NMR detection of protein 15N spins near paramagnetic lanthanide ions.
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Ions↗
Biomedical subjects
Michael John
Publications and source records attributed to Michael John.
Assignment of paramagnetic (15)N-HSQC spectra by heteronuclear exchange spectroscopy.
Paramagnetic metal ions in proteins provide a rich source of structural information, but the resonance assignments required to extract the information can be challenging. Here we demonstrate that paramagnetically shifted (15)N-HSQC cross-peaks can be assigned using N(Z)-exchange spectroscopy under conditions in which the paramagnetic form of the protein is in dynamic equilibrium with its diamagnetic form. Even slow exchange of specifically bound metal ions may be detected within the long lifetime of (15)N longitudinal magnetization of large proteins at high magnetic fields. Alternatively, the exchange can be accelerated using an excess of metal ions. In the resulting exchange spectra, paramagnetic (15)N resonances become visible for residues that are not directly observed in a conventional (15)N-HSQC spectrum due to paramagnetic (1)H(N) broadening. The experiments are illustrated by the 30 kDa lanthanide-binding epsilon186/theta complex of DNA polymerase III in the presence of sub-stoichiometric amounts of Dy(3+) or a mixture of Dy(3+) and La(3+).
Algorithms↗
The conformation of cyclo(-D-Pro-Ala4-) as a model for cyclic pentapeptides of the DL4 type.
The conformation of the cyclic pentapeptide cyclo(-D-Pro-Ala(4)-) in solution and in the solid state was reinvestigated using modern NMR techniques. To allow unequivocal characterization of hydrogen bonds, relaxation behavior, and intramolecular distances, differently labeled isotopomers were synthesized. The NMR results, supported by extensive MD simulations, demonstrate unambiguously that the preferred conformation previously described by us, but recently questioned, is indeed correct. The validation of the conformational preferences of this cyclic peptide is important given that this system is a template for several bioactive compounds and for controlled "spatial screening" for the search of bioactive conformations.
Alanine↗
Structure determination of protein-ligand complexes by transferred paramagnetic shifts.
Rational drug design depends on the knowledge of the three-dimensional (3D) structure of complexes between proteins and lead compounds of low molecular weight. A novel nuclear magnetic resonance (NMR) spectroscopy strategy based on the paramagnetic effects from lanthanide ions allows the rapid determination of the 3D structure of a small ligand molecule bound to its protein target in solution and, simultaneously, its location and orientation with respect to the protein. The method relies on the presence of a lanthanide ion in the protein target and on fast exchange between bound and free ligand. The binding affinity of the ligand and the paramagnetic effects experienced in the bound state are derived from concentration-dependent (1)H and (13)C spectra of the ligand at natural isotopic abundance. Combined with prior knowledge of the crystal or solution structure of the protein and of the magnetic susceptibility tensor of the lanthanide ion, the paramagnetic data define the location and orientation of the bound ligand molecule with respect to the protein from simple 1D NMR spectra. The method was verified with the ternary 30 kDa complex between the lanthanide-labeled N-terminal domain of the epsilon exonuclease subunit from the Escherichia coli DNA polymerase III, the subunit theta, and thymidine. The binding mode of thymidine was found to be very similar to that of thymidine monophosphate present in the crystal structure.
DNA Polymerase III↗
Efficient chi-tensor determination and NH assignment of paramagnetic proteins.
Anisotropic magnetic susceptibility tensors chi of paramagnetic metal ions are manifested in pseudocontact shifts, residual dipolar couplings, and other paramagnetic observables that present valuable long-range information for structure determinations of protein-ligand complexes. A program was developed for automatic determination of the chi-tensor anisotropy parameters and amide resonance assignments in proteins labeled with paramagnetic metal ions. The program requires knowledge of the three-dimensional structure of the protein, the backbone resonance assignments of the diamagnetic protein, and a pair of 2D 15N-HSQC or 3D HNCO spectra recorded with and without paramagnetic metal ion. It allows the determination of reliable chi-tensor anisotropy parameters from 2D spectra of uniformly 15N-labeled proteins of fairly high molecular weight. Examples are shown for the 185-residue N-terminal domain of the subunit epsilon from E. coli DNA polymerase III in complex with the subunit theta and La3+ in its diamagnetic and Dy3+, Tb3+, and Er3+ in its paramagnetic form.
