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Acta Crystallographica Section E: Structure Reports Online (1)
BMC Biotechnology (1)
Journal of Computational Biology (1)
Li, Xiangqian (3)
Bafna, Vineet (1)
Bandeira, Nuno (1)
Briggs, Steven P. (1)
Chen, Hongge (1)
Dost, Banu (1)
Ge, Chunhua (1)
Guo, Xiaodan (1)
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Accurate Mass Spectrometry Based Protein Quantification via Shared Peptides
Briggs, Steven P.
Journal of Computational Biology
In mass spectrometry-based protein quantification, peptides that are shared across different protein sequences are often discarded as being uninformative with respect to each of the parent proteins. We investigate the use of shared peptides which are ubiquitous (∼50% of peptides) in mass spectrometric data-sets for accurate protein identification and quantification. Different from existing approaches, we show how shared peptides can help compute the relative amounts of the proteins that contain them. Also, proteins with no unique peptide in the sample can still be analyzed for relative abundance. Our article uses shared peptides in protein quantification and makes use of combinatorial optimization to reduce the error in relative abundance measurements. We describe the topological and numerical properties required for robust estimates, and use them to improve our estimates for ill-conditioned systems. Extensive simulations validate our approach even in the presence of experimental error. We apply our method to a model of Arabidopsis thaliana root knot nematode infection, and investigate the differential role of several protein family members in mediating host response to the pathogen. Supplementary Material is available at www.liebertonline.com/cmb.
ITRAQ; linear programming; mass spectrometry optimization; protein quantification; shared peptides
Domain-swapping of mesophilic xylanase with hyper-thermophilic glucanase
Domain fusion is limited at enzyme one terminus. The issue was explored by swapping a mesophilic Aspergillus niger GH11 xylanase (Xyn) with a hyper-thermophilic Thermotoga maritima glucanase (Glu) to construct two chimeras, Xyn-Glu and Glu-Xyn, with an intention to create thermostable xylanase containing glucanase activity.
When expressed in E. coli BL21(DE3), the two chimeras exhibited bi-functional activities of xylanase and glucanase. The Xyn-Glu Xyn moiety had optimal reaction temperature (Topt) at 50 °C and thermal in-activation half-life (t1/2) at 50 °C for 47.6 min, compared to 47 °C and 17.6 min for the Xyn. The Glu-Xyn Xyn moiety had equivalent Topt to and shorter t1/2 (5.2 min) than the Xyn. Both chimera Glu moieties were more thermostable than the Glu, and the three enzyme Topt values were higher than 96 °C. The Glu-Xyn Glu moiety optimal pH was 5.8, compared to 3.8 for the Xyn-Glu Glu moiety and the Glu. Both chimera two moieties cooperated with each other in degrading substrates.
Domain-swapping created different effects on each moiety properties. Fusing the Glu domain at C-terminus increased the xylanase thermostability, but fusing the Glu domain at N-terminus decreased the xylanase thermostability. Fusing the Xyn domain at either terminus increased the glucanase thermostability, and fusing the Xyn domain at C-terminus shifted the glucanase pH property 2 units higher towards alkaline environments. Fusing a domain at C-terminus contributes more to enzyme catalytic activity; whereas, fusing a bigger domain at N-terminus disturbs enzyme substrate binding affinity.
Xylanase; Glucanase; Domain-swapping; Fusing
2,2′-(1,3,5,7-Tetraoxo-1,2,3,5,6,7-hexahydropyrrolo[3,4-f]isoindole-2,6-diyl)diacetic acid N,N-dimethylformamide disolvate
Acta Crystallographica Section E: Structure Reports Online
The asymmetric unit of the title compound, C14H8N2O8·2C3H7NO or L·2DMF (DMF = N,N-dimethylformamide), contains one half of the centrosymmetric molecule L and one solvent molecule, which is disordered between two orientations in a 0.555 (4):0.445 (4) ratio. Intermolecular O—H⋯O hydrogen bonds link one L and two DMF molecules into a centrosymmetric hydrogen-bonded cluster. The crystal packing is further stabilized by weak intermolecular C—H⋯O hydrogen bonds.
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