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PubMed2004

Rational design of lipid for membrane protein crystallization.

The lipidic cubic phase has been used to grow crystals of membrane proteins for high-resolution structure determination. However, the original, so-called, in meso method does not work reliably at low temperatures, where proteins are generally more stable, because the hosting lipid turns solid. The need existed therefore for a lipid that forms the cubic phase and that supports crystal growth at low temperatures. We created a database of phase diagrams and used it to design such a lipid. X-ray diffraction showed that the new lipid exhibits designed phase behavior. Further, it produces diffraction quality membrane protein crystals by the in meso method at 6 degrees C. This demonstrates that lipidic materials, like their protein counterparts are amenable to rational design. The same approach as used in this study should find application in extending the range of membrane proteins crystallizable by the in meso method and in tailoring transport of cubic phases for controlled delivery and uptake.

Carbon↗
PubMed2006

Attempts to rationalize protein crystallization using relative crystallizability.

Protein crystal growth (PCG) remains the bottleneck of crystallography despite many decades of study. The nucleation zone in the two-dimensional-phase diagram has been used to evaluate the relative crystallizability of proteins, which is expressed as a percentage over the phase area delineated by experimental protein and precipitating agent concentration ranges. For protein-salts which are subject to a direct temperature effect on solubility, as represented by Egg Lysozyme, a decrease in temperature augments the nucleation zone percentage whereas for those with retrograde solubility as a function of temperature, for example fructose-1,6-bisphosphatase in the presence and absence of AMP, an increase in temperature can significantly enhance the relative crystallizability. These results have been confirmed by the number of "hits" using PEGs as precipitating agents in Sparse Matrix Screen experiments for different proteins and are in excellent agreement with the relative crystallizability. The relationship between solubility dependence, relative crystallizability and crystallization success, has been evidenced. Such crystallizability can become a guide to identify efficient crystallization regions, providing a rational approach to PCG and structural biology.

Adenosine Monophosphate↗
PubMed2006

Rational proteomics V: structure-based mutagenesis has revealed key residues responsible for substrate recognition and catalysis by the dehydrogenase and isomerase activities in human 3beta-hydroxysteroid dehydrogenase/isomerase type 1.

Mammalian 3beta-hydroxysteroid dehydrogenase/isomerase (3beta-HSD) is a member of the short chain dehydrogenase/reductase. It is a key steroidogenic enzyme that catalyzes the first step of the multienzyme pathway conversion of circulating dehydroepiandrosterone and pregnenolone to active steroid hormones. A three dimensional model of a ternary complex of human 3beta-HSD type 1 (3beta-HSD_1) with an NAD cofactor and androstenedione product has been developed based upon X-ray structures of the ternary complex of E. coli UDP-galactose 4-epimerase (UDPGE) with an NAD cofactor and substrate (PDB_AC: 1NAH) and the ternary complex of human type 1 17beta-hydroxysteroid dehydrogenase (17beta-HSD_1) with an NADP cofactor and androstenedione (PDB_AC: 1QYX). The dimeric structure of the enzyme was built from two monomer models of 3beta-HSD_1 by respective 3D superposition with A and B subunits of the dimeric structure of Streptococcus suis DTDP-D-glucose 4,6-dehydratase (PDB_AC: 1KEP). The 3D model structure of 3beta-HSD_1 has been successfully used for the rational design of mutagenic experiments to further elucidate the key substrate binding residues in the active site as well as the basis for dual function of the 3beta-HSD_1 enzyme. The structure based mutant enzymes, Asn100Ser, Asn100Ala, Glu126Leu, His232Ala, Ser322Ala and Asn323Leu, have been constructed and functionally characterized. The mutagenic experiments have confirmed the predicted roles of the His232 and Asn323 residues in recognition of the 17-keto group of the substrate and identified Asn100 and Glu126 residues as key residues that participate for the dehydrogenase and isomerization reactions, respectively.

