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David K Smith

Publications and source records attributed to David K Smith.

35 records · Page 2Linked to original sources
PubMed2004

Self-assembly of two-component peptidic dendrimers: dendritic effects on gel-phase materials.

The self-assembly of diaminododecane solubilised by different dendritic peptides, possessing increasing levels of dendritic branching, was investigated. The dendritic peptides were based on l-lysine building blocks and were of first, second and third generation, containing one, three and seven amino acid repeat units respectively. By applying these structures as potential gelator units, the dendritic effect on gelation was investigated. The degree of structuring was modulated, with the dendritic peptide controlling the aggregate morphology and the ability of the self-assembled state to manifest itself macroscopically as gelation. First generation gelator units (G1) did not induce macroscopic gelation with diaminododecane under any conditions, whilst those self-assemblies based on second (G2) and third (G3) generation branches did form gel-phase materials. Furthermore, gel-phase materials based on G2 exhibited optimum gelation behaviour compared to those based on G3(in terms of the thermal strength of the materials). Circular dichroism showed that the dendritic effect, programmed in at the molecular level, is directly related to the degree of chiral organisation within the self-assembled state. The dendritic generation of the peptide controls the pattern of amide-amide hydrogen bonding in terms of binding strength and alignment as determined using NMR methods. The mode of self-assembly can be qualitatively rationalised in terms of an attractive enthalpic interaction (i.e., amide-amide hydrogen bonding), a repulsive interaction (i.e., steric interactions between dendritic peptides) and an entropic term related to the hierarchical organisation of the gelator building blocks. It is argued that the balance between these factors determines the nature of the dendritic effect.

Biocompatible Materials↗
PubMed2004

Two-component dendritic gel: effect of spacer chain length on the supramolecular chiral assembly.

The present study investigates in detail the physical gelation of toluene induced by the addition of simple aliphatic diamines to a dendritic L-lysine-based peptide. The gel-phase material obtained was characterized using differential scanning calorimetry, scanning electron microscopy, small-angle X-ray scattering, circular dichroism, 1H NMR, and X-ray diffraction. When the length of the aliphatic diamine is incrementally increased (C6-C12), the thermally reversible gel-sol transition temperature is dramatically increased (4-105 degrees C). This paper shows that the molecular information preset in the diamine is transcribed into the supramolecular assembly on the microscale and that this, in turn, controls the highly tunable macroscopic materials properties. The results also demonstrate the importance of chirality in the assembly process and highlight the role played by the aliphatic diamine in modulating the transcription of chirality from the molecular to the microscopic level.

Journal Article↗
PubMed2004

One-component gels based on peptidic dendrimers: dendritic effects on materials properties.

This paper describes the gelation of symmetric dendrimers based on building blocks constructed from L-lysine. These dendrimers form gel-phase materials in nonpolar organic solvents. The thermal properties and concentration dependence of the gelation were investigated, and it was found that there was a clear dendritic effect on the behavior of the soft materials formed, with higher generation dendrimers giving rise to more thermally stable gels. Variable temperature 1H NMR studies indicated that this behavior was probably a consequence of more extensive interdendrimer hydrogen bonding occurring between the peptidic groups in the higher generation dendrimers. The supramolecular aggregates were found to have a fibrillar structure, with the dimensions and alignment of the fibers being dependent on dendritic generation. Circular dichroism measurements confirmed that these fibers possessed chiral organization of the peptidic groups on the supramolecular (nano) scale, assigned as helicity. This paper indicates that dendritic functionalization provides a useful way of tuning gel-phase materials properties, with clear dendritic effects on gel formation being quantified for the first time, hence illustrating the way dendritic functionalization can play a positive role in the formation of highly functional organic materials with desirable properties.

Journal Article↗
PubMed2004

NMR and ESR investigations of the interaction between a carboxylic acid and an amine at the focal point of L-lysine based dendritic branches.

