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H Senn

Publications and source records attributed to H Senn.

At least 37 records · Page 2Linked to original sources
PubMed1993

Determination of the disulphide bonding pattern in proteins by local and global analysis of nuclear magnetic resonance data. Application to flavoridin.

This paper describes a new method for the elucidation of the disulphide bonding pattern in a protein from an initial set of unrefined nuclear magnetic resonance solution structures. The use of both local and global proton-proton nuclear Overhauser enhancement (NOE) distance information for the identification of the disulphide bridge network in cysteine-rich polypeptides was investigated by statistical analysis of the crystal structures of a selected group of proteins. There are six different types of inter-cysteine proton-proton distances which can potentially be used for the prediction of disulphide links. The uniqueness and the extent to which disulphide bonds could be identified by these distances was evaluated. Only NOEs between C beta H/C beta H and C alpha H/C beta H were shown to have positive predictive values for the characterization of disulphide links. Contrarily, the observation of an NOE between C alpha H and NH is a strong indication for the absence of a disulphide bridge between the two residues. The global analysis of the nuclear magnetic resonance data starts with the calculation of an initial set of conformers. First, pairing weights wij were assigned to all putative cysteine pairs in the protein according to a Gaussian-type distribution function from the C beta-C beta interatomic distances. In a second step, all conceivable disulphide patterns were formed by an exhaustive combinatorial enumeration. Statistical weights were then assigned to all patterns from the weights of the participating cysteine pairs. This method was validated with protein crystal structures deposited in the Brookhaven Protein Data Bank having three or more cysteine residues. It was then used to determine the previously unknown disulphide bonding pattern of the 12 cysteine residues of flavoridin.

Crotalid Venoms↗
PubMed1993

The nuclear magnetic resonance solution structure of flavoridin, an antagonist of the platelet GP IIb-IIIa receptor.

The snake venom protein flavoridin, a polypeptide of 70 amino acid residues, is a potent inhibitor of blood platelet aggregation. It binds to cell-surface integrin receptors such as the fibrinogen receptor glycoprotein IIb/IIIa. The inhibitory properties of flavoridin have been attributed to the tripeptide segment Arg-Gly-Asp (residues 49 to 51). This paper describes the determination of the three-dimensional structure of flavoridin in aqueous solution based on two-dimensional nuclear magnetic resonance spectroscopy. A family of 18 conformers was selected to characterize the solution structure. The molecule comprises two structural domains, an N-terminal unit extending from residues 1 to 25, and a C-terminal unit from residues 26 to 70. Whereas the mutual spatial orientation of these regions is not well defined, each one is well organized within itself. The segment 26 to 70, which is homologous to the sequence of the snake toxins echistatin and eristostatin, shows an average value of 1.0 A for the root-mean-square deviations of the backbone atoms among the 18 conformers. The structure of flavoridin consists essentially of non-repetitive elements such as tight turns and loops, whose location and conformation are characterized in this paper. With the exception of two short regions of antiparallel beta-sheet, no classic element of protein secondary structure is present. The six disulphide bridges, which have been mapped by applying a novel computational strategy (see accompanying paper), are the dominant organizational feature of the polypeptide fold of flavoridin. Two of the bridges are located in the N-terminal domain, three in the C-terminal domain and one connects the two structural units. The mobile RGD recognition sequence for integrins is located peripheral to the core region of the C-terminal domain at the most exposed end of a nine residue loop structure, which is attached to a short beta-sheet. The C terminus is close to this loop structure.

Amino Acid Sequence↗
PubMed1991

Selective 13C-labelling of cyclosporin A.

Cyclosporin A is biosynthetically labelled with 13C by growing an overproducing strain of Tolypocladium inflatum on minimal media containing either [1-13C]-, [2-13C]-, [3-13C]- or [6-13C]glucose as the only carbon source. NMR analysis of the 13C-labelled peptide showed a labelling pattern in which 13C occurs at specific sites. These can be predicted by consideration of the relevant biosynthetic pathways. Quantitation of the site-specific enrichments revealed that the 13C-label incorporation is efficient and selective. Metabolic fluxes through alternative pathways can also be estimated from these results. Isotopically labelled peptides will be a very useful tool for the study of molecular interactions with their receptors.

Amino Acid Sequence↗
PubMed1991

Interferon alfa-2b with VMCP compared to VMCP alone for induction and interferon alfa-2b compared to controls for remission maintenance in multiple myeloma: interim results.