Amino Acid Sequence↗
PubMed2006

Rational drug sequencing of paclitaxel, gemcitabine and carboplatin in patients with untreated stage IV and select stage IIIB non-small cell lung cancer.

INTRODUCTION: To conduct a phase II study evaluating the efficacy of rationally sequenced paclitaxel, gemcitabine, and carboplatin in patients with stage IV or select stage IIIB non-small cell lung cancer (NSCLC). METHODS: Patients with select stages IIIB (pleural effusion) and IV NSCLC with an ECOG performance status of 0-1 and no prior chemotherapy for their disease were eligible to participate. Treatment was delivered as follows: paclitaxel at 70 mg/m2 followed by gemcitabine at 300 mg/m2 on day 1, with carboplatin (AUC 5) on day 2 of a 28-day cycle. Response was assessed after every two cycles of therapy. The primary endpoint of this trial was response rate, with secondary endpoints of time to progression and 1 year overall survival. RESULTS: Twenty patients were enrolled on protocol, one of whom never received chemotherapy. The median number of cycles delivered was 3 (range 0-8). A partial response rate of 42% (8/19; 95% CI: 20-67%) and a stable disease rate of 11% (2/19; 95% CI: 1-33%) were observed. The median overall survival time was 9.6 months (95% CI: 4.6-16.6), with a 1 year overall survival rate of 42.1% (95% CI: 24.9-71.3%). Eight patients (42%) stopped treatment due to toxicity. CONCLUSION: Paclitaxel followed by gemcitabine and then carboplatin is an active, albeit complex, regimen in the treatment of patients with advanced NSCLC with insufficient advantage to justify continuation of this regimen.

Aged↗
PubMed2005

The use of animal models to guide rational vaccine design.

Although there are several varieties of animal models of tuberculosis, the mouse and the guinea pig are by far the most validated and useful. These provide information about vaccine-induced protection, immunogenicity, toxicity, and immunopathological effects. There is still much to be learned, however, in terms of rational vaccine design, especially in the context of therapeutic or anti-latent vaccine formulations and animal models of these situations.

Animals↗
PubMed2005

Rational vaccine strategies against AIDS: background and rationale.

New vaccine candidates exploiting the rational combination of regulatory and structural HIV gene products are being developed within the program of the AIDS Vaccine Integrated Project (AVIP) and will be tested in comparative preclinical and clinical trials with the ultimate goal of selecting proper candidates for advanced clinical testing in developing countries.

AIDS Vaccines↗
PubMed2006

Overexpression, purification and characterization of a hexahistidine-tagged recombinant extended nucleotide-binding domain 1 (NBD1) of the Cryptosporidium parvum CpABC3 for rational drug design.

Its natural resistance to antiprotozoal chemotherapy characterizes the intestinal protozoan parasite Cryptosporidium parvum and the P-glycoprotein-related multidrug resistance proteins such as CpABC3 could be involved. In order to design and study specific inhibitors of the CpABC3 nucleotide-binding domain, a hexahistidine-tagged recombinant protein encompassing the N-terminal cytosolic NBD1 domain was overexpressed in E. coli and purified. The 45 kDa H6-NBD1 displayed intrinsic fluorescent properties consistent with the presence of two Trp residues in a hydrophobic environment. The binding of ATP and the fluorescent analogue TNP-ATP produced a dose-dependent quenching as well as progesterone and the flavone quercetin. The extrinsic fluorescence of TNP-ATP was enhanced upon binding to H6-NBD1, which was only partially displaced by the natural substrate ATP. The recombinant protein hydrolyzed ATP (K(m)=145.4+/-18.2 microM), but ADP (K(m)=4.3+/-0.6mM) and AMP (K(m)=5.4+/-1.5 microM) were also substrates. TNP-ATP is a competitive inhibitor of the catalytic activity (K(i)=36.6+/-4.5 microM), but quercetin and progesterone were not inhibitors, evidencing different binding sites. The recombinant C. parvum H6-NBD1 should be a valuable tool for rational drug design and will allow the discrimination between specific inhibitors of the catalytic site and molecules binding to other sites.

