57 research outputs found
Exclusively heteronuclear NMR experiments for the investigation of intrinsically disordered proteins: focusing on proline residues
NMR represents a key spectroscopic technique that contributes to the emerging field of highly flexible, intrinsically disordered proteins (IDPs) or protein regions (IDRs) that lack a stable three-dimensional structure. A set of exclusively heteronuclear NMR experiments tailored for proline residues, highly abundant in IDPs/IDRs, are presented here. They provide a valuable complement to the widely used approach based on amide proton detection, filling the gap introduced by the lack of amide protons in proline residues within polypeptide chains. The novel experiments have very interesting properties for the investigations of IDPs/IDRs of increasing complexity.</p
Focusing on \u201cthe important\u201d through targeted NMR experiments: An example of selective 13C-12C bond detection in complex mixtures
Band-selective universal 90° and 180° rotation pulses covering the aliphatic carbon chemical shift range for triple resonance experiments on 1.2 GHz spectrometers
Biomolecular NMR spectroscopy requires large magnetic field strengths for high spectral resolution. Today’s highest fields comprise proton Larmor frequencies of 1.2 GHz and even larger field strengths are to be expected in the future. In protein triple resonance experiments, various carbon bandwidths need to be excited by selective pulses including the large aliphatic chemical shift range. When the spectrometer field strength is increased, the length of these pulses has to be decreased by the same factor, resulting in higher rf-amplitudes being necessary in order to cover the required frequency region. Currently available band-selective pulses like Q3/Q5 excite a narrow bandwidth compared to the necessary rf-amplitude. Because the maximum rf-power allowed in probeheads is limited, none of the selective universal rotation pulses reported so far is able to cover the full C aliphatic region on 1.2 GHz spectrometers. In this work, we present band-selective 90° and 180° universal rotation pulses (SURBOP90 and SURBOP180) that have a higher ratio of selective bandwidth to maximum rf-amplitude than standard pulses. Simulations show that these pulses perform better than standard pulses, e. g. Q3/Q5, especially when rf-inhomogeneity is taken into account. The theoretical and experimental performance is demonstrated in offset profiles and by implementing the SURBOP pulses in an HNCACB experiment at 1.2 GHz
Selective 1Hα NMR methods to reveal functionally relevant proline cis/trans isomers in IDPs
It is important to identify proline cis/trans isomers that appear in several regulatory mechanisms of proteins, and to characterize minor species that are present due to the conformational heterogeneity in intrinsically disordered proteins (IDPs). To obtain residue level information on these mobile systems we introduce two H-1(alpha)-detected, proline selective, real-time homodecoupled NMR experiments and analyze the proline abundant transactivation domain of p53. The measurements are sensitive enough to identify minor conformers present in 4-15 % amounts; moreover, we show the consequences of CK2 phosphorylation on the cis/trans-proline equilibrium. Using our results and available literature data we perform a statistical analysis on how the amino acid type effects the cis/trans-proline distribution. The methods are applicable under physiological conditions, they can contribute to find key proline isomers in proteins, and statistical analysis results may help in amino acid sequence optimization for biotechnological purposes
Thermal Equilibrium as an Initial State for Quantum Computation by NMR
We present a method of using a nuclear magnetic resonance computer to solve
the Deutsch-Jozsa problem in which: (1) the number of molecules in the NMR
sample is irrelevant to the number of qubits available to an NMR quantum
computer, and (2) the initial state is chosen to be the state of thermal
equilibrium, thereby avoiding the preparation of pseudopure states and the
resulting exponential loss of signal as the number of qubits increases. The
algorithm is described along with its experimental implementation using four
active qubits. As expected, measured spectra demonstrate a clear distinction
between constant and balanced functions.Comment: including 4 figure
A stapled chromogranin A-derived peptide is a potent dual ligand for integrins αvβ6 and αvβ8
Combining 2D STD-NMR, computation, biochemical assays and click-chemistry, we have identified a chromogranin-A derived compound (5) that has high affinity and bi-selectivity for αvβ6 and αvβ8 integrins and is stable in microsomal preparations
The Fantastic Four: A plug 'n' play set of optimal control pulses for enhancing nmr spectroscopy
We present highly robust, optimal control-based shaped pulses designed to
replace all 90{\deg} and 180{\deg} hard pulses in a given pulse sequence for
improved performance. Special attention was devoted to ensuring that the pulses
can be simply substituted in a one-to-one fashion for the original hard pulses
without any additional modification of the existing sequence. The set of four
pulses for each nucleus therefore consists of 90{\deg} and 180{\deg}
point-to-point (PP) and universal rotation (UR) pulses of identical duration.
These 1 ms pulses provide uniform performance over resonance offsets of 20 kHz
(1H) and 35 kHz (13C) and tolerate reasonably large radio frequency (RF)
inhomogeneity/miscalibration of (+/-)15% (1H) and (+/-)10% (13C), making them
especially suitable for NMR of small-to-medium-sized molecules (for which
relaxation effects during the pulse are negligible) at an accessible and widely
utilized spectrometer field strength of 600 MHz. The experimental performance
of conventional hard-pulse sequences is shown to be greatly improved by
incorporating the new pulses, each set referred to as the Fantastic Four
(Fanta4).Comment: 28 pages, 19 figure
Broadband 180 degree universal rotation pulses for NMR spectroscopy designed by optimal control
Broadband inversion pulses that rotate all magnetization components 180
degrees about a given fixed axis are necessary for refocusing and mixing in
high-resolution NMR spectroscopy. The relative merits of various methodologies
for generating pulses suitable for broadband refocusing are considered. The de
novo design of 180 degree universal rotation pulses using optimal control can
provide improved performance compared to schemes which construct refocusing
pulses as composites of existing pulses. The advantages of broadband universal
rotation by optimized pulses (BURBOP) are most evident for pulse design that
includes tolerance to RF inhomogeneity or miscalibration. We present new
modifications of the optimal control algorithm that incorporate symmetry
principles and relax conservative limits on peak RF pulse amplitude for short
time periods that pose no threat to the probe. We apply them to generate a set
of pulses suitable for widespread use in Carbon-13 spectroscopy on the majority
of available probes
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