Harri Koskela - Academia.edu (original) (raw)

Papers by Harri Koskela

Research paper thumbnail of CHEMSEA Findings

Jacek Bełdowski | Scientific & Project Coordinator +48 600 397 282; +48 58 731 17 37 | hyron@iopa... more Jacek Bełdowski | Scientific & Project Coordinator +48 600 397 282; +48 58 731 17 37 | hyron@iopan.gda.pl Joanna Potrykus | Project Communication +48 58 731 17 18 | potrykus@iopan.gda.pl Marta Szubska | Laboratory Manager +48 58 731 17 34 | szubi@iopan.gda.pl Zygmunt Klusek | Scientific Coordinator of Detection +48 58 731 16 25 | klusek@iopan.gda.pl Polish Naval Academy (PNA / AMW)

Research paper thumbnail of CAGEBIRD: improving the GBIRD filter with a CPMG sequence

Journal of Magnetic Resonance, 2004

An improvement of the GBIRD-filter is presented. The current approach utilizes Carr–Purcell–Meibo... more An improvement of the GBIRD-filter is presented. The current approach utilizes Carr–Purcell–Meiboom–Gill type pulse train during the BIRD delay. The method enables recording of purely absorptive 1D spectrum using only one isotope editing element. In the current method, the parent signal leakage due to JHH evolution during the BIRD delay is considerably smaller than in the conventional approach. As a

Research paper thumbnail of Evaluation of Different Sample Preparation Methods for Detection of Degradation Products of Mustard Gas in Decontamination Solutions

Several sample preparation methods were evaluated to find conditions for determination of the mai... more Several sample preparation methods were evaluated to find conditions for determination of the main reaction pathways and degradation products of mustard gas in four different decontamination solutions, i.e. Finnish emulsion E-2000, BX-24, GD-5 and GDS-2000.

Research paper thumbnail of Degradation Products of Mustard Gas in Decontamination

Four decontamination solutions were investigated to determine the main reaction pathways and degr... more Four decontamination solutions were investigated to determine the main reaction pathways and degradation products of mustard gas in short reaction times. Several sample preparation and analytical methods, including GC, GC-MS, LC-MS, LC-MSMS and NMR, were used. In addition, AMDIS software was applied to LC-MS studies.

Research paper thumbnail of 1H, 13C and 15N resonance assignments of the human filamin A tandem immunoglobulin-like domains 16–17 and 18–19

Biomolecular NMR Assignments, 2009

Filamins are large actin-binding and cross-linking proteins which act as linkers between the cyto... more Filamins are large actin-binding and cross-linking proteins which act as linkers between the cytoskeleton and various signaling proteins. Filamin A (FLNa) is the most abundant of the three filamin isoforms found in humans. FLNa contains an N-terminal actin-binding domain and 24 immunoglobulin-like (Ig) domains. The Ig domains are responsible for the FLNa dimerization and most of the interactions that FLNa has with numerous other proteins. There are several crystal and solution structures from isolated single Ig domains of filamins in the PDB database, but only few from longer constructs. Here, we present nearly complete chemical shift assignments of FLNa tandem Ig domains 16-17 and 18-19. Chemical shift mapping between FLNa tandem Ig domain 16-17 and isolated domain 17 suggests a novel domain-domain interaction mode.

Research paper thumbnail of Nuclear Magnetic Resonance Spectroscopy in Analysis of Chemicals Related to the Chemical Weapons Convention

Applications, Theory and Instrumentation, 2006

ABSTRACT

Research paper thumbnail of Rapid Chemical Characterisation of Stilbenes in the Root Bark of Norway Spruce by Off-line HPLC/DAD-NMR

Phytochemical Analysis, 2014

Introduction -Stilbenes are plant secondary metabolites that have shown promising and varied biol... more Introduction -Stilbenes are plant secondary metabolites that have shown promising and varied biological activities. Stilbenes are presently actively studied for the exploitation of this primary raw material resource, involving the concept of biorefining. Methods for the rapid discovery of new and known stilbene structures from various plant sources are thus keenly sought. Objective -To establish a simple and rapid technique of off-line HPLC with a diode-array detector (DAD) and NMR for the unambiguous structural elucidation of stilbene structures in the root bark of Norway spruce [Picea abies (L.) Karst.]. Material and methods -The stilbene containing fraction was extracted from the plant bark with an ethanol:water mixture (95:5, v/v) preceded by defatting of hydrophobic compounds with n-hexane using the accelerated solvent extraction technique. A portion of the ethanol-water soluble extract was hydrolysed with β-glucosidase to prepare stilbene aglycones. The extracts were further purified and enriched using a polymeric adsorbent. Stilbene-enriched extracts were directly characterised by off-line HPLC/DAD-NMR in conjunction with HPLC/DAD and HPLC/DAD with electrospray ionisation MS n . Results -Trans-isorhapontin and trans-astringin were identified as the major, and trans-piceid as a minor, stilbene glucosides of the bark of roots of Picea abies. Not only stilbene glucosides but also the corresponding stilbene aglycones, such as trans-resveratrol, trans-piceatannol and trans-isorhapontigenin, were rapidly identified from the hydrolysed extract. The acquired heteronuclear single-quantum coherence and heteronuclear multiple bond correlation spectra were used to assign the complete carbon NMR chemical shifts of trans-isorhapontin and trans-astringin without the need of acquiring a 13 C-NMR spectrum. Conclusion -The off-line HPLC/DAD-NMR method is expedient for the unambiguous identication of structurally similar stilbenes in plant extracts.

