PubMed Health⌕ Search

Biomedical subjects

O W Sørensen

Publications and source records attributed to O W Sørensen.

17 recordsLinked to original sources
PubMed2001

A sequential HNCA NMR pulse sequence for protein backbone assignment.

The conventional HNCA pulse sequence suffers from the ambiguity that it cannot distinguish inter- and intraresidue correlations because the one-bond and two-bond J(NC(alpha)) coupling constants are of similar magnitude. This paper presents a novel pulse sequence, sequential HNCA, that leads to a spectrum exhibiting exclusively interresidue correlations. This important sequential information has so far usually been obtained by an HN(CO)CA experiment that for medium field strengths typically also is more sensitive than HNCA. However, for increasing static magnetic fields the chemical shift anisotropy relaxation mechanism of carbonyl carbons becomes more and more efficient, leading to a degradation of the HN(CO)CA sensitivity. Hence there is a point where the sequential HNCA experiment becomes the most sensitive option for sequential N-C(alpha) correlation.

Journal Article↗
PubMed2001

Sequential HNCACB and CBCANH protein NMR pulse sequences.

The pulse sequences HNCACB and CBCANH correlating side chain C(beta) resonances with amide resonances in the protein backbone do not distinguish between inter- and intraresidue correlations. The new pulse sequences sequential HNCACB and sequential CBCANH make this distinction by suppressing coherence transfer between 13C(alpha) and 15N via the one-bond J(NC(alpha)) coupling so that only the sequential correlations are observed in the spectrum. The experimental results of applying sequential HNCACB in a clean-TROSY-adapted implementation to the protein Chymotrypsin Inhibitor 2 at 800 MHz are presented.

Carbon Isotopes↗
PubMed2001

Conformation of alamethicin in oriented phospholipid bilayers determined by (15)N solid-state nuclear magnetic resonance.

The conformation of the 20-residue antibiotic ionophore alamethicin in macroscopically oriented phospholipid bilayers has been studied using (15)N solid-state nuclear magnetic resonance (NMR) spectroscopy in combination with molecular modeling and molecular dynamics simulations. Differently (15)N-labeled variants of alamethicin and an analog with three of the alpha-amino-isobutyric acid residues replaced by alanines have been investigated to establish experimental structural constraints and determine the orientation of alamethicin in hydrated phospholipid (dimyristoylphosphatidylcholine) bilayers and to investigate the potential for a major kink in the region of the central Pro(14) residue. From the anisotropic (15)N chemical shifts and (1)H-(15)N dipolar couplings determined for alamethicin with (15)N-labeling on the Ala(6), Val(9), and Val(15) residues and incorporated into phospholipid bilayer with a peptide:lipid molar ratio of 1:8, we deduce that alamethicin has a largely linear alpha-helical structure spanning the membrane with the molecular axis tilted by 10-20 degrees relative to the bilayer normal. In particular, we find compatibility with a straight alpha-helix tilted by 17 degrees and a slightly kinked molecular dynamics structure tilted by 11 degrees relative to the bilayer normal. In contrast, the structural constraints derived by solid-state NMR appear not to be compatible with any of several model structures crossing the membrane with vanishing tilt angle or the earlier reported x-ray diffraction structure (Fox and Richards, Nature. 300:325-330, 1982). The solid-state NMR-compatible structures may support the formation of a left-handed and parallel multimeric ion channel.

Alamethicin↗
PubMed2001

Editing and diagonal peak suppression in three-dimensional HCCH protein NMR correlation experiments.

A novel three-dimensional (3D) HCCH NMR experiment is introduced. It involves 13C-13C COSY or TOCSY coherence transfer plus two independent editing steps according to the number of protons attached to the individual carbons before and after the 13C-13C homonuclear mixing. This double editing leads to simplification of HCCH protein side chain spectra that otherwise are prone to spectral overlap. Another interesting feature is amino acid selectivity, i.e. that the presence of certain correlations in a doubly edited HCCH subspectrum gives a clue as to assignment to a particular subgroup of amino acids or segments thereof. Finally, the selection of two different multiplicities in the two editing steps leads to diagonal peak suppression in the 1H-1H (3D spectrum recorded with two 1H and one 13C dimension) or the 13C-13C (3D spectrum recorded with one 1H and two 13C dimensions) two-dimensional projection. The new experiment is demonstrated using a 13C,15N-labeled protein sample, chymotrypsin inhibitor 2, at 500 MHz.

Animals↗
PubMed1999

13C natural abundance S3E and S3CT experiments for measurement of J coupling constants between 13Calpha or 1Halpha and other protons in a protein.