Algorithms↗
Characterization of human saposins by NMR spectroscopy.
Saposins are lipid-binding and membrane-perturbing glycoproteins of the mammalian lysosomes involved in sphingolipid and membrane digestion. Although the four human saposins (Saps), A-D, are sequence-related, they are responsible for the activation of different steps in the cascade of lysosomal glycosphingolipid degradation. Saposin activity is maximal under acidic conditions, and the pH dependence of lipid and membrane binding has been assigned to conformational variability. We have employed solution NMR spectroscopy to all four (15)N-labeled human saposins at both neutral and acidic pH. Using backbone NOEs and residual dipolar couplings, the "saposin fold" comprising five alpha-helices was confirmed for Sap-A, Sap-C, and Sap-D. Structural variations within these proteins are in the order of variations between the known structures of Sap-C and NK-lysin. In contrast, Sap-B yielded spectra of very poor quality, presumably due to conformational heterogeneity and molecular association. Sap-D exists in a slow dynamic equilibrium of two conformational states with yet unknown function. At pH 4.0, where all saposins are highly unstable, Sap-C undergoes a transition to a specific dimeric state, which is likely to resemble the structure recently found in both Sap-C in a detergent environment and crystals of Sap-B.
Amino Acid Sequence↗
Inter-domain orientation and motions in VAT-N explored by residual dipolar couplings and 15N backbone relaxation.
The N-terminal domain of VAT (Valosine-containing protein-like ATPase of Thermoplasma acidophilum), VAT-N (20.5 kDa), is considered to be the primary substrate-recognition site of the complex. The solution structure of VAT-N derived in our laboratory using conventionally obtained NMR restraints shows the existence of two equally sized sub-domains, VAT-Nn and VAT-Nc, together forming a kidney-shaped overall structure. The putative substrate-binding site of VAT-N involves free loops and a highly charged groove located on the surface of the protein. Alternatively, the opening of the cleft between the domains to accommodate substrate has been proposed to be part of the functional mechanism. We have used the residual dipolar couplings (RDCs) obtained in a bicelle medium to refine the structure of VAT-N. The long-range information available from RDCs both defines the sub-domain orientation and probes possible inter-domain motions. In addition, 15N backbone relaxation data were obtained and analysed within the model-free framework. Together, the data provides a refined structure with improved local geometry, but with the overall kidney shape intact. Further, the protein is rigid overall, with no evidence of inter-domain motions.
Adenosine Triphosphatases↗
Weak alignment of paramagnetic proteins warrants correction for residual CSA effects in measurements of pseudocontact shifts.
Paramagnetic metal ions can induce molecular alignment with respect to the magnetic field. This alignment generates residual anisotropic chemical shifts (RACS) due to nonisotropic averaging over the molecular orientations. Using a 30 kDa protein-protein complex, the RACS effects are shown to be significant for heteronuclear spins with large chemical shift anisotropies, lanthanide ions with large anisotropic magnetic susceptibility tensors, and measurements at high magnetic field. Therefore, RACS must be taken into account when pseudocontact shifts are measured by comparison of chemical shifts observed between complexes with paramagnetic and diamagnetic lanthanide ions. The results are of particular importance when different pseudocontact shifts measured for the 1HN, 15N, and 13C' spins of a peptide group are used to restrain its orientation with respect to the electronic magnetic susceptibility tensor in structure calculations.
Anisotropy↗
Comprehensive assessment of clinical outcome and quality of life after resection interposition arthroplasty of the thumb saddle joint.
