Protein folding

After some general remarks on protein structure, there follows a discussion on primary, secondary, and tertiary organization. The account of primary structure includes a discussion of the conformation of disulfide bonds. Types of helices, sheets, and turns are described in the section on secondary structure, followed by a discussion of super-secondary structure and the effects of metals and prosthetic groups of protein fold. The crux of the review lies in an examination of tertiary structure, or specifically of domains that are defined, in part, as functional units within a polypeptide chain. An assembly of domains can in turn result in a protein whose function is quite sophisticated. Some consideration of domain recognition is given in the section on taxonomy and in the appendix. The key part of the tertiary structure section concentrates on a taxonomic protein classification dependent not only on structure but also on function. A discussion of the requirements by quaternary structure on a fold are omitted in this review. Finally, no review of this kind can escape a discussion of evolutionary convergence and divergence.

Structural analysis of human hemoglobin variants with field desorption mass spectrometry

Tryptic hydrolyzates of normal and abnormal human globin chains were analyzed with mass spectrometry, using field desorption ionization technique. All the peptides, including core peptides, were detected as protonated molecular ions in field desorption mass spectra. Since the technique makes it possible to determine the mass number of each peptide, it is very useful for structural analysis of human hemoglobin variants, even those with electrophoretically and chromatographically silent mutations.

Kinetics and mechanism of heme-induced refolding of human alpha-globin

Hemoglobin alpha and beta chains are tightly packed, highly (75%) helical stable molecules. Removal of the heme results in unfolded (30% helical) unstable globin chains that can be refolded to the native conformation by recombination with heme. We have studied the kinetics of heme binding and the ensuing conformational changes by using three stopped-flow techniques: (i) fluorescence quenching, which monitors the spatial orientation and distance between the bound heme and the A12(14)alpha tryptophan; (ii) absorption at the Soret band maxima, whose position and intensity depend on the local environment of the heme and the nature of the axial ligands; and (iii) far-UV circular dichroism, which directly gauges the recovery of secondary structure. The fluorescence quenching was biphasic: An initial second-order decay, representing 80-85% of the total amplitude, marked the binding of hemin dicyanide to a relatively well-defined site at a rate constant of 3.3 x 10(7) M(-1) sec(-1), corresponding to a half-time of 10 msec at 2.4 muM reactants. The Soret absorption and circular dichroism were also multiphasic, all three probes detecting a first-order process of half-time 25-40 sec, during which the final secondary and tertiary structures of the heme pocket were established, and the spatial relationship between the heme and the A12 tryptophan was fixed. A slower circular dichroism change, representing two-thirds of the total backbone refolding, with a half-time of 116 sec, marked the full acquisition of the native subunit conformation. The results show that the residues of the heme pocket achieve or closely approach their final three-dimensional structure well before the entire chain is folded. These measurements represent a direct observation of the rate of prosthetic group-induced secondary structure formation and illustrate the advantages of multiple probe analysis in outlining a protein folding pathway.

Stability of globin mRNA in terminally differentiating murine erythroleukemia cells

The stability of globin mRNA is terminally differentiating MEL cells has been reevaluated. Previously, it had been reported that globin mRNA has a half-life of approximately 17 hr in terminally differentiating MEL cells. We show that the previous measurements of this parameter were confounded by physical instability of differentiating MEL cells. By using culture conditions that physically stabilize end-stage cells we show that the stability of globin mRNA in terminally differentiating MEL cells is equal to the value observed for ribosomal RNA, a half-life greater than 60 hr.

Hemoglobin Hammersmith (beta 42 (CD1) Phe replaced by Ser) associated with severe hemolytic anemia

Hemoglobin Hammersmith was detected in a five year old white female suffering from severe anemia first noted at 18 months of age. She has been splenectomized and her peripheral blood red cells were found to contain inclusion bodies.

Transient haem-globin interactions in photodeligated carboxyhaemoglobin and subunits

Although the fixation of ligand to haemoglobin (Hb) is known to be accompanied by changes in protein conformation regulating the oxygen exchange in blood, the mechanism triggering these changes remains undecided. We now report a dynamic approach to this problem using results obtained in a nanosecond laser photolysis study of carboxyhaemoglobin (HbCO) and its isolated subunits. The study is based on our previous observation of a structural evolution of free Hb after photodeligation, manifested through slight variations of the protein spectrum in the microsecond range. It is now found that the isolated subunits also show this behaviour. The duration of the spectral evolution is approximately 2 microseconds for the three proteins and the activation energy of the process approximately 9 kcal mol-1. The spectral evolution is attributed to local conformation changes at the haem region, occurring during the structural relaxation of the freshly deliganded protein. The results for the isolated chains show that such changes exist even in the absence of the R-T transition.

