. The contribution to the circular dichroism of each of the nearest neighbor base pairs has been obtained. The circular dichroism is found to be very sequence-dependent and may be useful in distinguishing possible secondary structures. However, the nearest neighbor approximation for circular dichroism fails to give a quantitative measure of the circular dichroism of double-strand regions.     

DNA condensation with polyamines I. Spectroscopic studies

The addition of polyamines with three or four positive charges to very dilute solutions of phage T7 DNA leads to a co-operative condensation. The reaction is very rapid and the DNA remains in the B-form as characterized by circular dichroism. The particles which are formed are roughly the size of a phage particle when they are prepared for electron microscopy. This aspect is discussed more completely in the accompanying paper (Chattoraj et al., 1978).Most of the experiments were performed at low ionic strength (roughly 0.002 m) with the triamine, spermidine. The reaction also occurs in 0.15 m-sodium chloride but here the experiments are accompanied by slow irreversible effects which are evidently due to aggregation since they are accompanied by a commensurate increase in turbidity. Consequently, most of the experiments have been done under the reversible low ionic strength conditions.Neither Mg²⁺ nor the diamine putrescine produce the reaction at concentrations similar to those found in bacterial cells. The tetramer spermine, on the other hand, which is not found in bacterial cells, is a very strong condensation agent in the μm region. The spermidine analog, bis-(3-aminopropyl)amine is very similar in behavior to spermidine.The role which polyamines might play in the condensation of DNA in phage heads is discussed.     

Kinetic folding and assembly mechanisms differ for two homologous heptamers

Here we investigate the time-resolved folding and assembly mechanism of the heptameric co-chaperonin protein 10 (cpn10) in vitro. The structure of cpn10 is conserved throughout nature: seven beta-barrel subunits are non-covalently assembled through beta-strand pairings in an overall doughnut-like shape. Kinetic folding/assembly experiments of chemically denatured cpn10 from Homo sapiens (hmcpn10) and Aquifex aeolicus (Aacpn10) were monitored by far-UV circular dichroism and fluorescence. We find the processes to be complex, involving several kinetic steps, and to differ between the mesophilic and hyper-thermophilic proteins. The hmcpn10 molecules partition into two parallel pathways, one involving polypeptide folding before protein-protein assembly and another in which inter-protein interactions take place prior to folding. In contrast, the Aacpn10 molecules follow a single sequential path that includes initial monomer misfolding, relaxation to productive intermediates and, subsequently, final folding and heptamer assembly. An A. aeolicus variant lacking the unique C-terminal extension of Aacpn10 displays the same kinetic mechanism as Aacpn10, signifying that the tail is not responsible for the rapid misfolding step. This study demonstrates that molecular details can overrule similarity of native-state topology in defining apparent protein-biophysical properties.     

Reversible unfolding of the β2 subunit of Escherichia coli tryptophan synthetase and its proteolytic fragments

The guanidine hydrochloride-induced reversible unfolding transitions at 4 °C of the β₂ subunit of tryptophan synthetase (l-serine hydrolyase (adding indole) EC. 4.2.1.20) and of its two proteolytic fragments, F₁ and F₂, are compared. The unfolding of the β₂ subunit shows a multistate behaviour, as judged by circular dichroism and fluorescence measurements. When isolated, the two fragments have different stabilities. Within β₂, the region corresponding to the large fragment, F₁ behaves as the corresponding isolated fragment, and no stabilization arising from the interaction with the complementary fragment can be detected. The same behaviour is suggested for the small fragment, F₂. These results lead to the apparent conclusion that, at least under these experimental conditions, the interactions between domains do not contribute greatly to the energetics of the folding process of the large β₂ protein.     

Complex of fd gene 5 protein and double-stranded RNA

We report the formation of complexes of the single-stranded DNA binding protein encoded by gene 5 of fd virus, with natural double-stranded RNAs. In the first direct visualization of a complex of the fd gene 5 protein with a double-stranded nucleic acid, we show by electron microscopy that the double-stranded RNA complex has a structure which is distinct from that of complexes with single-stranded DNA and is consistent with uniform coating of the exterior of the double-stranded RNA helix by the protein. Circular dichroism spectral data demonstrate that the RNA double helix in the complex is undisrupted, and that perturbation of the 228-nm circular dichroism assigned to protein tyrosines can occur in the absence of intercalation of nucleotide bases with protein aromatic residues. Our findings emphasize the potential importance of interaction with the sugar-phosphate polynucleotide backbone in binding of the fd gene 5 protein to nucleic acids.     