OBJECTIVE: To explore the biometric and psychometric properties of clinical, generic, and condition-specific instruments and to assess quantitatively the outcome after resection interposition arthroplasty (RIAP) of the thumb saddle joint. METHODS: One hundred three patients requiring 112 arthroplasties were assessed in a 4.5-7.7-year cross-sectional catamnesis by means of 4 widely used questionnaires and clinical and radiographic examinations. RESULTS: In all dimensions of the Short Form 36 (SF-36), the outcome was equal or significantly better than expected by the norm. The Disability of the Arm, Shoulder and Hand questionnaire (DASH) revealed some small, mainly functional limitations (mean score 78.4, norm 86.4). The SF-36, the DASH, and the Patient Related Wrist Evaluation form (PRWE) correlated highly and loaded on the same factor. The Hand Function Index was independent of the clinical measurements (range of motion, strength, etc. on the specially designed Custom Form) and of the self rating. CONCLUSION: Long-term followup of 112 RIAP patients showed excellent health and quality of life. A questionnaire set consisting of the SF-36, the DASH (or alternatively the short PRWE), and the Custom Form is proposed for the comprehensive and specific assessment of thumb joint conditions.
Adult↗
Comprehensive assessment of clinical outcome and quality of life after total elbow arthroplasty.
OBJECTIVE: To assess quantitatively the outcome and to explore the physiometric and psychometric properties of clinical, generic, and condition-specific instruments after total elbow arthroplasty. METHODS: Seventy-nine patients were assessed in a 6-19-year cross-sectional catamnesis by means of 6 widely used questionnaires, clinical examinations, and radiographic examinations. RESULTS: With regard to pain, general physical health, and all the mental health dimensions of the Short Form 36 (SF-36), the patients showed scores comparable to normative values. Elbow joint stability and satisfaction were both good. Significant functional limitation was evidenced by the low mean scores of the SF-36 physical functioning measure (48.7, normative 69.9) and the Disabilities of the Arm, Shoulder and Hand questionnaire (DASH) function measure (51.1, normative 89.3). The SF-36 physical component summary and the DASH correlated highly (r = 0.76) and, in factor analysis, loaded on the factor "physical unspecific." The patient and clinical modified American Shoulder and Elbow Surgeons questionnaire (mASES) correlated with the Patient Related Elbow Evaluation form (r = 0.92 with the patient mASES) and loaded on "physical specific." The SF-36 mental component summary loaded on "mental quality of life." CONCLUSION: The patients' self-rated health, quality of life, and clinical outcome were good and were not affected by impairment in some specific functional abilities. A questionnaire set comprising the SF-36 and the patient and clinical mASES is proposed for the comprehensive and specific assessment of outcome after elbow arthroplasty.
Adult↗
Modification of soybean sucrose synthase by S-thiolation with ENOD40 peptide A.
The gene ENOD40 is expressed at an early stage of root nodule organogenesis and has been postulated to play a central regulatory role in the Rhizobium-legume interaction. In vitro translation of soybean ENOD40 mRNA showed that the gene encodes two peptides of 12 and 24aa residues (peptides A and B) that bind to sucrose synthase. Here we show that the small Cys-containing peptide A binds to sucrose synthase by disulfide bond formation, which may represent a novel form of posttranslational modification of this important metabolic enzyme. Assays using nanomolar concentrations of peptide A revealed that the monomeric reduced form of this peptide binds to purified sucrose synthase. Using a cysteinyl capture strategy combined with MALDI-TOF MS analysis we identified the Cys residue C264 of soybean sucrose synthase as the binding site of peptide A. Modification of sucrose synthase with ENOD40 peptide A activates sucrose cleavage activity whereas the synthesis activity of the enzyme is unaffected. The results are discussed in relation to the role of sucrose synthase in the control of sucrose utilization in nitrogen-fixing nodules.
Amino Acid Substitution↗
Clinical outcomes in the revision of unicondylar arthoplasties to bicondylar arthroplasties. A matched-pair study.