The present trial was designed to evaluate whether interferon (IFN) combined with standard induction chemotherapy and/or interferon remission maintenance treatment improve treatment results in patients with multiple myeloma. Up to now 89 patients have received IFN plus vincristine/melphalan/cyclophosphamide/prednisolone (VMCP) as induction therapy, and 86 conventional VMCP. The proportion of patients with progressive disease was significantly lower (P less than 0.005) under IFN + VMCP as compared to the VMCP treatment group. Survival times were significantly longer (P less than 0.02) after IFN + VMCP induction therapy than after VMCP alone. In the second phase of this investigation, 33 progression-free myeloma patients were assigned to receive IFN as maintenance therapy, and 41 patients served as untreated controls. Patients maintained with IFN showed a tendency towards increased progression-free survival. Haematological side effects were observed significantly more often in patients receiving IFN, with more severe haematological toxicity in patients on the combined IFN + VMCP regimen and an increased number of patients with mild haematological toxicity in the group maintained with IFN. Other side effects, such as fever and fatigue, remained within tolerable limits. In conclusion, the preliminary results of this current clinical trial indicate significant advantages of combined IFN + VMCP induction treatment in terms of reduced disease progression and prolonged survival and possible benefits of IFN maintenance therapy in patients with multiple myeloma.

Adult↗
PubMed1991

Ceftriaxone and amikacin versus ceftazidime and amikacin in febrile granulocytopenia.

The efficacy and safety of the two antibiotic combinations, ceftazidime plus amikacin and ceftriaxone plus amikacin were compared in an open randomized trial. 100 episodes of neutropenia caused by malignant diseases and/or cytostatic drugs were evaluated in 66 males and 34 females with a mean age of 49.4 years. The types of infections treated were: septicemia 38, fever of undetermined origin 26, pneumonia 13, ear, nose and throat infections 11 and others 12. 17 episodes were not evaluable (6 protocol violations, 6 doubtful infections and 5 non-bacterial infections). The overall results were comparable, with a 74% success rate for ceftazidime and a 70% rate for ceftriaxone (criteria of the European Organization for Research and Treatment of Cancer). In the patients with septicemia, the success rate was 64% in the ceftriaxone and 57% in the ceftazidime group. Eight patients died during the treatment, in 5 cases due to infectious complications. There were no differences between the two groups in respect of efficacy or toxicity.

Adolescent↗
PubMed1989

Stereospecific nuclear magnetic resonance assignments of the methyl groups of valine and leucine in the DNA-binding domain of the 434 repressor by biosynthetically directed fractional 13C labeling.

Stereospecific 1H and 13C NMR assignments were made for the two diastereotopic methyl groups of the 14 valyl and leucyl residues in the DNA-binding domain 1-69 of the 434 repressor. These results were obtained with a novel method, biosynthetically directed fractional 13C labeling, which should be quite widely applicable for peptides and proteins. The method is based on the use of a mixture of fully 13C-labeled and unlabeled glucose as the sole carbon source for the biosynthetic production of the protein studied, knowledge of the independently established stereoselectivity of the pathways for valine and leucine biosynthesis, and analysis of the distribution of 13C labels in the valyl and leucyl residues of the product by two-dimensional heteronuclear NMR correlation experiments. Experience gained with the present project and a previous application of the same principles with the cyclic polypeptide cyclosporin A provides a basis for the selection of the optimal NMR experiments to be used in conjunction with biosynthetic fractional 13C labeling of proteins and peptides.

Carbon Isotopes↗
PubMed1989

GEOM: a new tool for molecular modelling based on distance geometry calculations with NMR data.

GEOM is a new graphics tool which allows the use of distance geometry to compute linear and cyclic structures typically arising in drug design situations. Modified amino acids or monomeric organic entities can be easily constructed in an interactive way and deposited in the library of the distance geometry program together with geometric information required for structure calculation in dihedral angle space. In addition, GEOM is able to produce all files needed to calculate a structure based on NMR data (NOE and J-coupling constraints) and it permits the graphic analysis and comparison of computed structures. The application of GEOM is demonstrated in three examples: modelling of cyclosporin A structures with and without a limited set of H-bond constraints and modelling of a cyclic hexapeptide with a full NMR data set.

Computer Graphics↗
PubMed1989

[Pulmonary changes in AIDS].

We reviewed retrospectively the clinical records of 28 patients with AIDS staged group IV according to CDC-criteria. Among these, 19 had pulmonary disease: most of them (n = 17) had pneumocystis carinii pneumonia (Pcp). 12/17 patients with proven Pcp displayed typical x-ray findings with diffuse perihilar interstitial infiltration sparing lung periphery. 3/17 had atypical features and 2 normal chest x-ray findings. These data are important to identify patients with pulmonary complications of AIDS.

