Interruptions of (CG)n sequences by GG, TG and CA need not prevent B to Z transition in solution

Oligonucleotides containing alternating purines-pyrimidines with AT base pairs have been shown to exist in the Z-form preferably in solid state. We report that oligodeoxyribonucleotides with GG, TG and CA interruptions in their alternating CG sequences can undergo B to Z transition in solution in the absence of any chemical modification or topological constraint. The sequences, d(CGCGCGGCGCGC) and d(CGTGCGCACG) have been synthesised and shown to adopt Z- conformation in presence of millimolar concentrations of Ni2+ under low water activity conditions. Significance of GG, TG and CA interruptions in the B to Z transition is discussed.

Linear gramicidin activates neutrophil functions and the activation is blocked by chemotactic peptide receptor antagonist

The activation of functional responses in rabbit peritoneal neutrophils by gramicidin and the chemotactic peptide, N-formyl-methionyl-leucyl-phenylalanine methyl ester, was studied. Gramicidin activated superoxide generation, lysosomal enzyme release and a decrease in fluorescence of chlortetracycline-loaded cells, as for the chemotactic peptide. The maximum intensities of the responses by gramicidin were lower than that by chemotactic peptide. Responses by both these peptides could be inhibited by t-butyloxycarbonyl-methionyl-leucyl-phenylalanine, a chemotactic peptide receptor antagonist. Gramicidin gave responses at low doses comparable to that of the chemotactic peptide.

Beta-turns in nascent procollagen are sites of posttranslational enzymatic hydroxylation of proline

The selective hydroxylation of proline residues in nascent procollagen chains by prolyl hydroxylase (EC 1.14.11.2) can be understood in terms of the conformational feature of the -Pro-Gly-segments in linear peptides and globular proteins. The folded beta-turn conformation in such segments appears to be the conformational requirement for proline hydroxylation. The available data on the hydroxylation of native and synthetic substrates of prolyl hydroxylase are explained on the basis of the extent of beta-turn formation in them. Taken in conjunction with the conformational features of the hydroxyproline residue, our results bring out the conformational reason for the posttranslational proline hydroxylation which, it is proposed, leads to the "straightening" of the beta-turn segments into the linear triple-helical conformation.

Molecular conformation of alamethicin in dimethylsulfoxide solution A two-dimensional n.m.r. study

The solution conformation of alamethicin, a 20-residue antibiotic peptide, has been investigated using two-dimensional n.m.r. spectroscopy. Complete proton resonance assignments of this peptide have been carried out using COSY, SUPERCOSY, RELAY COSY and NOESY two-dimensional spectroscopies. Observation of a large number of nuclear Overhauser effects between sequential backbone amide protons, between backbone amide protons and CβH protons of preceding residues and extensive intramolecular hydrogen bonding patterns of NH protons has established that this polypeptide is in a largely helical conformation. This result is in conformity with earlier reported solid state X-ray results and a recent n.m.r. study in methanol solution (Esposito et al. (1987) Biochemistry26, 1043-1050) but is at variance with an earlier study which favored an extended conformation for the C-terminal half of alamethicin (Bannerjee et al.

Conformational analysis of the right-hand twisted antiparallel β-Structure

The conformational analysis of a pair of two-linked peptide units in the anti-parallel arrangement is reported here with a view to study the effect of association of one chain with the other. The pair of two-linked peptide units were fixed in space through the hydrogen bonds between them, in accordance with certain hydrogen bond criteria. Model building was undertaken to ascertain whether the proximity of the side-chains could be used to eliminate any one of the right-hand twisted, left-hand twisted or regular β-structures. Stereochemically, it was found possible with all of them. The preference for a right-hand twisted β-structure, however, was indicated by the classical energy calculations. The relevance of the results thus obtained is discussed in the context of the preferential right-hand twist of the β-pleated sheets present in globular proteins. The agreement between the minimum energy conformations obtained for the pair of two-linked peptide units and the globular protein data is also indicated.

Successive refinement of structures with data of increasing resolution: a theoretical study for triclinic space groups

The method of least squares could be used to refine an imperfectly related trial structure by adoption of one of the following two procedures: (i) using all the observed at one time or (ii) successive refinement in stages with data of increasing resolution. While the former procedure is successful in the case of trial structures which are sufficiently accurate, only the latter has been found to be successful when the mean positional error (i.e.<|[Delta]r|>) for the atoms in the trial structure is large. This paper makes a theoretical study of the variation of the R index, mean phase-angle error, etc. as a function of <|[Delta]r|> for data corresponding to different esolutions in order to find the best refinement procedure [i.e. (i) or (ii)] which could be successfully employed for refining trial structures in which <|[Delta]r|> has large, medium and low values. It is found that a trial structure for which the mean positional error is large could be refined only by the method of successive refinement with data of increasing resolution.