Biomedical subjects

Jeffrey C Hoch

Publications and source records attributed to Jeffrey C Hoch.

5 recordsLinked to original sources

PubMed2004

Accelerated acquisition of high resolution triple-resonance spectra using non-uniform sampling and maximum entropy reconstruction.

Non-uniform sampling is shown to provide significant time savings in the acquisition of a suite of three-dimensional NMR experiments utilized for obtaining backbone assignments of H, N, C', CA, and CB nuclei in proteins : HNCO, HN(CA)CO, HNCA, HN(CO)CA, HNCACB, and HN(CO)CACB. Non-uniform sampling means that data were collected for only a subset of all incremented evolution periods, according to a user-specified sampling schedule. When the suite of six 3D experiments was acquired in a uniform fashion for an 11 kDa cytoplasmic domain of a membrane protein at 1.5 mM concentration, a total of 146 h was consumed. With non-uniform sampling, the same experiments were acquired in 32 h and, through subsequent maximum entropy reconstruction, yielded spectra of similar quality to those obtained by conventional Fourier transform of the uniformly acquired data. The experimental time saved with this methodology can significantly accelerate protein structure determination by NMR, particularly when combined with the use of automated assignment software, and enable the study of samples with poor stability at room temperature. Since it is also possible to use the time savings to acquire a greater numbers of scans to increase sensitivity while maintaining high resolution, this methodology will help extend the size limit of proteins accessible to NMR studies, and open the way to studies of samples that suffer from solubility problems.

Carbon Isotopes↗

PubMed2003

Molecular dynamics of the long neurotoxin LSIII.

Long neurotoxins bind tightly and specifically to the nicotinic acetylcholine receptor (AChR) in postsynaptic membranes and are useful for exploring the biology of synapses. In crystallographic studies of long neurotoxins the principal binding loop appears disordered, but the NMR solution structure of the long neurotoxin LSIII revealed significant local order, even though the loop is disordered with respect to the globular core. A possible mechanism for conferring global disorder while preserving local order is rigid-body motion of the loop about a hinge region. Here we report investigations of LSIII dynamics based on (13)C(alpha) magnetic relaxation rates and molecular dynamics simulation. The relaxation rates and MD simulation both confirm the hypothesis of rigid-body motion of the loop and place bounds on the extent and time scale of the motion. The bending motion of the loop is slow compared to the rapid fluctuations of individual dihedral angles, reflecting the collective nature and largely entropic free energy profile for hinge bending. The dynamics of the central binding loop in LSIII illustrates two distinct mechanisms by which molecular dynamics directly impacts biological activity. The relative rigidity of key residues involved in recognition at the tip of the central binding loop lowers the otherwise substantial entropic cost of binding. Large excursions of the loop hinge angle may endow the protein with structural plasticity, allowing it to adapt to conformational changes induced in the receptor.

Computer Simulation↗

PubMed2003

Elimination of 13Calpha splitting in protein NMR spectra by deconvolution with maximum entropy reconstruction.

Homonuclear 13C-13C couplings can significantly reduce the sensitivity and resolution of multidimensional NMR experiments. The most important of these couplings is the 13Calpha-13Cbeta coupling, and several different methods have been developed to eliminate its effect from spectra used for backbone assignment, including short or constant-time evolution periods, selectively labeled amino acids, and multiple-band decoupling sequences. In this communication we show that postacquisition deconvolution of the spectra with a maximum entropy algorithm can be superior to experimental decoupling. The method is very robust, does not introduce shifts of the resonance positions, and simplifies the measurement of the most important NMR experiments for protein backbone assignment.

Carbon Isotopes↗

PubMed2003

Multiple-quantum magic-angle spinning spectroscopy using nonlinear sampling.

NMR spectroscopy is a relatively insensitive technique and many biomolecular applications operate near the limits of sensitivity and resolution. A particularly challenging example is detection of the quadrupolar nucleus 17O, due to its low natural abundance, large quadrupole couplings, and low gyromagnetic ratio. Yet the chemical shift of 17O spans almost 1000 ppm in organic molecules and it serves as a potentially unique reporter of hydrogen bonding in peptides, nucleic acids, and water, and as a valuable complement to 13C and 15N NMR. Recent developments including the multiple-quantum magic-angle spinning (MQMAS) experiment have enabled the detection of 17O in biological solids, but very long data acquisitions are required to achieve sufficient sensitivity and resolution. Here, we perform nonlinear sampling in the indirect dimension of MQMAS experiments to substantially reduce the total acquisition time and improve sensitivity and resolution. Nonlinear sampling prevents the use of the discrete Fourier transform; instead, we employ maximum entropy (MaxEnt) reconstruction. Nonlinearly sampled MQMAS spectra are shown to provide high resolution and sensitivity in several systems, including lithium sulfate monohydrate (LiSO(4)-H(2)17O) and L-asparagine monohydrate (H(2)17O). The combination of nonlinear sampling and MaxEnt reconstruction promises to make the application of 17O MQMAS practical in a wider range of biological systems.

Anisotropy↗

PubMed2002

Modern spectrum analysis in multidimensional NMR spectroscopy: comparison of linear-prediction extrapolation and maximum-entropy reconstruction.

NMR spectroscopy is an inherently insensitive technique, and many challenging applications such as biomolecular studies operate at the very limits of sensitivity and resolution. Advances in superconducting magnet, cryogenic probe, and pulse sequence technologies have resulted in dramatic improvements in both sensitivity and resolution in the past decade. Conversely, the signal-processing method used most widely in NMR spectroscopy, extrapolation of the time domain signal by linear prediction (LP) followed by discrete Fourier transformation (DFT), was developed in the early 1980s and has not been subjected to detailed scrutiny for its impact on sensitivity and resolution. Here we report the first systematic investigation of the accuracy and precision of spectra obtained by LP extrapolation followed by DFT. We compare the results to spectra obtained by maximum-entropy (MaxEnt) reconstruction, which was developed contemporaneously to LP extrapolation but is not widely employed in NMR spectroscopy. Although it reduces truncation artifacts and increases the amplitudes of strong peaks, we find that LP extrapolation generates false-positive peaks and introduces frequency errors. These defects of LP extrapolation become less pronounced for longer data records and higher signal-to-noise ratio. MaxEnt generally yields more detectable peaks for a given number of data samples, more accurate peak frequencies, and fewer false-positive peaks than LP extrapolation. MaxEnt also permits the use of nonlinear sampling, which can give dramatic improvements in resolution. These results show that the use of MaxEnt together with nonlinear sampling, rather than LP extrapolation, could reduce the amount of instrument time required for adequate sensitivity and resolution by a factor of 2 or more.

Fourier Analysis↗