Amino acid sequence of beta-galactosidase. XI. Peptide ordering procedures and the complete sequence.

The amino acid sequence of beta-galactosidase has been determined. The monomer contains 1,021 amino acid residues in a single polypeptide chain and has a molecular weight of 116,349. All 80 tryptic peptides as well as all 24 CNBr peptides have been isolated in pure form. Evidence is presented for the ordering of the CNBr peptides. The sequence determination was aided by analysis of cyanogen bromide peptides obtained from a polypeptide fragment produced by a lacZ termination mutant strain.     

Photochromic polypeptides as synthetic models of biological photoreceptors: a spectroscopic study.

L-Glutamic acid polypeptides containing photochromic nitrospiropyran bound to the side chains at various percentages ("local" concentration) have been synthesized and investigated as possible artificial models of biological photoreceptors. Absorption and fluorescence spectroscopy have been utilized to investigate the photophysical and photochemical properties of nitrospiropyrans, both inserted in the polypeptide chain and in solution as "free" dye. Conformational variations produced by dark storage and light exposure of the photochromic polypeptides have been studied by means of circular dichroism. Dark-kept "free" dyes in hexafluoro-2-propanol solution in the merocyanine form ("open" form) give rise to molecular aggregates, which have been characterized as merocyanine dimers. The equilibrium constant between the monomer and the dimer, K, and their molar extinction coefficients, epsilon, at several wavelengths have been determined. Fluorescence measurements on "free" and polypeptide-bound nitrospiropyrans suggest that the dimerization process between merocyanines is favored when the photochromic units are inserted in the polypeptide chain and that under these conditions an efficient energy transfer from the monomer (donor) to the dimer (acceptor) occurs. By varying "local" as well as total nitrospiropyran concentration, it has been shown that the dimeric species result from intermolecular interactions between photochromic groups inserted in the same polypeptide chain. The alpha-helix --> random coil transition of the polypeptide structure after dark storage has eventually been shown to be the result of the dimerization process and not of the dark isomerization per se from the "closed" spiropyran form to the "open" merocyanine form of the dye.     

Structural features of normal and complemented forms of the Neurospora isopropylmalate isomerase.

The isopropylmalate isomerase (EC 4.2.1.33) of Neurospora crassa is a globular protein consisting of a single polypeptide chain with a molecular weight of about 90,000. The isomerase cannot easily be freed of a contaminating protease which cleaves the enzyme into two major fragments, one of approximately 56,000 and the other 37,000 daltons. This suggests that the folded polypeptide chain may contain some hinge point or loop exposed on the surface which makes it susceptible to proteolytic attack. Most of the isomerase activity extracted from the wild-type strain is in monomer form. However, a small fraction of the activity in crude extracts is found in multimeric aggregates, and the active isomerase extracted from complementing leu-2 heterokaryons consists entirely of dimers and higher multimers. These observations suggest that, though active as a monomer, a significant fraction of the normal enzyme might be organized in multimeric form within the cell.     

Further characterisation of a nucleic acid binding protein.

A glycoprotein which binds to nucleic acids has now been purified from Ustilago maydis until free from detectable deoxyribonuclease activity. It binds to a variety of substrates and in doing so, makes them soluble in dilute trichloroacetic acid. Physical studies suggest that it forms a variety of aggregates under low ionic strength, but at high ionic strength the monomer consists of a single polypeptide chain. Preliminary experiments have detected this novel binding activity in bacterial, fungal and mammalian cells.     

Primary structure of human thyroglobulin deduced from the sequence of its 8448-base complementary DNA

The mRNA encoding human thyroglobulin has been cloned and sequenced. It is made up of a 8301-nucleotide segment encoding a preprotein monomer of 2767 amino acids, flanked by non-coding 5' and 3' regions of 41 and 106 nucleotides, respectively. This preprotein consists of a leader sequence of 19 amino acids, followed by the sequence of the mature monomer, corresponding to a polypeptide of 2748 amino acids (Mr = 302773). On its amino-terminal side, 70% of the monomer is characterized by the presence of three types of repetitive units. In contrast, the remaining 30% of the protein is devoid of repetitive units. This last region however shows an interesting homology (up to 64%) with the acetylcholinesterase of Torpedo californica. The sites of thyroid hormones synthesis are clustered at both ends of the thyroglobulin monomer. By contrast, the potential glycosylation sites are scattered along the polypeptide chain.     