This paper reports the characterisation of supramolecular complexes formed between the carboxylic acid group at the focal point of host dendritic branches based on l-lysine building blocks and an amine group on an appropriate guest molecule. (1)H NMR titration investigations indicate that the interaction is relatively weak. Interestingly the dendritic generation appears to have no effect on the thermodynamics of benzylamine recognition - in contrast to previous studies in which charged guests have been bound to dendritic hosts. Control experiments using dendritic branches in which the carboxylic acid is protected as a methyl ester indicate that there is only a small amount of non-specific binding of the amine functionalised guest molecule within the dendritic framework itself. ESR investigations clearly show the binding between the dendritic branch and amine functionalised TEMPO radicals. Most interestingly, rotational correlation times can be determined from the ESR studies and they indicate that the mobility of the TEMPO radical is diminished on binding to the dendritic branch. Notably this effect is generation dependent, with larger dendritic branches having a more dramatic effect on the tumbling of the radical. Control experiments clearly prove the importance of the acid-base interaction and also demonstrate that effective binding only occurs in non-polar solvents. These results therefore illustrate that using host-guest chemistry at the focal point of a dendritic structure is an effective way to control and modify the solution phase properties and mobility of active species such as radicals.

Amines↗
PubMed2004

Protein flexibility and intrinsic disorder.

Comparisons were made among four categories of protein flexibility: (1) low-B-factor ordered regions, (2) high-B-factor ordered regions, (3) short disordered regions, and (4) long disordered regions. Amino acid compositions of the four categories were found to be significantly different from each other, with high-B-factor ordered and short disordered regions being the most similar pair. The high-B-factor (flexible) ordered regions are characterized by a higher average flexibility index, higher average hydrophilicity, higher average absolute net charge, and higher total charge than disordered regions. The low-B-factor regions are significantly enriched in hydrophobic residues and depleted in the total number of charged residues compared to the other three categories. We examined the predictability of the high-B-factor regions and developed a predictor that discriminates between regions of low and high B-factors. This predictor achieved an accuracy of 70% and a correlation of 0.43 with experimental data, outperforming the 64% accuracy and 0.32 correlation of predictors based solely on flexibility indices. To further clarify the differences between short disordered regions and ordered regions, a predictor of short disordered regions was developed. Its relatively high accuracy of 81% indicates considerable differences between ordered and disordered regions. The distinctive amino acid biases of high-B-factor ordered regions, short disordered regions, and long disordered regions indicate that the sequence determinants for these flexibility categories differ from one another, whereas the significantly-greater-than-chance predictability of these categories from sequence suggest that flexible ordered regions, short disorder, and long disorder are, to a significant degree, encoded at the primary structure level.

Amino Acid Sequence↗
PubMed2003

Two-component dendritic gels: easily tunable materials.

This paper reports the tunability of a two-component gel system based on dendritic l-lysine with a focal point carboxylic acid group and aliphatic diamines. The microscopic structure and macroscopic properties of the gel can be modulated by changing the concentration of the components, altering their molecular structures, or tuning their relative molar ratio. In the latter case, there is a complete change in the morphology of the gel that has a direct impact on its macroscopic properties, specifically its gel-sol transition temperature.

Journal Article↗
PubMed2003

Syntheses of dendritic branches based on L-lysine: is the stereochemistry preserved throughout the synthesis?

This paper reports the syntheses of individual dendritic branches based on L-lysine and functionalised with either Boc or Bz surface groups. Convergent and divergent synthetic approaches were employed and the preservation of stereochemistry during the syntheses was monitored using polarmetry, NMR and HPLC. In addition, racemic dendritic branches based on D,L-lysine were synthesised for comparative purposes. It was observed that the preservation of stereochemistry in the dendritic peptide was dependent on the method of synthesis, with divergent methodology being preferred. The results are discussed in terms of the known stereochemical outcomes of traditional peptide coupling processes, and are generalised to the synthesis of other dendritic peptides. Such observations about the chirality of dendritic peptides are of relevance to chemists developing dendritic systems for applications where single enantiomer dendrimers would clearly be preferred, such as enantioselective catalysis or pharmaceutical chemistry.

