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At least 667 records · Page 37Linked to original sources
PubMed2005

Chemical biology of protein lipidation: semi-synthesis and structure elucidation of prenylated RabGTPases.

Rab/Ypt guanosine triphosphatases (GTPases) represent a family of key membrane traffic regulators in eukaryotic cells. For their function Rab/Ypt proteins require double modification with two covalently bound geranylgeranyl lipid moieties at the C-terminus. Generally, prenylated proteins are very difficult to obtain by recombinant or enzymatic methods. We generated prenylated RabGTPases using a combination of chemical synthesis and protein engineering. This semi-synthesis depends largely on the availability of functionalized prenylated peptides corresponding to the proteins' native structure or modifications. We developed solution phase and solid phase strategies for the generation of peptides corresponding to the prenylated C-terminus of Rab7 GTPase in preparative amounts enabling us to crystallize the mono-prenylated Ypt1:RabGDI complex. The structure of the complex provides a structural basis for the ability of RabGDI to inhibit the release of nucleotide by Rab proteins and a molecular basis for understanding a RabGDI mutant that causes mental retardation in humans.

Models, Molecular↗
PubMed1987

Semisynthesis of cytochrome c analogues. The effect of modifying the conserved residues 38 and 39.

We have used chemical and enzymic protein engineering techniques to create analogues of the semisynthetic two-fragment complex (1-37).(38-104) of mitochondrial cytochrome c. This complex, unlike the natural product of specific tryptic cleavage, (1-38).(39-104), from which it is prepared, quite closely resembles the parent protein in functional characteristics and is thus a suitable substrate for modifications designed to study structure-function relations. We have replaced the invariant Arg-38 and the conserved Lys-39 with a range of alternative amino acids and have studied the effects on the principal functional parameters. The hydrogen-bonding capacity of Arg-38 is crucial to the stabilization of the bottom omega-loop, while the positive charge of Lys-39 helps maintain the high redox potential by electrostatic effects at the haem iron.

Amino Acids↗
PubMed2006

Integration of microfluidics with biomedical infrared spectroscopy for analytical and diagnostic metabolic profiling.

We describe how infrared spectroscopy of dry films (IRDF) can provide diagnostic information, and how we expect integration with laminar fluid diffusion interface (LFDI) sample pre-processing to generate new analytical and diagnostic tests. LFDI pre-processing provides sample clean-up and analyte separation. The sensitivity of IRDF to certain analytes is enhanced through the depletion of sample constituents that otherwise obscure relevant spectral features, permitting the deposition of films with larger sample volumes and, hence, of greater effective optical pathlength for the targeted analytes. An integrated LFDI-IRDF technology holds promise both as a method for rapid point-of-care quantitative analysis of biological fluids and as the engine of discovery for a wide range of novel diagnostic methods based upon metabolic profiling. In particular, successful integration will provide a versatile and cost effective technology platform that will allow for the accurate quantification of low-concentration analytes that are otherwise inaccessible and will provide the basis for diagnostic and prognostic methods that would otherwise be impossible. The specific question addressed by the proof-of-concept study summarised here is whether the spectra of LFDI processed samples can provide analytical methods that are more accurate than otherwise possible without LFDI pre-processing. The enrichment of serum creatinine is accomplished, with subsequent enhancement of its spectral contribution permitting quantification of this clinically important analyte beyond that achievable with no pre-processing. Finally, to illustrate the potential in diagnostic applications, two recently initiated studies are outlined, one involving chronic kidney disease and the other for chronic and acute coronary artery disease.

Biomarkers↗
PubMed1998

Localization of a sigma70 binding site on the N terminus of the Escherichia coli RNA polymerase beta' subunit.

The Escherichia coli genome encodes genes for seven different sigma subunit species while only having single genes for the alpha, beta, and beta' subunits that make up the RNA polymerase core enzyme. The various sigma factors compete for binding to the core enzyme, upon which they confer promoter DNA-specific transcription initiation to the polymerase. We have mapped a major interaction site between one of the sigma species, sigma70, and beta'. Using far-Western blotting analysis of chemically cleaved and genetically engineered protein fragments, we have identified a N-terminal fragment of beta' (residues 60-309) that could bind sigma70. We were able to more precisely map the interaction domain to amino acid residues 260-309 of beta' using nickel nitrilotriacetic acid co-immobilization assays.

