RNA and DNA Binding Epitopes of the Cold Shock Protein TmCsp from the Hyperthermophile Thermotoga maritima.

Prokaryotic cold shock proteins (CSPs) are considered to play an important role in the transcriptional and translational regulation of gene expression, possibly by acting as transcription anti-terminators and "RNA chaperones". They bind with high affinity to single-stranded nucleic acids. Here we report the binding epitope of TmCsp from Thermotoga maritima for both single-stranded DNA and RNA, using heteronuclear 2D NMR spectroscopy. At "physiological" growth temperatures of TmCsp (≥ 343 K), all oligonucleotides studied have dissociation constants between 1.6 ((dT)7) and 25.2 ((dA)7) µM as determined by tryptophan fluorescence quenching. Reduction of the temperature to 303 K leads to a pronounced increase of affinity for thymidylate (dT)7 and uridylate (rU)7 heptamers with dissociation constants of 4.0 and 10.8 nM, respectively, whereas the weak binding of TmCsp to cytidylate, adenylate, and guanylate heptamers (dC)7, (dA)7, and (dT)7 is almost unaffected by temperature. The change of affinities of TmCsp for (dT)7 and (rU)7 by approximately 3 orders of magnitude shows that it represents a cold chock sensor that switches on the cold shock reaction of the cell. A temperature dependent conformational switch of the protein is required for this action. The binding epitope on TmCsp for the ssDNA and RNA heptamers is very similar and comprises ß-strands 1 and 2, the loop ß1-ß2 as well as the loops connecting ß3 with ß4 and ß4 with ß5. Besides the loop regions, surprisingly, mainly the RNA-binding motif RNP1 is involved in ssDNA and RNA binding, while only two amino acids, H28 and W29, of the postulated RNA-binding motif RNP2 interact with the uridylate and thymidylate homonucleotides, although a high affinity in the nanomolar range is achieved. This is in contrast to the binding properties of other CSPs or cold shock domains, where RNP1 as well as RNP2 are involved in binding. TmCsp takes up a unique position since it is the only one which possesses a tryptophan residue instead of a usually highly conserved phenylalanine or tyrosine residue at the end of RNP2. NMR titrations suggest that neither (dT)7 nor (rU)7 represent the full binding motif and that non-optimal intercalation of W29 into these oligonucleotides blocks the access of the RNP2 site to the DNA or RNA. NMR-experiments with (dA)7 suggest an interaction of W29 with the adenine ring. Full binding seems to require at least one single purine base well-positioned within a thymine- or uracil-rich stretch of nucleic acids.

Glucose control in intensive care: usability, efficacy and safety of Space GlucoseControl in two medical European intensive care units.

BACKGROUND: The Space GlucoseControl system (SGC) is a nurse-driven, computer-assisted device for glycemic control combining infusion pumps with the enhanced Model Predictive Control algorithm (B. Braun, Melsungen, Germany). We aimed to investigate the performance of the SGC in medical critically ill patients. METHODS: Two open clinical investigations in tertiary centers in Graz, Austria and Zurich, Switzerland were performed. Efficacy was assessed by percentage of time within the target range (4.4-8.3 mmol/L; primary end point), mean blood glucose, and sampling interval. Safety was assessed by the number of hypoglycemic episodes (≤2.2 mmol/L) and the percentage of time spent below this cutoff level. Usability was analyzed with a standardized questionnaire given to involved nursing staff after the trial. RESULTS: Forty medical critically ill patients (age, 62 ± 15 years; body mass index, 30.0 ± 8.9 kg/m2; APACHE II score, 24.8 ± 5.4; 27 males; 8 with diabetes) were included for a period of 6.5 ± 3.7 days (n = 20 in each center). The primary endpoint (time in target range 4.4 to 8.3 mmol/l) was reached in 88.3% ± 9.3 of the time and mean arterial blood glucose was 6.7 ± 0.4 mmol/l. The sampling interval was 2.2 ± 0.4 hours. The mean daily insulin dose was 87.2 ± 64.6 IU. The adherence to the given insulin dose advice was high (98.2%). While the percentage of time spent in a moderately hypoglycemic range (2.2 to 3.3 mmol/L) was low (0.07 ± 0.26% of the time), one severe hypoglycemic episode (<2.2 mmol/L) occurred (2.5% of patients or 0.03% of glucose readings). CONCLUSIONS: SGC is a safe and efficient method to control blood glucose in critically ill patients as assessed in two European medical intensive care units.

