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Youlin Xia

Publications and source records attributed to Youlin Xia.

10 recordsLinked to original sources
PubMed2005

NMR structure and Mg2+ binding of an RNA segment that underlies the L7/L12 stalk in the E.coli 50S ribosomal subunit.

Helix 42 of Domain II of Escherichia coli 23S ribosomal RNA underlies the L7/L12 stalk in the ribosome and may be significant in positioning this feature relative to the rest of the 50S ribosomal subunit. Unlike the Haloarcula marismortui and Deinococcus radiodurans examples, the lower portion of helix 42 in E.coli contains two consecutive G*A oppositions with both adenines on the same side of the stem. Herein, the structure of an analog of positions 1037-1043 and 1112-1118 in the helix 42 region is reported. NMR spectra and structure calculations support a cis Watson-Crick/Watson-Crick (cis W.C.) G*A conformation for the tandem (G*A)2 in the analog and a minimally perturbed helical duplex stem. Mg2+ titration studies imply that the cis W.C. geometry of the tandem (G*A)2 probably allows O6 of G20 and N1 of A4 to coordinate with a Mg2+ ion as indicated by the largest chemical shift changes associated with the imino group of G20 and the H8 of G20 and A4. A cross-strand bridging Mg2+ coordination has also been found in a different sequence context in the crystal structure of H.marismortui 23S rRNA, and therefore it may be a rare but general motif in Mg2+ coordination.

Adenine↗
PubMed2005

IP-COSY, a totally in-phase and sensitive COSY experiment.

The IP-COSY experiment presented in this paper gives an in-phase spectral presentation in both the F(1) and F(2) dimensions by a combined use of a constant evolution time (CT) in t(1) and a symmetrical refocusing period before t(2). Compared with DQF-COSY and CT-COSY, IP-COSY further alleviates the effect of signal reduction due to a small ratio p (= J/linewidth), showing (1) improved lineshape and cross-peak definition and (2) especially enhancement in signals of the peaks of small active J coupling constant and the peaks of broader linewidth. A new strategy was adopted to eliminate or reduce effectively artifactual peaks by adding a 0.1-0.2 ms variation to the time delays of the CT period used for each scan of the FID in IP-COSY and CT-COSY. (3)J(H,H) coupling constants of larger than 4 Hz in the fingerprint region of peptides can be directly derived from the separation of doublets. IP-COSY cross peaks are stronger than those in DQF-COSY by 4-20-fold for tested peptides and oligonucleotides (MW < 8 kDa) with acquisition and processing parameters used in the work, and they are easier to identify than those in CT-COSY. The overall improvement in IP-COSY should make the detection/autodetection of the COSY cross peaks and the measurements of the various coupling constants more easily achieved, providing valuable information for the structure elucidation of peptides/small proteins and oligonucleotides.

Nuclear Magnetic Resonance, Biomolecular↗
PubMed2004

(3,2)D GFT-NMR experiments for fast data collection from proteins.

High throughput structure determination of proteins will contribute to the success of proteomics investigations. The G-Matrix Fourier Transformation NMR (GFT-NMR) method significantly shortens experimental time by reducing the number of the dimensions of data acquisition for isotopically labeled proteins (Kim, S. and Szyperski, T. (2003) J. Am. Chem. Soc. 125, 1385). We demonstrate herein a suite of ten 3D-->2D or (3,2)D GFT-NMR experiments using (13)C/(15)N-labeled ubiquitin. These experiments were completed within 18 hours, representing a 4- to 18-fold reduction in data acquisition time compared to the corresponding conventional 3D experiments. A subset of the GFT-NMR experiments, (3,2)D HNCO, HNCACB, HN(CO)CACB, and 2D (1)H-(15)N HSQC, which are necessary for backbone assignments, were carried out within 6 hours. To facilitate the analysis of the GFT-NMR spectra, we developed automated procedures for viewing and analyzing the GFT-NMR spectra. Our overall strategy allows (3,2)D GFT-NMR experiments to be readily performed and analyzed. Nevertheless, the increase in spectral overlap and the reduction in signal sensitivity in these fast NMR experiments presently limit their application to relatively small proteins.

Carbon Isotopes↗
PubMed2004

TROSY-based correlation and NOE spectroscopy for NMR structural studies of large proteins.