Chromatography, High Pressure Liquid↗
PubMed2003

Solution structure of the C-terminal domain of the ciliary neurotrophic factor (CNTF) receptor and ligand free associations among components of the CNTF receptor complex.

The functional receptor complex of ciliary neurotrophic factor (CNTF), a member of the gp130 family of cytokines, is composed of CNTF, the CNTF receptor alpha (CNTFR), gp130, and the leukemia inhibitory factor receptor (LIFR). However, the nature of the receptor-mediated interactions in this complex has not yet been resolved. To address this issue we have determined the solution structure of the C-terminal or BC domain of CNTFR and studied the interactions of CNTFR with LIFR and gp130. We reported previously that the membrane distal cytokine-binding domain (CBD1) of LIFR could interact in vitro with soluble CNTFR (sCNTFR) in the absence of CNTF. Here we show that the CBD of human gp130 can also bind in vitro to sCNTFR in the absence of CNTF. In addition, the gp130 CBD could compete with the LIFR CBD1 for the binding of sCNTFR. Substitution of residues in the gp130 CBD, the LIFR CBD1, and the CNTFR BC domain that are expected to be involved in receptor-receptor interactions significantly reduced their interactions. An NMR chemical shift perturbation study of the interaction between the BC domains of CNTFR and gp130 further mapped the interaction surface. These data suggest that both the gp130 CBD and the LIFR CBD1 interact with CNTFR in a similar way and provide insights into the nature of the CNTF receptor complex.

Amino Acid Substitution↗
PubMed2003

Rapid screening of binding constants by calibrated competitive 1H NMR spectroscopy.

A calibrated competitive NMR method has been developed that is appropriate for the rapid screening of binding constants. This method involves the initial characterisation of a receptor-substrate binding event for which the (1)H NMR spectrum of a given receptor (calibrant) is modified by the substrate of interest at a range of concentrations. For all subsequent "unknown" receptors, K(a) values are then determined by using a competition assay (in the presence of the calibrant receptor) by measuring a single standard (1)H NMR spectrum. This enables a rapid assessment of the recognition properties of a library of potential receptors. Only the calibrant receptor needs to be NMR active, while the library of putative receptors, as well as the substrate, can be NMR silent. This method assumes the formation of complexes of 1:1 stoichiometry. To demonstrate this methodology, the binding of a number of crown ether type compounds with K+ ions has been studied. Comparison of the binding strengths obtained by using this approach with those in the literature shows excellent agreement. A range of new compounds that have recently been synthesised within our group has also been screened in order to illustrate how this approach can rapidly assess binding ability. This method has significance for chemists working in the fields of combinatorial receptor/substrate design and supramolecular chemistry as a means of rapid optimisation of binding strength.

Journal Article↗
PubMed2003

Improved amino acid flexibility parameters.

Protein molecules exhibit varying degrees of flexibility throughout their three-dimensional structures, with some segments showing little mobility while others may be so disordered as to be unresolvable by techniques such as X-ray crystallography. Atomic displacement parameters, or B-factors, from X-ray crystallographic studies give an experimentally determined indication of the degree of mobility in a protein structure. To provide better estimators of amino acid flexibility, we have examined B-factors from a large set of high-resolution crystal structures. Because of the differences among structures, it is necessary to normalize the B-factors. However, many proteins have segments of unusually high mobility, which must be accounted for before normalization can be performed. Accordingly, a median-based method from quality control studies was used to identify outliers. After removal of outliers from, and normalization of, each protein chain, the B-factors were collected for each amino acid in the set. It was found that the distribution of normalized B-factors followed a Gumbel, or extreme value distribution, and the location parameter, or mode, of this distribution was used as an estimator of flexibility for the amino acid. These new parameters have a higher correlation with experimentally determined B-factors than parameters from earlier methods.

