Search PubMed⌕ Search

Biomedical subjects

D A Phoenix

Publications and source records attributed to D A Phoenix.

At least 37 records · Page 2Linked to original sources
PubMed1998

The Escherichia coli low molecular mass penicillin-binding proteins and a putative membrane bound protein complex.

The Escherichia coli low molecular mass penicillin-binding proteins are enzymes associated with the periplasmic face of the inner membrane. This mini review discusses the membrane anchoring of these enzymes and their possible participation in a putative membrane bound protein complex involved in the regulation of peptidoglycan biosynthesis. The identification of such a complex may lead to the identification of new sites of action for antibacterial compounds.

Amino Acid Sequence↗
PubMed1998

The hydrophobic moment plot and its efficacy in the prediction and classification of membrane interactive proteins and peptides.

The central premise of hydrophobic moment plot methodology is that primary sequence information alone may be used to differentiate between amphiphilic structures which are likely to belong to either surface active or globular proteins. However, the boundaries delineating the regions of the plot appear to be based on information derived from a relatively small protein data set and are not well defined. This, coupled with the uncertainties associated with interpretation of the significance of the hydrophobic moment has led the reliability of this methodology to be questioned with respect to predicting membrane interactions. Accordingly, we have used hydrophobic plot methodology to predict the cellular locations of an expanded set of proteins with known membrane location, including those of the original study. The accuracy of prediction was subjected to chi-square statistical analysis and here we discuss the conclusion that the predictive abilities of this methodology are no better than chance.

Algorithms↗
PubMed1997

Alpha-helical conformation in the C-terminal anchoring domains of E. coli penicillin-binding proteins 4, 5 and 6.

The E. coli low molecular mass penicillin-binding proteins (PBP's) are penicillin sensitive, enzymes involved in the terminal stages of peptidoglycan biosynthesesis. These PBP's are believed to anchor to the periplasmic face of the inner membrane via C-terminal amphiphilic alpha-helices but to date the only support for this hypothesis has been obtained from theoretical analysis. In this paper, the conformational behaviour of synthetic peptides corresponding to these C-terminal anchoring domains was studied as a function of solvent, pH, sodium dodecyl sulphate micelles and phospholipid (DOPC, DOPG) vesicles using circular dichroism (CD) spectroscopy. The CD data showed that in 2,2,2-trifluoroethanol or sodium dodecylsulphate, all three peptides have the capacity to form an alpha-helical conformation but in aqueous solution or in the presence of phospholipid vesicles only those peptides corresponding to the PBP5 and PBP6 C-termini were observed to do so. A pH dependent loss of alpha-helical conformation in the peptide corresponding to the PBP5 C-terminus was found to correlate with the susceptibility of PBP5 to membrane extraction. This correlation would agree with the hypothesis that an alpha-helical conformation is required for membrane interaction of the PBP5 C-terminal region.

Amino Acid Sequence↗
PubMed1997

Evidence of rare codon clusters within Escherichia coli coding regions.

It is known that there is a high occurrence of rare codons at the start of coding region. Here it is shown that although the remainder of the gene is likely to contain a relatively low number of rare codons, rare and non-rare codons do not form a random sequence. It is apparent that throughout the coding region there is a higher than expected number of rare codon clusters. For example once a rare codon has occurred there is a greater chance than expected of the next six codons containing another rare codon. This non-random distribution implies that rare codons may have an as yet unidentified biological role.

Base Sequence↗
PubMed1997

An investigation into the ability of C-terminal homologues of Escherichia coli low molecular mass penicillin-binding proteins 4, 5 and 6 to undergo membrane interaction.

The Escherichia coli low molecular mass penicillin-binding proteins (PBP4, PBP5 and PBP6) are a group of penicillin-sensitive enzymes involved in the final stages of cell wall assembly. It has been suggested that these proteins may interact with the periplasmic face of the inner membrane via C-terminal amphiphilic alpha-helices. Theoretical analysis has predicted that these C-terminal helical regions may be membrane interactive. We have tested this hypothesis by assaying PBP C-terminal homologues (P4, P5 and P6) for haemolytic activity. Our results show that the PBP5 and PBP6 C-terminal homologues readily lyse sheep erythrocytes in a pH-dependent manner with LD50's of 3.5 x 10(-6) M and 6.8 x 10(-7) M respectively at pH 7. These results appear to support the present model for the membrane anchoring of PBP5 and PBP6. The PBP4 C-terminal homologue shows no evidence of haemolytic activity which could imply a different means of membrane association for PBP4.

Amino Acid Sequence↗
PubMed1997

Increased cytotoxicity and phototoxicity in the methylene blue series via chromophore methylation.

The cytotoxic and photodynamic activities of the commercially-available biological stains methylene blue (MB), 1,9-dimethyl MB (Taylor's Blue) and a newly synthesised compound, 1-methyl MB, were measured against the murine mammary tumour cell line, EMT-6. Both 1-methyl MB and 1,9-dimethyl MB exhibited increased dark toxicity with concomitant higher phototoxicity compared to MB at a light dose of 7.2 J cm-2. While increasing the light dose as a function of the fluence rate increased the photocytotoxicity of MB, this had little effect on the methylated derivatives. In vitro chemical testing proved that successive methylation rendered the phenothiazinium chromophore both more resistant to reduction to its inactive leuco form, and also led to increased levels of singlet-oxygen production, thus providing a possible explanation for the increased toxicities of the methylated derivatives. Comparisons are made with the benzo[a]phenothiazinium photosensitizer, EtNBS.

Animals↗
PubMed1997

An algorithm for the detection of surface-active alpha helices with the potential to anchor proteins at the membrane interface.