Metal phthalocyanine substituted hemoglobins. Complexes of manganese and zinc tetrasulfonated phthalocyanines with apohemoglobin

Artificial hemoglobins have been prepared with Mn(III) and Zn(II) tetrasulfonated phthalocyanines in place of heme. Their structure and properties have been investigated by difference spectroscopy, CD, epr, electrophoresis, and molecular weight estimation. Spectrophotometric titration data indicate the ratio of the reagents in this process to be 1:1. The visible absorption spectra show the main peak at 625 nm for the manganese compound and 681 nm for the zinc one. It is evident from CD experiments that incorporation of MN(III)L into apohemoglobin increases helical content of the protein whereas that of Zn(II)L increases its unfolding due to the change of electronic configuration of Zn(II) ion on coordination with the protein. On the basis of spectroscopic and epr data, the formula of the manganese complex is suggested to be (O)Mn(IV)L-globin, whereas that of the zinc complex Zn(II)L-globin. Electrophoresis and molecular weight estimation indicate both complexes to be dimers. Manganese complex binds additional ligands as CN-, imidazole, CO, and NO. Spectroscopic and epr data indicate reduction of the manganese complex and formation of the NO adduct with probable formula (NO) + Mn(II)L-globin. Mechanism of this process is suggested. Both phthalocyanine globins are not able to combine reversibly with oxygen and cannot act as physiological oxygen carriers.

Prenatal diagnosis of hemoglobinopathies: comparison of the results obtained by isoelectric focusing of hemoglobins and by chromatography of radioactive globin chains

Isoelectric focusing (IEF) of hemoglobin was compared to the classical chromatography of labeled globin chains for 22 antenatal diagnoses of hemoglobinopathies: 11 for beta thalassemia, and 11 for sickle cell disease. In all cases, the two methods gave identical results. The diagnosis was confirmed after birth or abortion. Three fetuses homozygous for beta thalassemia and one homozygous for sickle cell disease exhibited no Hb A by IEF, in contrast to normal fetuses or those heterozygous for one of the two hemoglobinopathies. In addition, blood samples obtained in other centers after abortion of 22 fetuses homozygous for beta + or beta 0 thalassemia exhibited no Hb A when analyzed by IEF. When Hb A was present, the respective proportions of Hb A and acetylated Hb F were determined by densitometry of the IEF gel. The Hb A/acetylated Hb F ratio obtained by IEF correlated well with the beta A/gamma ratio of globin chain synthesis, IEF requires 0.1 mg of unlabeled hemoglobin. It is performed in 90 min and several samples can be analyzed simultaneously. If present, maternal contamination of fetal blood must be eliminated by selective lysis of maternal (RBC) using the Orskov reaction. Improvements in this method to obtain suitable samples for IEF analysis are described.

Complete amino acid sequences of the major early embryonic alpha-like globins of the chicken

Vertebrate embryos contain hemoglobins composed of globin polypeptides structurally distinct from those of adults. Together with fetal and adult globin chains, these early embryonic globins are encoded by two developmentally regulated multigene families. To facilitate analysis of the structure and evolution of early embryonic alpha-globin genes, we have determined the complete amino acid sequences of the pi and pi' alpha-like globins of the chick embryo. While differing from each other by an alanine/glutamic acid interchange at position 124, this pair of sequences differs from the major and minor adult alpha-globins by 43%. The early embryonic and adult alpha-like sequences appear to have diverged following an ancient gene duplication. We discuss specific amino acid substitutions in functional positions as possible mediators of the reduced Bohr effect and elevated oxygen affinity, which are characteristic of early embryonic hemoglobins.

Solvent accessibility, protein surfaces, and protein folding

Studies of the native structures of proteins, together with measurements of the thermodynamic properties of the transition between unfolded and native states, have defined the major components of the forces that stabilize native protein structures. However, the nature of the intermediates in the folding process remains largely hypothetical. It is a fairly widespread and not implausible assumption that the intermediates in the folding of a monomeric protein contain the same kinds of secondary and tertiary structures that appear in the native conformation, and that, although unstable, their lifetimes are prolonged by forces similar to those that stabilize the native structure. We wished to examine what happens if, during the folding of a monomeric protein, regions of secondary structure come together to form an intermediate of reduced instability. We applied calculations of accessible surface area (a measure of hydrophobic stabilization) and parameterized nonbonded energy calculations (measuring the strengths of van der Waals forces) to identify the kinds of stabilizing interactions that might be available to such an intermediate. First, we analyzed the total buried surface area of two types of proteins into contributions from formation of secondary structure alone, interaction of pairs of secondary-structural elements, the formation of the structure alone, interaction of pairs of secondary-structural elements, the formation of the complete secondary structure without the turns, and the complete native structure. The formation of secondary structure alone, without tertiary-structural interactions, buries roughly half the surface that the complete structure does. We then analyzed in more detail the approach of two alpha-helices to form a complex, as an illustrative example of the nature of the interaction between compact structural units which remain fairly rigid during their interaction. Many features of the results are not limited to the interaction of alpha-helices. (The results therefore neither confirm nor refute the hypothesis that alpha-helices are intermediates in the folding proteins). We find that the first forces to be felt upon approach arise from solvent conditions on the relative position and orientation of the two helices as does the close packing which optimizes the van der Waals interactions at shorter distances apart. Therefore there appears to be a range of distances in which hydrophobic interactions could create a nonspecific complex between two helices in which the side chains might have sufficient time to seek the proper interdigitation observed in the native structure, where the two helices are in intimate contact. Indeed, we find that only in the final stages of approach is the native geometry the most stable; in the region in which solvent-exclusion forces predominate, the conformation with helix axes parallel is more stable than the native conformation, in the cases we examined...