ATP Binding Cassette Transporter, Subfamily B↗
PubMed2005

On-chip transfection of PC12 cells based on the rational understanding of the role of ECM molecules: efficient, non-viral transfection of PC12 cells using collagen IV.

Transfection microarrays (TMA) are important emerging tools for the study of genetic events in living cells in a high-throughput fashion and with significant material economy. However, the difficulty to transfect various relevant cell types on-chip hinders the use of TMAs. Herein we present the realization of a transfection microarray applicable to PC12 cells that heavily relies on the use of ECM molecules. Collagen IV and at a lesser extent laminin or collagen I, but not fibronectin or poly-l-lysine were found to significantly increase the solution-phase as well as on-chip transfection efficiency of PC12 cells. The highest transfection efficiency obtained was consistently above 60%. The observed correlations between the transfection efficiencies and the differential adhesion-induced events triggered by the studied ECMs provides the basis for the rationalization of the role of ECMs on the transfection process.

Animals↗
PubMed2005

A rationally assembled microbial community for growing Tagetes patula L. in a lunar greenhouse.

Well-defined plant-associated bacteria were used for growing French marigolds (Tagetes patula L.) in anorthosite, a substrate of low bioavailability, analogous to a lunar rock. The consortium was composed mainly of plant growth-promoting rhizobacteria and biocontrol agents that were used for seed inoculation. Simultaneously, the sterile substrate was inoculated with the siliceous bacterium Paenibacillus sp. IMBG156. The plant benefited from bacterial activity which resulted in stimulation of seed germination, better plant development, and finally in flowering of inoculated tagetes. In contrast, control plants grew poorly in sterile anorthosite and never flowered. Analysis of bacterial community composition showed that both species colonized plant roots, and there were no shifts in the consortium structure in the rhizosphere of French marigolds within 6 weeks. Paenibacillus sp. IMBG156 was able to release some elements (Ca, Fe, Si) from substrate anorthosite. It was assumed that a rationally assembled consortium of bacterial strains supported growth and development of the model plant under growth-limiting conditions, at least by means of bioleaching and delivering of essential nutritional elements to the plants, and by promoting plant growth.

Bacillaceae↗
PubMed2006

Rationalizing membrane protein overexpression.

Functional and structural studies of membrane proteins usually require overexpression of the proteins in question. Often, however, the 'trial and error' approaches that are mainly used to produce membrane proteins are not successful. Our rapidly increasing understanding of membrane protein insertion, folding and degradation means that membrane protein overexpression can be more rationalized, both at the level of the overexpression host and the overexpressed membrane protein. This change of mindset is likely to have a significant impact on membrane protein research.

Animals↗
PubMed2006

Computational methods to rationalize experimental strategies in biocatalysis.

Computational methods are more and more widely applied in biocatalysis to gain rational guidelines, to orient experimental planning and, ultimately, to avoid expensive and time-consuming experiments. In this respect, molecular modelling, multivariate statistical analysis and chemometrics in general are useful computational tools, although they follow completely different investigative approaches.

Biotechnology↗
PubMed2005

Rational monoclonal antibody development to emerging pathogens, biothreat agents and agents of foreign animal disease: The antigen scale.

Many factors influence the choice of methods used to develop antibody to infectious agents. In this paper, we review the current status of the main technologies used to produce monoclonal antibodies (mAbs) from the B cells of antigen-sensitized animals. While companies are adopting advanced high-throughput methods, the major technologies used by veterinary and medical research laboratories are classical hybridoma fusion and recombinant library selection techniques. These methods have inherent advantages and limitations but have many common aspects when using immunized rodents. Laboratories with expertise in both methods of antibody development have a distinct advantage in their ability to advance mAb technology. New and re-emerging infectious threats in today's world emphasize the need for quality immunoreagents and the need to maintain expertise in mAb development. We provide examples of some common applications for mAb reagents used to identify pathogens such as the SARS-coronavirus (SARS-CoV), Bacillus anthracis, and foot-and-mouth disease (FMD) virus. We also outline a framework for investigators to make rational decisions concerning which method to use to develop mAbs based upon characteristics of the pathogen under study and the intended downstream application. Lastly, we provide parameters for the immunisation of mice and a classification system which describes the expected outcome for mAb development strategies when using classes of immunogens to generate mAbs with desired activities.