Research paper thumbnail of Hafnium Bis(phenoxyimino) Dibenzyl Complexes and Their Activation toward Olefin Polymerization

Organometallics, 2007

ABSTRACT Hf bis(phenoxyimino) dibenzyl complexes bearing benzylimino and perfluorophenylimino gro... more ABSTRACT Hf bis(phenoxyimino) dibenzyl complexes bearing benzylimino and perfluorophenylimino groups were prepared by a direct reaction between the desired ligand precursors and Hf(CH2Ph)4. In the solid state, the Hf complexes adopt an octahedral configuration where imino nitrogens are in positions cis to each other and oxygens occupy apical vertices of the coordination polyhedron. According to 1H NMR and 2D-NOESY studies, this cis-N,N configuration was also maintained in solution. In addition, the structures of Hf bis(phenoxyimino) dibenzyl complexes were studied with DFT calculations. Activation of the Hf dibenzyl complexes with B(C6F5)3 led to the highly air-, moisture-, solvent-, and temperature-sensitive cationic bis(phenoxyimino) Hf monobenzyl species, which were further investigated by 1H and 19F NMR, 1H−13C heteronuclear correlation, 2D-NOESY, and ESI-MS methods. It was observed that the cationic, benzylimino-substituted Hf complexes have a propensity toward CH activation. The correlation between the stability of the cationic species toward CH activation and the catalytic behavior of the MAO-activated dibenzyl complexes was established. Accordingly, the MAO-activated Hf bis(phenoxyimino) dibenzyl complexes and their dichloro analogues, depending on the ligand substitution, have from low to very high catalytic activities (up to 14 000 kg of PE/((mol of cat.) h (bar of ethylene))) in ethylene polymerizations. In general, the produced polyethylene had a monomodal molar mass distribution with relatively narrow polydispersity. Polypropylene produced with perfluorophenyl-substituted Hf complexes had a large amount of 2,1-misinsertions in the polymer chains. To further shed light on the catalytic reaction, polymerizations of ethylene and propylene with the cationic species generated from Hf bis(phenoxyimino) dibenzyl complexes with B(C6F5)3 were studied with 1H NMR.

Research paper thumbnail of Evaluation of protein15N relaxation times by inverse Laplace transformation

Magnetic Resonance in Chemistry, 2004

Relaxation times (T 1 , T 2 , T 1r ) are usually evaluated from exponential decay data by least-s... more Relaxation times (T 1 , T 2 , T 1r ) are usually evaluated from exponential decay data by least-squares fitting methods. For this procedure, the integrals or amplitudes of signals must be determined, which can be laborious with large data sets. Moreover, the fitting requires a priori knowledge of the number of exponential components responsible for the decay. We have adapted inverse Laplace transformation (ILT) for the analysis of relaxation data. Exponential components are resolved with ILT to reciprocal space on their corresponding relaxation rate values. The ILT approach was applied to 3D linewidth-resolved 15 N HSQC experiments to evaluate 15 N T 1 and T 2 relaxation times of ubiquitin. The resulting spectrum is a true 3D spectrum, where the signals are separated by their 1 H and 15 N chemical shifts (HSQC correlations) and by their relaxation rate values (R 1 or R 2 /. From this spectrum, the relaxation times can be obtained directly with a simple peak-picking procedure.

Research paper thumbnail of Quantitative determination of aliphatic hydrocarbon compounds by 2D NMR

Magnetic Resonance in Chemistry, 2002

ABSTRACT

Research paper thumbnail of Continuous H/D exchange of aromatic hydrocarbons using near-critical deuterium oxide

The Journal of Supercritical Fluids, 2007

Near-and supercritical D 2 O is both a relatively cheap deuterium source and an environmentally b... more Near-and supercritical D 2 O is both a relatively cheap deuterium source and an environmentally benign solvent for batch-wise H/D exchange reactions. In this work, a new continuous flow reactor online-coupled with liquid-liquid extraction was constructed for the selective deuteration of aromatic hydrocarbons in pressurized hot D 2 O at short contact times. Exchange positions were identified by GC-MS, 1 H NMR, and FTIR analysis. Four aromatic hydrocarbons (eugenol, 9-fluorenone, 4-hydroxyacetophenone, and xanthone) were screened for H/D exchange in conventional batch reactors with use of near-and supercritical D 2 O (p = 300 bar, t = 2 h, T = 250-450 • C) alone and with basic or metal catalyst (Na 2 CO 3 , Pd/C). Highest isotopic purities were obtained for deuteration of eugenol (d 1 = 59%) and 4-hydroxyacetophenone (d 5 = 91%) in the absence of catalyst. 2 H-labelling of these two compounds was then investigated in continuous flow experiments (p = 300 bar, T = 250-350 • C, τ = 1-4 min). Under optimized conditions, high isotopic purities were obtained for eugenol (d 1 = 61%) and 4-hydroxyacetophenone (d 5 = 82%), as before in batch runs, but the contact time, and the probability of decomposition, were significantly reduced. The continuous process developed offers good potential for the deuteration of thermally sensitive substrates.