Amino Acid Sequence↗
PubMedDate not supplied

Quantitative regioselectivity of glucuronidation of quercetin by recombinant UDP-glucuronosyltransferases 1A9 and 1A3 using enzymatic kinetic parameters.

Quercetin has been suggested to exert its pharmacological effects, at least in part, via its metabolites, such as glucuronides. Quantitative regioselectivity analyses are important to understand the contributions of UDP-glucuronosyltransferases (UGTs) to the pharmacological activity of quercetin. The present work obtained active UGT1A9 and UGT1A3 enzymes with a Bac-to-Bac expression system, and quercetin was metabolized by each of them to four monoglucuronides (7-, 3-, 4'- and 3'-glucuronide). Enzymatic kinetic parameters of each glucuronide were calculated to elucidate quantitatively UGT1A9's and UGT1A3's regioselectivities for quercetin. UGT1A3's highest glucuronidation efficiency was observed for the 3'-glucuronide, then the 3-, 4'- and 7-glucuronide. The catalytic efficiency order for UGT1A9 was 3->7->3'->4'-glucuronide.

Computer Simulation↗
PubMed2004

Filtering of ineffective siRNAs and improved siRNA design tool.

MOTIVATION: Short interfering RNAs (siRNAs) can be used to suppress gene expression and possess many potential applications in therapy, but how to design an effective siRNA is still not clear. Based on the MPI (Max-Planck-Institute) basic principles, a number of siRNA design tools have been developed recently. The set of candidates reported by these tools is usually large and often contains ineffective siRNAs. In view of this, we initiate the study of filtering ineffective siRNAs. RESULTS: The contribution of this paper is 2-fold. First, we propose a fair scheme to compare existing design tools based on real data in the literature. Second, we attempt to improve the MPI principles and existing tools by an algorithm that can filter ineffective siRNAs. The algorithm is based on some new observations on the secondary structure, which we have verified by AI techniques (decision trees and support vector machines). We have tested our algorithm together with the MPI principles and the existing tools. The results show that our filtering algorithm is effective. AVAILABILITY: The siRNA design software tool can be found in the website http://www.cs.hku.hk/~sirna/ CONTACT: smyiu@cs.hku.hk

Algorithms↗
PubMedDate not supplied

Enhancing tumor targeting and apoptosis using noncovalent antibody homodimers.

A rare type of antibody that spontaneously binds to each self (homodimerizes) has been described. This self-binding (autophilic) antibody provides stronger protection against bacterial infection than a non self-binding antibody with identical specificity and affinity due to increase of polymeric avidity. A peptide derived from the self-binding domain of the autophilic antibody was crosslinked to the Fc carbohydrate of two monoclonal antibodies specific for the B-cell receptor (BCR) of a murine and a human B-cell tumor. Peptide-crosslinked antibodies bind to themselves on solid phase ELISA as homodimer and establish in solution a monomer-dimer equilibrium. Autophilic antibodies bind to their respective tumor target cells with increased efficiency as determined by FACS analysis. They also induce twice the amount of apoptosis of target tumor cells than the control antibodies. Furthermore, the modified antibodies inhibit tumor growth in culture more efficiently than the control antibodies. Criss-cross protocols in FACS, apoptosis, and growth inhibition indicate the specificity of targeting the BCR with autophilic antitumor antibodies. The chemical approach of increasing the binding of antibodies without creating chemically crosslinked dimers mimics naturally occurring autophilic antibodies and represents a simple and attractive alternative to chemical dimerizing and antibody engineering techniques for improving their antitumor effect. Furthermore, these results provide a guide to incorporate the self-binding peptide into the structure of antibodies using modeling and molecular crafting techniques.

Animals↗
PubMed2003

Cluster-doping approach for wide-gap semiconductors: the case of p-type ZnO.