Structure of glycogen phosphorylase a at 3.0 A resolution and its ligand binding sites at 6 A.

A model of the polypeptide backbone of the dimer of glycogen phosphorylase a (EC 2.4.1.1) was built from a 3 A resolution electron density map derived from x-ray diffraction analysis of native tetragonal crystals and two heavy atom isomorphous replacement derivatives. Each identical subunit of the dimer has a compact shape with overall dimensions of 85 X 75 X 55 A and is tightly associated with its 2-fold symmetry related subunit. There are three major excursions of the polypeptide chain of one monomer across the 2-fold axis to make extensive contacts with the other subunit. The active site, of which there are two per dimer, is shared between the two subunits at their interface and comprises a pocket-like region within a "V"-shaped framework of two alpha helices. Within this region are found the binding sites for the substrates, glucose-1-P and arsenate, a competitive inhibitor, UDP-glucose, and the allosteric effector, AMP. The site of metabolic control, Ser-14 phosphate, is hydrogen-bonded to a side chain on the outside of one of the alpha helices forming the active site and is 15 A from the AMP binding site. Maltoheptaose, a glycogen analogue and substrate for these enzymatically active crystals, binds in a second region of interest. Even at concentrations above its Km, when binding is sufficiently tight that all seven glucose moieties may be discerned, the closest of these is 25 A from the glucose-1-P binding site. We suggest that this polysaccharide binding site may represent a storage site whereby phosphorylase is bound to the glycogen particle in the muscle cell. The polypeptide chain in a third region has the same topological structure as has been observed for the nucleotide binding domains in the dehydrogenases. Adenine or adenosine (but not AMP) bind here in a position similar to the adenine ring of NAD in the dehydrogenases while glucose binds 17 A away in an interior crevice near the center of the monomer.     

Physicochemical properties of T4 polynucleotide kinase.

Some physicochemical properties of T4 polynucleotide kinase (EC2.7.1.78) have been studied. The enzyme is an oligomer of one polypeptide chain. The molecular weight of the monomer is 33000, as determined from the amino acid analysis. Phenylalanine is the N-terminal amino acid. Each monomer contains two --SH groups, one exposed and one more buried. Circular dichroic spectra suggest a high content of alpha-helical structure, 45--55%. Excitation at 280 nm gave a strong emission fluorescence spectrum with a maximum centering at 340 nm. Sedimentation studies suggested the enzymically active form to be a tetramer. High ionic strength (0.1 M KC1), spermine, and the substrates ATP and thymidine 3'-monophosphate were found to be essential factors in order to stabilize the protein in an oligomeric structure. The association constants for ATP, thymidine 3'-monphosphate, and P1 were determined fluorimetrically to be 7.9 x 105, 4.8 x 105, and 7.2 x 10(2) M-1 respectively.     

Ligand interactions of the cation-independent mannose 6-phosphate receptor. The stoichiometry of mannose 6-phosphate binding

The interaction of the bovine cation-independent mannose 6-phosphate receptor with a variety of phosphorylated ligands has been studied using equilibrium dialysis and immobilized receptor to measure ligand binding. The dissociation constants for mannose 6-phosphate, pentamannose phosphate, bovine testes beta-galactosidase, and a high mannose oligosaccharide with two phosphomonoesters were 7 X 10(-6) M, 6 X 10(-6) M, 2 X 10(-8) M, and 2 X 10(-9) M, and the mol of ligand bound/mol of receptor monomer were 2.17, 1.85, 0.9, and 1.0, respectively. We conclude that the cation-independent mannose 6-phosphate receptor has two mannose 6-phosphate-binding sites/polypeptide chain.     

Secondary structure and assembly mechanism of an oligomeric channel protein

The alpha-toxin of Staphylococcus aureus is secreted as a water-soluble, monomeric polypeptide (Mr 33 182) that can assemble into an oligomeric membrane channel. By chemical cross-linking, we have confirmed that the major form of the channel is a hexamer. The circular dichroism spectrum of this hexamer in detergent revealed that it contains a high proportion of beta-sheet that we deduce must lie within the lipid bilayer when the protein is associated with membranes. The circular dichroism spectrum of the monomeric toxin in the presence or absence of detergent was closely similar to the spectrum of the hexamer, suggesting that the secondary structure of the polypeptide is little changed on assembly. Results of experiments involving limited proteolysis of the monomer and hexamer are consistent with the idea that assembly involves the movement of two rigid domains about a hinge located near the midpoint of the polypeptide chain. The hydrophilic monomer is thereby converted to an amphipathic rod that becomes a subunit of the hexamer.     