MOTIVATION: Surface-active peptides are amphiphilic in nature and have been shown to have the potential to interact at the membrane interface, possibly by lying parallel to the membrane surface. Present methodology for the identification of these helices uses a fixed window size, is based on a two-dimensional sum of hydrophobicity vectors and gives no measure of the statistical significance for any region identified as amphiphilic. Identification of weakly surface-active structures is difficult and here we have attempted to remedy this by introducing an algorithm which considers three-dimensional geometries and variable window size. RESULTS: A new measure of membrane-interactive potential is proposed, called the depth-weighted inserted hydrophobicity (DWIH), which is based on the sequestration of hydrophobic residues within a hydrophobic compartment, such as that produced by a membrane bilayer. A statistical significance for this measure has been derived using Monte Carlo techniques. The algorithm is applied to a set of proteins which are thought to anchor to the membrane via C-terminal amphiphilic alpha helices. The DWIH measure appears to allow the identification of this category of membrane-interactive helices which lie near the boundary of the hydrophobic moment plot and which have previously been hard to classify.

Algorithms↗
PubMed1997

In-vitro photobactericidal activity of aminoacridines.

The toxicities of several aminoacridines were measured against pathogenic strains of both Gram-positive (Staphylococcus aureus, Enterococcus faecalis, Bacillus cereus) and Gram-negative (Escherichia coli, Pseudomonas aeruginosa) organisms. In several cases, illumination at a light dose of 6.3 J/cm2 resulted in considerable decreases in the minimum lethal drug concentrations required, giving up to 50-fold increases in bactericidal activity. Derivatives of 9-aminoacridine (aminacrine) exhibited phototoxicity against one or more of the test organisms, but the established photosensitizing acridines proflavine and acridine orange were photobactericidal against all strains.

Aminoacridines↗
PubMed1997

A study of photobactericidal activity in the phenothiazinium series.

The photodynamic antibacterial properties of a closely related series of commercially available phenothiazinium dyes were tested against a range of pathogenic strains of Gram-positive (Staphylococcus aureus, Enterococcus faecalis, Bacillus cereus) and Gram-negative organisms (Escherichia coli, Pseudomonas aeruginosa). The photosensitisers were illuminated using a non-laser light source at a fluence of 1.75 mW cm-2 and this resulted in the enhancement of antibacterial activity in liquid culture. In several cases, illumination resulted in considerable decreases in the minimum lethal concentrations required, giving up to 100-fold increases in bactericidal activity.

Acridine Orange↗
PubMed1997

MIRs are present in coding regions of human genes.

By using a weighted function and the method of enlarged similarity a search has been performed to identify mammalian interspersed repeats (MIRs) in DNA sequences from the EMBL data bank. The existence of MIRs is shown in coding regions of human genes and also in chicken and duck genomes. It is possible to conclude from the results obtained that MIRs were established in the coding regions of some genes and may have taken part in gene evolution. Furthermore, MIRs may have been amplified in vertebrate genomes before the origin of mammals.

Algorithms↗
PubMed1997

Latent periodicity of DNA sequences of many genes.

A method of latent periodicity search being developed. Mutual information is used to reveal of DNA or mRNA sequence latent periodicity. The latent periodicity of DNA sequence is a periodicity with low level of homology between any two periods inside DNA sequence. The mutual information between artificial numerical sequence and DNA sequence is calculated. The length of the artificial sequence period is varied from 2 to 150. The high level of the mutual information between artificial and DNA sequences allows to find any type of latent periodicity of DNA sequence. The latent periodicity of many DNA coding regions has been found. Potential significance of latent periodicity is discussed.

Base Sequence↗
PubMed1996

On the targeting and membrane assembly of the Escherichia coli outer membrane porin, PhoE.

Within gram-negative bacteria such as Escherichia coli, the outer membrane porins provide a relatively non-specific uptake route which is utilised by a wide range of solutes including many antibiotics. Understanding the targeting and membrane assembly of these proteins is therefore of importance and this mini review aims to discuss this process in light of present knowledge.

Bacterial Proteins↗
PubMed1996

Development of a bacterial model for studying anthracycline-membrane interactions.

Growth of wild-type Escherichia coli strain MRE600 was severely affected up to 9 h following treatment with the anthracycline doxorubicin (15 microM), however, after 9 h, the cells became resistant. The onset of resistance coincided with some changes in the relative proportions of total saturated, monounsaturated and cyclopropane fatty acids. The anionic lipid content in E. coli strain HDL11 is under lac control and synthesis can be induced by incubation with the lac inducer IPTG. HDL11, with low levels of anionic phospholipid, was unaffected by doxorubicin (100 microM) over 9 h, with only slight inhibition of growth seen over 24 h. When the anionic lipid content of HDL11 was increased, there was a slight increase in the efficacy of doxorubicin, providing evidence for a membrane-based step in doxorubicin action.

Antibiotics, Antineoplastic↗
PubMed1995

Depletion of anionic phospholipids has no observable effect on the anchoring of penicillin binding protein 5 to the inner membrane of Escherichia coli.

Escherichia coli penicillin-binding protein 5 (PBP5) is anchored to the periplasmic face of the inner membrane via a C-terminal amphiphilic alpha-helix. The results of washing experiments have suggested an electrostatic contribution to the anchoring mechanism which may involve the cationic region of the C-terminal alpha-helix. Similarities between this anchor domain and some surface active agents, such as melittin, suggest that the cationic region of the PBP5 anchor may require the presence of anionic phospholipids for membrane interaction. Washing experiments performed on membranes of HDL11, an E. coli mutant in which the expression of the major anionic phospholipids is under lac control, found no such requirement. The results are discussed in relation to the hypothesis that the cationic region may interact with other sources of negative charge, possibly arising from a PBP complex.

Bacterial Proteins↗