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PubMed1993

Atomic structure of a cytochrome c' with an unusual ligand-controlled dimer dissociation at 1.8 A resolution.

The crystallographic structure of cytochrome c' from the purple phototrophic bacterium Chromatium vinosum (CVCP) has been determined at 1.8 A resolution using multiple isomorphous replacement. The molecule is a dimer, with each 131-residue chain folding as a four-helical bundle incorporating a covalently bound heme group at the core. This structure is the third of the ubiquitous cytochromes c' to be solved and is similar to the known structures of cytochrome c' from R. molischianum (RMCP) and R. rubrum (RRCP). CVCP is unique in exhibiting ligand-controlled dimer dissociation while RMCP and RRCP do not. The Tyr16 side-chain, which replaced Met16 in RMCP and Leu14 in RRCP, is parallel to the heme plane and located directly above the sixth ligand site of the heme Fe. Any ligand binding to this site, such as CO or CN-, must move the Tyr16 side-chain, which would be expected to cause other conformational changes of helix A, which contributes to the dimer interface, and consequently disrupting the dimer. Thus, the crystallographic structure of CVCP suggests a mechanism for dimer dissociation upon ligand binding. The dimer interface specificity is due to a lock and key shape complementarity of hydrophobic residues and not to any charge complementarity or cross-interface hydrogen bonds as is common in other protein-protein interfaces. The co-ordinates have been deposited in the Brookhaven Data Bank (entry P1BBH).

Amino Acid Sequence↗

PubMed2005

MAGIC Tool: integrated microarray data analysis.

SUMMARY: Several programs are now available for analyzing the large datasets arising from cDNA microarray experiments. Most programs are expensive commercial packages or require expensive third party software. Some are freely available to academic researchers, but are limited to one operating system. MicroArray Genome Imaging and Clustering Tool (MAGIC Tool) is an open source program that works on all major platforms, and takes users 'from tiff to gif'. Several unique features of MAGIC Tool are particularly useful for research and teaching. AVAILABILITY: http://www.bio.davidson.edu/MAGIC

Algorithms↗

PubMedDate not supplied

A method for the in vitro exposure of human cells to environmental and complex gaseous mixtures: application to various types of atmosphere.

The application of in vitro methods to the analysis of the effects of airborne materials is still limited, because there are no generally accepted concepts and technologies for efficiently exposing adherent growing cells to test atmospheres, especially those comprising complex mixtures of gaseous and particulate phases. The introduction of in vitro research into the field of inhalation toxicology offers a unique possibility for using human cells and tissues for pre-screening studies, thus reducing the necessity for animal experiments, and cutting the numbers of animals used in toxicological testing. We therefore developed a novel experimental concept that uses an exposure device based on the cell cultivation system CULTEX (Patent No. DE 198011763; PCT/EP99/00295). This allowed us to investigate environmental atmospheres, which were chemically and physically unmodified, in an in vitro system, by exposing the target cells directly at the air/liquid interface. The exposure device itself is small and flexible enough to be connected to a variety of aerosol-generating systems without the need for an incubator, as it fulfils all the requirements for maintaining cell viability over a defined period. The general applicability and the sensitivity of this in vitro approach for testing various generated atmospheres under the same cell-exposure conditions were demonstrated by studying dose-dependent cytotoxic effects in human lung epithelial cells exposed to air contaminated with single gases or complex mixtures, such as diesel exhaust fumes and side-stream cigarette smoke.

Adenosine↗

PubMed1993

Family practice informatics: research issues in computerized medical records.

There are unique features of family and general practice which lead to unique issues in medical informatics for family physicians. The nature of practice in office based community settings and the discipline of dealing with all ages, sexes, and health conditions over the lifetime of a patient and his/her family lead to models of the thinking that are different from those used in most other specialties. Research is urgently needed to verify the models of thinking that physicians use during patient care encounters and the associated nomenclatures and classifications which support them. User interfaces need to be optimized for accuracy and speed. Standards for medical records computing in family practice need testing and validation.

Ambulatory Care Information Systems↗

PubMed2005

Novel nucleotide-binding sites in ATP-sensitive potassium channels formed at gating interfaces.

