Folding of apominimyoglobin

Structural characterization of recombinant streptokinase following recovery from inclusion bodies using different chemical solubilization treatments

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Protein solubilization from E. coli inclusion bodies was done using various concentrations of chemicals.

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After protein solubilization from inclusion bodies by various concentrations of chemicals, intensities of rSK CD signals were varied.

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The obtained rSK contained different amounts of secondary structures and biological potency.

Circular dichroism (CD) in far-UV region was employed to study the extent of changes occurred in the secondary structures of recombinant streptokinase (rSK), solubilized from inclusion bodies (IBs) by different chemicals and refolded/purified by chromatographic techniques. The secondary structure distribution of rSK, obtained following different chemical solubilization systems, was varied and values in the range of 12.4–14.5% α-helices, 40–51% β-sheets and 35.5–48.3% turns plus residual structures were found. With reducing the concentration of chemicals during IB solubilization, the content of turns plus random coils was diminished and simultaneously the amounts of α- and β-sheets were increased. These changes in the secondary structures would lower the hydrophobicity along with the chance of protein aggregation and expose the hydrophilic regions of the protein. Therefore, these alterations in the secondary structures, occurred following efficient IBs solubilization by low concentration of chemicals, could be related to enhancement in rSK biological potency previously observed.

A molecule for all seasons: The heme

If life without heme-Fe were at all possible, it would definitely be different. Indeed this complex and versatile iron-porphyrin macrocycle upon binding to different “globins” yields hemeproteins crucial to sustain a variety of vital functions, generally classified, for convenience, in a limited number of functional families. Over-and-above the array of functions briefly outlined below, the spectacular progress in molecular genetics seen over the last 30 years led to the discovery of many hitherto unknown novel hemeproteins in prokaryotes and eukaryotes. Here, we highlight a few basic aspects of the chemistry of the hemeprotein universe, in particular those that are relevant to the control of heme-Fe reactivity and specialization, as sculpted by a variety of interactions with the protein moiety.

Selective and efficient extraction of recombinant proteins from the periplasm of Escherichia coli using low concentrations of chemicals

Experiments were conducted to determine chemicals at low concentrations, which can be utilized for selective release of periplasmic proteins. It was revealed that 80-100 % of the activity of alpha-amylase, beta-lactamase, and Fab D1.3 was retained in the presence of 0.05 and 0.1 % Triton X-100, 0.1 % Tween 20, 0.1 % DOC, 0.01 % BAC, 0.01 % CTAB, 10 mM EDTA, 1 mM and 10 mM DEA, 10 mM NTA, 0.1 and 1 % SHMP, 200 mM urea, 100-500 mM GndCl, and 1 % solvents (hexane, xylene, toluene, benzene, pyridine and isoamyl alcohol). Performance of these chemicals, recognized as generally safe, for selective release of proteins from the periplasm of Escherichia coli was investigated. DOC was a general and very efficient agent, and at concentrations as low as 0.05, 0.1, and 0.025 %, released beta-lactamase, alpha-amylase, and Fab D1.3 selectively with yield factors of 2.7, 2.3, and 3.6 times greater than osmotic shock procedure, respectively. EDTA (1 and 10 mM) discharged Fab D1.3 with efficiency more than osmotic shock (target protein yield of 110 and 138 %, correspondingly). Isoamyl alcohol (10 % v/v) was effective for periplasmic release of alpha-amylase and particularly Fab D1.3, with target protein yields of 75 and 168 %, respectively.

Collapse and search dynamics of apomyoglobin folding revealed by submillisecond observations of alpha-helical content and compactness

The characterization of protein folding dynamics in terms of secondary and tertiary structures is important in elucidating the features of intraprotein interactions that lead to specific folded structures. Apomyoglobin (apoMb), possessing seven helices termed A-E, G, and H in the native state, has a folding intermediate composed of the A, G, and H helices, whose formation in the submillisecond time domain has not been clearly characterized. In this study, we used a rapid-mixing device combined with circular dichroism and small-angle x-ray scattering to observe the submillisecond folding dynamics of apoMb in terms of helical content (f(H)) and radius of gyration (R(g)), respectively. The folding of apoMb from the acid-unfolded state at pH 2.2 was initiated by a pH jump to 6.0. A significant collapse, corresponding to approximately 50% of the overall change in R(g) from the unfolded to native conformation, was observed within 300 micros after the pH jump. The collapsed intermediate has a f(H) of 33% and a globular shape that involves >80% of all its atoms. Subsequently, a stepwise helix formation was detected, which was interpreted to be associated with a conformational search for the correct tertiary contacts. The characterized folding dynamics of apoMb indicates the importance of the initial collapse event, which is suggested to facilitate the subsequent conformational search and the helix formation leading to the native structure.

