Semirational design of active tumor suppressor p53 DNA binding domain with enhanced stability

We have designed a p53 DNA binding domain that has virtually the same binding affinity for the gadd45 promoter as does wild-type protein but is considerably more stable. The design strategy was based on molecular evolution of the protein domain. Naturally occurring amino acid substitutions were identified by comparing the sequences of p53 homologues from 23 species, introducing them into wild-type human p53, and measuring the changes in stability. The most stable substitutions were combined in a multiple mutant. The advantage of this strategy is that, by substituting with naturally occurring residues, the function is likely to be unimpaired. All point mutants bind the consensus DNA sequence. The changes in stability ranged from +1.27 (less stable Q165K) to −1.49 (more stable N239Y) kcal mol−1, respectively. The changes in free energy of unfolding on mutation are additive. Of interest, the two most stable mutants (N239Y and N268D) have been known to act as suppressors and restored the activity of two of the most common tumorigenic mutants. Of the 20 single mutants, 10 are cancer-associated, though their frequency of occurrence is extremely low: A129D, Q165K, Q167E, and D148E are less stable and M133L, V203A and N239Y are more stable whereas the rest are neutral. The quadruple mutant (M133LV203AN239YN268D), which is stabilized by 2.65 kcal mol−1 and Tm raised by 5.6°C is of potential interest for trials in vivo.

Specific molecular recognition of mixed nucleic acid sequences: An aromatic dication that binds in the DNA minor groove as a dimer

Phenylamidine cationic groups linked by a furan ring (furamidine) and related compounds bind as monomers to AT sequences of DNA. An unsymmetric derivative (DB293) with one of the phenyl rings of furamidine replaced with a benzimidazole has been found by quantitative footprinting analyses to bind to GC-containing sites on DNA more strongly than to pure AT sequences. NMR structural analysis and surface plasmon resonance binding results clearly demonstrate that DB293 binds in the minor groove at specific GC-containing sequences of DNA in a highly cooperative manner as a stacked dimer. Neither the symmetric bisphenyl nor bisbenzimidazole analogs of DB293 bind significantly to the GC containing sequences. DB293 provides a paradigm for design of compounds for specific recognition of mixed DNA sequences and extends the boundaries for small molecule-DNA recognition.

Rational design of a bacterial transcriptional cascade for amplifying gene expression capacity

Cascade regulatory circuits have been described that control numerous cell processes, and may provide models for the design of artificial circuits with novel properties. Here we describe the design of a transcriptional regulatory cascade to amplify the cell response to a given signal. We used the salicylate-responsive activators of Pseudomonas putida NahR of the naphthalene degradation plasmid NAH7 and XylS2, a mutant regulator of the TOL plasmid for catabolism of m-xylene and their respective cognate promoters Psal and Pm. Control of the expression of xylS2 with the nahR/Psal system permitted either their selective activation with specific effectors for each protein or the simultaneous activation of both of them with salicylate. When cells face the common effector of the two regulators, both the increase in XylS2 concentration and the stimulation of its activity act synergistically on the Pm promoter, amplifying the gene expression capacity by at least one order of magnitude with respect to the individual systems. By changing the hierarchy of regulators, we showed that the specific features of the downstream regulator were crucial for the amplification effect. Directed changes in the effector profile of the regulators allowed the extension of the amplifying system to other molecular signals.

Deciphering the design of the tropomyosin molecule

The crystal structure at 2.0-Å resolution of an 81-residue N-terminal fragment of muscle α-tropomyosin reveals a parallel two-stranded α-helical coiled-coil structure with a remarkable core. The high alanine content of the molecule is clustered into short regions where the local 2-fold symmetry is broken by a small (≈1.2-Å) axial staggering of the helices. The joining of these regions with neighboring segments, where the helices are in axial register, gives rise to specific bends in the molecular axis. We observe such bends to be widely distributed in two-stranded α-helical coiled-coil proteins. This asymmetric design in a dimer of identical (or highly similar) sequences allows the tropomyosin molecule to adopt multiple bent conformations. The seven alanine clusters in the core of the complete molecule (which spans seven monomers of the actin helix) promote the semiflexible winding of the tropomyosin filament necessary for its regulatory role in muscle contraction.