The coupling of cell metabolism to membrane electrical activity is a vital process that regulates insulin secretion, cardiac and neuronal excitability and the responses of cells to ischemia. ATP-sensitive potassium channels (K(ATP); Kir6.x) are a major part of this metabolic-electrical coupling system and translate metabolic signals such as the ATP:ADP ratio to changes in the open or closed state (gate) of the channel. The localization of the nucleotide-binding site (NBS) on Kir6.x channels and how nucleotide binding gates these K(ATP) channels remain unclear. Here, we use fluorescent nucleotide binding to purified Kir6.x proteins to define the peptide segments forming the NBS on Kir6.x channels and show that unique N- and C-terminal interactions from adjacent subunits are required for high-affinity nucleotide binding. The short N- and C-terminal segments comprising the novel intermolecular NBS are next to helices that likely move with channel opening/closing, suggesting a lock-and-key model for ligand gating.

Adenosine Triphosphate↗

PubMed2006

Histamine regulates placental cytokine expression--in vivo study on HDC knockout mice.

Successful pregnancy is closely related to polarization toward a Th2 type immune response. As histamine is known to initiate Th2 dominance during inflammatory processes we raised the question whether histamine has any effect on the actual tuning of proper cytokine balance for the proceeding of the gestation. Histamine has multiple functions in the process of pregnancy, different studies have shown the direct and/or indirect presence of histamine action in the placenta as well. As HDC is the unique histamine producing enzyme in eukaryotes, we used HDC (so endogenous histamine)-deficient knockout mice as reliable model for studying histamine-related processes in vivo. We examined the placental histamine content and the expression of histamine receptors and Th1/Th2/Th3 type cytokines in the placenta. We showed for the first time the influence of histamine on the orchestrated regulation of placental cytokine expression. In the absence of local histamine the cytokine balance is shifted toward Th1 types at the maternal-placental interface, threatening pregnancy. We also measured splenic lymphocyte subpopulation ratios in pregnant and non-pregnant mice and found that in pregnancy they are independent of the presence of histamine.

Animals↗

PubMed1996

Structure of chymopapain at 1.7 A resolution.

The X-ray structure of chymopapain, a cysteine proteinase isolated from the latex of the fruits of Carica papaya L., has been determined by molecular replacement methods and refined to a conventional R factor of 0.19 for all observed reflections in the range from 9.5 to 1.7 A resolution. The crystals used in this study contained a unique molecular species of chymopapain with two moles of thiomethyl attached to the two free cysteines per mole of enzyme. A comparison is made with the other known papaya proteinase X-ray structures: papain, caricain, and glycyl endopeptidase. Their backbone conformations are extremely similar except for two loop regions. Both regions are located at the surface of the protein and far away of the active site cleft. In each X-ray structure the same water network was found at the interface between the two domains of the enzyme. A close examination of the active site groove showed that the specificity restrictions dictated by the S2 subsite did not differ significantly among the four proteinases.

Amino Acid Sequence↗

PubMed1996

Local dynamics of the M13 major coat protein in different membrane-mimicking systems.

The local environment of the transmembrane and C-terminal domain of M13 major coat protein was probed by site-directed ESR spin labeling when the protein was introduced into three membrane-mimicking systems, DOPC vesicles, sodium cholate micelles, and SDS micelles. For this purpose, we have inserted unique cysteine residues at specific positions in the transmembrane and C-terminal region, using site-directed mutagenesis. Seven viable mutants with reasonable yield were harvested: A25C, V31C, T36C, G38C, T46C, A49C, and S50C. The mutant coat proteins were indistinguishable from wild type M13 coat protein with respect to their conformational and aggregational properties. The ESR data suggest that the amino acid positions 25 and 46 of the coat protein in DOPC vesicles are located close to the membrane-water interface. In this way the lysines at positions 40, 43, and 44 and the phenylalanines at positions 42 and 45 act as hydrophilic and hydrophobic anchors, respectively. The ESR spectra of site specific maleimido spin-labeled mutant coat proteins reconstituted into DOPC vesicles and solubilized in sodium cholate or SDS indicate that the local dynamics of the major coat protein is significantly affected by its structural environment (micellar vs bilayer), location (aqueous vs hydrophobic), and lipid/protein ratio. The detergents SDS and sodium cholate sufficiently well solubilize the major coat protein and largely retain its secondary structure elements. However, the results indicate that they have a poorly defined protein-amphiphilic structure and lipid-water interface as compared to bilayers and thus are not a good substitute for lipid bilayers in biophysical studies.

Capsid↗

PubMed1999

Structure and function of an archaeal topoisomerase VI subunit with homology to the meiotic recombination factor Spo11.

