FMP Publications

Our publications are recorded in a searchable database since 2010, updates will be added regularly.

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Identification of hydroxyl protons, determination of their exchange dynamics, and characterization of hydrogen bonding in a microcrystallin protein
Agarwal, V., Linser, R., Fink, U., Faelber, K.; Reif, B.
J Am Chem Soc, 132:3187-3195

Tags: Solid-State NMR Spectroscopy (Reif)

Abstract: Heteronuclear correlation experiments employing perdeuterated proteins enable the observation of all hydroxyl protons in a microcrystalline protein by MAS solid-state NMR. Dipolar-based sequences allow magnetization transfers that are >50 times faster compared to scalar-coupling-based sequences, which significantly facilitates their assignment. Hydroxyl exchange rates were measured using EXSY-type experiments. We find a biexponential decay behavior for those hydroxyl groups that are involved in side chain-side chain C-O-H...O horizontal lineC hydrogen bonds. The quantification of the distances between the hydroxyl proton and the carbon atoms in the hydrogen-bonding donor as well as acceptor group is achieved via a REDOR experiment. In combination with X-ray data and isotropic proton chemical shifts, availability of (1)H,(13)C distance information can aid in the quantitative description of the geometry of these hydrogen bonds. Similarly, correlations between backbone amide proton and carbonyl atoms are observed, which will be useful in the analysis of the registry of beta-strand arrangement in amyloid fibrils.

Cyclative cleavage through dipolar cycloaddition: polymer-bound azidopeptidylphosphoranes deliver locked cis-triazolylcyclopeptides as privileged protein binders
Ahsanullah, R.J.; Rademann, J.
Angew Chem Int Ed Engl, 49:5378-5382

Tags: Medicinal Chemistry (Rademann)

Dynamic nuclear polarization of deuterated proteins
Akbey, Ü., Franks, W. T., Linden, A., Lange, S., Griffin(*), R. G., van Rossum, B. J.; Oschkinat, H.
Angew Chem Int Ed Engl, 49:7803-7806

Tags: Protein Structure (Oschkinat)

Optimum levels of exchangeable protons in perdeuterated proteins for proton detection in MAS solid-state NMR spectroscopy
Akbey, Ü., Lange, S., Trent Franks, W., Linser, R., Rehbein, K., Diehl, A., van Rossum, B. J., Reif, B.; Oschkinat, H.
J Biomol NMR, 46:67-73

Tags: Protein Structure (Oschkinat), Solid-State NMR Spectroscopy (Reif)

Abstract: We present a systematic study of the effect of the level of exchangeable protons on the observed amide proton linewidth obtained in perdeuterated proteins. Decreasing the amount of D(2)O employed in the crystallization buffer from 90 to 0%, we observe a fourfold increase in linewidth for both (1)H and (15)N resonances. At the same time, we find a gradual increase in the signal-to-noise ratio (SNR) for (1)H-(15)N correlations in dipolar coupling based experiments for H(2)O concentrations of up to 40%. Beyond 40%, a significant reduction in SNR is observed. Scalar-coupling based (1)H-(15)N correlation experiments yield a nearly constant SNR for samples prepared with < or =30% H(2)O. Samples in which more H(2)O is employed for crystallization show a significantly reduced NMR intensity. Calculation of the SNR by taking into account the reduction in (1)H T (1) in samples containing more protons (SNR per unit time), yields a maximum SNR for samples crystallized using 30 and 40% H(2)O for scalar and dipolar coupling based experiments, respectively. A sensitivity gain of 3.8 is obtained by increasing the H(2)O concentration from 10 to 40% in the CP based experiment, whereas the linewidth only becomes 1.5 times broader. In general, we find that CP is more favorable compared to INEPT based transfer when the number of possible (1)H,(1)H interactions increases. At low levels of deuteration (> or =60% H(2)O in the crystallization buffer), resonances from rigid residues are broadened beyond detection. All experiments are carried out at MAS frequency of 24 kHz employing perdeuterated samples of the chicken alpha-spectrin SH3 domain.