The molecular biology of apoptosis.

All multicellular organisms have mechanisms for killing their own cells, and use physiological cell death for defence, development, homeostasis, and aging. Apoptosis is a morphologically recognizable form of cell death that is implemented by a mechanism that has been conserved throughout evolution from nematode to man. Thus homologs of the genes that implement cell death in nematodes also do so in mammals, but in mammals the process is considerably more complex, involving multiple isoforms of the components of the cell death machinery. In some circumstances this allows independent regulation of pathways that converge upon a common end point. A molecular understanding of this mechanism may allow design of therapies that either enhance or block cell death at will.

The molecular role of the common gamma c subunit in signal transduction reveals functional asymmetry within multimeric cytokine receptor complexes.

The specific signal transduction function of the gamma c subunit in the interleukin (IL) 2, IL-4, IL-7, IL-9, and IL-15 receptor complexes remains undefined. The present structure-function analyses demonstrated that the entire cytoplasmic tail of gamma c could be functionally replaced in the IL-2 receptor (IL-2R) signaling complex by a severely truncated erythropoietin receptor cytoplasmic domain lacking tyrosine residues. Heterodimerization of IL-2R beta with either gamma c or the truncated erythropoietin receptor chain led to an array of specific signals normally derived from the native IL-2R despite the substitution of Janus kinase JAK2 for JAK3 in the receptor complex. These findings thus suggest a model in which the gamma c subunit serves as a common and generic "trigger" chain by providing a nonspecific Janus kinase for signaling program initiation, while signal specificity is determined by the unique "driver" subunit in each of the gamma c- containing receptor complexes. Furthermore, these results may have important functional implications for the asymmetric design of many cytokine receptor complexes and the evolutionary design of receptor subfamilies that share common trigger or driver subunits.

Crystal and molecular structure of paclitaxel (taxol).

Paclitaxel (formerly called taxol), an important anticancer drug, inhibits cell replication by binding to and stabilizing microtubule polymers. As drug-receptor interactions are governed by the three-dimensional stereochemistries of both participants, we have determined the crystal structure of paclitaxel to identify its conformational preferences that may be related to biological activity. The monoclinic crystals contain two independent paclitaxel molecules in the asymmetric unit plus several water and dioxane solvent molecules. Taxane ring conformation is very similar in both paclitaxel molecules and is similar to the taxane ring conformation found in the crystal structure of the paclitaxel analogue docetaxel (formerly called taxotere). The two paclitaxel molecules have carbon-13 side-chain conformations that differ from each other and from that of the corresponding side chain in the docetaxel crystal structure. The carbon-13 side-chain conformation of one paclitaxel molecule is similar to what was proposed from NMR studies done in polar solvents, while that of the other paclitaxel molecule is different and hitherto unobserved. The paclitaxel molecules interact with each other and with solvent atoms through an extensive network of hydrogen bonds. Analysis of the hydrogen-bonding network together with structure-activity studies may suggest which atoms of paclitaxel are important for binding to microtubule receptors.

Mimics of the binding sites of opioid receptors obtained by molecular imprinting of enkephalin and morphine.

Molecular imprinting of morphine and the endogenous neuropeptide [Leu5]enkephalin (Leu-enkephalin) in methacrylic acid-ethylene glycol dimethacrylate copolymers is described. Such molecular imprints possess the capacity to mimic the binding activity of opioid receptors. The recognition properties of the resultant imprints were analyzed by radioactive ligand binding analysis. We demonstrate that imprinted polymers also show high binding affinity and selectivity in aqueous buffers. This is a major breakthrough for molecular imprinting technology, since the binding reaction occurs under conditions relevant to biological systems. The antimorphine imprints showed high binding affinity for morphine, with Kd values as low as 10(-7) M, and levels of selectivity similar to those of antibodies. Preparation of imprints against Leu-enkephalin was greatly facilitated by the use of the anilide derivative rather than the free peptide as the print molecule, due to improved solubility in the polymerization mixture. Free Leu-enkephalin was efficiently recognized by this polymer (Kd values as low as 10(-7) M were observed). Four tetra- and pentapeptides, with unrelated amino acid sequences, were not bound. The imprints showed only weak affinity for two D-amino acid-containing analogues of Leu-enkephalin. Enantioselective recognition of the L-enantiomer of phenylalanylglycine anilide, a truncated analogue of the N-terminal end of enkephalin, was observed.