Research paper thumbnail of Some aspects of quantitative 2D NMR

Journal of Magnetic Resonance, 2005

We have studied the application of 2D HSQC for quantitative measurements and propose some improve... more We have studied the application of 2D HSQC for quantitative measurements and propose some improvements to the previously published Q-HSQC method. Application of CPMG-INEPT for polarization transfer period suppresses the evolution of J(HH), and thus corrects the shape of the cross-peaks. The better cross-peak shape makes phase correction and integration of the cross-peaks easier. Further, the (13)C resonance offset dependency can have a significant influence to the results. The offset effects can be compensated either by correcting results with a proper coefficient, or using 90 degrees composite (13)C pulses in the pulse sequence. The results show that these modifications improve the applicability of 2D HSQC for quantitative analysis when studying molecules possessing large J(HH) couplings and wide (13)C chemical shift range.

Research paper thumbnail of Quantitative two-dimensional HSQC experiment for high magnetic field NMR spectrometers

Journal of Magnetic Resonance, 2010

The finite RF power available on carbon channel in proton-carbon correlation experiments leads to... more The finite RF power available on carbon channel in proton-carbon correlation experiments leads to non-uniform cross peak intensity response across carbon chemical shift range. Several classes of broadband pulses are available that alleviate this problem. Adiabatic pulses provide an excellent magnetization inversion over a large bandwidth, and very recently, novel phase-modulated pulses have been proposed that perform 90 degrees and 180 degrees magnetization rotations with good offset tolerance. Here, we present a study how these broadband pulses (adiabatic and phase-modulated) can improve quantitative application of the heteronuclear single quantum coherence (HSQC) experiment on high magnetic field strength NMR spectrometers. Theoretical and experimental examinations of the quantitative, offset-compensated, CPMG-adjusted HSQC (Q-OCCAHSQC) experiment are presented. The proposed experiment offers a formidable improvement to the offset performance; (13)C offset-dependent standard deviation of the peak intensity was below 6% in range of+/-20 kHz. This covers the carbon chemical shift range of 150 ppm, which contains the protonated carbons excluding the aldehydes, for 22.3 T NMR magnets. A demonstration of the quantitative analysis of a fasting blood plasma sample obtained from a healthy volunteer is given.

Research paper thumbnail of LR-CAHSQC: an application of a Carr–Purcell–Meiboom–Gill-type sequence to heteronuclear multiple bond correlation spectroscopy

Journal of Magnetic Resonance, 2003

A new pulse sequence, long-range CPMG-adjusted heteronuclear single quantum coherence (LR-CAHSQC)... more A new pulse sequence, long-range CPMG-adjusted heteronuclear single quantum coherence (LR-CAHSQC), is proposed for the determination of long-range JCH coupling constants from a long-range 1H-13C correlation experiment. The long-range heteronuclear coupling constants can be directly extracted from COSY-type antiphase peak patterns. The current approach utilizes CPMG-sequences for polarization transfer, and thus avoids the evolution of homonuclear JHH couplings, which normally may introduce abnormalities into the cross peak pattern. The differences between LR-CAHSQC and normal LR-HSQC are discussed.

Research paper thumbnail of Application of Quantitative Artificial Neural Network Analysis to 2D NMR Spectra of Hydrocarbon Mixtures

Journal of Chemical Information and Modeling, 2002

Understanding relationships between the structure and composition of molecular mixtures and their... more Understanding relationships between the structure and composition of molecular mixtures and their chemical properties is a main industrial aim. One central field of research is oil chemistry where the key question is how the molecular characteristics of composite hydrocarbon mixtures can be associated with the macroscopic properties of the oil products. Apparently these relationships are complex and often nonlinear and therefore call for advanced spectroscopic techniques. An informative and an increasingly used approach is two-dimensional nuclear magnetic resonance (2D NMR) spectroscopy. In the case of composite hydrocarbons the application of 2D NMR methodologies in a quantitative manner pose many technical difficulties, and, in any case, the resulting spectra contain many overlapping resonances that challenge the analytical work. Here, we present a general methodology, based on quantitative artificial neural network (ANN) analysis, to resolve overlapping information in 2D NMR spectra and to simultaneously assess the relative importance of multiple spectral variables on the sample properties. The results in a set of 2D NMR spectra of oil samples illustrate, first, that use of ANN analysis for quantitative purposes is feasible also in 2D and, second, that this methodology offers an intrinsic opportunity to assess the complex and nonlinear relationships between the molecular composition and sample properties. The presented ANN methodology is not limited to the analysis of NMR spectra but can also be applied in a manner similar to other (multidimensional) spectroscopic data.