First-principles calculations on p-type doping of the paradigm wide-gap ZnO semiconductor reveal that successful doping depends much on engineering a stable local chemical bonding environment. We suggest a cluster-doping approach in which a locally stable chemical environment is realized by using few dopant species. We explain two puzzling experimental observations, i.e., that monodoping N in ZnO via N2 fails to produce p-type behavior, whereas using an NO source produces metastable p-type behavior, which disappears over time.

Journal Article↗
PubMed2004

De novo proteins from designed combinatorial libraries.

Combinatorial libraries of de novo amino acid sequences can provide a rich source of diversity for the discovery of novel proteins with interesting and important activities. Randomly generated sequences, however, rarely fold into well-ordered proteinlike structures. To enhance the quality of a library, features of rational design must be used to focus sequence diversity into those regions of sequence space that are most likely to yield folded structures. This review describes how focused libraries can be constructed by designing the binary pattern of polar and nonpolar amino acids to favor proteins that contain abundant secondary structure, while simultaneously burying hydrophobic side chains and exposing hydrophilic side chains to solvent. The "binary code" for protein design was used to construct several libraries of de novo proteins, including both alpha-helical and beta-sheet structures. The recently determined solution structure of a binary patterned four-helix bundle is well ordered, thereby demonstrating that sequences that have neither been selected by evolution (in vivo or in vitro) nor designed by computer can form nativelike proteins. Examples are presented demonstrating how binary patterned libraries have successfully produced well-ordered structures, cofactor binding, catalytic activity, self-assembled monolayers, amyloid-like nanofibrils, and protein-based biomaterials.

Models, Chemical↗
PubMed2003

Structure of Rab GDP-dissociation inhibitor in complex with prenylated YPT1 GTPase.

Rab/Ypt guanosine triphosphatases (GTPases) represent a family of key membrane traffic regulators in eukaryotic cells whose function is governed by the guanosine diphosphate (GDP) dissociation inhibitor (RabGDI). Using a combination of chemical synthesis and protein engineering, we generated and crystallized the monoprenylated Ypt1:RabGDI complex. The structure of the complex was solved to 1.5 angstrom resolution and provides a structural basis for the ability of RabGDI to inhibit the release of nucleotide by Rab proteins. Isoprenoid binding requires a conformational change that opens a cavity in the hydrophobic core of its domain II. Analysis of the structure provides a molecular basis for understanding a RabGDI mutant that causes mental retardation in humans.

Binding Sites↗
PubMed1996

Full-scale studies of factors related to coliform regrowth in drinking water.

An 18-month survey of 31 water systems in North America was conducted to determine the factors that contribute to the occurrence of coliform bacteria in drinking water. The survey included analysis of assimilable organic carbon (AOC), coliforms, disinfectant residuals, and operational parameters. Coliform bacteria were detected in 27.8% of the 2-week sampling periods and were associated with the following factors: filtration, temperature, disinfectant type and disinfectant level, AOC level, corrosion control, and operational characteristics. Four systems in the study that used unfiltered surface water accounted for 26.6% of the total number of bacterial samples collected but 64.3% (1,013 of 1,576) of the positive coliform samples. The occurrence of coliform bacteria was significantly higher when water temperatures were > 15 degrees C. For filtered systems that used free chlorine, 0.97% of 33,196 samples contained coliform bacteria, while 0.51% of 35,159 samples from chloraminated systems contained coliform bacteria. The average density of coliform bacteria was 35 times higher in free-chlorinated systems than in chloraminated water (0.60 CFU/100 ml for free-chlorinated water compared with 0.017 CFU/100 ml for chloraminated water). Systems that maintained dead-end free chlorine levels of < 0.2 mg/liter or monochloramine levels of < 0.5 mg/liter had substantially more coliform occurrences than systems that maintained higher disinfectant residuals. Free-chlorinated systems with AOC levels greater than 100 micrograms/liter had 82% more coliform-positive samples and 19 times higher coliform levels than free-chlorinated systems with average AOC levels less than 99 micrograms/liter. Systems that maintained a phosphate-based corrosion inhibitor and limited the amount of unlined cast iron pipe had fewer coliform bacteria. Several operational characteristics of the treatment process or the distribution system were also associated with increased rates of coliform occurrence. The study concludes that the occurrence of coliform bacteria within a distribution system is dependent upon a complex interaction of chemical, physical, operational, and engineering parameters. No one factor could account for all of the coliform occurrences, and one must consider all of the parameters described above in devising a solution to the regrowth problem.

