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Dusan Uhrín

Publications and source records attributed to Dusan Uhrín.

12 recordsLinked to original sources
PubMed2006

Disease-associated sequence variations congregate in a polyanion recognition patch on human factor H revealed in three-dimensional structure.

Mutations and polymorphisms in the regulator of complement activation, factor H, have been linked to atypical hemolytic uremic syndrome (aHUS), membranoproliferative glomerulonephritis, and age-related macular degeneration. Many aHUS patients carry mutations in the two C-terminal modules of factor H, which normally confer upon this abundant 155-kDa plasma glycoprotein its ability to selectively bind self-surfaces and prevent them from inappropriately triggering the complement cascade via the alternative pathway. In the current study, the three-dimensional solution structure of the C-terminal module pair of factor H has been determined. A binding site for a fully sulfated heparin-derived tetrasaccharide has been delineated using chemical shift mapping and the C3d/C3b-binding site inferred from sequence comparisons and computational docking. The resultant information allows assessment of the likely consequences of aHUS-associated amino acid substitutions in this critical region of factor H. It is striking that, excepting those likely to perturb the three-dimensional structure, aHUS-associated missense mutations congregate in the polyanion-binding site delineated in this study, thus potentially disrupting a vital mechanism for control of complement on self-surfaces in the microvasculature of the kidney. It is intriguing that a single nucleotide polymorphism predisposing to age-related macular degeneration occupies another region of factor H that harbors a polyanion-binding site.

Amino Acid Sequence↗
PubMed2006

Measurement of one-bond 13Calpha-1Halpha residual dipolar coupling constants in proteins by selective manipulation of CalphaHalpha spins.

We have developed new 2D and 3D experiments for the measurement of C(alpha)-H(alpha) residual dipolar coupling constants in (13)C and (15)N labelled proteins. Two experiments, 2D (HNCO)-(J-CA)NH and 3D (HN)CO-(J-CA)NH, sample the C(alpha)-H(alpha) splitting by means of C(alpha) magnetization, while 2D (J-HACACO)NH and 3D J-HA(CACO)NH use H(alpha) magnetization to achieve a similar result. In the 2D experiments the coupling evolution is superimposed on the evolution of the (15)N chemical shifts and the IPAP principle is used to obtain (1)H-(15)N HSQC-like spectra from which the splitting is determined. The use of a third dimension in 3D experiments reduces spectral overlap to the point where use of an IPAP scheme may not be necessary. The length of the sampling interval in the J-dimension of these experiments is dictated solely by the relaxation properties of C(alpha) or H(alpha) nuclei. This was made possible by the use of C(alpha) selective pulses in combination with either a DPFGSE or modified BIRD pulses. Inclusion of these pulse sequence elements in the J-evolution periods removes unwanted spin-spin interactions. This allows prolonged sampling periods ( approximately 25 ms) yielding higher precision C(alpha)-H(alpha) splitting determination than is achievable with existing frequency based methods.

Algorithms↗
PubMed2005

Conformation of glycosaminoglycans by ion mobility mass spectrometry and molecular modelling.

We have performed conformational analyses of heparin-derived oligosaccharide ions in the gas phase using a combination of ion-mobility mass spectrometry and molecular modelling. Negative mode electrospray ionisation was used to generate singly (disaccharide, [C12H15NO19S3Na3]-) and doubly charged (tetrasaccharides, [C24H30N2O38S6Na6]2- and [C24H31N2O35S5Na5]2-) ions containing three and six Na+ ions, respectively. Good agreement was obtained between the experimental and theoretical cross sections. The latter were obtained using modelled structures generated by the AMBER-based force field. Analysis of the conformations of the oligosaccharide ions shows that sodium cations play a major role in stabilizing these ions in the gas phase. This was seen in the formation of oligomers of the disaccharide ion and "compact" structures of tetrasaccharide ions. Interestingly, the gas phase conformations of the three tetrasaccharide ions with different primary structures were significantly different.

Carbohydrate Conformation↗
PubMed2005

1H-detected double-J-modulated INEPT-INADEQUATE for simultaneous determination of one-bond and long-range carbon-carbon connectivities and the measurement of all carbon-carbon coupling constants.