Transverse relaxation-optimized spectroscopy (TROSY) is based on the fact that cross-correlation relaxation rates associated with the interferences between chemical shift anisotropy and dipole-dipole interactions can be dramatically reduced. TROSY selects these slowly relaxing components of 15N-1HN or 13C-1H antiphase coherences to significantly enhanced signal sensitivity and spectral resolution for large proteins (>30 kD). The basic principles and applications of three- and four-dimensional TROSY-based triple-resonance experiments and NOESY experiments for structure-function studies of proteins are discussed in this chapter. To make applications of these experiments easier, some of the experimental setups are also described.

Carbon Isotopes↗
PubMed2004

TROSY-based NMR experiments for the study of macromolecular dynamics and hydrogen bonding.

Transverse relaxation-optimized spectroscopy (TROSY)-based nuclear magnetic resonance (NMR) experiments can be exploited to obtain chemical shift assignment and values of J-coupling constants, residual dipolar couplings, and nuclear Overhauser effects (NOEs) for structural studies of proteins, as discussed in Chapter 5. Furthermore, the application of TROSY-based NMR experiments can be extended to the measurements of molecule dynamics, amide proton exchange rates, and hydrogen bonds. This chapter describes these experiments.

Hydrogen Bonding↗
PubMed2003

1H(C) and 1H(N) total NOE correlations in a single 3D NMR experiment. 15N and 13C time-sharing in t1 and t2 dimensions for simultaneous data acquisition.

Simultaneous data acquisition in time-sharing (TS) multi-dimensional NMR experiments has been shown an effective means to reduce experimental time, and thus to accelerate structure determination of proteins. This has been accomplished by spin evolution time-sharing of the X and Y heteronuclei, such as (15)N and (13)C, in one of the time dimensions. In this work, we report a new 3D TS experiment, which allows simultaneous (13)C and (15)N spin labeling coherence in both t(1) and t(2) dimensions to give four NOESY spectra in a single 3D experiment. These spectra represent total NOE correlations between (1)H(N) and (1)H(C) resonances. This strategy of double time-sharing (2TS) results in an overall four-fold reduction in experimental time compared with its conventional counterpart. This 3D 2TS CN-CN-H HSQC-NOESY-HSQC pulse sequence also demonstrates improvements in water suppression, (15)N spectral resolution and sensitivity, which were developed based on 2D TS CN-H HSQC and 3D TS H-CN-H NOESY-HSQC experiments. Combining the 3D TS and the 3D 2TS NOESY experiments, NOE assignment ambiguities and errors are considerably reduced. These results will be useful for rapid protein structure determination to complement the effort of discerning the functions of diverse genomic proteins.

Amino Acid Sequence↗
PubMed2002

Novel projected 4D triple resonance experiments for polypeptide backbone chemical shift assignment.

Here we present a novel suite of projected 4D triple-resonance NMR experiments for efficient sequential assignment of polypeptide backbone chemical shifts in 13C/15N doubly labeled proteins. In the 3D HNN[CAHA] and 3D HNN(CO)[CAHA] experiments. the 13C(alpha) and lHalpha chemical shifts evolve in a common dimension and are simultaneously detected in quadrature. These experiments are particularly useful for the assignment of glycine-rich polypeptide segments. Appropriate setting of the 1H radiofrequency carrier allows one to place cross peaks correlating either backbone 15N/1H(N)/13C(alpha) or 15N/1H(N)/H(alpha) chemical shifts in separate spectral regions. Hence, peak overlap is not increased when compared with the conventional 3D HNNCA and HNN(CA)HA. 3D HNN[CAHA] and 3D HNN(CO)[CAHA] are complemented by 3D reduced-dimensionality (RD) HNN COCA and NNCACO, where 13C(alpha) and 13C' chemical shifts evolve in a common dimension. The 13C(alpha), shift is detected in quadrature, which yields peak pairs encoding the 13C' chemical shift in an in-phase splitting. This suite of four experiments promises to be of value for automated high-throughput NMR structure determination in structural genomics, where the requirement to independently sample many indirect dimensions in a large number of NMR experiments may prevent one from accurately adjusting NMR measurement times to spectrometer sensitivity.

Nuclear Magnetic Resonance, Biomolecular↗