It is demonstrated that the spin-state-selective pulse sequence elements, S3E and S3CT, previously introduced for measurement of J coupling constants in 15N-labeled proteins can be applied for work with peptides and proteins with 13C at the natural abundance level. In addition, a method is described for suppression of crosstalk caused by passive spin flips and pulse imperfections, which otherwise results in systematically underestimated J coupling constants and thereby inaccurate structural constraints. This method is also applicable for crosstalk suppression in applications of S3E and S3CT to 13C- or 15N-labeled samples. Experimental confirmation is obtained using a 10 mM BPTI sample focusing on 13C in the alpha position. The measured J coupling constants include 3J(HN-Halpha) and 3J(Halpha-Hbeta) related to the phi and chi1 angles, respectively.

Carbon Isotopes↗
PubMed1999

Spin-state-selective TPPI: a new method for suppression of heteronuclear coupling constants in multidimensional NMR experiments.

A novel multidimensional NMR pulse sequence tool, spin-state-selective time-proportional phase incrementation (S(3) TPPI), is introduced. It amounts to application of different TPPIs on the two components of doublets so that their frequencies can be manipulated independently. The chief application is for suppression of large heteronuclear one-bond coupling constants in indirect dimensions of multidimensional experiments without interchanging the two transverse magnetization components of doublets as conventional decoupling does, which is advantageous when they relax at different rates such as by partial compensation of dipolar and CSA relaxation contributions. For experimental confirmation we use a sample of (15)N-labeled neural cell adhesion molecule modules 1 and 2, a protein with a molecular weight of about 20 kDa. The new tool is general and can be combined with many multidimensional NMR experiments for proteins.

Magnetic Resonance Spectroscopy↗
PubMed1999

The role of coherence transfer efficiency in design of TROSY-type multidimensional NMR experiments.

An improved method for TROSY-type (Pervushin et al., Proc. Natl. Acad. Sci. USA 94, 12366-12371 (1997)) heteronuclear two-dimensional correlation involving protons of negligible CSA is presented. Rather than applying a simple INEPT sequence for back-transfer to protons (Pervushin et al., J. Am. Chem. Soc. 120, 6394-6400 (1998)), we replace the pi/2 proton pulse in INEPT by a spin-state-selective coherence transfer element (Sorensen et al., J. Biomol. NMR 10, 181-186 (1997)) and maintain broadband decoupling during acquisition. Theoretically that results in a sensitivity enhancement of a factor of 2. The new method is demonstrated using a (13)C,(15)N-labeled protein sample, RAP 18-112 (N-terminal domain of alpha(2)-macroglobulin receptor associated protein), at 750 MHz.

Magnetic Resonance Spectroscopy↗
PubMed1999

Pulse sequences for measurement of one-bond (15)N-(1)H coupling constants in the protein backbone.

A set of three improved two-dimensional (2D) NMR methods for measuring one-bond (15)N-(1)H coupling constants in the protein backbone is presented. They are tailored to suit the size of the TROSY effect, i.e., the degree of interference between dipolar and chemical shift anisotropy relaxation mechanisms. The methods edit 2D spectra into two separate subspectra corresponding to the two possible spin states of the coupling partner. Cross talk between the two subspectra is a second order effect in the difference between the actual coupling constants and the one used in setting the pertinent delays of the pulse sequences. This relatively high degree of editing accuracy makes the methods useful for applications to molecules subjected to weak alignment where the one-bond coupling constants are linear combinations of a scalar J and a residual dipolar contribution containing important structural information. A demonstration of the new methods is shown for the (15)N-labeled protein chymotrypsin inhibitor 2 in a lipid bicelle mixture.

Hydrogen↗
PubMed1999

Suppression of diagonal peaks in TROSY-type 1H NMR NOESY spectra of 15N-labeled proteins.

A novel method for suppression of diagonal peaks in the amide region of NOESY NMR spectra of 15N-labeled proteins is presented. The method is particularly useful for larger proteins at high magnetic fields where interference between dipolar and chemical shift anisotropy relaxation mechanisms results in large TROSY effects, i.e. , large differences in 1HN linewidths depending on the spin state of attached 15N nuclei. In this limit the new TROSY NOESY method does not compromise sensitivity. It is demonstrated using a perdeuterated 15N-labeled protein sample, Neural Cell Adhesion Molecule 213-308 (NCAM) from rat, in H2O at 800 MHz.

Animals↗
PubMed1998

Simultaneous and independent rotations with arbitrary flip angles and phases for I, ISalpha, and ISbeta spin systems.