We describe a new NMR experiment, (1)H-detected double-J-modulated (DJM)-INEPT-INADEQUATE, for tracing out the carbon skeleton of molecules. This experiment allows simultaneous correlation of directly bonded carbon atoms and those separated by multiple bonds, while at the same time also providing the values of all J(CC) coupling constants. This is achieved by replacing both fixed carbon-carbon coupling evolution intervals of the INEPT-INADEQUATE experiment by variable time intervals, which are incremented in concert with the DQ evolution period (t(1)). We show that the analysis of the fine structure of cross-peaks in DJM-INEPT-INADEQUATE spectra leads to accurate values of coupling constants and give guidelines for the proper usage of the method. The proposed experiment is two times less sensitive that the original INEPT-INADEQUATE experiment. We show that, using a 600-MHz cryoprobe and 20 mg of a monosaccharide, spectra that are suitable for the analysis of coupling constants as small as 2 Hz can be obtained within 24 h. Instead of performing multiple experiments, a single DJM-INEPT-INADEQUATE experiment can thus provide a wealth of information for the structural analysis of small molecules.

Algorithms↗
PubMed2004

Functional insights from the structure of the multifunctional C345C domain of C5 of complement.

The complement protein C5 initiates assembly of the membrane attack complex. This remarkable process results in lysis of target cells and is fundamental to mammalian defense against infection. The 150-amino acid residue domain at the C terminus of C5 (C5-C345C) is pivotal to C5 function. It interacts with enzymes that convert C5 to C5b, the first step in the assembly of the membrane attack complex; it also binds to the membrane attack complex components C6 and C7 with high affinity. Here a recombinant version of this C5-C345C domain is shown to adopt the oligosaccharide/oligonucleotide binding fold, with two helices packed against a five-stranded beta-barrel. The structure is compared with those from the netrin-like module family that have a similar fold. Residues critical to the interaction with C5-convertase cluster on a mobile, hydrophobic inter-strand loop that protrudes from the open face of the beta-barrel. The opposite, helix-dominated face of C5-C345C carries a pair of exposed hydrophobic side chains adjacent to a striking negatively charged patch, consistent with affinity for positively charged factor I modules in C6 and C7. Modeling of homologous domains from complement proteins C3 and C4, which do not participate in membrane attack complex assembly, suggests that this provisionally identified C6/C7-interacting face is indeed specific to C5.

Amino Acid Sequence↗
PubMed2004

Determination of sugar structures in solution from residual dipolar coupling constants: methodology and application to methyl beta-D-xylopyranoside.

We have developed methodology for the determination of solution structures of small molecules from residual dipolar coupling constants measured in dilute liquid crystals. The power of the new technique is demonstrated by the determination of the structure of methyl beta-d-xylopyranoside (I) in solution. An oriented sample of I was prepared using a mixture of C(12)E(5) and hexanol in D(2)O. Thirty residual dipolar coupling constants, ranging from -6.44 to 4.99 Hz, were measured using intensity-based J-modulated NMR techniques. These include 15 D(HH), 4 (1)D(CH), and 11 (n)D(CH) coupling constants. The accuracy of the dipolar coupling constants is estimated to be < +/- 0.02 Hz. New constant-time HMBC NMR experiments were developed for the measurement of (n)D(CH) coupling constants, the use of which was crucial for the successful structure determination of I, as they allowed us to increase the number of fitted parameters. The structure of I was refined using a model in which the directly bonded interatom distances were fixed at their ab initio values, while 16 geometrical and 5 order parameters were optimized. These included 2 CCC and 6 CCH angles, and 2 CCCC and 6 CCCH dihedral angles. Vibrationally averaged dipolar coupling constants were used during the refinement. The refined solution structure of I is very similar to that obtained by ab initio calculations, with 11 bond and dihedral angles differing by 0.8 degrees or less and the remaining 5 parameters differing by up to 3.3 degrees . Comparison with the neutron diffraction structure showed larger differences attributable to crystal packing effects. Reducing the degree of order by using dilute liquid crystalline media in combination with precise measurement of small residual dipolar coupling constants, as shown here, is a way of overcoming the limitation of strongly orienting liquid crystals associated with the complexity of (1)H NMR spectra for molecules with more than 12 protons.

Carbohydrate Conformation↗
PubMed2004

In phase selective excitation of overlapping multiplets by gradient-enhanced chemical shift selective filters.