Similarity of force-induced unfolding of apomyoglobin to its chemical-induced unfolding: an atomistic molecular dynamics simulation approach

We have compared force-induced unfolding with traditional unfolding methods using apomyoglobin as a model protein. Using molecular dynamics simulation, we have investigated the structural stability as a function of the degree of mechanical perturbation. Both anisotropic perturbation by stretching two terminal atoms and isotropic perturbation by increasing the radius of gyration of the protein show the same key event of force-induced unfolding. Our primary results show that the native structure of apomyoglobin becomes destabilized against the mechanical perturbation as soon as the interhelical packing between the G and H helices is broken, suggesting that our simulation results share a common feature with the experimental observation that the interhelical contact is more important for the folding of apomyoglobin than the stability of individual helices. This finding is further confirmed by simulating both helix destabilizing and interhelical packing destabilizing mutants.

Fast purification of the Apo form and of a non-binding heme mutant of recombinant sperm whale myoglobin

As molecular biology has developed it has become possible to abundantly produce heterologous proteins in bacteria and to design serial amino acid substitutions for the generation of modified proteins, an approach also known as protein engineering. Sperm whale myoglobin, a protein of broad interest, has been cloned for several years now and a large collection of mutants has been produced. The presence of heme stabilizes the protein, which is recovered soluble from the bacterial pellet, and most purification protocols take advantage of this property for myoglobin purification directly from the pellet. However, recovery from the column resin is poor with these methods making them expensive and the procedure for removing heme is laborious and drastic when the apo form of Mb is required. In the case of proteins with severe mutations, which bind heme weakly or do not bind it at all, such methods cannot be employed without massive loss of productivity. Here, we describe a modified method, which is both low cost and rapid, for the purification of the soluble apo form of Mb from Escherichia coli inclusion bodies. Biophysical characterization of the protein after purification shows that the purified apoMb retains its native conformation and is soluble. This modified method is also used for the purification of a non-heme-binding apoMb mutant, demonstrating its efficiency when dealing with drastic mutations.

Construction and characterization of a chimeric myoglobin

In order to investigate the functional and structural role of modular structure in globins, we have engineered a chimeric myoglobin (ChimMb) in which the first and third exon come from the gene coding for the sperm whale Mb and the second exon from the gene coding for Aplysia limacina Mb. This ChimMb, fused to the Maltose Binding Protein (MBP) and expressed in Escherichia coli as an apoprotein, binds protoheme in a 1:1 stoichiometric ratio. Based on some functional and spectroscopic properties, we conclude that the central core of the ChimMb (which derives from A. limacina) is native-like. On the other hand, the ChimMb deprived (by proteolytic digestion) of the fused MBP displays a considerably reduced stability. These results suggest that the sperm whale A-G-H nucleus does not contribute significantly to the overall stability of the ChimMb.

Unfolding of the loggerhead sea turtle (Caretta caretta) myoglobin: A (1)H-NMR and electronic absorbance study

The effect of urea concentration on the backbone solution structure of the cyanide derivative of ferric Caretta caretta myoglobin (at pH 5.4) is reported. By addition of urea, sequential and long-range nuclear Overhauser effects (NOEs) are gradually lost. By using the residual NOE constraints to build the molecular model, a picture of the unfolding pathway was obtained. When the urea concentration is raised to 2.2 M, helices A and B appear largely disordered; helices C, D, and F loose structural constraints at 3.0 M urea. At urea concentration >6 M, the protein appears to be fully unfolded, including the GH hairpin and helix E stabilizing the prosthetic group. Reversible and cooperative denaturation isotherms obtained by following NOE peaks are considerably different from those obtained by monitoring electronic absorption changes. The reversible and cooperative urea-dependent folding-unfolding process of C. caretta myoglobin follows the minimum three-state mechanism N long left and right arrow X long left and right arrow D, where X represents a disordered globin structure (occurring at approximately 4 M urea) that still binds the heme.

