Charged End Groups Research Articles

Interaction of synthetic analogues of distamycin and netropsin with nucleic acids. Does curvature of ligand play a role in distamycin-DNA interactions?

Distamycin and netropsin, a class of minor groove binding nonintercalating agents, are characterized by their B-DNA and A-T base-specific interactions. To understand the conformational and chemical basis of the above specificities, the DNA-binding characteristics of a novel synthetic analogue of distamycin have been studied. The analogue, mPD derivative, has the requisite charged end groups and a number of potential hydrogen-bonding loci equal to those of distamycin. The difference in the backbone curvatures of the ligands, distamycin, the mPD derivative, and NSC 101327 (another structurally analogous compound), is a major difference between these ligands. UV and CD spectroscopic studies reported here show the following salient features: The mPD derivative recognizes only B-DNA, to which it binds via the minor groove. On the other hand, unlike distamycin, it binds with comparable affinities to A-T and G-C base pairs in a natural DNA. These DNA-binding properties are compared with those reported earlier for distamycin and NSC 101327 [Zimmer, Ch., & Wahnert, U. (1986) Prog. Biophys. Mol. Biol. 47, 31-112]. The backbone structures of these three ligands were compared to show the progressive decrease in curvatures in the order distamycin, mPD derivative, and NSC 101327. The plausible significance of the backbone curvature vis-à-vis the characteristic B-DNA and AT-specific binding of distamycin is discussed. To our knowledge, this is the first attempt (with a model synthetic analogue) to probe the possible influence of backbone curvature upon the specificity of interactions of the distamycin class of groove-binding ligands with DNA.

Netropsin, a DNA-binding oligopeptide structural and binding studies

The crystal structure of netropsin, an oligopeptide which binds to DNA, has been determined. The molecule is bowed with the amide groups on the concave side, and the carbonyl and methyl groups on the convex side. The amide groups participate in extensive hydrogen bonding with water molecules; the charged amino end groups interact with the sulfate anions. Binding of netropsin to poly(dA) · poly(dT) under conditions of different ionic strength was also studied. Utilizing the crystallographic as well as the binding data, it is possible to build a model which explains the specificity of this antibiotic.

Kinetic mechanism and specificity of the phosphorylase kinase reaction.

The kinetic mechanism of the phosphorylase kinase reaction was studied using a synthetic tetradecapeptide and phosphorylase b as substrates. The synthetic peptide contained the amino acid sequence, Se+Asp-Gln-Glu-LysArg1”-Lys-Gln-Ile-Ser-Va115-Arg-Gly-Leu as found in rabbit muscle phosphorylase 6. From initial rate studies and from the use of substrate analogs as competitive inhibitors, it was determined that the initial rate data were consistent with the Random Ri Ri mechanism for the phosphorylase kinase reaction. Although the synthetic tetradecapeptide appeared to be a good substrate for phosphorylase kinase (V, was only one-half of that with phosphorylase b as substrate), the K, of the peptide was 75-fold larger than the K,, of phosphorylase b. Various peptide analogs of the synthetic substrate were used to study the effect of size, charge at the NH,-terminal and the COOH-terminal residue, and substitution of arginine-16 on the kinetic parameters of activated phosphorylase kinase. Deletion of the first 4 residues and charged end groups on the peptide affected the rate of phosphorylation. Replacement of arginine-16 with a conservative or nonconservative substitution affected both the K, and rate of phosphorylation. A cyanogen bromide fragment derived from and containing the NH,-terminal segment of phosphorylase was tested for its ability to serve as substrate for activated phosphorylase kinase. The K,,, for activated phosphorylase kinase was intermediate for that of tetradecapeptide and phosphorylase b, while the V,,, was lower than with tetradecapeptide as substrate.

Conformational changes of polypeptides in intense electric fields.

AbstractEmploying a simple “all or none” statistical theory, a calculation is given of the phase diagram in electric field–temperature space for the helix–coil transition of a polypeptide with nonpolar residues but charged end groups. The principal results are (i) the transition field extrapolated to absolute zero is on the order of millions of volts per centimeter, (ii) the normal transition temperature of large molecules is predicted to be significantly affected by fields as low as 30,000 V/cm, and (iii) for temperatures just above the helix‐coil transition temperature, the application of a field to a large molecule causes an initial transition to the helix state and with a further isothermal increase of field the coil state returns. The theory is extended to the case of the unfolding of a globular protein in an electric field. The fields are somewhat lower than those for the helix‐coil transition and are always single‐valued at a given temperature. Lastly the effect of including the presence of charged residues is shown to decrease the estimated critical fields but keep them of the same order of magnitude as those given for the case of nonpolar residues.

Studies on aqueous dextran-poly(ethylene glycol) two-phase systems containing charged poly(ethylene glycol) I. Partition of albumins

1. 1. Methods for the synthesis of trimethylamino-poly(ethylene glycol) and poly(ethylene glycol)-sulfonate are described. 2. 2. Three albumins have been partitioned in a dextran-poly(ethylene glycol)-water system, containing different amounts of poly(ethylene glycol) with charged end-groups. It is shown that the partition of proteins is strongly affected by the charged poly(ethylene glycol), and in opposite ways when the net charge of the protein changes sign.

The composition and some structural features of the principal gastric glycoprotein.

Gel chromatography on Sephadex G150 or Bio-gel P150 resolved the gastric secretions into three fractions. The non-retarded fraction contained 70–90% of the total carbohydrate eluted in the three fractions. The gastric secretions before gel filtration and the non-retarded fraction contained the same carbohydrate residues and the three carbohydrate components, galactose, glucosamine and galactosamine, in the same quantitative proportions. The amino-acid composition of the non-retarded fraction showed marked similarities and characteristic quantitative relationships. Threonine and serine were found to constitute 45–50% of the total aminoacid content. The analytical data, ultracentrifugation and light scattering studies suggest that the non-retarded fraction is composed of macromolecules which have a common basic composition but which are polydisperse with reference to their charged end groups, fucose and size.

Rates of termination in polymerizations initiated by benzoyl peroxide and by ammonium persulfate

AbstractPolymerizations of styrene have been carried out in solution using as initiators benzoyl peroxide or ammonium persulfate. It has been shown that the ammonium persulfate initiated polymerizations proceed at a faster rate and produce polymers of higher molecular weight than those initiated by benzoyl peroxide, although all the conditions for polymerization remained identical in both cases. This behavior is explained in terms of a reduced rate of termination. It is suggested tentatively that the reduction in the rate of termination may be due to the mutual electrostatic repulsion of the chains caused by the presence of electrically charged end groups arising from initiation by the sulfate ion radical. Calculations are presented showing the essential conditions that have to be fulfilled to make the explanation tenable.