Research paper thumbnail of Solution structure of the first immunoglobulin domain of human myotilin

Journal of Biomolecular NMR, 2009

Myotilin is a 57 kDa actin-binding and -bundling protein that consists of a unique serine-rich am... more Myotilin is a 57 kDa actin-binding and -bundling protein that consists of a unique serine-rich amino-terminus, two Ig-domains and a short carboxy-terminus with a PDZ-binding motif. Myotilin localizes in sarcomeric Z-discs, where it interacts with several sarcomeric proteins. Point mutations in myotilin cause muscle disorders morphologically highlighted by sarcomeric disarray and aggregation. The actin-binding and dimerization propensity of myotilin has been mapped to the Ig-domains. Here we present high-resolution structure of the first Ig-domain of myotilin (MyoIg1) determined with solution state NMR spectroscopy. Nearly complete chemical shift assignments of MyoIg1 were achieved despite several missing backbone 1H-15N-HSQC signals. The structure derived from distance and dihedral angle restraints using torsion angle dynamics was further refined using molecular dynamics. The structure of MyoIg1 exhibits I-type Ig-fold. The absence of several backbone 1H-15N-HSQC signals can be explained by conformational exchange taking place at the hydrophobic core of the protein.

Research paper thumbnail of Rapid and accurate processing method for amide proton exchange rate measurement in proteins

Journal of Biomolecular NMR, 2007

Exchange between protein backbone amide hydrogen and water gives relevant information about solve... more Exchange between protein backbone amide hydrogen and water gives relevant information about solvent accessibility and protein secondary structure stability. NMR spectroscopy provides a convenient tool to study these dynamic processes with saturation transfer experiments. Processing of this type of NMR spectra has traditionally required peak integration followed by exponential fitting, which can be tedious with large data sets. We propose here a computer-aided method that applies inverse Laplace transform in the exchange rate measurement. With this approach, the determination of exchange rates can be automated, and reliable results can be acquired rapidly without a need for manual processing.

Research paper thumbnail of Atomic Structures of Two Novel Immunoglobulin-like Domain Pairs in the Actin Cross-linking Protein Filamin

Journal of Biological Chemistry, 2009

Filamins are actin filament cross-linking proteins composed of an N-terminal actin-binding domain... more Filamins are actin filament cross-linking proteins composed of an N-terminal actin-binding domain and 24 immunoglobulin-like domains (IgFLNs). Filamins interact with numerous proteins, including the cytoplasmic domains of plasma membrane signaling and cell adhesion receptors. Thereby filamins mechanically and functionally link the cell membrane to the cytoskeleton. Most of the interactions have been mapped to the C-terminal IgFLNs 16-24. Similarly, as with the previously known compact domain pair of IgFLNa20-21, the two-domain fragments IgFLNa16-17 and IgFLNa18-19 were more compact in small angle x-ray scattering analysis than would be expected for two independent domains. Solution state NMR structures revealed that the domain packing in IgFLNa18-19 resembles the structure of IgFLNa20-21. In both domain pairs the integrin-binding site is masked, although the details of the domain-domain interaction are partly distinct. The structure of IgFLNa16-17 revealed a new domain packing mode where the adhesion receptor binding site of domain 17 is not masked. Sequence comparison suggests that similar packing of three tandem filamin domain pairs is present throughout the animal kingdom, and we propose that this packing is involved in the regulation of filamin interactions through a mechanosensor mechanism.

Research paper thumbnail of NMR properties of conjugated linoleic acid (CLA) methyl ester hydroperoxides

Chemistry and Physics of Lipids, 2008

a b s t r a c t NMR data on lipid hydroperoxides is scarce. In this study, hydroperoxides were pr... more a b s t r a c t NMR data on lipid hydroperoxides is scarce. In this study, hydroperoxides were produced from methyl 9-cis,11-trans-octadecadienoate and from methyl 10-trans,12-cis-octadecadienoate by autoxidation in the presence of 20% of ␣-tocopherol. Ten different hydroperoxides were isolated from the autoxidation mixtures of the two conjugated linoleic acid (CLA) methyl esters by SPE and HPLC. The assignment of the 1 H and 13 C NMR spectra of these hydroperoxides was accomplished by 2D NMR experiments and by spectral simulations. Substitution of a hydroperoxyl group at the allylic position in CLA methyl esters induced a 53.93 ppm downfield shift on the hydroperoxyl-bearing carbon resonance. The effects on the olefinic ␣, ␤, ␥, and ␦ carbon resonances were −3.45, +4.96, −1.22, and +4.42 ppm, respectively. Furthermore, the solvent effects of deuterochloroform, deuteroacetone, and deuterobenzene on the 13 C resonances of the hydroperoxides suggest that deuterochloroform is the appropriate solvent for 13 C NMR studies on mixtures of lipid hydroperoxides.

Research paper thumbnail of Solution structure of the parvulin-type PPIase domain of Staphylococcus aureus PrsA – Implications for the catalytic mechanism of parvulins

BMC Structural Biology, 2009

Background: Staphylococcus aureus is a Gram-positive pathogenic bacterium causing many kinds of i... more Background: Staphylococcus aureus is a Gram-positive pathogenic bacterium causing many kinds of infections from mild respiratory tract infections to life-threatening states as sepsis. Recent emergence of S. aureus strains resistant to numerous antibiotics has created a need for new antimicrobial agents and novel drug targets. S. aureus PrsA is a membrane associated extracytoplasmic lipoprotein which contains a parvulin-type peptidyl-prolyl cis-trans isomerase domain. PrsA is known to act as an essential folding factor for secreted proteins in Gram-positive bacteria and thus it is a potential target for antimicrobial drugs against S. aureus.