The 109 residue nerve tissue minihemoglobin from Cerebratulus lacteus highlights striking structural plasticity of the alpha-helical globin fold

A very short hemoglobin (CerHb; 109 amino acids) binds O(2) cooperatively in the nerve tissue of the nemertean worm Cerebratulus lacteus to sustain neural activity during anoxia. Sequence analysis suggests that CerHb tertiary structure may be unique among the known globin fold evolutionary variants. The X-ray structure of oxygenated CerHb (R factor 15.3%, at 1.5 A resolution) displays deletion of the globin N-terminal A helix, an extended GH region, a very short H helix, and heme solvent shielding based on specific aromatic residues. The heme-bound O(2) is stabilized by hydrogen bonds to the distal TyrB10-GlnE7 pair. Ligand access to heme may take place through a wide protein matrix tunnel connecting the distal site to a surface cleft located between the E and H helices.

Cloning, overexpression and characterization of micro-myoglobin, a minimal heme-binding fragment

We report the cloning and expression of micro-myoglobin, a 78-amino-acid fragment containing residues 29-105 of sperm whale myoglobin, and spanning the region from mid-helix B to mid-helix G of the globin fold. In contrast to full-length myoglobin and to mini-myoglobin (residues 32-129), the micro-myoglobin apoprotein is almost unfolded. However, circular dichroism and absorption spectroscopy data indicate that this fragment is capable of folding into a functional heme-binding unit forming a complex with the prosthetic group with characteristics similar to native myoglobin. Therefore, this case represents a new example of cofactor-assisted folding. The experimental data suggest independence between myoglobin subdomains.

Folding of an isolated ribonuclease H core fragment

Based on results from both equilibrium and kinetic hydrogen exchange studies of Escherichia coli ribonuclease HI (RNase H), a fragment of RNase H (eABCD) was designed. The sequence of eABCD contains less than half of the protein's primary sequence and includes the regions that were shown to be the most protected from hydrogen exchange in all previous studies of RNase H. This core fragment of RNase H encodes a well-ordered protein with native-like properties. When isolated from the full-length monomeric protein, the eABCD fragment forms a stable dimer. However, we show indirectly that the monomeric form of eABCD is folded and has an overall secondary structure similar to the dimeric form.

The N-terminal sequence affects distant helix interactions in hemoglobin. Implications for mutant proteins from studies on recombinant hemoglobin felix

The N-terminal 18-amino acid sequence of the beta-chain of hemoglobin, as far as the end of the A helix, has been replaced by the corresponding sequence of the gamma-chain of fetal hemoglobin with the remaining sequence of the beta-chain retained (helices B through H). The gamma-beta-chain had the correct mass, and its entire sequence was established by mass spectrometric analysis of its tryptic peptides; the alpha-chain also had the correct mass. This recombinant hemoglobin (named Hb Felix) retains cooperativity and has an oxygen affinity like that of HbA both in the presence and absence of the allosteric regulators, 2,3-diphosphoglycerate or chloride but differs from HbF in its 2,3-diphosphoglycerate response. However, Hb Felix has some features that resemble fetal hemoglobin, i.e. its significantly decreased tetramer-dimer dissociation and its circular dichroism spectrum, which measure the strength of the tetramer-dimer interface in the oxy conformation and its rearrangement to the deoxy conformation, respectively. Even though Hb Felix contains the HbA amino acids at its tetramer-dimer interface, which is located at a distance from the substitution sites, its interface properties resemble those of HbF. Therefore, the N-terminal sequence and not just those amino acids directly involved at the subunit interface contacts with alpha-chains must have a strong influence on this region of the molecule. The results reinforce the concept of fluid long range relationships among various parts of the hemoglobin tetramer (Dumoulin, A., Manning, L. R., Jenkins, W. T., Winslow, R. M., and Manning, J. M. (1997) J. Biol. Chem. 272, 31326-31332) and demonstrate the importance of the N-terminal sequence, especially in some mutant hemoglobins, in influencing its overall structure by affecting the relationship between helices.