Animal Diseases↗
PubMed2005

Rational design of a plasmid DNA vaccine capable of eliciting cell-mediated immune responses to multiple HIV antigens in mice.

Given the importance of the HIV-specific cell-mediated immune response in the early control and resolution of HIV infection and the observed correlation between pre-challenge vaccine elicited CTL responses and post challenge outcome in SHIV/rhesus macaque experiments, we sought to identify several candidate plasmid DNA (pDNA) vaccine designs capable of eliciting robust and balanced cell-mediated immune responses to multiple HIV-1 derived antigens in mice for further vaccine development. To rationally construct candidate vaccines for immunogenicity testing, we determined the relative immunogenicity of the individual HIV-derived vaccine antigens (env, gag, pol, nef, tat and vif) and the relative strength of various transcriptional control elements (HCMV, SCMV, HSV Lap1) in Balb/c mice. Next, a number of 1-, 2-, 3- and 4-vector pDNA vaccine designs were tested for their ability to elicit HIV-1 antigen-specific CMI responses. For these studies, Balb/c mice were immunized with a fixed total pDNA vaccine dose of 100 mcg in combination with 25 mcg plasmid-based murine IL-12 and tested for the induction of HIV-1 antigen-specific CMI responses by IFN-gamma ELISpot analysis. The results of this study indicate that all pDNA vaccine designs were capable of eliciting CMI responses to multiple HIV-1 antigens. As a result of this iterative comparative analysis, we have identified a number of pDNA vaccine candidates capable of eliciting potent, balanced CMI responses to multiple HIV-1 derived antigens. These results have important implications for the design and development of an efficacious vaccine for the prevention of HIV-1 infection.

Animals↗
PubMed2006

Rational design of Salmonella-based vaccination strategies.

A permanently growing body of information is becoming available about the quality of protective immune responses induced by mucosal immunization. Attenuated live bacterial vaccines can be administered orally and induce long-lasting protective immunity in humans without causing major side effects. An attenuated Salmonella enterica serovar Typhi strain is registered as live oral vaccine against typhoid fever and has been in use for more than two decades. Recombinant attenuated Salmonella strains are also an attractive means of delivering heterologous antigens to the immune system, thereby, stimulating strong mucosal and systemic immune responses and consequently provide an efficient platform technology to design novel vaccination strategies. This includes the choice of heterologous protective antigens and their expression under the control of appropriate promoters within the carrier strain. The availability of well-characterized attenuated mutants of Salmonella concomitantly supports fine tuning of immune response triggered against heterologous antigens. Exploring different mucosal sites as a potential route of immunization has to be taken into account as an additional important way to modulate immune responses according to clinical requirements. This article focuses on the rational design of strategies to modulate appropriate immunological effector functions on the basis of selection of (i) attenuating mutations of the Salmonella strains, (ii) specific expression systems for the heterologous antigens, and (iii) route of mucosal administration.

Animals↗
PubMed1986

A rational approach to the selection of an assist device for the failing right ventricle.

Assist devices have become available for the treatment of right ventricular (RV) failure. The present study assesses the efficacy of pulmonary artery balloon counterpulsation (PABC) in restoring RV output to normal levels. In a porcine model of RV failure during left heart bypass, PABC restored RV output to normal, provided that the RV output was not depressed to less than 50% of baseline values. When RV failure was more severe, PABC was not effective in restoring RV output to base line. This study suggests that a rational approach should be developed for the use of right heart assist devices. In moderately severe RV failure, PABC may be successful in restoring cardiac output to normal. However, in extreme failure a right heart bypass is necessary.