Research paper thumbnail of CHEMSEA Findings

Jacek Bełdowski | Scientific & Project Coordinator +48 600 397 282; +48 58 731 17 37 | hyron@iopa... more Jacek Bełdowski | Scientific & Project Coordinator +48 600 397 282; +48 58 731 17 37 | hyron@iopan.gda.pl Joanna Potrykus | Project Communication +48 58 731 17 18 | potrykus@iopan.gda.pl Marta Szubska | Laboratory Manager +48 58 731 17 34 | szubi@iopan.gda.pl Zygmunt Klusek | Scientific Coordinator of Detection +48 58 731 16 25 | klusek@iopan.gda.pl Polish Naval Academy (PNA / AMW)

Research paper thumbnail of CAGEBIRD: improving the GBIRD filter with a CPMG sequence

Journal of Magnetic Resonance, 2004

An improvement of the GBIRD-filter is presented. The current approach utilizes Carr–Purcell–Meibo... more An improvement of the GBIRD-filter is presented. The current approach utilizes Carr–Purcell–Meiboom–Gill type pulse train during the BIRD delay. The method enables recording of purely absorptive 1D spectrum using only one isotope editing element. In the current method, the parent signal leakage due to JHH evolution during the BIRD delay is considerably smaller than in the conventional approach. As a

Research paper thumbnail of Evaluation of Different Sample Preparation Methods for Detection of Degradation Products of Mustard Gas in Decontamination Solutions

Several sample preparation methods were evaluated to find conditions for determination of the mai... more Several sample preparation methods were evaluated to find conditions for determination of the main reaction pathways and degradation products of mustard gas in four different decontamination solutions, i.e. Finnish emulsion E-2000, BX-24, GD-5 and GDS-2000.

Research paper thumbnail of Degradation Products of Mustard Gas in Decontamination

Four decontamination solutions were investigated to determine the main reaction pathways and degr... more Four decontamination solutions were investigated to determine the main reaction pathways and degradation products of mustard gas in short reaction times. Several sample preparation and analytical methods, including GC, GC-MS, LC-MS, LC-MSMS and NMR, were used. In addition, AMDIS software was applied to LC-MS studies.

Research paper thumbnail of 1H, 13C and 15N resonance assignments of the human filamin A tandem immunoglobulin-like domains 16–17 and 18–19

Biomolecular NMR Assignments, 2009

Filamins are large actin-binding and cross-linking proteins which act as linkers between the cyto... more Filamins are large actin-binding and cross-linking proteins which act as linkers between the cytoskeleton and various signaling proteins. Filamin A (FLNa) is the most abundant of the three filamin isoforms found in humans. FLNa contains an N-terminal actin-binding domain and 24 immunoglobulin-like (Ig) domains. The Ig domains are responsible for the FLNa dimerization and most of the interactions that FLNa has with numerous other proteins. There are several crystal and solution structures from isolated single Ig domains of filamins in the PDB database, but only few from longer constructs. Here, we present nearly complete chemical shift assignments of FLNa tandem Ig domains 16-17 and 18-19. Chemical shift mapping between FLNa tandem Ig domain 16-17 and isolated domain 17 suggests a novel domain-domain interaction mode.

Research paper thumbnail of Nuclear Magnetic Resonance Spectroscopy in Analysis of Chemicals Related to the Chemical Weapons Convention

Applications, Theory and Instrumentation, 2006

ABSTRACT

Research paper thumbnail of Rapid Chemical Characterisation of Stilbenes in the Root Bark of Norway Spruce by Off-line HPLC/DAD-NMR

Phytochemical Analysis, 2014

Introduction -Stilbenes are plant secondary metabolites that have shown promising and varied biol... more Introduction -Stilbenes are plant secondary metabolites that have shown promising and varied biological activities. Stilbenes are presently actively studied for the exploitation of this primary raw material resource, involving the concept of biorefining. Methods for the rapid discovery of new and known stilbene structures from various plant sources are thus keenly sought. Objective -To establish a simple and rapid technique of off-line HPLC with a diode-array detector (DAD) and NMR for the unambiguous structural elucidation of stilbene structures in the root bark of Norway spruce [Picea abies (L.) Karst.]. Material and methods -The stilbene containing fraction was extracted from the plant bark with an ethanol:water mixture (95:5, v/v) preceded by defatting of hydrophobic compounds with n-hexane using the accelerated solvent extraction technique. A portion of the ethanol-water soluble extract was hydrolysed with β-glucosidase to prepare stilbene aglycones. The extracts were further purified and enriched using a polymeric adsorbent. Stilbene-enriched extracts were directly characterised by off-line HPLC/DAD-NMR in conjunction with HPLC/DAD and HPLC/DAD with electrospray ionisation MS n . Results -Trans-isorhapontin and trans-astringin were identified as the major, and trans-piceid as a minor, stilbene glucosides of the bark of roots of Picea abies. Not only stilbene glucosides but also the corresponding stilbene aglycones, such as trans-resveratrol, trans-piceatannol and trans-isorhapontigenin, were rapidly identified from the hydrolysed extract. The acquired heteronuclear single-quantum coherence and heteronuclear multiple bond correlation spectra were used to assign the complete carbon NMR chemical shifts of trans-isorhapontin and trans-astringin without the need of acquiring a 13 C-NMR spectrum. Conclusion -The off-line HPLC/DAD-NMR method is expedient for the unambiguous identication of structurally similar stilbenes in plant extracts.