The mini-hemoglobins in neural and body wall tissue of the nemertean worm, Cerebratulus lacteus

Hemoglobin (Hb) occurs in circulating red blood cells, neural tissue, and body wall muscle tissue of the nemertean worm, Cerebratulus lacteus. The neural and body wall tissue each express single major Hb components for which the amino acid sequences have been deduced from cDNA and genomic DNA. These 109-residue globins form the smallest stable Hbs known. The globin genes have three exons and two introns with splice sites in the highly conserved positions of most globin genes. Alignment of the sequences with those of other globins indicates that the A, B, and H helices are about one-half the typical length. Phylogenetic analysis indicates that shortening results in a small tendency of globins to group together regardless of their actual relationships. The neural and body wall Hbs in situ are half-saturated with O2 at 2.9 and 4.1 torr, respectively. The Hill coefficient for the neural Hb in situ, approximately 2.9, suggests that the neural Hb self-associates in the deoxy state at least to tetramers at the 2-3 mM (heme) concentration estimated in the cells. The Hb must dissociate upon oxygenation and dilution because the weight-average molecular mass of the HbO2 in vitro is only about 18 kDa at 2-3 microM heme concentration. Calculations suggest that the Hb can function as an O2 store capable of extending neuronal activity in an anoxic environment for 5-30 min.

Apomyoglobin folding intermediates characterized by the hydrophobic fluorescent probe 8-anilino-1-naphthalene sulfonate

Folding apomyoglobin intermediates were investigated by optical techniques including steady-state fluorescence, frequency domain fluorometry, and absorption spectroscopy. The investigated chromophores were the aromatic residues, i.e., tyrosyl and tryptophanyl residues, and the extrinsic probe (8-anilino-1-naphthalenesulfonate, ANS) which is particularly useful for studying partly structured forms appearing in the early stage of protein folding. The emission decay of the extrinsic probe as well as resonance energy transfer from tryptophanyl residues to ANS permitted to identify and characterize partly folded forms obtained under different experimental conditions. The results indicate that the intermediates so far detected (I-1 and I-2 states) are distinct structural states. The differences concern the solvent accessibility to the aromatic side chains and the conformational dynamics of the protein region forming the binding site for the extrinsic fluorophore.

Unfolding of apomyoglobin from Aplysia limacina: the effect of salt and pH on the cooperativity of folding

The equilibrium unfolding pathway of Aplysia apomyoglobin has been studied under various solvent conditions. The protein exhibits a single unfolding transition in acid in contrast to the two transitions observed for the mammalian apomyoglobins with which it shares a common fold but a low level of sequence identity (24%). This acid-unfolded species has considerable residual structure as evidenced by both tryptophan fluorescence and far-UV CD spectroscopy. It remains 40% alpha-helical under low salt conditions (2 mM citrate, 4 degrees C); the folded form is 65% helical. A similar species is observed for the mammalian globins in mild acid conditions. Titration with GdnHCl at pH 7 reveals two unfolding transitions, the first having common features with that observed in acid and the second resulting in a completely unfolded state. Under the same conditions, urea unfolds the protein completely in an apparently single cooperative transition. Assuming a simple three-state model (F<-->I<-->U), data from GdnHCl and urea titrations over a range of pH conditions were used to derive values for the apparent stability (delta Gw(app) and solvent accessibility (n(app)) of the folded (F) and intermediate (I) forms of the protein. Urea titrations were then repeated over a range of KCl concentrations in order to understand the contribution of Cl- to the different unfolding activity of GdnHCl. A three-state scheme is justified when changes in delta G(w(app)) occur without changes in n(app). The change in free energy of folding of I<-->F (delta Gw(F/I)) decreases to 0 at pH 4 as expected from the acid unfolding curve. delta Gw(I/U) reaches its maximum at pH 4.5, the isoelectric point of the protein. Variations of this value with pH and chloride are as much as 3 kcal mol-1 and correlate closely with changes in n(app) although there is no change in the alpha-helical content of I across the pH range. This observation is interpreted here as a deviation of the unfolding of the I state of Aplysia apomyoglobin from a cooperative behaviour.