INTRODUCTION: The aim of the following study was to find out how much a previously implanted unicondylar prosthesis affects the clinical and functional outcome of a total knee arthroplasty in case of revision surgery. MATERIALS AND METHODS: A matched-pair comparative analysis was performed on 28 patients (group A) who required bicondylar knee arthroplasty following failed unicondylar arthroplasty and 28 patients (group B) with primary bicondylar knee arthroplasty. Both groups were matched according to age, sex, weight, height, type of prosthesis, and follow-up time after bicondylar arthroplasty. The patients' evaluation was based on the Knee Society Score and the WOMAC Score. Radiographs (AP weight-bearing and lateral) were taken of the knee. The average follow-up time after bicondylar arthroplasty was 55+/-15 months in group A and 56+/-13 months in group B. RESULTS: The knee score was 71.8+/-18 and 80.4+/-10 points (p=0.01) and the function score 56.1+/-15 and 64.1+/-19 points (p=0.1) for group A and group B, respectively. The subjective assessment according to the WOMAC Score was statistically significant in terms of the functional outcome. Increased postoperative range of motion of 109 degrees +/-11 degrees was noticed for group B in comparison with group A (101 degrees +/-8 degrees ; p=0.004). Patients revised from an unicondylar arthroplasty required a significantly thicker polyethylene inlay (12.9+/-3 mm) compared with the primarily implanted group (10.3+/-3 mm; p=0.004). CONCLUSION: Revision of an unicondylar to a bicondylar knee replacement showed inferior functional results in comparison to primary bicondylar knee arthroplasty. Patients are satisfied after conversion of an unicondylar to bicondylar prosthesis, but not quite as much as patients who received a primary bicondylar arthroplasty. However, in the small number of patients where revision surgery after failed unicondylar prosthesis is required, the patient had already been successfully treated for many years.
Aged↗
NMR studies on the substrate-binding domains of the thermosome: structural plasticity in the protrusion region.
Group II chaperonins close their cavity with the help of conserved, helical extensions, the so-called protrusions, which emanate from the apical or substrate-binding domains. A comparison of previously solved crystal structures of the apical domains of the thermosome from Thermoplasma acidophilum showed structural plasticity in the protrusion parts induced by extensive packing interactions. In order to assess the influence of the crystal contacts we investigated both the alpha and beta-apical domains (alpha-ADT and beta-ADT) in solution by NMR spectroscopy. Secondary structure assignments and 15N backbone relaxation measurements showed mostly rigid structural elements in the globular parts of the domains, but revealed intrinsic structural disorder and partial helix fraying in the protrusion regions. On the other hand, a beta-turn-motif conserved in archaeal group II chaperonins might facilitate substrate recognition. Our results help us to specify the idea of the open, substrate-accepting state of the thermosome and may provide an additional jigsaw piece in understanding the mode of substrate binding of group II chaperonins.
Archaeal Proteins↗
Expression of the GM2-activator protein in the methylotrophic yeast Pichia pastoris, purification, isotopic labeling, and biophysical characterization.
The GM2-activator protein (GM2AP) belongs to a group of five small, nonenzymatic proteins that are essential cofactors for the degradation of glycosphingolipids in the lysosome. It mediates the interaction between the water-soluble enzyme beta-hexosaminidase A and its membrane-embedded substrate, ganglioside GM2, at the lipid-water interphase. Inherited defects in the gene encoding this glycoprotein cause a fatal neurological storage disorder, the AB variant of GM2 gangliosidosis. With the aim to establish a convenient eukaryotic system that allows the efficient production of functionally folded, glycosylated GM2AP and offers the potential of cost-efficient isotopic labeling for structural studies by NMR spectroscopy, we established the expression of recombinant GM2AP in the methylotrophic yeast Pichia pastoris. For the construction of expression plasmids, either the full cDNA encoding human GM2AP preproprotein was cloned in the expression vector pPIC3.5K, or the cDNA encoding only the mature form of GM2AP was inserted in the vector pPIC9K under control of the alcohol oxidase 1 promoter. Both plasmids led to the successful secretory expression of active, glycosylated GM2AP, which could easily be purified by Ni-NTA chromatography due to the hexahistidine tag introduced at the C-terminus. Remarkably, the expression of this membrane-active protein in P. pastoris was accompanied by two peculiarities which were not encountered in other expression systems for GM2AP: First, a significant fraction of the secreted protein existed in the form of aggregates, and second, considerable amounts of noncovalently bound lipids were associated with the recombinant protein. A three-step purification scheme was therefore devised consisting of Ni-NTA, reversed phase, and gel filtration chromatography, which finally yielded 10-12 mg of purified, monomeric GM2AP per liter of expression supernatant. MALDI- and ESI-TOF mass spectrometry were employed to assess the processing, homogeneity, and glycosylation pattern of the recombinant protein. Surface plasmon resonance spectroscopy allowed the interaction of GM2AP with immobilized liposomes to be studied. A modified version of FM22 minimal medium was then used in the cost-effective (15)N-labeling of GM2AP to assess its amenability for the structural investigation by NMR spectroscopy. Initial (15)N,(1)H-HSQC experiments show a well-folded protein and provide evidence for extensive conformational exchange processes within the molecule.