Acquired Immunodeficiency Syndrome↗
PubMed1987

15N-labeled P22 c2 repressor for nuclear magnetic resonance studies of protein-DNA interactions.

The salmonella phage P22 c2 repressor was produced with 90% 15N isotope labeling of all leucines, using the expression system E. coli W3110 lac IQ¿P 125. The N-terminal DNA-binding domain 1-76 was obtained by chymotrypsin cleavage. Its characterization by biochemical techniques, mass spectrometry, and one- and two-dimensional nuclear magnetic resonance (NMR) showed that highly residue-selective isotope labeling was achieved with the minimal growth medium used. The ability to obtain such isotope labeling opens new avenues for NMR studies of protein-DNA interactions in the P22 operator system.

Escherichia coli↗
PubMed1985

Secondary hypertension and neurofibromatosis: bilateral renal artery stenosis and coarctation of the abdominal aorta.

A 34-year-old white man with generalized neurofibromatosis was found to have severe renal vascular hypertension due to a coarctation of the abdominal aorta and bilateral renal artery stenosis with saccular aneurysms. Increased renal venous renin activity showed the active involvement of the renin-angiotensin system in maintaining the hypertension. Because the patient refused surgical treatment, antihypertensive treatment with Captopril, a specific inhibitor of the angiotensin converting enzyme was used, resulting in normal blood pressure being restored over an 18 month observation period.

Adult↗
PubMed1984

The spatial structure of the axially bound methionine in solution conformations of horse ferrocytochrome c and Pseudomonas aeruginosa ferrocytochrome c551 by 1H NMR.

A generally applicable method for the determination of the spatial structure of the heme iron-bound methionine in c-type ferrocytochromes at atomic resolution is presented. It relies primarily on measurements of nuclear Overhauser effects between the individual hydrogen atoms of the axial methionine, and between individual hydrogens of the methionine and the heme group. Four different methionine conformers, corresponding to the four possible stereospecific assignments for the methionine methylene proton resonances, are generated by a structural interpretation of the nuclear Overhauser effects with the use of an interactive computer graphics technique. A unique structure and unique stereospecific resonance assignments are then obtained by discriminating between these four conformers on the basis of van der Waals' constraints and heme ring current effects on the chemical shifts. The use of the method is illustrated with studies of horse ferrocytochrome c and Pseudomonas aeruginosa ferrocytochrome c 551. Comparison with the crystal structures shows close coincidence between the methionine conformations in solution and in single crystals of these proteins.

Animals↗
PubMed1983

Coordination of the heme iron in the low-potential cytochromes c-553 from Desulfovibrio vulgaris and Desulfovibrio desulfuricans. Different chirality of the axially bound methionine in the oxidized and reduced states.

The coordination geometry at the heme iron of the cytochromes c-553 from Desulfovibrio vulgaris and Desulfovibrio desulfuricans was investigated by 1H-nuclear magnetic resonance and circular dichroism spectroscopy. Individual assignments were obtained for heme c and the axial ligands. From studies of nuclear Overhauser enhancements the axial histidine imidazole ring orientation relative to the heme group was found to coincide with other c-type cytochromes. In contrast, a new structure was observed for the axial methionine in the reduced cytochromes c-553. This includes S chirality at the iron-bound sulfur atom, but compared to cytochromes c-551 from Pseudomonads and Rhodopseudomonas gelatinosa and cytochrome c5 from Pseudomonas mendocina, which also contain S-chiral methionine, a different spatial arrangement of the gamma- and beta-methylene groups and the alpha carbon of methionine prevails. For the ferricytochromes c-553 R chirality was found for the iron-bound sulfur. This is the first observation of different methionine chirality in different oxidation states of the same c-type cytochrome.

Binding Sites↗
PubMed1983

A new spatial structure for the axial methionine observed in cytochrome c5 from Pseudomonas mendocina. Correlations with the electronic structure of heme c.

Cytochrome c5 from Pseudomonas mendocina has been isolated and the coordination geometry at the heme iron was investigated by 1H nuclear magnetic resonance and circular dichroism spectroscopy. Individual assignments were obtained for heme c and the axial ligands. From studies of nuclear Overhauser enhancements the axial histidine imidazole ring orientation relative to the heme group was found to coincide with that of other c-type cytochromes. In contrast, a new structure was observed for the axial methionine. This includes S chirality at the iron-bound sulfur atom, but compared to cytochromes c-551 from Pseudomonads and Rhodopseudomonas gelatinosa, which also contain S-chiral methionine, the spatial arrangement of the gamma- and beta-methylene groups and the alpha carbon of methionine is markedly different. Analysis of the electron spin density distribution in ferricytochrome c5 in the light of this new coordination geometry provides additional support for the hypothesis that the electronic structure of heme c is primarily governed by the orientation of the sp3 lone-pair orbital of the axial sulfur atom with respect to the heme plane.