Mechanism and evolution of protein dimerization.

We have investigated the mechanism and the evolutionary pathway of protein dimerization through analysis of experimental structures of dimers. We propose that the evolution of dimers may have multiple pathways, including (1) formation of a functional dimer directly without going through an ancestor monomer, (2) formation of a stable monomer as an intermediate followed by mutations of its surface residues, and (3), a domain swapping mechanism, replacing one segment in a monomer by an equivalent segment from an identical chain in the dimer. Some of the dimers which are governed by a domain swapping mechanism may have evolved at an earlier stage of evolution via the second mechanism. Here, we follow the theory that the kinetic pathway reflects the evolutionary pathway. We analyze the structure-kinetics-evolution relationship for a collection of symmetric homodimers classified into three groups: (1) 14 dimers, which were referred to as domain swapping dimers in the literature; (2) nine 2-state dimers, which have no measurable intermediates in equilibrium denaturation; and (3), eight 3-state dimers, which have stable intermediates in equilibrium denaturation. The analysis consists of the following stages: (i) The dimer is divided into two structural units, which have twofold symmetry. Each unit contains a contiguous segment from one polypeptide chain of the dimer, and its complementary contiguous segment from the other chain. (ii) The division is repeated progressively, with different combinations of the two segments in each unit. (iii) The coefficient of compactness is calculated for the units in all divisions. The coefficients obtained for different cuttings of a dimer form a compactness profile. The profile probes the structural organization of the two chains in a dimer and the stability of the monomeric state. We describe the features of the compactness profiles in each of the three dimer groups. The profiles identify the swapping segments in domain swapping dimers, and can usually predict whether a dimer has domain swapping. The kinetics of dimerization indicates that some dimers which have been assigned in the literature as domain swapping cases, dimerize through the 2-state kinetics, rather than through swapping segments of performed monomers. The compactness profiles indicate a wide spectrum in the kinetics of dimerization: dimers having no intermediate stable monomers; dimers having an intermediate with a stable monomer structure; and dimers having an intermediate with a stable structure in part of the monomer. These correspond to the multiple evolutionary pathways for dimer formation. The evolutionary mechanisms proposed here for dimers are applicable to other oligomers as well.     

The conformation and aggregation of bovine β-casein A. I. Molecular aspects of thermal aggregation

The conformation of β-casein A in the monomeric and thermally aggregated states has been investigated by a range of techniques. β-Casein exists as a monomer in solution at 4°C and at concentrations up to at least 3 g/dl. The molecule is flexible and exhibits a lot of segmental motion, but its secondary structure is not wholly random coil; about one-third of the polypeptide chain is ordered and the likely locations of these regions are discussed. The radius of gyration, representing the time-average distribution of the flexible chain, is 46 Å. Increasing temperature leads to aggregation of the β-casein molecules. The degree of association is very sensitive to experimental conditions, and under our conditions a 14-mer exists at 20°C. The aggregate is spherical with a radius of about 100 Å. The interior of the aggregate is relatively disordered, and the β-casein molecules remain in a largely flexible, hydrated conformation. The volume restriction of the protein molecules which occurs on association leads to some immobilization of the hydrophobic C-terminal region, which is packed toward the center of the aggregate.     

Radiation inactivation of galactose oxidase,a monomeric enzyme with a stable free radical

To determine the radiation sensitivity of galactose oxidase, a 68 kDa monomeric enzyme containing a mononuclear copper ion coordinated with an unusually stable cysteinyl‐tyrosine (Cys‐Tyr) protein free radical. Both active enzyme and reversibly rendered inactive enzyme were irradiated in the frozen state with high‐energy electrons. Surviving polypeptides and surviving enzyme activity were analyzed by radiation target theory giving the radiation sensitive mass for each property. In both active and inactive forms, protein monomer integrity was lost with a single radiation interaction anywhere in the polypeptide, but enzymatic activity was more resistant, yielding target sizes considerably smaller than that of the monomer. These results suggest that the structure of galactose oxidase must make its catalytic activity unusually robust, permitting the enzymatic properties to survive in molecules following cleavage of the polymer chain. Radiation target size for loss of monomers yielded the mass of monomers indicating a polypeptide chain cleavage after a radiation interaction anywhere in the monomer. Loss of enzymatic activity yielded a much smaller mass indicating a robust structure in which catalytic activity could be expressed in cleaved polypeptides.     