Dimeric and tetrameric hemoglobins from the mollusc Scapharca inaequivalvis: Structural and functional properties

The bivalve mollusc Scapharca inaequivalvis contains in the coelomic fluid erythrocytes with a dimeric (HbI) and a tetrameric (HbII) hemoglobin like the other members of the arcid family. The tetrameric protein is made up from two types of polypeptide chain, while the dimeric protein is made from a single type of chain which differs from the other two in terms of molecular weight and isoelectric point.The optical and circular dichroism spectra show that the heme environment in HbI and HbII resembles that of vertebrate hemoglobins, although distinctive features are present in the deoxygenated derivative. p]The dimeric HbI in the pH range 6 to 9 does not change its association state upon deoxygenation, while the tetrameric HbII polymerizes as indicated by the appearance of a fast peak in the sedimentation velocity patterns. The dependence of the areas and sedimentation coefficients of the fast and slow peaks on protein concentration is characteristic of a rapidly established association-dissociation equilibrium between tetramers and polymers higher than octamers. The pH, ionic strength and temperature dependence of polymer formation indicate that both hydrophobic and ionic interactions stabilize the polymers.The functional properties of HbI and HbII differ. HbI shows co-operative oxygen binding (h = 1·5) and a constant oxygen affinity ($\text{p}{}_{\mathrm{<mtext>1</mtext><mtext>2</mtext>}}\text{= 7.8}\text{mm Hg}$) over the pH range 5.5 to 9.5. HbII likewise shows co-operativity in oxygen binding (h = 2·0). Its oxygen affinity at neutral and alkaline pH values is slightly lower ($\text{p}{}_{\mathrm{<mtext>1</mtext><mtext>2</mtext>}}\text{= 9.1}\text{mm Hg}$) than that of the dimeric protein, but becomes higher at pH values below 6.5 due to the presence of an acid Bohr effect. At high protein concentrations, under conditions of extensive polymerization of the deoxygenated derivative, the oxygen affinity is lowered and co-operativity slightly increased. Both phenomena require that the oxygen affinity of the polymer be lower than that of the tetramer, consistent with the predictions of linkage theory.     

A ferredoxin from the thermohalophilic bacterium Rhodothermus marinus

A [3Fe–4S]^1+/0 ferredoxin was isolated from the thermohalophilic and strict aerobic bacterium Rhodothermus marinus. It is a small protein, with an apparent molecular mass of 9 kDa. Its N-terminal amino acid sequence reveals the capability of binding two tetranuclear clusters. However, upon purification, it contains a single [3Fe–4S]^1+/0, with an unusually low reduction potential of ?650 mV, determined by cyclic voltammetry at pH 7.6. [¹H]NMR spectroscopy shows that the protein contains a single, homogeneous, trinuclear centre. When purified under anaerobic conditions, the EPR [3Fe–4S]^1+/0 centre signal is also observed. However, it can now be reduced by dithionite and a new signal attributed to a [4Fe–4S]^2+/1+ cluster develops. This can also be observed upon reconstitution of the prosthetic groups. The function of this ferredoxin in R. marinus is still unknown but it is very sensitive to oxygen, an unexpected characteristic for a protein from an aerobic organism.The thermodynamic stability of the R. marinus ferredoxin was also investigated and was shown to be high. Thermal and chemical unfolding reactions appear as single, cooperative transitions. The midpoint (T_m) for thermally induced unfolding is 102±2 °C (pH 7). Unfolding induced by the chemical denaturant guanidine hydrochloride (GuHCl) shows a transition midpoint at 5.0 M GuHCl (pH 7.0, 20 °C). The iron–sulfur cluster degrades upon polypeptide unfolding, resulting in an irreversible denaturation process.     

Single amino acid mutations block a late step in the folding of beta-lactamase from Staphylococcus aureus

Two single amino acid mutant proteins of beta-lactamase PC1 from Staphylococcus aureus, P2 Thr40----Ile and P54 Asp146----Asn, have been investigated using urea-gradient polyacrylamide gel electrophoresis, circular dichroism and sedimentation velocity. Investigation of the folded states of the mutants has shown that compared to wild-type PC1 they are slightly more expanded, and have reduced aromatic circular dichroism, but the same content of secondary structure as PC1. The mutants exhibit fast refolding kinetics to the folded state, in contrast to PC1, which refolds only slowly. We conclude from these results that the folded mutants are in a state close to but distinct from the native state of PC1 and have certain properties in common with the compact intermediate in the folding of beta-lactamase. Therefore, these single amino acid substitutions result in a folding pathway blocked at a point located after collapse of the already folded structural units into a globular shape, and close to the final reshuffling step that leads to the native state of the wild-type enzyme.     