Data Collection↗
PubMed1998

Development of hybrid strains for the mineralization of chloroaromatics by patchwork assembly.

The persistence of chloroaromatic compounds can be caused by various bottlenecks, such as incomplete degradative pathways or inappropriate regulation of these pathways. Patchwork assembly of existing pathways in novel combinations provides a general route for the development of strains degrading chloroaromatics. The recruitment of known complementary enzyme sequences in a suitable host organism by conjugative transfer of genes might generate a functioning hybrid pathway for the mineralization of some chloroaromatics not degraded by the parent organisms. The rational combination uses (a) peripheral, funneling degradation sequences originating from aromatics-degrading strains to fulfill the conversion of the respective analogous chloroaromatic compound to chlorocatechols as the central intermediates; (b) a central chlorocatechol degradation sequence, the so-called modified ortho pathway, which brings about elimination of chlorine substituents; and (c) steps of the 3-oxoadipate pathway to reach the tricarboxylic acid cycle. The genetic organization of these pathway segments has been well characterized. The specificity of enzymes of the xylene, benzene, biphenyl, and chlorocatechol pathways and the specificity of the induction systems for the chlorinated substrates are analyzed in various organisms to illustrate eventual bottlenecks and to provide alternatives that are effective in the conversion of the "new" substrate. Hybrid pathways are investigated in "new" strains degrading chlorinated benzoates, toluenes, benzenes, and biphenyls. Problems occurring after the conjugative DNA transfer and the "natural" solution of these are examined, such as the prevention of misrouting into the meta pathway, to give a functioning hybrid pathway. Some examples clearly indicate that patchwork assembly also happens in nature.

Benzene↗
PubMed2006

The potential risks of nanomaterials: a review carried out for ECETOC.

During the last few years, research on toxicologically relevant properties of engineered nanoparticles has increased tremendously. A number of international research projects and additional activities are ongoing in the EU and the US, nourishing the expectation that more relevant technical and toxicological data will be published. Their widespread use allows for potential exposure to engineered nanoparticles during the whole lifecycle of a variety of products. When looking at possible exposure routes for manufactured Nanoparticles, inhalation, dermal and oral exposure are the most obvious, depending on the type of product in which Nanoparticles are used. This review shows that (1) Nanoparticles can deposit in the respiratory tract after inhalation. For a number of nanoparticles, oxidative stress-related inflammatory reactions have been observed. Tumour-related effects have only been observed in rats, and might be related to overload conditions. There are also a few reports that indicate uptake of nanoparticles in the brain via the olfactory epithelium. Nanoparticle translocation into the systemic circulation may occur after inhalation but conflicting evidence is present on the extent of translocation. These findings urge the need for additional studies to further elucidate these findings and to characterize the physiological impact. (2) There is currently little evidence from skin penetration studies that dermal applications of metal oxide nanoparticles used in sunscreens lead to systemic exposure. However, the question has been raised whether the usual testing with healthy, intact skin will be sufficient. (3) Uptake of nanoparticles in the gastrointestinal tract after oral uptake is a known phenomenon, of which use is intentionally made in the design of food and pharmacological components. Finally, this review indicates that only few specific nanoparticles have been investigated in a limited number of test systems and extrapolation of this data to other materials is not possible. Air pollution studies have generated indirect evidence for the role of combustion derived nanoparticles (CDNP) in driving adverse health effects in susceptible groups. Experimental studies with some bulk nanoparticles (carbon black, titanium dioxide, iron oxides) that have been used for decades suggest various adverse effects. However, engineered nanomaterials with new chemical and physical properties are being produced constantly and the toxicity of these is unknown. Therefore, despite the existing database on nanoparticles, no blanket statements about human toxicity can be given at this time. In addition, limited ecotoxicological data for nanomaterials precludes a systematic assessment of the impact of Nanoparticles on ecosystems.

Journal Article↗