Research paper thumbnail of Hafnium Bis(phenoxyimino) Dibenzyl Complexes and Their Activation toward Olefin Polymerization

Organometallics, 2007

ABSTRACT Hf bis(phenoxyimino) dibenzyl complexes bearing benzylimino and perfluorophenylimino gro... more ABSTRACT Hf bis(phenoxyimino) dibenzyl complexes bearing benzylimino and perfluorophenylimino groups were prepared by a direct reaction between the desired ligand precursors and Hf(CH2Ph)4. In the solid state, the Hf complexes adopt an octahedral configuration where imino nitrogens are in positions cis to each other and oxygens occupy apical vertices of the coordination polyhedron. According to 1H NMR and 2D-NOESY studies, this cis-N,N configuration was also maintained in solution. In addition, the structures of Hf bis(phenoxyimino) dibenzyl complexes were studied with DFT calculations. Activation of the Hf dibenzyl complexes with B(C6F5)3 led to the highly air-, moisture-, solvent-, and temperature-sensitive cationic bis(phenoxyimino) Hf monobenzyl species, which were further investigated by 1H and 19F NMR, 1H−13C heteronuclear correlation, 2D-NOESY, and ESI-MS methods. It was observed that the cationic, benzylimino-substituted Hf complexes have a propensity toward CH activation. The correlation between the stability of the cationic species toward CH activation and the catalytic behavior of the MAO-activated dibenzyl complexes was established. Accordingly, the MAO-activated Hf bis(phenoxyimino) dibenzyl complexes and their dichloro analogues, depending on the ligand substitution, have from low to very high catalytic activities (up to 14 000 kg of PE/((mol of cat.) h (bar of ethylene))) in ethylene polymerizations. In general, the produced polyethylene had a monomodal molar mass distribution with relatively narrow polydispersity. Polypropylene produced with perfluorophenyl-substituted Hf complexes had a large amount of 2,1-misinsertions in the polymer chains. To further shed light on the catalytic reaction, polymerizations of ethylene and propylene with the cationic species generated from Hf bis(phenoxyimino) dibenzyl complexes with B(C6F5)3 were studied with 1H NMR.

Research paper thumbnail of Evaluation of protein15N relaxation times by inverse Laplace transformation

Magnetic Resonance in Chemistry, 2004

Relaxation times (T 1 , T 2 , T 1r ) are usually evaluated from exponential decay data by least-s... more Relaxation times (T 1 , T 2 , T 1r ) are usually evaluated from exponential decay data by least-squares fitting methods. For this procedure, the integrals or amplitudes of signals must be determined, which can be laborious with large data sets. Moreover, the fitting requires a priori knowledge of the number of exponential components responsible for the decay. We have adapted inverse Laplace transformation (ILT) for the analysis of relaxation data. Exponential components are resolved with ILT to reciprocal space on their corresponding relaxation rate values. The ILT approach was applied to 3D linewidth-resolved 15 N HSQC experiments to evaluate 15 N T 1 and T 2 relaxation times of ubiquitin. The resulting spectrum is a true 3D spectrum, where the signals are separated by their 1 H and 15 N chemical shifts (HSQC correlations) and by their relaxation rate values (R 1 or R 2 /. From this spectrum, the relaxation times can be obtained directly with a simple peak-picking procedure.

Research paper thumbnail of Quantitative determination of aliphatic hydrocarbon compounds by 2D NMR

Magnetic Resonance in Chemistry, 2002

ABSTRACT

Research paper thumbnail of Continuous H/D exchange of aromatic hydrocarbons using near-critical deuterium oxide

The Journal of Supercritical Fluids, 2007

Near-and supercritical D 2 O is both a relatively cheap deuterium source and an environmentally b... more Near-and supercritical D 2 O is both a relatively cheap deuterium source and an environmentally benign solvent for batch-wise H/D exchange reactions. In this work, a new continuous flow reactor online-coupled with liquid-liquid extraction was constructed for the selective deuteration of aromatic hydrocarbons in pressurized hot D 2 O at short contact times. Exchange positions were identified by GC-MS, 1 H NMR, and FTIR analysis. Four aromatic hydrocarbons (eugenol, 9-fluorenone, 4-hydroxyacetophenone, and xanthone) were screened for H/D exchange in conventional batch reactors with use of near-and supercritical D 2 O (p = 300 bar, t = 2 h, T = 250-450 • C) alone and with basic or metal catalyst (Na 2 CO 3 , Pd/C). Highest isotopic purities were obtained for deuteration of eugenol (d 1 = 59%) and 4-hydroxyacetophenone (d 5 = 91%) in the absence of catalyst. 2 H-labelling of these two compounds was then investigated in continuous flow experiments (p = 300 bar, T = 250-350 • C, τ = 1-4 min). Under optimized conditions, high isotopic purities were obtained for eugenol (d 1 = 61%) and 4-hydroxyacetophenone (d 5 = 82%), as before in batch runs, but the contact time, and the probability of decomposition, were significantly reduced. The continuous process developed offers good potential for the deuteration of thermally sensitive substrates.