Efficacy and safety of glucose control with Space GlucoseControl in the medical intensive care unit--an open clinical investigation.

BACKGROUND: We aimed to investigate the performance of the Space GlucoseControl system (SGC) (B. Braun, Melsungen, Germany) in medical critically ill patients. The SGC is a nurse-driven, computer-assisted device for glycemic control combining infusion pumps with the enhanced Model Predictive Control algorithm. SUBJECTS AND METHODS: The trial was designed as a single-center, open clinical investigation in a nine-bed medical intensive care unit in a tertiary center in Graz, Austria. Efficacy was assessed by percentage of time within the target range (4.4-8.3 mmol/L; primary end point), mean blood glucose, and sampling interval. Safety was assessed by the number of hypoglycemic episodes (≤2.2 mmol/L). RESULTS: Twenty mechanically ventilated patients (age, 63±16 years; body mass index, 31.0±10.7 kg/m(2); Acute Physiology and Chronic Health Evaluation II score, 25.4±6.3; 14 males; six with diabetes) were included for a period of 7.0±3.6 days. Time within target range was 83.4±8.9% (mean±SD), and mean arterial blood glucose was 6.8±0.4 mmol/L. No severe hypoglycemic episodes (<2.2 mmol/L) occurred, and the percentage of time within 2.2 and 3.3 mmol/L was low (0.03±0.07%). The sampling interval was 2.0±0.4 h. The mean insulin dose was 93.5±80.1 IU/day, and the adherence to the given insulin dose advice was high (98.3%). A total of 11 unintended therapy interruptions (0.08 events/treatment day) caused by software problems occurred in four patients. CONCLUSIONS: SGC is a safe and efficient method to control blood glucose in critically ill patients in the medical intensive care unit.

Hospital glucose control: safe and reliable glycemic control using enhanced model predictive control algorithm in medical intensive care unit patients.

BACKGROUND: The aim of this study was to investigate the performance of the enhanced Model Predictive Control (eMPC) algorithm for glycemic control in medical critically ill patients for the whole length of intensive care unit (ICU) stay. METHODS: The trial was designed as a single-center, open, noncontrolled clinical investigation in a nine-bed medical ICU in a tertiary teaching hospital. In 20 patients, blood glucose (BG) was controlled with a laptop-based bedside version of the eMPC. Efficacy was assessed by percentage of time within the target range (4.4-6.1 mM; primary end point), mean BG, and BG sampling interval. Safety was assessed by the number of severe hypoglycemic episodes (<2.2 mM). RESULTS: Twenty patients (69 +/- 11 years old; body mass index, 27.4 +/- 4.5 kg/m(2); APACHE II, 25.5 +/- 5.2) were included for a period of 7.3 days (median; interquartile range, 4.4-10.2 days) in the study. Time within target range was 58.12 +/- 10.05% (mean +/- SD). For all patients with at least 7 days in the ICU, there was no statistically significant difference between the daily mean percentage of times in target range in respect of the averages. Mean arterial BG was 5.8 +/- 0.5 mM, insulin requirement was 101.3 +/- 50.7 IU/day, and mean carbohydrate intake (enteral and parenteral nutrition) was 176.4 +/- 61.9 g/day. Three hypoglycemic episodes occurred in three subjects, corresponding to a rate of 0.02 per treatment day. CONCLUSIONS: In our single-center, noncontrolled study the eMPC algorithm was a safe and reliable method to control BG in critically medical ICU patients for the whole length of ICU stay.

Evaluation of implementation of a fully automated algorithm (enhanced model predictive control) in an interacting infusion pump system for establishment of tight glycemic control in medical intensive care unit patients.

