Biomedical subjects

Shangwu Ding

Publications and source records attributed to Shangwu Ding.

5 recordsLinked to original sources

PubMed2006

Towards uniform enhancement in solid-state cross polarization magic [corrected] angle spinning NMR: a scheme incorporating cross polarization with rotational resonance.

A recently proposed experimental scheme for achieving uniform cross polarization enhancement of low-gamma nuclear species in solids under magic angle spinning, termed quantitative cross polarization (QUCP) [Hou et al., Chem. Phys. Lett. 421, 356 (2006)], is described, supported with comprehensive theoretical analysis, numerical simulation, and experimental investigation with both uniformly labeled and naturally abundant solids. This method combines cross polarization with dipolar-assisted rotational resonance (DARR) [Takegoshi et al., Chem. Phys. Lett. 344, 631 (2001)] broadband homonuclear recoupling technique to achieve quantitative CP spectra under fast magic angle spinning. In addition to the correct and systematical interpretation on the phenomenon we reported in the previous Letter, a number of general guidelines for performing QUCP experiments are presented in this work. It is firmly established that while the enhancement factor in QUCP depends on the CP contact time, uniform enhancement can nevertheless be realized for all types of carbon group. For natural abundance samples, the polarization transfer rate is generally slower than that in labeled samples, but quasi-equilibrium among dilute spins in the mixing period can always be reached and uniform enhancement can be achieved albeit the DARR irradiation time needed can be much longer. For labeled samples, the time gain of QUCP experiment is almost the same as that of conventional CP. For natural abundance samples, it is generally much better than single-pulse experiment. Various representative systems, including uniformly (13)C-labeled DL-alanine and (13)C, (15)N labeled L-tyrosine, as well as naturally abundant alanine, tyrosine, and monoethyl fumarate, are used to verify the validity of our theoretical analysis and numerical simulation and to demonstrate the utility and advantages of the present approach.

Journal Article↗

PubMed2006

A realistic potential model for N-H vector diffusion in proteins.

A realistic model for the potential energy for the diffusion of N-H vectors in a protein is proposed, massively modifying the simplistic models currently used in the literature. In particular, a quantitative and analytical connection between the order parameter of the N-H vector diffusion in a protein and the number of potential minima is established, offering a significant insight into the longstanding question of how protein dynamics is affected by the potential-energy landscape. The largest number of potential minima in a protein is estimated to be no more than around 25. In addition, the conformational entropies derived from classical statistical mechanics and quantum statistical mechanics are proved to be identical. Based on the presented theoretical formula, the number of potential minima for each residue of five representative proteins is evaluated and shows a good correlation between local structural flexibility and the number of potential minima.

Diffusion↗

PubMed2006

One and two dimensional 1H and 13C high resolution NMR investigation of lariat ethers and their alkali metal ionic complexes: a more tangible evidence for the presence of less common C-H***O hydrogen bonds.

The possible existence of less common hydrogen bonds in three lariat ethers and their alkali-metal ionic complexes have been investigated with one- and two-dimensional (1D and 2D) proton and carbon-13 high resolution liquid state NMR spectroscopy. The occurrence of hydrogen-bonding induced by the addition of metal ions has been identified with the observation of indirect dipolar coupling between the coupling partners involved in the hydrogen-bonding. The addition of metal ions, moreover, causes appreciable change of chemical shift of several protons and carbons. The chemical shift change depends on the ion radius, larger ions causing smaller change. Moreover, the change of chemical shift is in coincidence with the occurrence of hydrogen-bonding. The values of the coupling constants have been obtained for each of these hydrogen bonds and were used for evaluating the hydrogen-bond strength. An intriguing and surprising observation is that a C-H***O hydrogen bond identified in solution by this work was not found in the previous study with X-ray diffraction or other methods.

Alkalies↗

PubMed2004

A computer simulation study of water drying at the interface of protein chains.

This study investigated the water drying (cavitation) in the interfacial region of two chains of a dimeric protein by nanosecond molecular dynamics simulations using explicit water representation. Separation-induced cavity of water was directly observed in the region. We evaluated the separation length scale of two chains on which the drying transition occurs, and the average number of water molecules that are expelled from the interfacial region during the transition. The obtained values can be rationalized by Kelvin equation for finite lateral size of confinement [K. Lum and A. Luzar, Phys. Rev. E 56, R6283 (1997)]. Also, we found that the drying transition is accompanied by an exponential reduction in the average hydrogen-bond number per interfacial water molecule. The results of this study may deepen the understanding of how hydrophobic interaction drives the assembly of protein chains.

Amino Acid Sequence↗

PubMed2004

Effects of pulse strength, width, and sample spinning speed on the spectral spin diffusion of multiquantum coherences of spin-3/2 quadrupolar nuclei.

The effects of radio-frequency pulse strength, width, and sample spinning speed on the spin-diffusion spectrum of half-integer quadrupolar spins in solids have been studied by theoretical, numerical, and experimental investigations. It is revealed that the line shape of the cross peaks changes nonmonotonically with respect to the change of pulse strength, pulse width, or sample spinning speed. It is also found that the sample spinning speed has much more pronounced influence on the spin diffusion spectral line shape. In many cases of practical importance, the effect of sample spinning must be included in spectral analysis, in contrast to the practice of previous studies. Moreover, this effect can be exploited to further improve the precision in the determination of relative orientation of the electric-field gradient tensors of the exchange partners.

Journal Article↗