Wenzhou Li

The University of Arizona, Tucson, AZ, United States

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Publications (7)24.78 Total impact

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    ABSTRACT: Soluble guanylyl/guanylate cyclase (sGC) converts GTP to cGMP after binding nitric oxide, leading to smooth muscle relaxation and vasodilation. Impaired sGC activity is common in cardiovascular disease and sGC stimulatory compounds are greatly sought. sGC is a 150 kDa heterodimeric protein with two H-NOX domains (one with heme, one without), two PAS domains, a coiled-coil domain and two cyclase domains. Binding of NO to the sGC heme leads to proximal histidine release and stimulation of catalytic activity. To begin understanding how binding leads to activation, we examined truncated sGC proteins from Manduca sexta (tobacco hornworm) that bind NO, CO and stimulatory compound YC-1, but lack the cyclase domains. We determined the overall shape of truncated Ms sGC using analytical ultracentrifugation and small angle X-ray scattering (SAXS), revealing an elongated molecule 115 Å by 90 Å by 75 Å. Binding of NO, CO or YC-1 had little effect on shape. Using chemical cross-linking and tandem mass spectrometry, we identified 20 intermolecular contacts, allowing us to fit homology models of the individual domains into the SAXS-derived molecular envelope. The resulting model displays a central parallel coiled-coil platform upon which the H-NOX and PAS domains are assembled. The β1 H-NOX and α1 PAS domains are in contact and form the core signaling complex, while the α1 H-NOX domain can be removed without significant effect on ligand binding or overall shape. Removal of 21 residues from the C-terminus yields a protein with dramatically increased proximal histidine release rates upon NO binding.
    Biochemistry 01/2013; · 3.38 Impact Factor
  • Article: SQID-XLink
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    ABSTRACT: Peptide identification algorithm is a major bottleneck for mass spectrometry based chemical cross-linking experiments. Our lab recently developed an intensity-incorporated peptide identification algorithm, and here we implemented this scheme for cross-linked peptide discovery. Our program, SQID-XLink, searches all regular, dead-end, intra and inter cross-linked peptides simultaneously, and its effectiveness is validated by testing a published dataset. This new algorithm provides an alternative approach for high confidence cross-linking identification. Availability: SQID-XLink program is freely available for download from http://quiz2.chem.arizona.edu/wysocki/bioinformatics.htm Supplementary information: Supplementary data are available at Bioinformatics online. Contact: vwysocki@email.arizona.edu
    Bioinformatics. 10/2012; 28(19):2548-2550.
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    ABSTRACT: Peptide identification algorithm is a major bottleneck for mass spectrometry based chemical cross-linking experiments. Our lab recently developed an intensity-incorporated peptide identification algorithm, and here we implemented this scheme for cross-linked peptide discovery. Our program, SQID-XLink, searches all regular, dead-end, intra and inter cross-linked peptides simultaneously, and its effectiveness is validated by testing a published dataset. This new algorithm provides an alternative approach for high confidence cross-linking identification. SQID-XLink program is freely available for download from http://quiz2.chem.arizona.edu/wysocki/bioinformatics.htm Supplementary data are available at Bioinformatics online. vwysocki@email.arizona.edu.
    Bioinformatics 07/2012; 28(19):2548-50. · 5.47 Impact Factor
  • Source
    Wenzhou Li, Vicki H Wysocki
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    ABSTRACT: Electron transfer dissociation (ETD) is an alternative technique used in mass spectrometry-based proteomics experiments. Because it is newer, most of the protein identification algorithms for ETD are still a simple derivation of well-established collision-activated dissociation algorithms without the consideration of many unique ETD spectral features. Sridhara and coworkers recently reported removing the charge-reduced precursors and corresponding neutral loss peaks to improve ETD peptide identification with the Open Mass Spectrometry Search Algorithm (OMSSA). These peaks were also used to deduce the charge of the precursors for low resolution data. The scheme is a concrete example of implementing known ETD fragmentation features to improve a protein identification algorithm.
    Expert Review of Proteomics 06/2012; 9(3):241-3. · 3.90 Impact Factor
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    ABSTRACT: Electron transfer dissociation (ETD) is an alternative peptide dissociation method developed in recent years. Compared with the traditional collision induced dissociation (CID) b and y ion formation, ETD generates c and z ions and the backbone cleavage is believed to be less selective. We have reported previously the application of a statistical data mining strategy, K-means clustering, to discover fragmentation patterns for CID, and here we report application of this approach to ETD spectra. We use ETD data sets from digestions with three different proteases. Data analysis shows that selective cleavages do exist for ETD, with the fragmentation patterns affected by protease, charge states, and amino acid residue compositions. It is also noticed that the c(n-1) ion, corresponding to loss of the C-terminal amino acid residue, is statistically strong regardless of the residue at the C-terminus of the peptide, which suggests that the peptide gas phase conformation plays an important role in the dissociation pathways. These patterns provide a basis for mechanism elucidation, spectral prediction, and improvement of ETD peptide identification algorithms.
    Analytical Chemistry 12/2011; 83(24):9540-5. · 5.70 Impact Factor
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    ABSTRACT: To interpret LC-MS/MS data in proteomics, most popular protein identification algorithms primarily use predicted fragment m/z values to assign peptide sequences to fragmentation spectra. The intensity information is often undervalued, because it is not as easy to predict and incorporate into algorithms. Nevertheless, the use of intensity to assist peptide identification is an attractive prospect and can potentially improve the confidence of matches and generate more identifications. On the basis of our previously reported study of fragmentation intensity patterns, we developed a protein identification algorithm, SeQuence IDentfication (SQID), that makes use of the coarse intensity from a statistical analysis. The scoring scheme was validated by comparing with Sequest and X!Tandem using three data sets, and the results indicate an improvement in the number of identified peptides, including unique peptides that are not identified by Sequest or X!Tandem. The software and source code are available under the GNU GPL license at http://quiz2.chem.arizona.edu/wysocki/bioinformatics.htm.
    Journal of Proteome Research 01/2011; 10(4):1593-602. · 5.06 Impact Factor
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    ABSTRACT: Tandem mass spectrometry is a widely used tool in proteomics. This section will address the properties that describe how protonated peptides fragment when activated by collisions in a mass spectrometer and how that information can be used to identify proteins. A review of the mobile proton model is presented, along with a summary of commonly observed peptide cleavage enhancements, including the proline effect. The methods used to elucidate peptide dissociation chemistry by using both small groups of model peptides and large datasets are also discussed. Finally, the role of peak intensity in commercially available and developmental peptide identification algorithms is examined.
    Methods in molecular biology (Clifton, N.J.) 01/2010; 604:73-94. · 1.29 Impact Factor