A new pulse sequence element for simultaneous and independent rotations with arbitrary flip angles and phases for isolated I, ISalpha, and ISbeta resonances without the use of selective radiofrequency pulses is introduced and experimentally demonstrated. S is a directly attached heteronucleus either at natural abundance or isotopically enriched. This pulse sequence element, dubbed TIG-BIRD (triselective independent gyrations BIRD), generalizes earlier elements like BIRD, TANGO, BANGO, and BIG-BIRD, the latter of which allows for arbitrary selection of flip angles and phases for I and IS spin systems without discriminating between ISalpha and ISbeta resonances. For ISalpha and ISbeta spin systems it also generalizes the spin-state-selective excitation (S3E) element selectively exciting only one of the ISalpha or ISbeta resonances. TIG-BIRD is a nonselective addition to the NMR toolkit which effects the equivalent of three independent selective rotations for I, ISalpha, and ISbeta resonances.

Hydrocarbons, Iodinated↗
PubMed1998

New multidimensional editing experiments for measurement of amide deuterium isotope effects on Cbeta chemical shifts in 13C, 15N-labeled proteins.

Novel multidimensional NMR pulse sequences for measurement of the three- and four-bond amide deuterium isotope effect on the chemical shifts of 13Cbeta in proteins are presented. The sequences result in editing into two subspectra of a heteronuclear triple resonance spectrum ¿omega(N), omega(Cbeta), omega(Halpha)¿ according to there being a deuterium or a proton attached to 15N for the pertinent correlations. The new experiments are demonstrated by an application to the first module of the 13C,15N-labeled protein RAP 18-112 (N-terminal module of alpha2-macroglobulin receptor associated protein).

Amides↗
PubMed1994

A general enhancement scheme in heteronuclear multidimensional NMR employing pulsed field gradients.

General pulse sequence elements that achieve sensitivity-enhanced coherence transfer from a heteronucleus to protons of arbitrary multiplicity are introduced. The building blocks are derived from the sensitivity-enhancement scheme introduced by Cavanagh et al. ((1991) J. Magn. Reson., 91, 429-436), which was used in conjunction with gradient coherence selection by Kay et al. ((1992) J. Am. Chem. Soc., 114, 10663-10665), as well as from a multiple-pulse sequence effecting a heteronuclear planar coupling Hamiltonian. The building blocks are incorporated into heteronuclear correlation experiments, in conjunction with coherence selection by the formation of a heteronuclear gradient echo. This allows for efficient water suppression without the need for water presaturation. The methods are demonstrated in HSQC-type experiments on a sample of a decapeptide in H2O. The novel pulse sequence elements can be incorporated into multidimensional experiments.

Amino Acid Sequence↗
PubMed1994

A new 2D NMR method for measurement of JHH coupling constants.

A new 2D NMR pulse sequence for E.COSY-type measurement of J(HH) coupling constants is introduced. It exploits a heteronuclear spin, e.g., 13C, for displacement in the omega(1) frequency dimension via a large heteronuclear J coupling. The experiment is demonstrated by application to a heptapeptide at the natural abundance 13C level. It is suitable, for example, for measurement of 3J(HH) and 4J(HH) coupling constants in peptides and proteins.

Amino Acid Sequence↗
PubMed1988

Three-dimensional NMR spectroscopy of a protein in solution.

The geometric information used to solve three-dimensional (3D) structures of proteins by NMR spectroscopy resides in short (less than 5 A) interproton-distance data. To obtain these distances, the 1H-NMR spectrum must first be assigned using correlation and nuclear Overhauser effect (NOE) experiments to demonstrate through-bond (scalar) and through-space connectivities, respectively. Because the NOE is proportional to r-6, distance information can then be derived. The increased resolution afforded by extending NMR experiments into a second dimension enables one to detect and interpret effects that would not be possible in one dimension owing to extensive spectral overlap and much reduced information. A number of small protein structures have previously been solved in this way. Extending this methodology to larger proteins, however, requires yet an additional improvement in resolution as overlap of cross-peaks in the two-dimensional (2D) NMR spectra present a major barrier to their unambiguous identification. One way of increasing the resolution is to extend the 2D-NMR experiments into a third dimension. We report here the applicability of three-dimensional NMR to macromolecules using the 46-residue protein alpha 1-purothionin as an example.

Antimicrobial Cationic Peptides↗
PubMed1983

Improved spectral resolution in cosy 1H NMR spectra of proteins via double quantum filtering.

A double quantum filter is inserted into a two-dimensional correlated (COSY) 1H NMR experiment to obtain phase-sensitive spectra in which both cross peak and diagonal peak multiplets have anti-phase fine structure, and in which the cross peaks and the major contribution to the diagonal peaks have absorption lineshapes in both dimensions. The elimination of the dispersive character of the diagonal peaks in phase-sensitive, double quantum-filtered COSY spectra allows identification of cross peaks lying immediately adjacent to the diagonal, which represents a significant improvement over the conventional COSY experiment.

Magnetic Resonance Spectroscopy↗