Research paper thumbnail of Some aspects of quantitative 2D NMR

Journal of Magnetic Resonance, 2005

We have studied the application of 2D HSQC for quantitative measurements and propose some improve... more We have studied the application of 2D HSQC for quantitative measurements and propose some improvements to the previously published Q-HSQC method. Application of CPMG-INEPT for polarization transfer period suppresses the evolution of J(HH), and thus corrects the shape of the cross-peaks. The better cross-peak shape makes phase correction and integration of the cross-peaks easier. Further, the (13)C resonance offset dependency can have a significant influence to the results. The offset effects can be compensated either by correcting results with a proper coefficient, or using 90 degrees composite (13)C pulses in the pulse sequence. The results show that these modifications improve the applicability of 2D HSQC for quantitative analysis when studying molecules possessing large J(HH) couplings and wide (13)C chemical shift range.

Research paper thumbnail of Quantitative two-dimensional HSQC experiment for high magnetic field NMR spectrometers

Journal of Magnetic Resonance, 2010

The finite RF power available on carbon channel in proton-carbon correlation experiments leads to... more The finite RF power available on carbon channel in proton-carbon correlation experiments leads to non-uniform cross peak intensity response across carbon chemical shift range. Several classes of broadband pulses are available that alleviate this problem. Adiabatic pulses provide an excellent magnetization inversion over a large bandwidth, and very recently, novel phase-modulated pulses have been proposed that perform 90 degrees and 180 degrees magnetization rotations with good offset tolerance. Here, we present a study how these broadband pulses (adiabatic and phase-modulated) can improve quantitative application of the heteronuclear single quantum coherence (HSQC) experiment on high magnetic field strength NMR spectrometers. Theoretical and experimental examinations of the quantitative, offset-compensated, CPMG-adjusted HSQC (Q-OCCAHSQC) experiment are presented. The proposed experiment offers a formidable improvement to the offset performance; (13)C offset-dependent standard deviation of the peak intensity was below 6% in range of+/-20 kHz. This covers the carbon chemical shift range of 150 ppm, which contains the protonated carbons excluding the aldehydes, for 22.3 T NMR magnets. A demonstration of the quantitative analysis of a fasting blood plasma sample obtained from a healthy volunteer is given.

Research paper thumbnail of LR-CAHSQC: an application of a Carr–Purcell–Meiboom–Gill-type sequence to heteronuclear multiple bond correlation spectroscopy

Journal of Magnetic Resonance, 2003

A new pulse sequence, long-range CPMG-adjusted heteronuclear single quantum coherence (LR-CAHSQC)... more A new pulse sequence, long-range CPMG-adjusted heteronuclear single quantum coherence (LR-CAHSQC), is proposed for the determination of long-range JCH coupling constants from a long-range 1H-13C correlation experiment. The long-range heteronuclear coupling constants can be directly extracted from COSY-type antiphase peak patterns. The current approach utilizes CPMG-sequences for polarization transfer, and thus avoids the evolution of homonuclear JHH couplings, which normally may introduce abnormalities into the cross peak pattern. The differences between LR-CAHSQC and normal LR-HSQC are discussed.

Research paper thumbnail of Application of Quantitative Artificial Neural Network Analysis to 2D NMR Spectra of Hydrocarbon Mixtures

Journal of Chemical Information and Modeling, 2002

Understanding relationships between the structure and composition of molecular mixtures and their... more Understanding relationships between the structure and composition of molecular mixtures and their chemical properties is a main industrial aim. One central field of research is oil chemistry where the key question is how the molecular characteristics of composite hydrocarbon mixtures can be associated with the macroscopic properties of the oil products. Apparently these relationships are complex and often nonlinear and therefore call for advanced spectroscopic techniques. An informative and an increasingly used approach is two-dimensional nuclear magnetic resonance (2D NMR) spectroscopy. In the case of composite hydrocarbons the application of 2D NMR methodologies in a quantitative manner pose many technical difficulties, and, in any case, the resulting spectra contain many overlapping resonances that challenge the analytical work. Here, we present a general methodology, based on quantitative artificial neural network (ANN) analysis, to resolve overlapping information in 2D NMR spectra and to simultaneously assess the relative importance of multiple spectral variables on the sample properties. The results in a set of 2D NMR spectra of oil samples illustrate, first, that use of ANN analysis for quantitative purposes is feasible also in 2D and, second, that this methodology offers an intrinsic opportunity to assess the complex and nonlinear relationships between the molecular composition and sample properties. The presented ANN methodology is not limited to the analysis of NMR spectra but can also be applied in a manner similar to other (multidimensional) spectroscopic data.