Amino Acids↗
PubMed2002

Membrane distal cytokine binding domain of LIFR interacts with soluble CNTFR in vitro.

Ciliary neurotrophic factor (CNTF) is a member of the gp130 family of cytokines. The functional receptor complex of CNTF is composed of the CNTF receptor alpha (CNTFR), gp130 and the leukemia inhibitory factor receptor (LIFR). Three regions on CNTF have been identified as binding sites for its receptors. The ligand-receptor interactions are mediated through the cytokine binding domains (CBDs) and/or the immunoglobulin-like domains of the receptors. However, in the case of CNTF, the precise nature of the protein-protein contacts in the signaling complex has not yet been resolved. In this study, we provide the first demonstration that the membrane distal CBD (CBD1) of LIFR associates in vitro with soluble CNTFR in the absence of CNTF. Moreover, purified CBD1 partially blocks CNTF signaling, but not that of interleukin-6 or LIF, in human embryonal carcinoma cell line Ntera/D1 cells. These data raise the possibility that LIFR has the capability to form a ligand-free complex with CNTFR.

Animals↗
PubMed2002

Ferrocene encapsulated within symmetric dendrimers: a deeper understanding of dendritic effects on redox potential.

Ferrocene has been encapsulated within a symmetric ether-amide dendritic shell and its redox potential monitored in a variety of solvents. The dendritic effect generated by the branched shell is different in different solvents. In less polar, non hydrogen bond donor solvents, attachment of the branched shell to ferrocene increases its E(1/2), indicating that oxidation to ferrocenium (charge buildup) becomes thermodynamically hindered by the dendrimer, a result explained by the dendrimer providing a less polar medium than that of the surrounding electrolyte solution. The effect of electrolyte concentration on redox potential was also investigated, and it was shown that the concentration of "innocent" electrolyte has a significant effect on the redox potential by increasing the overall polarity of the surrounding medium. Dendritic destabilization of charge buildup is in agreement with the majority of reported dendritic effects. A notable exception to this is provided by the asymmetric ferrocene dendrimers previously reported by Kaifer and co-workers, in which the branching facilitated oxidation, and it is proposed that in this case the dendritic effect is generated by a different mechanism. Interestingly, in methanol, the new symmetric ferrocene dendrimer exhibited almost no dendritic effect, a result explained by the ability of methanol to interact extensively with the branched shell, generating a more open superstructure. By comparison of all the new data with other reports, this study provides a key insight into the structure-activity relationships which control redox processes in dendrimers and also an insight into the electrochemical process itself.

Journal Article↗
PubMedDate not supplied

Dendrons with spermine surface groups as potential building blocks for nonviral vectors in gene therapy.

This paper investigates a series of dendrons based on the Newkome dendritic scaffold that displays a naturally occurring polyamine (spermine) on their surface. These dendrons have previously been shown to interact with DNA in a generation dependent manner with the more highly branched dendrons exhibiting a strong multivalency effect for the spermine surface groups. In this paper, we investigate the ability of these dendrons to transfect DNA into cells (human breast carcinoma cells, MDA-MB-231, and murine myoblast cells, C2C12) as determined by the luciferase assay. Although the dendrons are unable to transfect DNA in their own right, they are capable of delivering DNA in vitro when administered with chloroquine, which assists with escape from endocytic vesicles. The cytotoxicity of the dendrons was determined using the XTT assay, and it was shown that the dendrons were nontoxic either alone or in the presence of DNA. However, when administered with DNA and chloroquine, the most highly branched dendron did exhibit some cytotoxicity. This paper elucidates the relationship between in vitro transfection efficiency and toxicity. While transfection efficiencies are modest, the low toxicity of the dendrons, both in their own right, and in the presence of DNA, provides encouragement that this type of building block, which has a relatively high affinity for DNA, will provide a useful starting point for the further synthetic development of more effective gene transfection agents.

Animals↗