Chromatography↗
Backbone 1H, 15N and 13C resonance assignments of alpha-ADT and beta-ADT.
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Carbon Isotopes↗
Performance of the TechLab C. DIFF CHEK-60 enzyme immunoassay (EIA) in combination with the C. difficile Tox A/B II EIA kit, the Triage C. difficile panel immunoassay, and a cytotoxin assay for diagnosis of Clostridium difficile-associated diarrhea.
We compared a recently marketed enzyme immunoassay for glutamate dehydrogenase (GDH), TechLab's C. DIFF CHEK-60 (TL-GDH), in combination with the C. difficile Tox A/B II enzyme immunoassay (Tox-A/B) with (i) the Triage C. difficile test, which detects both GDH (TR-GDH) and toxin A (TR-Tox-A); (ii) an in-house cytotoxin assay (C-Tox); and (iii) stool cultures for C. difficile. All C. difficile isolates were tested for the presence of the toxin genes by PCR. If a toxin gene-positive strain of Clostridium difficile was recovered and a toxin was detected by any method, the result was considered to be truly positive. Eighty-seven of 93 and 79 of 93 C. difficile culture-positive samples were also TL-GDH and TR-GDH positive, respectively. No test was able to detect toxin in all samples with true-positive results. Tox-A/B and TR-Tox-A in combination with the GDH detection tests and C-Tox were able to identify 52 and 50 samples with true-positive results. Tox-A/B and TR-Tox-A would have missed 15 and 31% of cases of C. difficile-associated diarrhea, respectively, if used alone.
Bacterial Proteins↗
Serum sickness-like reaction possibly associated with meropenem use.
Serum sickness-like reactions most commonly occur secondary to drug administration. We describe a serum sickness-like reaction that was possibly associated with meropenem therapy.
Adult↗
Oral everolimus inhibits in-stent neointimal growth.
BACKGROUND: Rapamycin (sirolimus)-eluting stents are associated with reduced restenosis rates in animal studies and initial human trials. The present study evaluated whether orally administered everolimus (a macrolide of the same family as sirolimus) inhibits in-stent neointimal growth in rabbit iliac arteries. METHODS AND RESULTS: New Zealand white rabbits were randomized to everolimus 1.5 mg/kg per day starting 3 days before stenting and reduced to 1 mg/kg per day from days 14 to 28 (group 1), everolimus 1.5 mg/kg given 1 day before stenting followed by 0.75 mg/kg per day for 28 days (group 2), or matching placebo for each group. Drugs were administered by oral gavage. Stents were deployed in both iliac arteries, and arteries were harvested 28 days after stenting. Group 1 everolimus-treated rabbits experienced weight loss and anorexia, which resolved after the everolimus dose was lowered on day 14. Group 2 animals were healthy for the duration of everolimus dosing. Both everolimus treatment groups significantly reduced in-stent neointimal growth (46% reduction and 42% reduction in intimal thickness in groups 1 and 2, respectively). In group 2 everolimus-treated animals, the neointima was healed or healing, characterized by stent struts covered by a thin neointima, overlying endothelial cells, and only small foci of fibrin. Scanning electron microscopy showed >80% stent surface endothelialization in group 2 everolimus-treated rabbits. CONCLUSIONS: Oral everolimus suppresses in-stent neointimal growth in the rabbit iliac artery. At a dose of 1.5 mg/kg given 1 day before stenting followed by 0.75 mg/kg per day for 28 days, everolimus was well tolerated and was associated with significant neointimal healing.
Administration, Oral↗