Design of continuously reinforced concrete pavements using glass fiber reinforced polymer rebars /

"October 2005."

The design of planar gradient coils. Part ll: A weighted superposition method

In this work a superposition technique for designing gradient coils for the purpose of magnetic resonance imaging is outlined, which uses an optimized weight function superimposed upon an initial winding similar to that obtained from the target field method to generate the final wire winding. This work builds on the preliminary work performed in Part I on designing planar insertable gradient coils for high resolution imaging. The proposed superposition method for designing gradient coils results in coil patterns with relatively low inductances and the gradient coils can be used as inserts into existing magnetic resonance imaging hardware. The new scheme has the capacity to obtain images faster with more detail due to the deliver of greater magnetic held gradients. The proposed method for designing gradient coils is compared with a variant of the state-of-the-art target field method for planar gradient coils designs, and it is shown that the weighted superposition approach outperforms the well-known the classical method.

Synthesis of polymers and copolymers of lactide through titanium initators

The research described in this thesis explored the synthesis tlnd characteristltion of biocompatible and biodegradable polymers of lactide through non-toxic titanium alkoxide nitiators. The research objectives focused on the preparation of polylactides in both solvent and solventless media, to produce materials with a wide range of molecular weights. The polylactides were fully characterised using gel permeation chromatography and 1H and 13C NMR spectroscopy. NMR spectroscopy was carried out in the study the reaction mechanisms. Kinetic studies of the ring opening polymerisation of lactide with titanium alkoxide initiators were also conducted using NMR spectroscopy. The objectives of this research were also focused on the enhancement of the flexibility of the polymer chains by synthesising random and block copolymers of lactide and ε-caprolactone using Ti(0-i-Pr)4 as an initiator, This work involved extensive characterisalion of the synthesised copolymers using gel permeation chromatography and 1H and 13C NMR spectroscopic analysis. Kinetic studies of the ring opening polymerisation of ε-caplrolactone and of the copolymerisation of lactide and ε-caprolactone with Ti(O-i-Pr)4 as an initiator were also carried out. The last section of this work involved the synthesis of block and star-shaped copolymers of lactide and poly(ethylene glycol) [PEG]. The preparation of lactide/PEG block copolymers was carried out by ring opening polymerisation of L-Iactide using Ti(O-i-Pr)4 as an initiator and hydroxyl-terminated PEG's with different numbers of hydroxyl groups as co-initiators both in solution and solventless media. These all-in-one polymersations yielded the synthesis of both lactide homopolymer and lactide/PEG block copolymer. In order to selectively synthesise copolymers of lactide and PEG, the experiment was carried out in two steps. The first step consisted of the synthesis of a titanium macro-initiator by exchanging the iso-propoxide ligands by PEG with different numbers of hydroxyl groups. The second step involved the ring opening polymerisation of lactide using the titanium macrocatalyst that was prepared as an initiator. The polymerisations were carried out in a solventless media. The synthesis of lactide/PEG copolymers using polyethylene glycol with amino terminal groups was also discussed. Extensive characterisation of the lactide block copolymers and macroinitiators was carried out using techniques such as, gel permeation chromatography (GPC), NMR spectroscopy and differential scanning calorimeter (DeS).