BACKGROUND: The objective of this study was to investigate the performance of a newly developed decision support system for the establishment of tight glycemic control in medical intensive care unit (ICU) patients for a period of 72 hours. METHODS: This was a single-center, open, non-controlled feasibility trial including 10 mechanically ventilated ICU patients. The CS-1 decision support system (interacting infusion pumps with integrated enhanced model predictive control algorithm and user interface) was used to adjust the infusion rate of administered insulin to normalize blood glucose. Efficacy and safety were assessed by calculating the percentage of values within the target range (80-110 mg/dl), hyperglycemic index, mean glucose, and hypoglycemic episodes (<40 mg/dl). RESULTS: The percentage of values in time in target was 47.0% (+/-13.0). The average blood glucose concentration and hyperglycemic index were 109 mg/dl (+/-13) and 10 mg/dl (+/-9), respectively. No hypoglycemic episode (<40 mg/dl) was detected. Eleven times (1.5% of all given advice) the nurses did not follow and, thus, overruled the advice of the CS-1 system. Several technical malfunctions of the device (repetitive error messages and missing data in the data log) due to communication problems between the new hardware components are shortcomings of the present version of the device. As a consequence of these technical failures of system integration, treatment had to be stopped ahead of schedule in three patients. CONCLUSIONS: Despite technical malfunctions, the performance of this prototype CS-1 decision support system was, from a clinical point of view, already effective in maintaining tight glycemic control. Accordingly, and with technical improvement required, the CS-1 system has the capacity to serve as a reliable tool for routine establishment of glycemic control in ICU patients.

Species-specific differences in the intermediate states of human and Syrian hamster prion protein detected by high pressure NMR spectroscopy.

Human (huPrP) and Syrian hamster (ShaPrP) prion proteins have barriers for mutual infectivity, although they fold into almost an identical structure. The pressure responses of huPrP and ShaPrP characterized by high pressure NMR spectroscopy show differences in their excited states, as monitored by pressure-induced chemical shifts and intensity changes of individual residues in the (15)N/(1)H HSQC spectra. Both proteins fluctuate rapidly between two well folded (native) conformations N(1) and N(2) and less frequently between N and the excited states I(1) and I(2) with local disorder that may present structural intermediates on the way to PrP(Sc). These four structural states can be observed in the hamster and human PrP. At ambient pressure, less than 5 molecules of 10,000 are in the intermediate state I(2). From the structural point of view, the different states are mutually different, particularly in positions strategically important for generating species barriers for infection. The results point to the notion that excited state conformers are important for infection and that their structural differences may crucially determine species barriers for infection.

Observation of intermediate states of the human prion protein by high pressure NMR spectroscopy.

BACKGROUND: Prions as causative agents of transmissible spongiform encephalopathies (TSEs) in humans and animals are composed of the infectious isomer, PrPSc, of the cellular prion protein, PrPC. The conversion and thus the propensity of PrPC to adopt alternative folds leads to the species-specific propagation of the disease. High pressure is a powerful tool to study the physico-chemical properties of proteins as well as the dynamics and structure of folding intermediates. RESULTS: Conformational intermediates of the human prion protein huPrPC were characterized by a combination of hydrostatic pressure (up to 200 MPa) with two-dimensional NMR spectroscopy. All pressure effects showed to be reversible and there is virtually no difference in the overall pressure response between the folded core of the N-terminal truncated huPrPC(121-230) and the full-length huPrPC(23-230). The only significant differences in the pressure response of full-length and truncated PrP suggest that E168, H187, T192, E207, E211 and Y226 are involved in a transient interaction with the unfolded N-terminus. High-pressure NMR spectroscopy indicates that the folded core of the human prion protein occurs in two structural states N1 and N2 in solution associated with rather small differences in free enthalpies (3.0 kJ/mol). At atmospheric pressure approximately 29% of the protein are already in the pressure favored conformation N2. There is a second process representing two possible folding intermediates I1 and I2 with corresponding average free enthalpies of 10.8 and 18.6 kJ/mol. They could represent preaggregation states of the protein that coexist at ambient pressure with a very small population of approximately 1.2% and less than 0.1%. Further the pressure response of the N-terminus indicates that four different regions are in a fast equilibrium with non-random structural states whose populations are shifted by pressure. CONCLUSION: We identified pressure stabilized folding intermediates of the human prion protein. The regions reflecting most strongly the transition to the intermediate states are the beta1/alpha1-loop and the solvent exposed side of alpha3. The most pressure-sensitive region (representing mainly intermediate I1) is the loop between beta-strand 1 and alpha-helix 1 (residue 139-141), indicating that this region might be the first entry point for the infectious conformer to convert the cellular protein.