In all organisms, type II DNA topoisomerases are essential for untangling chromosomal DNA. We have determined the structure of the DNA-binding core of the Methanococcus jannaschii DNA topoisomerase VI A subunit at 2.0 A resolution. The overall structure of this subunit is unique, demonstrating that archaeal type II enzymes are distinct from other type II topoisomerases. However, the core structure contains a pair of domains that are also found in type IA and classic type II topoisomerases. Together, these regions may form the basis of a DNA cleavage mechanism shared among these enzymes. The core A subunit is a dimer that contains a deep groove that spans both protomers. The dimer architecture suggests that DNA is bound in the groove, across the A subunit interface, and that the two monomers separate during DNA transport. The A subunit of topoisomerase VI is homologous to the meiotic recombination factor, Spo11, and this structure can serve as a template for probing Spo11 function in eukaryotes.

Amino Acid Sequence↗

PubMed1996

When and how to eradicate Helicobacter pylori: role of histamine receptor antagonists.

Peptic ulcer is today frequently considered to be an infectious disease. The bacteria assumed to be the cause of gastric or duodenal ulcer was first called Campylobacter pyloridis and later C. pylori because of its structural similarity to other Campylobacter species. Later, unique characteristics were reported, and it was renamed Helicobacter pylori (Hp). In retrospect, it was presumably first described in man in 1938 (Doenges 1938), although the clinical significance was not established until 1983 (Warren 1983, Warren and Marshall 1983). It is a spiral-shaped, gram-negative bacteria with four to six flagella and dimensions of 0.5 x 3.0 micron. . With the help of these flagella, it moves into the mucous layer overlying the gastric epithelium where it colonizes at the interface of the mucous layer and the surface epithelial cells. It can be found in any part of the gastrointestinal tract demonstrating gastric epithelium, i.e. the stomach and metaplastic areas of the esophagus or the duodenum. One characteristic of this bacteria is the production of a urease enzyme that catalyzes urea to ammonium and bicarbonate. The production of ammonium causes the development of an alkaline microenvironment that protects it from the gastric acid. In the presence of urea, the organism will therefore replicate to a pH as low as 4.3 and survive without replication to a pH as low as 2.3. In Western countries, an increase in the prevalence of Hp infection is observed in the population with progressing age. In childhood, infection before the age of 20 years is rare. At the age of 60 years or older, however, the prevalence rate is on the order of 40% to 60% (Dooley et al. 1989, Perez-Perez et al. 1988, Marshall 1994). The seroconversion rate in adults is lower than 1% per year (Parsonnet et al. 1992). The infection seems to be stable, probably persisting for many years or even a lifetime.

Adolescent↗

PubMed1996

Safety and security of information systems.

This paper discusses some of the similarities and differences between the attributes of safety and security. It places these attributes within the broader topic of dependability and tries to identify what aspects of safety and security are unique and which aspects may be viewed within the attributes of reliability and availability. The paper then suggests that, rather than analyse systems from the single perspective of safety or security, they should be analysed from the broader perspective of dependability.

Computer Security↗

PubMed1995

Beta 1 integrins in epithelial tissues: a unique distribution in the lens.

Integrins have been shown to play a role in directing and maintaining cell differentiation and polarization. The embryonic lens provides a good system in which to examine their role in epithelial cell differentiation, because all stages of lens development are represented in an individual embryonic lens. Therefore, we examined the expression and distribution of beta 1 integrin heterodimers in both the lens epithelium and the differentiated lens fiber cells. In lens epithelial cells beta 1 integrin was found to be localized to all membrane surfaces. Lens fiber cells contained beta 1 integrin all along their lateral borders as well as at the site of their attachment to the lens capsule and at their interface with lens epithelial cells. The distribution of beta 1 integrin in the lens was distinct from that observed in simple epithelia, the retinal pigment epithelium (RPE), kidney, and intestine, where it was limited to a basal lateral localization. We examined the specific beta 1 integrin heterodimers expressed in the lens by Western blot analysis for the integrin alpha subunits following beta 1 immunoprecipitation and compared them with those expressed in RPE cells. In the lens we detected alpha 3 and alpha 6 subunits but not alpha 1, alpha 5, or alpha v. When the lens was separated into epithelial and fiber cells, we found that alpha 3 was expressed at a higher level in the epithelial cells, while alpha 6 was primarily associated with the fiber cells. In the RPE the primary beta 1 integrin detected was alpha 3. Unlike in lens and kidney, alpha 6 beta 1 integrin in RPE cells was expressed only at a low level. alpha v was also expressed in RPE cells but not as a beta 1 heterodimer. As in the lens, neither alpha 5 beta 1 nor alpha 1 beta 1 integrin was detected in RPE. Both lens and RPE cells express a specific subset of beta 1 integrin heterodimers which are likely to be important to the initiation and maintenance of their differentiated phenotype.