Enzymic imbalance in serine metabolism in rat hepatomas.

The renaturation of the tetrameric enzyme phosphoglycerate mutase from baker's yeast after denaturation in guanidinium chloride was studied. Three proteinases (trypsin, chymotrypsin and thermolysin) cause extensive loss of activity of samples taken during the early stages of refolding. As judged by SDS/polyacrylamide-gel electrophoresis, the proteinases cause substantial degradation of the polypeptide chain with no evidence for large quantities of fragments of Mr greater than 6500. These data suggest that the early intermediates in the refolding, especially the folded monomer, possess a number of sites that are susceptible to proteolysis.     

Structure of tetanus toxin. I. Breakdown of the toxin molecule and discrimination between polypeptide fragments.

Tetanus toxin was digested with papain, yielding one major polypeptide (Fragment C) with a molecular weight corresponding to 47,000 +/- 5%, thus comprising about one-third of the toxin molecule. Fragment C was antigenically active, atoxic, and stimulated the formation of antibodies neutralizing the lethal action of tetanus toxin in vivo. Furthermore, a second split product (Fragment B) was isolated from the papain digest, containing two polypeptide chains linked together via a disulfide bond. Fragment B (Mr = 95,000 +/- 5%) was atoxic and showed a reaction of nonidentity with Fragment C on immunodiffusion analysis against tetanus antitoxin. The basic two-chain structure (heavy and light chain polypeptide, cf. Matsuda, M., and Yoneda, M. (1975) Infect. Immun. 12, 1147-1153) of tetanus toxin has been confirmed and the relationship between Fragments B and C within this framework has been established. Fragment C was distinguished from the light chain by electrophoresis in sodium dodecyl sulfate and by immunodiffusion analysis, indicating that this fragment constitutes a portion of the heavy chain polypeptide. Fragment B showed a reaction of partial identity with the light as well as the heavy chain from tetanus toxin. Reduction of Fragment B with dithiothreitol followed by gel chromatography yielded a fraction which was indistinguishable from the light chain portion of the toxin molecule. It is concluded that Fragment B comprises the complementary portion of the heavy chain (remaining after scission of the polypeptide bond(s) releasing Fragment C) linked to the light chain by a disulfide bond.     

A stable prostacyclin-like substance produced by the medicinal leech Hirudo medicinalis.

The medicinal leech Hirudo medicinalis produces a low-molecular mass compound with properties similar to those of prostacyclin. It extracted with organic solvent, had affinity to 6-keto-PGF1alpha antibodies, inhibited human platelet aggregation induced in vitro by thrombin (by 50% at 4 pg/ml), and caused hypotension and secretion of plasminogen (t-PA) into the blood stream of rats. A main distinction from prostacyclin is stability of the substance due to covalent binding with the polypeptide chain of destabilase. Because of the high aggregability of destabilase, the molecules of the protein-lipid complex are organized into micelles that can change their spatial orientation depending on the nature of the solvent. Incorporation of hirudin and blood plasma kallikrein inhibitor into the micelle structure causes the formation of liposomes (with a molecular mass of the structural monomer 25 kDa). This complex with polypeptides provides not only stability but also rapid transmembrane penetration. The pure prostacyclin-like substance has a molecular mass of 391 Da and can be produced on destruction of the destabilase polypeptide chain.     