High-resolution structure of the histidine-containing phosphocarrier protein (HPr) from Staphylococcus aureus and characterization of its interaction with the bifunctional HPr kinase/phosphorylase.

A high-resolution structure of the histidine-containing phosphocarrier protein (HPr) from Staphylococcus aureus was obtained by heteronuclear multidimensional nuclear magnetic resonance (NMR) spectroscopy on the basis of 1,766 structural restraints. Twenty-three hydrogen bonds in HPr could be directly detected by polarization transfer from the amide nitrogen to the carbonyl carbon involved in the hydrogen bond. Differential line broadening was used to characterize the interaction of HPr with the HPr kinase/phosphorylase (HPrK/P) of Staphylococcus xylosus, which is responsible for phosphorylation-dephosphorylation of the hydroxyl group of the regulatory serine residue at position 46. The dissociation constant Kd was determined to be 0.10 +/- 0.02 mM at 303 K from the NMR data, assuming independent binding. The data are consistent with a stoichiometry of 1 HPr molecule per HPrK/P monomer in solution. Using transversal relaxation optimized spectroscopy-heteronuclear single quantum correlation, we mapped the interaction site of the two proteins in the 330-kDa complex. As expected, it covers the region around Ser46 and the small helix b following this residue. In addition, HPrK/P also binds to the second phosphorylation site of HPr at position 15. This interaction may be essential for the recognition of the phosphorylation state of His15 and the phosphorylation-dependent regulation of the kinase/phosphorylase activity. In accordance with this observation, the recently published X-ray structure of the HPr/HPrK core protein complex from Lactobacillus casei shows interactions with the two phosphorylation sites. However, the NMR data also suggest differences for the full-length protein from S. xylosus: there are no indications for an interaction with the residues preceding the regulatory Ser46 residue (Thr41 to Lys45) in the protein of S. xylosus. In contrast, it seems to interact with the C-terminal helix of HPr in solution, an interaction which is not observed for the complex of HPr with the core of HPrK/P of L. casei in crystals.

Structure determination and ligand interactions of the PDZ2b domain of PTP-Bas (hPTP1E): splicing-induced modulation of ligand specificity.

Two versions of the PDZ2 domain of the protein tyrosine phosphatase PTP-Bas/human PTP-BL are generated by alternative splicing. The domains differ by the insertion of five amino acid residues and their affinity to the tumour suppressor protein APC. Whereas PDZ2a is able to bind APC in the nanomolar range, PDZ2b shows no apparent interaction with APC. Here the solution structure of the splicing variant of PDZ2 with the insertion has been determined using 2D and 3D heteronuclear NMR experiments. The structural reason for the changed binding specificity is the reorientation of the loop with extra five amino acid residues, which folds back onto beta-strands two and three. In addition the side-chain of Lys32 closes the binding site of the APC binding protein and the two helices, especially alpha-helix 2, change their relative position to the protein core. Consecutively, the binding site is sterically no longer fully accessible. From the NMR-titration studies with a C-terminal APC-peptide the affinity of the peptide with the protein can be estimated as 540(+/-40)microM. The binding site encompasses part of the analogous binding site of PDZ2a as already described previously, yet specific interaction sites are abolished by the insertion of amino acids in PDZ2b. As shown by high-affinity chromatography, GST-PDZ2b and GST-PDZ2a bind to phosphatidylinositol 4,5-bisphosphate (PIP(2)) micelles with a dissociation constant K(D) of 21 microM and 55 microM, respectively. In line with these data PDZ2b binds isolated, dissolved PIP(2) and PIP(3) (phosphatidylinositol 3,4,5-trisphosphate) molecules specifically with a lower K(D) of 230(+/-20)microM as detected by NMR spectroscopy. The binding site could be located by our studies and involves the residues Ile24, Val26, Val70, Asn71, Gly77, Ala78, Glu85, Arg88, Gly91 and Gln92. PIP(2) and PIP(3) binding takes place in the groove of the PDZ domain that is normally part of the APC binding site.