Animals↗

PubMed2000

A heterodimeric coiled-coil peptide pair selected in vivo from a designed library-versus-library ensemble.

Novel heterodimeric coiled-coil pairs were selected simultaneously from two DNA libraries using an in vivo protein-fragment complementation assay with dihydrofolate reductase, and the best pair was biophysically characterized. We randomized the interface-flanking e and g positions to Gln, Glu, Arg or Lys, and the core a position to Asn or Val in both helices simultaneously, using trinucleotide codons in DNA synthesis. Selection cycles with three different stringencies yielded sets of coiled-coil pairs, of which 80 clones were statistically analyzed. Thereby, properties most crucial for successful heterodimerization could be distinguished from those mediating more subtle optimization. A strong bias towards an Asn pair in the core a position indicated selection for structural uniqueness, and a reduction of charge repulsions at the e/g positions indicated selection for stability. Increased stringency led to additional selection for heterospecificity by destabilizing the respective homodimers. Interestingly, the best heterodimers did not contain exclusively complementary charges. The dominant pair, WinZip-A1B1, proved to be at least as stable in vitro as naturally occurring coiled coils, and was shown to be dimeric and highly heterospecific with a K(D) of approximately 24 nM. As a result of having been selected in vivo it possesses all characteristics required for a general in vivo heterodimerization module. The combination of rational library design and in vivo selection presented here is a very powerful strategy for protein design, and it can reveal new structural relationships.

Amino Acid Sequence↗

PubMed2005

Three-dimensional solution structure of a unique S100 protein.

S100A13 is a homodimeric protein that belongs to the S100 subfamily of EF-hand Ca2+-binding proteins. S100A13 exhibits unique physical and functional properties not observed in other members of the S100 family. S100A13 is crucial for the non-classical export of acidic fibroblast growth factors (FGFs-1), which lack signal peptide at their N-terminal end. In the present study, we report the three-dimensional solution structure of Ca2+-bound S100A13 using a variety of 3D NMR experiments. The structure of S100A13 is globular with four helices and an antiparallel beta-sheet in each subunit. The dimer interface is formed mainly by an antiparallel arrangement of helices H1, H1', H4, and H4'. Isothermal titration calorimetry (ITC) experiments show that S100A13 binds non-cooperatively to four calcium ions. Prominent differences exist between the three-dimensional structures of S100A13 and other S100 proteins. The hydrophobic pocket that largely contributes to protein-protein interactions in other S100 proteins is absent in S100A13. The structure of S100A13 is characterized by a large patch of negatively charged residues flanked by dense cationic clusters contributed largely by the positively charged residues located at the C-terminal end. Results of ITC experiments reveal that S100A13 lacking the C-terminal segment (residues 88-98) fails to bind FGF-1. The three-dimensional structure of S100A13 not only provides useful clues on its role in the non-classical export of signal peptide-less proteins such as FGF-1 but also paves the way for rational design of drugs against FGF-induced tumors.

Amino Acid Sequence↗

PubMed2005

NMR structural study of TcUBP1, a single RRM domain protein from Trypanosoma cruzi: contribution of a beta hairpin to RNA binding.

TcUBP1 is a trypanosome cytoplasmic RNA-binding protein containing a single, conserved RNA-recognition motif (RRM) domain involved in selective destabilization of U-rich mRNAs such as the Trypanosoma cruzi small mucin gene family mRNA, TcSMUG. TcUBP1 binds specific transcripts in vivo and co-localizes in the perinuclear part of the cell with components of the mRNA-stability determinant pathway such as poly(A)-binding protein 1 (PABP1) and TcUBP2, a closely related RRM-containing protein. In TcUBP proteins, the RRM domain is flanked by N-terminal Gln-rich and C-terminal Gly-Gln-rich extensions, which are involved in protein-protein interactions. In this work, we determined the solution structure of the TcUBP1 RRM domain by nuclear magnetic resonance (NMR) spectroscopy. The domain has a characteristic betaalphabetabetaalphabeta fold, consisting of a beta sheet composed of four antiparallel betastrands and two alpha helices packed against one face of the beta sheet. A unique aspect of TcUBP1 is the participation of a beta hairpin (beta4-beta5) in the beta sheet, resulting in an enlarged RNA-binding surface. Detailed analysis of the TcUBP1 interaction with a short single-stranded RNA derived from the 3' UTR of TcSMUG was carried out by titration experiments using both NMR spectroscopy and isothermal titration calorimetry. This analysis revealed that amino acids located within the beta hairpin (beta4-beta5) contribute to complex formation. This enlarged protein-RNA interface could compensate for the lack of additional RNA-binding domains in TcUBP1, as observed in many other RRM-containing proteins. The structure of TcUBP1 reveals new aspects of single RRM-RNA interactions and insight into how N- and C-terminal extensions can contribute to RNA binding.

