Journal of Protein Chemistry

We examined the dephosphorylation of p36, a protein ofD. discoideum that has previously been shown to be phosphorylated in a GDP-dependent manner (Anschutzet al., 1989). Specific dephosphorylation of p36 was found to occur in cell preparations but the activity responsible was strongly dependent upon the concentration of proteins in those extracts. When preparations were diluted, this activity was no longert detectable and the radiolabeled phosphate incorporated into p36 was stable. In contrast, p36 phosphorylation was seemingly unaffected by this treatment. Under the conditions where endogenous dephosphorylating activity was not detectable, the addition of GDP to the reaction resulted in substantial dephosphorylation of p36. The stimulation of this dephosphorylation process occurred at concentrations of GDP that were distinct from those that led to an increased p36 phosphorylation due to the previously reported stimulation of p36 protein kinase activity. Characterization of the dephosphorylation of p36 indicates that the same enzyme is responsible for the endogenous and GDP-stimulated activities. Additionally, these activities are identical when assayed with p36 that had been phosphortylated with ATP or GTP. In contrast to p36 kinase activity, the dephosphorylation of p36 did not display any developmental changes with respect to its regulatory features.

Chloride ion is a major allosteric regulator for many hemoglobins and particularly for bovine hemoglobin. A site-directed reagent for amino groups, methyl acetyl phosphate, when used forglobal rather thanselective modification of R (oxy) and T (deoxy) state bovine hemoglobin, can acetylate those functional amino groups involved in binding of chloride; the extensively acetylated hemoglobin tetramer retains nearly full cooperativity. The chloride-induced decrease in the oxygen affinity parallels the acetylation of bovine hemoglobin (i.e., their effects are mutually exclusive), suggesting that methyl acetyl phosphate is a good probe for the functional chloride binding sites in hemoglobins. Studies on theoverall alkaline Bohr effect indicates that the part of the contribution dependent on chloride and reduced by 60% after acetylation is due to amino groups, Val-1(α) and Lys-81(β); the remaining 40% is contributed by the imidazole side chain of His-146(β), which is not acetylated by methyl acetyl phosphate, and is not dependent on chloride. The five amino groups—Val-1(α), Lys-99(α), Met-1(β), Lys-81(β), and Lys-103(β)—of bovine hemoglobin that are acetylated in an oxygen-linked fashion are consideredfunctional chloride binding sites. Molecular modeling indicates that these functional chloride binding sites are contiguous from one end of the central cavity of hemoglobin to the other; some of them are aligned within a chloride channel connecting each end of the dyad axis. A generalization that can be made about hemoglobin function from these studies is that the blocking of positive charges within this channel either by binding of chloride or other anions, by covalent chemical modification such as acetylation, or by site-specific mutagenesis to create additional chloride binding sites each accomplish the same function of lowering the oxygen affinity of hemoglobin.

In the present study on enzymatic peptide bond formation the proteosynthetic potential of several proteases was explored. Trypsin, α-chymotrypsin, papain, carboxypeptidase Y (CPD-Y), and thermolysin served as catalysts for the protease-controlled synthesis of some fragments of melanocyte-stimulating hormones. To obviate possible proteolytic cleavage of preexisting peptide bonds—a drawback often encountered during enzymatic peptide syntheses—several expedients leading to the target peptides were developed. The enzymatic procedure enabled under mild conditions the preparation of the desired peptides whose amino acid composition may give rise to severe complications during conventional syntheses.

An improved multiple linear regression (MLR) method is proposed to predict a protein's secondary structural content based on its primary sequence. The amino acid composition, the autocorrelation function, and the interaction function of side-chain mass derived from the primary sequence are taken into account. The average absolute errors of prediction over 704 unrelated proteins with the jackknife test are 0.088, 0.081, and 0.059 with standard deviations 0.073, 0.066, and 0.055 for α-helix, β-sheet, and coil, respectively. That the sum of predicted secondary structure content should be close to 1.0 was introduced as a criterion to evaluate whether the prediction is acceptable. While only the predictions with the sum of predicted secondary structure content between 0.99 and 1.01 are accepted (about 11% of all proteins), the absolute errors are 0.058 for α-helix, 0.054 for β-sheet, and 0.045 for coil.

Clostridial neurotoxins are the most powerful toxins known. Nevertheless, derivatives of these toxins may find broad applications both in science and medicine because of their unique abilities to recognize neurons and deliver small and large molecules into them. In this paper we describe the construction of two types of such derivatives. Proteins belonging to the first class were designed to allow direct conjugation with one or few molecules of interest. Proteins belonging to the second class contain biotin residue and therefore could be easily connected to streptavidin loaded with multiple molecules of interest. Only C-terminal regions of neurotoxin heavy chains were incorporated in the structure of recombinant proteins. Nevertheless, recombinant proteins were found to be able to recognize specific neuronal receptors and target model molecules to rat synaptosomes and human neuroblastoma cells.