Increase in the susceptibility of hemoglobin to trypsin on treatment with glutathione or cysteine

1. Native human hemoglobin A was digested with proteases after treatment with reduced or oxidized glutathione, cysteine, or cystine. 2. The treatment of hemoglobin with a 40-fold molar excess of reduced glutathione or cysteine at 37 degrees C for 4 enhanced its susceptibility to trypsin 4 or 6 times, respectively. However, oxidized glutathione and cystine had little or no effect on its susceptibility to the protease. 3. The enhanced susceptibility was not due to conformational change in hemoglobin, such as dissociation to dimers or monomers, or to unfolding of alpha-helical structure, but was due to dissociation of heme from the globin moiety, judging from measurements of the absorption spectrum and circular dichroism spectrum, and gel-filtration analysis.

Variable rate of polypeptide chain elongation in vitro. Effect of spermidine

Translation of rabbit globin mRNA and tobacco mosaic virus mRNA was studied in a wheat germ system. After a short pulse with labeled methionine, the reaction products were separated by polyacrylamide gel electrophoresis in sodium dodecyl sulfate and visualized by fluorography. Discrete bands corresponding to incomplete products were detected both with globin and tobacco mosaic virus RNA as messenger at a time when no release of peptides from tRNA could be detected. In the absence of spermidine certain intermediate products accumulated during the chase period. With increasing incubation time, the radioactivity of most bands was chased into higher-molecular-weight products. This change in size distribution was more pronounced when magnesium was partially replaced by spermidine. Evidence is presented that some of the incomplete products had in part been released from tRNA. No such release of polypeptides could be detected in experiments using the artificial messenger poly(U), indicating that non-specific peptidyl-tRNA hydrolases were not present in the system. The transient accumulation of discrete bands during the chase period indicates that in the wheat germ system polypeptide chain elongation occurs at discontinuous rates. The fact that spermidine increases the rate of elongation and the yield of full-length translation products may be due to its ability to facilitate the movement of the ribosomes beyond regions where the elongation is retarded.

Peptide separations on substituted polystyrene resins. Effect of cross-linkage

The effect of copolymer cross-linkage on the resolution of soluble tryptic peptides of human globin (alpha- and beta-chains) separated in columns containing substituted polystyrene resin classified to 11 +/- 1 micrometer has been examined. With both the cation and anion exchange resins, polymers of lower cross-linkage provided better resolution; inferior resolution was obtained with 12% cross-linked resins. It was also observed that microparticle anion-exchange resins could be used in columns maintained at 55 degrees instead of 35 degrees as used traditionally. Resolution and yield with 20 x 1 cm resin beds were generally as good as or superior to much longer columns of crushed bead resin of the same chemical structure.

Hemoglobin variants and methods used for their characterization during 7 years of screening at the Center for Disease Control

During 7 years of screening for hemoglobin variants, over 75 rare variants have been characterized. Of these, 18 were described for the first time. This report presents tabulated data regarding the structural and functional defects that were observed, information on the ethnic origin, and other special properties exhibited by these variants. The strategy and procedures for characterizing these variants are also summarized.

Structural comparisons of heme binding proteins

Of the 82 three dimensionally characterized residues of cytochrome c551, 49 are found to be structurally and topologically equivalent to the globin fold and 41 are equivalent to the cytochrome b5 fold, with a respective root mean square separation of 3.5 and 4.9 A between equivalenced Calpha atoms. The common fold represents a central heme binding core, corresponding to the middle exon of certain globin genes. After superposition of the protein folds, the heme irons are found to be separated by 5.4 and 1.6 A, while their heme normals are inclined by 6 degrees and 32 degrees, respectively. Furthermore, the heme "face", determined by the asymmetric attachment of the vinyl and propionyl side chains, is directed similarly in all three heme proteins. The heme itself is rotated by 72 degrees and 116 degrees about its normal, respectively. The minimum base change per codon for the three pairwise comparisons corresponds to the expected value of random sequence comparisons. While all three heme proteins may have diverged from a common ancestor, their similarity may have arisen from the requirements of heme binding or the utilization of a particularly stable fold. Known structures within commonly accepted divergent families were superimposed in order to discriminate better between convergence and divergence. Minimum base changes per codon, number of deletions and insertions, percentage of equivalenced residues, precision of heme superposition, and root mean square separation of equivalenced Calpha atoms were tested as measures of evolutionary relationships.