Amino Acid Motifs↗

PubMed2000

Osmomechanics of the Propionigenium modestum F(o) motor.

In Propionigenium modestum, ATP is manufactured from ADP and phosphate by the enzyme ATP synthase using the free energy of an electrochemical gradient of Na+ ions. The P. modestum ATP synthase is a clear member of the family of F-type ATP synthases and the only major distinction is an extension of the coupling ion specificity to H+, Li+, or Na+, depending on the conditions. The use of Na+ as a coupling ion offers unique experimental options to decipher the ion-translocation mechanism and the osmotic and mechanical behavior of the enzyme. The single a subunit and the oligomer of c subunits are part of the stator and rotor, respectively, and operate together in the ion-translocation mechanism. During ATP synthesis, Na+ diffuses from the periplasm through the a subunit channel onto the Na+ binding site on a c subunit. From there it dissociates into the cytoplasm after the site has rotated out of the interface with subunit a. In the absence of a membrane potential, the rotor performs Brownian motions into either direction and Na+ ions are exchanged between the two compartments separated by the membrane. Upon applying voltage, however, the direction of Na+ flux and of rotation is biased by the potential. The motor generates torque to drive the rotation of the gamma subunit, thereby releasing tightly bound ATP from catalytic sites in F(1). Hence, the membrane potential plays a pivotal role in the torque-generating mechanism. This is corroborated by the fact that for ATP synthesis, at physiological rates, the membrane potential is indispensable. We propose a catalytic mechanism for torque generation by the F(o) motor that is in accord with all experimental data and is in quantitative agreement with the requirement for ATP synthesis.

Adenosine Triphosphate↗

PubMed2001

Crystal structure and kinetic analysis of beta-lactamase inhibitor protein-II in complex with TEM-1 beta-lactamase.

The structure of the 28 kDa beta-lactamase inhibitor protein-II (BLIP-II) in complex with the TEM-1 beta-lactamase has been determined to 2.3 A resolution. BLIP-II is a secreted protein produced by the soil bacterium Streptomyces exfoliatus SMF19 and is able to bind and inhibit TEM-1 with subnanomolar affinity. BLIP-II is a seven-bladed beta-propeller with a unique blade motif consisting of only three antiparallel beta-strands. The overall fold is highly similar to the core structure of the human regulator of chromosome condensation (RCC1). Although BLIP-II does not share the same fold with BLIP, the first beta-lactamase inhibitor protein for which structural data was available, a comparison of the two complexes reveals a number of similarities and provides further insights into key components of the TEM-1-BLIP and TEM-1-BLIP-II interfaces. Our preliminary results from gene knock-out studies and scanning electron microscopy also reveal a critical role of BLIP-II in sporulation.

Amino Acid Sequence↗

PubMedDate not supplied

Improving pediatric chemotherapy safety through voluntary incident reporting: lessons from the field.

BACKGROUND: A multidisciplinary team within Vanderbilt Children's Hospital (VCH) designed, developed, and implemented a pediatric chemotherapy incident reporting and improvement system (CIRIS) for pediatric oncology nurse and pharmacists. The aim of this collaboration was to improve pediatric chemotherapy by translating recommendations made by the Institute of Medicine into an operational safety improvement system that is embedded into daily care processes. METHODS: CIRIS improves chemotherapy safety by linking two distinct components: (a) a technical component that uses desktop, laptop, and portable wireless handheld computers to interface the Web-based software application for point-of-care incident reporting and on-demand retrieval of patient support information, and (b) a human component that performs process analysis, data reporting, and clinical improvement. This integrated system facilitates and supports a blame-free culture for reporting of near misses and preventable adverse drug events. RESULTS: Between February 8, 2002, and March 9, 2003, pediatric oncology nurses and chemotherapy pharmacists electronically reported 97 chemotherapy-related incidents associated with 96 unique patients. Ordering errors were the most commonly reported incidents. CIRIS improved reporting performance demonstrated using the conventional paper-based reporting system.

Antineoplastic Agents↗