Arndt(*), H. D., Hackenberger(*), C. P. R.; Schwarzer, D.
Chem Unserer Zeit, 44:130-137

Tags: Protein Chemistry (Schwarzer)

High Resolution H-1-Detected Solid-State NMR Spectroscopy of Protein Aliphatic Resonances: Access to Tertiary Structure Information
Asami, S., Schmieder, P.; Reif, B.
J. Am. Chem. Soc., 132:15133-15135

Tags: Solid-State NMR Spectroscopy (Reif), Solution NMR (Schmieder)

Abstract: Biological magic angle spinning (MAS) solid-state nuclear magnetic resonance spectroscopy has developed rapidly over the past two decades. For the structure determination of a protein by solid-state NMR, routinely C-13,C-13 distance restraints as well as dihedral restraints are employed. In protonated samples, this is achieved by growing the bacterium on a medium which contains [1,3]-C-13 glycerol or [2]-C-13 glycerol to dilute the C-13 spin system. Labeling schemes, which rely on heteronuclei, are insensitive both for detection and in terms of quantification of distances, since they are relying on low-gamma nuclei. Proton detection can in principle provide a gain in sensitivity by a factor of 8 and 31, compared to the C-13 or N-15 detected version of the experiment. We report here a new labeling scheme, which enables H-1-detection of aliphatic resonances with high resolution in MAS solid-state NMR spectroscopy. We prepared microcrystals of the SH3 domain of chicken a-spectrin with 5% protonation at nonexchangeable sites and obtained line widths on the order of 25 Hz for aliphatic H-1 resonances. We show further that C-13 resolved 3D-H-1,H-1 correlation experiments yield access to long-range proton-proton distances in the protein.

Synthesis and thermodynamic characterization of small cyclic antimicrobial arginine and tryptophan-rich peptides with selectivity for Gram-negative bacteria
Bagheri, M.
Methods Mol Biol, 618:87-109

Tags: Peptide-Lipid-Interaction/ Peptide Transport (Dathe)

Abstract: One promising strategy to combat the proliferation of bacteria resistance toward current antibiotics is the development of peptide-based drug. Among these compounds is a group of small cyclic peptides rich in arginine (Arg) and tryptophan (Trp) residues with selective toxicity toward Gram-negative bacteria. The small size of these peptides with improved toxicity toward Gram-negative bacteria makes them an interesting candidate to understand the forces responsible for their selectivity and paves the way to develop new therapeutics with potent activity toward multi-resistant Gram-negative bacteria. To reach this goal, isothermal titration calorimetry (ITC) is a useful technique which may provide the complete set of thermodynamic parameters of the interaction of peptides with lipid bilayers mimicking the properties of bacterial membranes within a few hours. The purpose of this chapter is to describe the synthesis of this group of small synthetic antimicrobial peptides together with the application of ITC to study their interaction with lipid membranes.

New function for an old enzyme: NEP deficient mice develop late-onset obesity
Becker, M., Siems, W. E., Kluge(*), R., Gembardt(*), F., Schultheiss(*), H. P., Schirner(*), M.; Walther(*), T.
Plos One, 5

Tags: Biochemical Neurobiology (Siems)