A two-active site one-polypeptide enzyme: the isomaltase from sea lion small intestinal brush-border membrane. Its possible phylogenetic relationship with sucrase-isomaltase

The enzyme responsible for all of the isomaltase activity and much of the maltase activity in the small intestine of the Californian sea lion (Zalophus californianus) was isolated by detergent solubilization of the brush-border membrane, followed by immunoadsorption chromatography using antibodies directed against rabbit sucrase-isomaltase. In 0.1% Triton X-100, sea lion isomaltase occurs as a monomer of Mr = 245,000 and is composed of a single polypeptide chain. As judged from the stoichiometry of the covalent binding of the affinity label, conduritol-B-epoxide, this polypeptide chain carries two enzymatically active sites; they are apparently identical and do not show either positive or negative cooperativity. In addition to cross-reacting immunologically with rabbit sucrase-isomaltase, sea lion isomaltase has similar overall enzymatic properties, with the exception of not hydrolyzing sucrose. The Alaskan fur seal (Collarhinus ursinus) has a two-active site isomaltase; however, in contrast to the sea lion, this animal is endowed with a small but significant sucrase activity. Along with (fully active) pro-sucrase-isomaltase, sea lion isomaltase is one of the very few examples of enzymes with more than one active site on a single polypeptide chain acting "in parallel" (rather than "in series"). Furthermore, this enzyme triggers some interesting questions on the phylogenetical pedigree of small intestinal sucrase-isomaltase.     

Nicotinamide adenine dinucleotide-specific glutamate dehydrogenase of Neurospora crassa. IX. Isolation and sequences of several large cyanogen bromide peptides.

The isolation and sequences of several large peptides from cyanogen bromide cleavage of the 1030-residue polypeptide chain of the NAD-specific glutamate dehydrogenase of Neurospora crassa are described. One of these is in the 669-residue sequence of the COOH-terminal end of the protein. The remaining peptides have been aligned in two partial sequences in the NH2-terminal portion of the polypeptide chain.     

Solution studies on heme proteins. Circular dichroism and optical rotation of Glycera dibranchiata hemoglobins

Circular dichroism (CD) and optical rotatory dispersion (ORD) spectra of several liganded derivatives of the monomer and polymer hemoglobin components of the marine annelid, Glycera dibranchiata were measured over the wavelength range 650--195 nm. The differences observed between the monomer and polymer components for the heme dichroic bands in the visible, Soret and ultraviolet wavelength regions seem to result from changes in the heme environment, geometry and coordination state of the central heme iron in these proteins. Within the Soret region, the liganded derivatives of the monomer hemoglobin exhibit predominantly negative circular dichroic bands. The heme band at 260 nm is also absent for the monomer hemoglobin. The ORD and CD spectra in the far-ultraviolet, peptide absorbing region suggest also differences in the alpha-helix content of the monomer and polymer hemoglobins. The values for the single-chain G. dibranchiata hemoglobin are in the expected range (about 70% alpha-helix) as predicted by the X-ray structure of this protein. The lower estimates of the alpha-helix content for the polymer hemoglobin (approx. 50%), may reflect the differences in amino acid composition, primary structure and polypeptide chain foldings. Changes in oxidation state and ligand binding appears to have no pronounced effect on the helicity of either the monomer or polymer hemoglobins. The removal of the heme moiety from the monomer hemoglobin did result in a major decrease in its helix content similar to the loss of heme from myoglobin.     

The amino acid sequence of human insulin-like growth factor I and its structural homology with proinsulin

The complete amino acid sequence of human insulin-like growth factor I (IGF-I), a polypeptide isolated from serum, has been determined. IGF-I is a single chain polypeptide of 70 amino acid residues cross-linked by three disulfide bridges. The calculated molecular weight is 7649. IGF-I displays obvious homology to proinsulin: positions 1 to 29 are homologous to insulin B chain and positions 42 to 62 to insulin A chain. A shortened "connecting" peptide with 12 residues (positions 30 to 41) compared to 30 to 35 in proinsulins shows no homology to proinsulin C peptide. An octapeptide sequence at the COOH-terminal end is also a feature not found in proinsulins. The number of differences in amino acid positions between IGF-I and insulins suggests that duplication of the gene of the common ancestor of proinsulin and IGF occurred before the time of appearance of the vertebrates. Of the 19 residues known to be invariant in all insulins so far sequenced, only glutamine A5 and asparagine A21 are replaced in IGF-I by glutamic acid and alanine, respectively. The fact that all half-cystine and glycine residues and most nonpolar core residues of the insulin monomer are conserved is compatible with a three-dimensional structure of IGF-I similar to that of insulin.