Animals↗
PubMed2003

A peptide mimetic of an anti-CD4 monoclonal antibody by rational design.

The development of rational methods to design 'continuous' sequence mimetics of discontinuous regions of protein sequence has, to now, been only marginally successful. This has been largely due to the difficulty of constraining the recognition elements of a mimetic structure to the relative conformational and spatial orientations present in the parent molecule. Using peptide mapping to determine 'active' antigen recognition residues, molecular modeling, and a molecular dynamics trajectory analysis, we have developed a peptide mimic of an anti-CD4 antibody, containing antigen contact residues from multiple CDRs. The design described is a 27-residue peptide formed by juxtaposition of residues from 5 CDR regions. It displays an affinity for the antigen (CD4) of 0.9nM, compared to 2nM for the parent antibody ST40. Nevertheless, the mimetic shows low biological activity in an anti-retroviral assay.

Amino Acid Sequence↗
PubMed2000

Biomimetic transport and rational drug delivery.

Medicine and pharmaceutics are encountering critical needs and opportunities for transvascular drug delivery that improves site targeting and tissue permeation by mimicking natural tissue addressing and transport mechanisms. This is driven by the accelerated development of genomic agents requiring targeted controlled release. Although rationally designed for in vitro activity, such agents are not highly effective in vivo, due to opsonization and degradation by plasma constituents, and failure to transport across the local vascular endothelium and tissue matrix. A growing knowledge of the addresses of the body can be applied to engineer "Bio-Logically" staged delivery systems with sequential bioaddressins complementary to the discontinuous compartments encountered--termed discontinuum pharmaceutics. Effective tissue targeting is accomplished by leukocytes, bacteria, and viruses. We are increasingly able to mimic their bioaddressins by genomic means. Approaches described in this commentary include: (a) endothelial-directed adhesion mediated by oligosaccharides and carbohydrates (e.g. dermatan sulfate as a mimic of sulfated CD44) and peptidomimetics interacting with adhesins, selectins, integrins, hyaluronans, and locally induced growth factors (e.g. vascular endothelial growth factor, VEGF) and coagulation factors (e.g. factor VIII antigen); (b) improved tissue permeation conferred by hydrophilically "cloaked" carrier systems; (c) "uncloaking" by matrix dilution or selective triggering near the target cells; and (d) target binding-internalization by terminally exposed hydrophobic moieties, cationic polymers, and receptor-binding lectins, peptides, or carbohydrates. This commentary also describes intermediate technology solutions (e.g. "hybrid drugs"), and highlights the high-resolution, dynamic magnetic resonance imaging and radiopharmaceutical imaging technologies plus the groups and organizations capable of accelerating these important initiatives.

Biological Transport, Active↗
PubMed2003

Rationalization of membrane protein crystallization with polyethylene glycol using a simple depletion model.

Based on the importance of crystallizing membrane proteins in a rational way, cytochrome bc(1) complex (BC1) was crystallized using polyethylene glycol (PEG) as a sole crystallization agent. Interaction between protein-detergent complexes of BC1 was estimated by dynamic light scattering, and was compared with the numerical calculation using the Derjaguin-Landau-Verwey-Overbeek potential plus a depletion potential, without considering specific surface properties of the protein-detergent complexes. The experiments and calculation were found to be consistent and we obtained a relation between PEG molecular weight M and the range of depletion zone delta as delta approximately M(0.48+/-0.02). The stability of liquid phase of BC1 solutions was controlled by a ratio of (the range of depletion zone)/(the radius of a BC1 particle), which was consistent with recent theoretical predictions. The crystallization was most successful under a condition where the stability of the liquid phase changed from stable to unstable. The PEG molecular weight that fulfilled this condition coincided with the one used empirically to crystallize BC1 in the past by a number of groups. These results are compared to the fact that membrane proteins were often successfully crystallized close to the detergent cloud point.

Animals↗