Botulinum neurotoxin (NT) serotype A is a ∼150-kDa dichain protein. Posttranslational nicking of the single-chain NT (residues Pro 1–Leu 1295) by the protease(s) endogenous to Clostridium botulinum excises 10 residues, leaving Pro 1–Lys 437 and Ala 448–Leu 1295 in the ∼50-kDa light (L) and ∼100-kDa heavy (H) chains, respectively, connected by a Cys 429–Cys 453 disulfide and noncovalent bonds [Krieglstein et al. (1994), J. Protein Chem. 13, 49–57]. The L chain is a metalloprotease, while the amino- and carboxy-terminal halves of the H chain have channel-forming and receptor-binding activities, respectively [Montecucco and Schiavo (1995), Q. Rev. Biophys. 28, 423–472]. Endoproteinase Glu-C and α-chymotrypsin were used for controlled digestion at pH 7.4 of the ∼150-kDa dichain NT and the isolated ∼100-kDa H chain (i.e., freed from the L chain) in order to map the cleavage sites and isolate the proteolytic fragments. The dichain NT appeared more resistant to cleavage by endoproteinase Glu-C than the isolated H chain. In contrast, the NT with its disulfide(s) reduced showed rapid digestion of both chains, including a cleavage between Glu 251 and Met 252 (resulting in ∼30- and ∼20-kDa fragments of the L chain) which was not noted unless the NT was reduced. Interestingly, an adjacent bond, Tyr 249–Tyr 250, was noted earlier [DasGupta and Foley (1989), Biochimie 71, 1193–1200] to undergo “self-cleavage” following reductive separation of the L chain from the H chain. The site Tyr–Tyr–Glu–Met (residues 249–252) appears to become exposed following reduction of Cys 429–Cys 453 disulfide. Identification of Glu 669–Ile 670 and Tyr 683–Ile 684 as protease-susceptible sites demonstrated for the first time that at least two peptide bonds in the segment of the H chain (residues 659–684), part of which (residues 659–681) is thought to interact with the endosomal membranes and forms channels [Oblatt-Montal et al., (1995), Protein Sci. 4, 1490–1497], are exposed on the surface of the NT. Two of the fragments of the H chain we generated and purified by chromatography are suitable for structure–function studies; the ∼85- and ∼45-kDa fragments beginning at residue Leu 544 and Ser 884, respectively (both extend presumably to Leu 1295) contain the channel-forming segment and receptor-binding segments, respectively. In determining partial amino acid sequences of 10 fragments, a total of 149 amino acids in the 1275-residue NT were chemically identified.

To investigate the structure ofEscherichia coli ribosomal protein S13 in 30S ribosomal subunits, we have previously generated 22 S13 specific monoclonal antibodies and mapped their specific epitopes to the S13 sequence. The availability of these S13 epitopesin situ has been further examined by incubating these monoclonal antibodies with 30S ribosomal subunits and analyzing formation of monoclonal antibody-linked ribosome dimers by sucrose gradients centrifugation. We have found that none of the 22 monoclonal antibodies makes ribosome dimers individually as do typical antisera. However, one monoclonal antibody, designated AS13-MAb 2, reacts with 30S ribosomal subunits to form immunocomplexes sedimenting faster than subunit monomers. When AS13-MAb 2 is paired with any one of three monoclonal antibodies directed to the S13 C-terminal epitopes, dimer formation is observed. Other pairs of monoclonal antibodies directed to distinct S13 epitopes have been tested similarly for dimer formation. Monoclonal antibody AS13-MAb 22, directed to the N-terminal region of 22 residues, also causes subunits to form typical dimers, but only if paired with one of the three monoclonal antibodies directed to the S13 C-terminal region. The close proximity of the epitopes recognized by AS13-MAbs 2 and 22 has been established by the mutual competition between the antibodies binding to intact 30S subunits. These results corroborate our previous observation, using polyclonal antibodies, that S13 has more than one epitope exposed on 30S subunits. Our finding that sequences on both ends of the S13 molecule are immunochemically accessible provides information about the molecular organization of S13in situ.

IKP104, a novel antimitotic drug, has two classes of binding sites on bovine brain tubulin with different affinities. IKP104, by itself, enhances the decay of tubulin, but in the presence of colchicine or podophyllotoxin, it stabilizes tubulin instead of opening up the hydrophobic areas [Luduena et al. (1995), Biochemistry 34, 15751–15759], Here, we have dissected these two apparently contradictory effects of IKP104 by cleaving the C-terminal ends of both α and β subunits of tubulin with subtilisin. We have found that the selective removal of the C-terminal ends from both the α and β subunits of αβ tubulin lowers the sulfhydryl titer by approximately 1.5 mol/mol of dimer. Interestingly, IKP104 does not increase either the sulfhydryl liter or the exposure of hydrophobic areas of this subtilisin-treated tubulin (αsβs). Moreover, IKP104 lowers the sulfhydryl titer of αsβs tubulin approximately by 1 mol/mol and appears to inhibit completely the time-dependent decay of αsβs tubulin. The cleavage at the C-terminal ends of both α and β modulates the effect of IKP104 on the β subunit, but not on the α subunit. Fluorometric binding data analysis suggests that IKP104 binds to the αsβs tubulin only at the high-affinity site; the low-affinity site(s) disappear almost completely. The sulfhydryl titer data for α and β and the fluoromelric data therefore suggest that the interaction of IKP104 at the high-affinity site on tubulin is not regulated by the C-terminal domains of α and β and the effect of the high-affinity site is restricted largely to the α subunit, while the low-affinity-site binding is modulated by the C-terminal domain of β. It also appears that the stabilization and the acceleration of the decay of tubulin are mediated by distinct interactions of IKP104 with its high- and low-affinity sites on tubulin, respectively.

The thermal stability of acid-soluble collagens was studied by circular dichroism (CD) spectroscopy. Adult bovine dermal collagen (BDC), rat-tail tendon collagen (RTC), and calf skin collagen (CSC) were compared. Despite some variability in amino acid composition and apparent molecular weight, the CD spectra for helical and unordered collagen structures were essentially the same for all the sources. The melting of these collagens occurs as a two-stage process characterized by a pretransition (T p) followed by complete denaturation (T d). The characteristic temperatures vary with the source of the collagen; for mature collagens (BDC, RTC) T p = 30°C and T d = 36deg;C, and for CSC T p = 34°C and T d = 40°C. Neutral salts, NaCl or KCl, at low concentrations (0.02–0.2 M) appear to bind to the collagens and shift the thermal transitions of these collagens to lower temperatures.