Some aspects of the microbiological properties of polymers and composite materials

The interaction of microorganisms with glass-reinforced polyester resins(GRP), both under laboratory and simulated operating conditions, has been examined following reports of severl! fungal biodeterioration. Although GRP was not previously associated with substantial microbial growth, small amounts of microbial activity would pose problems for products associated with comestible materials. The microbiology of the raw materials was investigated, two ingredients were supportive to microbial populations whilst five materials were biostatic or inhibitory in their action. Production laminate was not susceptible to microbial deterioration or inhibitory to microbes. Incorporation of zinc stearate, one of the supportive ingredients, at 300% manufacturing level or drastic undercuring produced laminate capable of supporting microbial growth but only after a non-biotic stage of degradation. Study of the long-term population dynamics of cisterns of GRP and competitive materials under conditions simulating in-service conditions, monitoring microbial numbers within the experimental vessels and comparing with the populations of the supply water, suggests that the performance of GRP cisterns is slightly superior to conventional competitive materials. An investigation of the biological performance of GRP cisterns in an isolated area of known microbiological hazard was conducted. Severe biodeterioration had been experienced with Preform GRP articles moulded using different production techniques, but substitution of current GRP articles resulted in no recurrence of the problem. All attempts to establish the fungal isolate responsible for the phenomena in cisterns under controlled conditions failed. Scanning Electron Microscopy of GRP surfaces showed that although differences exist between current and Preform laminates, these could not satisfactorily explain the differences in service behaviour. These results and the results of the British Plastics Federation Expert Working Group interlaboratory study are discussed in relation to the original report of gross fungal biodeterioration and, to the design of future testing programmes for the products of industrial concerns.

The design of novel antifolates against pneumocystis carinii

The pneumonia caused by Pneumocystis carinii is ultimately responsible for the death of many acquired immunodeficiency syndrome (AIDS) patients. Large doses of trimethoprim and pyrimethamine in combination with a sulphonamide and/or pentamidine suppress the infection but produce serious side-effects and seldom prevent recurrence after treatment withdrawal. However, the partial success of the aforementioned antifolates, and also trimetrexate used alone, does suggest dihydrofolate reductase (DHFR) as a target for the development of antipneumocystis agents. From the DHFR inhibitory activities of 3'-substituted pyrimethamine analogues it was suggested that the 3'-(3'',3''-dimethyltriazen-1''-yl) substituent may be responsible for the greater activity for the P.carinii over the mammalian enzyme. Crystallographic and molecular modeling studies revealed considerable geometrical and electronic differences between the triazene and the chemically related formamidine functions that may account for the differences in DHFR inhibitory profiles. Structural and electronic parameters calculated for a series of 3'-(3'',3''-disubstitutedtriazen-1''-yl) pyrimethamine analogues did not correlate with the DHFR inhibitory activities. However, the in vitro screening against P.carinii DHFR revealed that the 3''-hydroxyethyl-3''-benzyl analogue was the most active and selective. Models of the active sites of human and P.carinii DHFRs were constructed using DHFR sequence and structural homology data which had identified key residues involved in substrate and cofactor binding. Low energy conformations of the 3'',3''-dimethyl and 3''-hydroxyethyl-3''-benzyle analogues, determined from nuclear magnetic resonance studies and theoretical calculations, were docked by superimposing the diaminopyrimidine fragment onto a previously docked pyrimethamine analogue. Enzyme kinetic data supported the 3''-hydroxyethyl-3''-benzyl moiety being located in the NADPH binding groove. The 3''-benzyl substituent was able to locate to within 3 AA of a valine residue in the active site of P.carinii DHFR thereby producing a hydrophobic contact. The equivalent residue in human DHFR is threonine, more hydrophilic and less likely to be involved in such a contact. This difference may account for the greater inhibitory activity this analogue has for P.carinii DHFR and provide a basis for future drug design. From an in vivo model of PCP in immunosuppressed rats it was established that the 3"-hydroxyethyl-3"-benzyl analogue was able to reduce the.P.carinii burden more effectively with increasing doses, without causmg any visible signs of toxicity. However, equivalent doses were not as effective as pentamidine, a current treatment of choice for Pneumocystis carinii pneumonia.