Protein folding kinetics provides a context-independent assessment of beta-strand propensity in the Fyn SH3 domain

Structural database-derived propensities for amino acids to adopt particular local protein structures, such as alpha-helix and beta-strand, have long been recognized and effectively exploited for the prediction of protein secondary structure. However, the experimental verification of database-derived propensities using mutagenesis studies has been problematic, especially for beta-strand propensities, because local structural preferences are often confounded by non-local interactions arising from formation of the native tertiary structure. Thus, the overall thermodynamic stability of a protein is not always altered in a predictable manner by changes in local structural propensity at a single position. In this study, we have undertaken an investigation of the relationship between beta-strand propensity and protein folding kinetics. By characterizing the effects of a wide variety of amino acid substitutions at two different beta-strand positions in an SH3 domain, we have found that the observed changes in protein folding rates are very well correlated to beta-strand propensities for almost all of the substitutions examined. In contrast, there is little correlation between propensities and unfolding rates. These data indicate that beta-strand conformation is well formed in the structured portion of the SH3 domain transition state, and that local structure propensity strongly influences the stability of the transition state. Since the transition state is known to be packed more loosely than the native state and likely lacks many of the non-local stabilizing interactions seen in the native state, we suggest that folding kinetics studies may generally provide an effective means for the experimental validation of database-derived local structural propensities.     

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

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

Linear correlation between thermal stability and folding kinetics of lysozyme

We have studied the refolding and thermal denaturation of hen egg white lysozyme in a wide range of pH values (from 1.5 to 9.4) using stopped-flow circular dichroism (CD) and differential scanning calorimetry (DSC). A linear correlation was found between the thermal denaturation temperature (T(m)) and the logarithm of the refolding rate of the slow folding phase of hen egg white lysozyme (lnk(2)).     

Kinetics and energetics of the translocation of maltose binding protein folding mutants

Protein translocation in Escherichia coli is mediated by the translocase that, in its minimal form, comprises a protein-conducting pore (SecYEG) and a motor protein (SecA). The SecYEG complex forms a narrow channel in the membrane that allows passage of secretory proteins (preproteins) in an unfolded state only. It has been suggested that the SecA requirement for translocation depends on the folding stability of the mature preprotein domain. Here we studied the effects of the signal sequence and SecB on the folding and translocation of folding stabilizing and destabilizing mutants of the mature maltose binding protein (MBP). Although the mutations affect the folding of the precursor form of MBP, these are drastically overruled by the combined unfolding stabilization of the signal sequence and SecB. Consequently, the translocation kinetics, the energetics and the SecA and SecB dependence of the folding mutants are indistinguishable from those of wild-type preMBP. These data indicate that unfolding of the mature domain of preMBP is likely not a rate-determining step in translocation when the protein is targeted to the translocase via SecB.     

Agar Processed from Gracilaria foliifera of Florida

Agar producing a firm gel with specific rheological properties as well as a good commercial value was processed from Gracilaria foliifera (Forsskal) Børgesen, a red alga harvested along the Florida west coast. The alkali pretreatment of the seaweed based on the Funaki-Kojima’s method was applied before the process of agar extraction. The chemical and physical properties of the processed agar were compared with other typical agar experimentally processed.     

Hydrophobic effect on the stability and folding of a hyperthermophilic protein

Ribonuclease HII from hyperthermophile Thermococcus kodakaraensis (Tk-RNase HII) is a kinetically robust monomeric protein. The conformational stability and folding kinetics of Tk-RNase HII were measured for nine mutant proteins in which a buried larger hydrophobic side chain is replaced by a smaller one (Leu/Ile to Ala). The mutant proteins were destabilized by 8.9 to 22.0 kJ mol^− 1 as compared with the wild-type protein. The removal of each -CH₂- group burial decreased the stability by 5.1 kJ mol^− 1 on average in the mutant proteins of Tk-RNase HII examined. This is comparable with the value of 5.3 kJ mol^− 1 obtained from experiments for proteins from organisms growing at moderate temperature. We conclude that the hydrophobic residues buried inside protein molecules contribute to the stabilization of hyperthermophilic proteins to a similar extent as proteins at normal temperature. In the folding experiments, the mutant proteins of Tk-RNase HII examined exhibited faster unfolding compared with the wild-type protein. These results indicate that the buried hydrophobic residues strongly contribute to the kinetic robustness of Tk-RNase HII. This is the first report that provides a practical cause of slow unfolding of hyperthermostable proteins.