Structural heterogeneity of the various forms of apomyoglobin: implications for protein folding

Temperature-induced denaturation transitions of different structural forms of apomyoglobin were studied monitoring intrinsic tryptophan fluorescence. It was found that the tryptophans are effectively screened from solvent both in native and acid forms throughout most of the temperature range tested. Thus, the tryptophans' surrounding do not show a considerable change in structure where major protein conformational transitions have been found in apomyoglobin using other techniques. At high temperatures and under strong destabilizing conditions, the tryptophans' fluorescence parameters show sigmoidal thermal denaturation. These results, combined with previous studies, show that the structure of this protein is heterogeneous, including native-like (tightly packed) and molten globule-like substructures that exhibit conformation (denaturation) transitions under different conditions of pH and temperature (and denaturants). The results suggest that the folding of this protein proceeds via two "nucleation" events whereby native-like contacts are formed. One of these events, which involves AGH "core" formation, appears to occur very early in the folding process, even before significant hydrophobic collapse in the rest of the protein molecule. From the current studies and other results, a rather detailed picture of the folding of myoglobin is presented, on the level of specific structures and their thermodynamical properties as well as formation kinetics.

Fast events in protein folding: relaxation dynamics of secondary and tertiary structure in native apomyoglobin

We report the fast relaxation dynamics of "native" apomyoglobin (pH 5.3) following a 10-ns, laser-induced temperature jump. The structural dynamics are probed using time-resolved infrared spectroscopy. The infrared kinetics monitored within the amide I absorbance of the polypeptide backbone exhibit two distinct relaxation phases which have different spectral signatures and occur on very different time scales (nu = 1633 cm(-1),tau = 48 ns; nu = 1650 cm(-1),tau = 132 micros). We assign these two spectral components to discrete substructures in the protein: helical structure that is solvated (1633 cm(-1)) and native helix that is protected from solvation by interhelix tertiary interactions (1650 cm(-1)). Folding rate coefficients inferred from the observed relaxations at 60 degrees C are k(f)(solvated) = (7 to 20) x 10(6) s(-1) and k(f)(native) = 3.6 x 10(3) s(-1), respectively. The faster rate is interpreted as the intrinsic rate of solvated helix formation, whereas the slower rate is interpreted as the rate of formation of tertiary contacts that determine a native helix. Thus, at 60 degrees C helix formation precedes the formation of tertiary structure by over three orders of magnitude in this protein. Furthermore, the distinct thermodynamics and kinetics observed for the apomyoglobin substructures suggest that they fold independently, or quasi-independently. The observation of inhomogeneous folding for apomyoglobin is remarkable, given the relatively small size and structural simplicity of this protein.

The native state of apomyoglobin described by proton NMR spectroscopy: the A-B-G-H interface of wild-type sperm whale apomyoglobin

Proton nuclear magnetic resonance spectroscopy was applied to sperm whale apomyoglobin to describe the conformation adopted by the protein under native conditions. The study focused on the A-B-G-H interface, a region known to form a compact subdomain in the apoprotein (Hughson and Baldwin, Biochemistry 28:4415-4422, 1989). Two histidine residues located in this subdomain, His24 and His119, interact and are thought to play a role in the acid denaturation process (Barrick et al., J. Mol. Biol. 237:588-601, 1994). A stable double mutant at these positions (His24Val/His119Phe sperm whale apomyoglobin) was compared with wild-type apomyoglobin. The amino acid replacements result in chemical shift perturbations near the mutations, in particular in the AB interhelical region, and in a deceleration of backbone amide hydrogen exchange in the B helix from position 27 to position 33. The double mutant data were used to expand and confirm the wild-type spectral analysis. Signals from the D helix were identified that demonstrate the formation of holoprotein-like structure. The assigned wild-type nuclear Overhauser effects, although in small number, were sufficient to construct a model of the compact subdomain of the apoprotein. This was achieved by using the structure of the holoprotein and restraining it with the geometrical information on the apoprotein in a simulated annealing procedure. The experimental restraints define a low-resolution model of the A-B-G-H interface in apomyoglobin.