Circular Dichroism↗
PubMed1983

Determination of the coordination geometry at the heme iron in three cytochromes c from Saccharomyces cerevisiae and from Candida krusei based on individual 1H-NMR assignments for heme c and the axially coordinated amino acids.

The 1H-NMR lines of heme c and the axial ligands in reduced and oxidized Iso-1 and Iso-2 cytochromes c from Saccharomyces cerevisiae and in cytochrome c from Candida krusei were individually assigned and the conformation of the coordination sphere of the heme iron was investigated with the use of proton-proton Overhauser enhancement measurements and circular dichroism spectroscopy. The coordination geometry of the axial methionine and the axial histidine and the electronic structure of the heme were found to be closely similar in these yeast cytochromes c and in mammalian cytochromes c. In particular, R chirality at the sulfur atom of the iron-bound methionine was observed in both groups of proteins. Additional nuclear Overhauser enhancement studies of the spatial arrangement relative to the heme group of amino acid side-chains in the heme crevice of yeast ferrocytochromes c showed that the conformational homologies extend beyond the immediate coordination sphere of the heme iron. These data provide a conformational basis for observations on the functional properties of cytochromes c from yeast and mammalian species, which were reported previously by other groups.

Binding Sites↗
PubMed1983

Individual 1H-NMR assignments for the heme groups and the axially bound amino acids and determination of the coordination geometry at the heme iron in a mixture of two isocytochromes c-551 from Rhodopseudomonas gelatinosa.

This paper describes chemical and physicochemical studies of two small isocytochromes c-551 (approx. 9000 dalton) from Rhodopseudomonas gelatinosa. In spite of numerous amino acid substitutions in the N-terminal half of the sequence the two isoproteins could not be separated by the procedures used, presumably because they have identical size, charge and isoelectric points. Individual assignments of the 1H-NMR lines of heme c and the axial ligands to the heme iron were therefore obtained by nuclear Overhauser enhancement measurements and saturation transfer experiments in a mixed solution of the two isocytochromes c-551. The conformation of the coordination sphere was investigated by additional 1H-NMR and circular dichroism studies. For both isoproteins the electronic structure of the heme and the chirality of the methionine attachment to the iron were found to coincide with those in Pseudomonas cytochromes c-551, i.e., S chirality was observed for the axial methionine. The Rps. gelatinosa cytochromes c-551 thus differ from mammalian, yeast, Euglena gracilis and Rhodospirillum rubrum cytochromes c, which all have R chirality at the axial methionine and concomitantly a characteristically different electronic heme structure. This is the first observation of S chirality of the axially bound methionine in a species outside the Pseudomonas family. The redox potentials of the two isocytochromes c-551 of Rps. gelatinosa differ by approx. 120 mV, and there is no cross-exchange of electrons between the two species. The two isoproteins could thus function in two different, parallel electron-transfer chains or at two different locations in a single transfer sequence.

Amino Acids↗
PubMed1980

3-Trifluoromethyl-3-phenyldiazirine. A new carbene generating group for photolabeling reagents.

The synthesis of 3-trifluoromethyl-3-phenyldiazirine (TPD) is reported in an overall yield of 60% based on 2,2,2-trifluoroacetophenone as starting material. TPD is rapidly photolyzed on irradiation near 350 nm to yield 35% of the diazoisomer and 65% of the corresponding carbene. No internal rearrangement of the latter compound by fluorine migration was detected. Photolysis in methanol yielded the product of a formal OH insertion in greater than 95% yield. Photolysis in cyclohexane gave at least a 50% yield of the CH insertion product at a diazirine concentration of 15 mM. The products were identified by gas chromatographic mass spectra and by 19F NMR spectra. In the dark the diazirine is stable in 1 M acid or base and at temperatures as high as 75 degrees C for at least 30 min. The diazoisomer is much less photolabile and is stable in 0.1 M acetic acid for at least 12 h. The synthesis of a derivative of TPD containing the 2-hydroxyethyl[O-tosylate] group on the para position of the phenyl ring is described. This compound permits the easy attachment of the TPD function to other molecules. It is suggested that the ease of synthesis, dark stability, rapid photolysis, and reactivity of the carbene may make this group useful in the preparation of various photochemical probes.

Affinity Labels↗