We have developed gradient-enhanced chemical shift selective filters (ge-CSSF) for inphase excitation of overlapping multiplets 1H. This method relies on the constructive addition of on resonance signal while off resonance magnetization is eliminated by destructive interference due to variable chemical shift evolution. This is achieved by co-addition of several FIDs acquired with a gradually incremented chemical shift evolution period. Two variable-time and one constant-time ge-CSSFs are proposed that can be combined with TOCSY, NOESY, and ROESY mixing schemes yielding highly selective 1D experiments. Analytical and numerical expressions are derived to calculate the excitation profiles of the ge-CSSFs and to examine the effects of spin-spin relaxation, the length of the CSSF increment, and selective inversion pulses. We demonstrate, both theoretically and experimentally, that CSSFs yield fast signal separation for compounds with a range of spin-spin relaxation times and chemical shift differences as small as 1-2 Hz. The use of pulsed field gradients ensures that very clean spectra are obtained. The main application of these techniques lies in analysis of mixtures where severe spectral overlap prevents the use of simple 1D selective methods.

Journal Article↗
PubMed2002

Measurement of small one-bond proton-carbon residual dipolar coupling constants in partially oriented (13)C natural abundance oligosaccharide samples: analysis of heteronuclear (1)J(CH)-modulated spectra with the BIRD inversion pulse.

Two 2D J-modulated HSQC-based experiments were designed for precise determination of small residual dipolar one-bond carbon-proton coupling constants in (13)C natural abundance carbohydrates. Crucial to the precision of a few hundredths of Hz achieved by these methods was the use of long modulation intervals and BIRD pulses, which acted as semiselective inversion pulses. The BIRD pulses eliminated effective evolution of all but (1)J(CH) couplings, resulting in signal modulation that can be described by simple modulation functions. A thorough analysis of such modulation functions for a typical four-spin carbohydrate spin system was performed for both experiments. The results showed that the evolution of the (1)H-(1)H and long-range (1)H-(13)C couplings during the BIRD pulses did not necessitate the introduction of more complicated modulation functions. The effects of pulse imperfections were also inspected. While weakly coupled spin systems can be analyzed by simple fitting of cross peak intensities, in strongly coupled spin systems the evolution of the density matrix needs to be considered in order to analyse data accurately. However, if strong coupling effects are modest the errors in coupling constants determined by the "weak coupling" analysis are of similar magnitudes in oriented and isotropic samples and are partially cancelled during dipolar coupling calculation. Simple criteria have been established as to when the strong coupling treatment needs to be invoked.

Carbon↗
PubMed2002

Solution structure of the calponin CH domain and fitting to the 3D-helical reconstruction of F-actin:calponin.

Calponin is involved in the regulation of contractility and organization of the actin cytoskeleton in smooth muscle cells. It is the archetypal member of the calponin homology (CH) domain family of actin binding proteins that includes cytoskeletal linkers such as alpha-actinin, spectrin, and dystrophin, and regulatory proteins including VAV, IQGAP, and calponin. We have determined the first structure of a CH domain from a single CH domain-containing protein, that of calponin, and have fitted the NMR-derived coordinates to the 3D-helical reconstruction of the F-actin:calponin complex using cryo-electron microscopy. The tertiary fold of this single CH domain is typical of, yet significantly different from, those of the CH domains that occur in tandem pairs to form high-affinity ABDs in other proteins. We thus provide a structural insight into the mode of interaction between F-actin and CH domain-containing proteins.

Actins↗
PubMed2002

3D HSQC-HSQMBC--increasing the resolution of long-range proton-carbon correlation experiments.

A 3D HSQC-HSQMBC experiment is proposed for increasing the separation of proton-carbon long-range correlation cross peaks, the lack of which is occasionally seen in corresponding 2D experiments. It is aimed at complex molecules with many protonated carbons exhibiting a narrow spread of 13C chemical shifts e.g., complex carbohydrates. It does not yield long-range correlation of quaternary carbons. An extra indirectly detected 1H dimension of this experiment provides additional separation of long-range correlation cross peaks by utilising the chemical shifts of protons directly attached to 13C. Evolution of single-quantum coherences throughout the entire pulse sequence ensures that the cross peaks are inphase pure absorption singlets in both indirectly detected dimensions, thus maximising the resolution and sensitivity of the experiment. Partial signal cancellation can be expected due to the antiphase character of peaks in the directly detected dimension. The intensity of cross peaks depends on the length of a single long-range evolution interval and values of both active and passive long-range coupling constants of each carbon. The 3D HSQC-HSQMBC experiment provided high quality long-range correlation spectra of a 2 mg pentasaccharide sample in 27 h. The technique can also be used for measurement of long-range heteronuclear coupling constants from pure antiphase multiplets in the directly detected dimension.

Carbon↗