Research paper thumbnail of Solution structure of the first immunoglobulin domain of human myotilin

Journal of Biomolecular NMR, 2009

Myotilin is a 57 kDa actin-binding and -bundling protein that consists of a unique serine-rich am... more Myotilin is a 57 kDa actin-binding and -bundling protein that consists of a unique serine-rich amino-terminus, two Ig-domains and a short carboxy-terminus with a PDZ-binding motif. Myotilin localizes in sarcomeric Z-discs, where it interacts with several sarcomeric proteins. Point mutations in myotilin cause muscle disorders morphologically highlighted by sarcomeric disarray and aggregation. The actin-binding and dimerization propensity of myotilin has been mapped to the Ig-domains. Here we present high-resolution structure of the first Ig-domain of myotilin (MyoIg1) determined with solution state NMR spectroscopy. Nearly complete chemical shift assignments of MyoIg1 were achieved despite several missing backbone 1H-15N-HSQC signals. The structure derived from distance and dihedral angle restraints using torsion angle dynamics was further refined using molecular dynamics. The structure of MyoIg1 exhibits I-type Ig-fold. The absence of several backbone 1H-15N-HSQC signals can be explained by conformational exchange taking place at the hydrophobic core of the protein.

Research paper thumbnail of Rapid and accurate processing method for amide proton exchange rate measurement in proteins

Journal of Biomolecular NMR, 2007

Exchange between protein backbone amide hydrogen and water gives relevant information about solve... more Exchange between protein backbone amide hydrogen and water gives relevant information about solvent accessibility and protein secondary structure stability. NMR spectroscopy provides a convenient tool to study these dynamic processes with saturation transfer experiments. Processing of this type of NMR spectra has traditionally required peak integration followed by exponential fitting, which can be tedious with large data sets. We propose here a computer-aided method that applies inverse Laplace transform in the exchange rate measurement. With this approach, the determination of exchange rates can be automated, and reliable results can be acquired rapidly without a need for manual processing.

Research paper thumbnail of Atomic Structures of Two Novel Immunoglobulin-like Domain Pairs in the Actin Cross-linking Protein Filamin

Journal of Biological Chemistry, 2009

Filamins are actin filament cross-linking proteins composed of an N-terminal actin-binding domain... more Filamins are actin filament cross-linking proteins composed of an N-terminal actin-binding domain and 24 immunoglobulin-like domains (IgFLNs). Filamins interact with numerous proteins, including the cytoplasmic domains of plasma membrane signaling and cell adhesion receptors. Thereby filamins mechanically and functionally link the cell membrane to the cytoskeleton. Most of the interactions have been mapped to the C-terminal IgFLNs 16-24. Similarly, as with the previously known compact domain pair of IgFLNa20-21, the two-domain fragments IgFLNa16-17 and IgFLNa18-19 were more compact in small angle x-ray scattering analysis than would be expected for two independent domains. Solution state NMR structures revealed that the domain packing in IgFLNa18-19 resembles the structure of IgFLNa20-21. In both domain pairs the integrin-binding site is masked, although the details of the domain-domain interaction are partly distinct. The structure of IgFLNa16-17 revealed a new domain packing mode where the adhesion receptor binding site of domain 17 is not masked. Sequence comparison suggests that similar packing of three tandem filamin domain pairs is present throughout the animal kingdom, and we propose that this packing is involved in the regulation of filamin interactions through a mechanosensor mechanism.

Research paper thumbnail of NMR properties of conjugated linoleic acid (CLA) methyl ester hydroperoxides

Chemistry and Physics of Lipids, 2008

a b s t r a c t NMR data on lipid hydroperoxides is scarce. In this study, hydroperoxides were pr... more a b s t r a c t NMR data on lipid hydroperoxides is scarce. In this study, hydroperoxides were produced from methyl 9-cis,11-trans-octadecadienoate and from methyl 10-trans,12-cis-octadecadienoate by autoxidation in the presence of 20% of ␣-tocopherol. Ten different hydroperoxides were isolated from the autoxidation mixtures of the two conjugated linoleic acid (CLA) methyl esters by SPE and HPLC. The assignment of the 1 H and 13 C NMR spectra of these hydroperoxides was accomplished by 2D NMR experiments and by spectral simulations. Substitution of a hydroperoxyl group at the allylic position in CLA methyl esters induced a 53.93 ppm downfield shift on the hydroperoxyl-bearing carbon resonance. The effects on the olefinic ␣, ␤, ␥, and ␦ carbon resonances were −3.45, +4.96, −1.22, and +4.42 ppm, respectively. Furthermore, the solvent effects of deuterochloroform, deuteroacetone, and deuterobenzene on the 13 C resonances of the hydroperoxides suggest that deuterochloroform is the appropriate solvent for 13 C NMR studies on mixtures of lipid hydroperoxides.

Research paper thumbnail of Solution structure of the parvulin-type PPIase domain of Staphylococcus aureus PrsA – Implications for the catalytic mechanism of parvulins

BMC Structural Biology, 2009

Background: Staphylococcus aureus is a Gram-positive pathogenic bacterium causing many kinds of i... more Background: Staphylococcus aureus is a Gram-positive pathogenic bacterium causing many kinds of infections from mild respiratory tract infections to life-threatening states as sepsis. Recent emergence of S. aureus strains resistant to numerous antibiotics has created a need for new antimicrobial agents and novel drug targets. S. aureus PrsA is a membrane associated extracytoplasmic lipoprotein which contains a parvulin-type peptidyl-prolyl cis-trans isomerase domain. PrsA is known to act as an essential folding factor for secreted proteins in Gram-positive bacteria and thus it is a potential target for antimicrobial drugs against S. aureus.