Abstract: BACKGROUND: According to the World Health Organization (WHO) there is a pandemic of obesity with approximately 300 million people being obese. Typically, human obesity has a polygenetic causation. Neutral endopeptidase (NEP), also known as neprilysin, is considered to be one of the key enzymes in the metabolism of many active peptide hormones. METHODOLOGY/PRINCIPAL FINDINGS: An incidental observation in NEP-deficient mice was a late-onset excessive gain in body weight exclusively from a ubiquitous accumulation of fat tissue. In accord with polygenetic human obesity, mice were characterized by deregulation of lipid metabolism, higher blood glucose levels, with impaired glucose tolerance. The key role of NEP in determining body mass was confirmed by the use of the NEP inhibitor candoxatril in wild-type mice that increased body weight due to increased food intake. This is a peripheral and not a central NEP action on the switch for appetite control, since candoxatril cannot cross the blood-brain barrier. Furthermore, we demonstrated that inhibition of NEP in mice with cachexia delayed rapid body weight loss. Thus, lack in NEP activity, genetically or pharmacologically, leads to a gain in body fat. CONCLUSIONS/SIGNIFICANCE: In the present study, we have identified NEP to be a crucial player in the development of obesity. NEP-deficient mice start to become obese under a normocaloric diet in an age of 6-7 months and thus are an ideal model for the typical human late-onset obesity. Therefore, the described obesity model is an ideal tool for research on development, molecular mechanisms, diagnosis, and therapy of the pandemic obesity.

Genetic defects, thyroid growth and malfunctions of the TSHR in pediatric patients
Biebermann(*), H., Winkler(*), F.; Kleinau, G.
Front Biosci-Landmrk, 15:913-933

Tags: Structural Bioinformatics and Protein Design (Krause, G.)

Abstract: Naturally occurring activating and inactivating mutations of the thyrotropin receptor (TSHR) were found as a molecular cause of diseases in patients suffering from non-autoimmune hyperthyroidism and syndromes of thyrotropin resistance, respectively. These mutations are mostly functionally characterized in vitro and therefore, they represent an excellent tool to study structure-function relationships of this G-protein-coupled receptor. In this review, we summarize published germline mutations of the TSHR with focus on 1) the phenotype of (pediatric) patients, 2) potential genotype/phenotype correlations, 3) structural implications for receptor activation and inactivation, 4) the impact on thyroid growth, and 5) finally on aspects of TSHR dimerization. In conclusion, this comprehensive analysis of medical and biological data opens an avenue to understand genetic defects and malfunctions of the TSHR in molecular detail and in their entirety. This knowledge is important to refine our insights in non-autoimmune diseases caused by defects of the TSHR gene and it might help to develop pharmacological means for compensation of uncontrolled thyroid growth.

Alpha-helical transmembrane peptides: a "divide and conquer" approach to membrane proteins
Bordag, N.; Keller, S.
Chem Phys Lipids, 163:1-26

Tags: Biophysics of Membrane Proteins (Keller)

Abstract: Alpha-helical membrane proteins fulfill many vital roles in all living cells and constitute the majority of drug targets. However, their relevance is in no way paralleled by our current understanding of their structures and functions. This is because membrane proteins present a number of experimental obstacles that are difficult to surmount by classical methods developed for water-soluble proteins. Moreover, membrane proteins are not only challenging on their very own but, when embedded in a biological membrane, also reside in an outstandingly complex milieu. These difficulties have fostered a "divide and conquer" approach, in which a membrane protein is dissected into shorter and easier-to-handle transmembrane (TM) peptides. Under suitable conditions, such peptides fold independently and retain many of the properties displayed in the context of the full-length parent protein. This contribution reviews some of the most notable insights into alpha-helical membrane proteins gleaned from experiments on protein-derived TM peptides. We recapitulate some peculiar properties of lipid bilayers that render them such a complex and unique environment and discuss generic features pertaining to hydrophobic peptides derived from alpha-helical membrane proteins. The main part of the review is devoted to a critical discussion of particularly interesting examples of TM peptides studied in membrane-mimetic systems of increasing complexity: isotropic solvents, detergent micelles, lipid bilayers, and biological membranes. The unifying theme is to explore to what extent TM peptides in combination with different membrane-mimetic systems can aid in advancing our knowledge and comprehension of alpha-helical membrane proteins as well as in developing new pharmacological tools.

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Leibniz-Forschungsinstitut für Molekulare Pharmakologie im Forschungsverbund Berlin e.V. (FMP)
Campus Berlin-Buch
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