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Differences in the fractional abundances of carbohydrates of natural and recombinant human tissue factor.

ABSTRACT: Tissue factor (TF) is a single polypeptide integral membrane glycoprotein composed of 263 residues and is essential to life in its role as the initiator of blood coagulation. Previously we have shown that the activity of the natural placental TF (pTF) and the recombinant TF (rTF) from Sf9 insect cells is different (Krudysz-Amblo, J. et al (2010) J. Biol. Chem. 285, 3371-3382).In this study, using mass spectrometry, we show by quantitative analysis that the extent of glycosylation varies on each protein.Fractional abundance of each glycan composition at each of the three glycosylation sites reveals the most pronounced difference to be at asparagine (Asn) 11. This residue is located in the region of extensive TF-factor VIIa (FVIIa) interaction. Carbohydrate fractional abundance at Asn11 revealed that glycosylation in the natural placental TF is much more prevalent (~76%) than in the recombinant protein (~20%). The extent of glycosylation on Asn124 and Asn137 is similar in the two proteins, despite the pronounced differences in the carbohydrate composition. Additionally, 77% of rTF exists as TF des-1, 2 (missing the first two amino acids from the N-terminus). In contrast, only 31% of pTF is found in the des-1, 2 form.These observations may attribute to the difference in the ability of TF-FVIIa complex to activate factor X (FX).Structural and functional comparison of the recombinant and natural protein advances our understanding and knowledge on the biological activity of TF.

SUBMITTER: Krudysz-Amblo J

PROVIDER: S-EPMC3048926 | biostudies-literature | 2011 Apr

REPOSITORIES: biostudies-literature

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Differences in the fractional abundances of carbohydrates of natural and recombinant human tissue factor.

Krudysz-Amblo Jolanta J Jennings Mark E ME Matthews Dwight E DE Mann Kenneth G KG Butenas Saulius S

Biochimica et biophysica acta 20101221 4

<h4>Background</h4>Tissue factor (TF) is a single polypeptide integral membrane glycoprotein composed of 263 residues and is essential to life in its role as the initiator of blood coagulation. Previously we have shown that the activity of the natural placental TF (pTF) and the recombinant TF (rTF) from Sf9 insect cells is different (Krudysz-Amblo, J. et al (2010) J. Biol. Chem. 285, 3371-3382).<h4>Methods</h4>In this study, using mass spectrometry, we show by quantitative analysis that the exte ...[more]

PMID: 21172408

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Project description:Most implementations of mass spectrometry-based proteomics involve enzymatic digestion of proteins, expanding the analysis to multiple proteolytic peptides for each protein. Currently, there is no consensus of how to summarize peptides' abundances to protein concentrations, and such efforts are complicated by the fact that error control normally is applied to the identification process, and do not directly control errors linking peptide abundance measures to protein concentration. Peptides resulting from suboptimal digestion or being partially modified are not representative of the protein concentration. Without a mechanism to remove such unrepresentative peptides, their abundance adversely impacts the estimation of their protein's concentration. Here, we present a relative quantification approach, Diffacto, that applies factor analysis to extract the covariation of peptides' abundances. The method enables a weighted geometrical average summarization and automatic elimination of incoherent peptides. We demonstrate, based on a set of controlled label-free experiments using standard mixtures of proteins, that the covariation structure extracted by the factor analysis accurately reflects protein concentrations. In the 1% peptide-spectrum match-level FDR data set, as many as 11% of the peptides have abundance differences incoherent with the other peptides attributed to the same protein. If not controlled, such contradicting peptide abundance have a severe impact on protein quantifications. When adding the quantities of each protein's three most abundant peptides, we note as many as 14% of the proteins being estimated as having a negative correlation with their actual concentration differences between samples. Diffacto reduced the amount of such obviously incorrectly quantified proteins to 1.6%. Furthermore, by analyzing clinical data sets from two breast cancer studies, our method revealed the persistent proteomic signatures linked to three subtypes of breast cancer. We conclude that Diffacto can facilitate the interpretation and enhance the utility of most types of proteomics data.

Project description:PurposeTo test the hypothesis that fractional kidney hypoxia, measured by using blood oxygen level-dependent (BOLD) magnetic resonance (MR) imaging, correlates with renal blood flow (RBF), tissue perfusion, and glomerular filtration rate (GFR) in patients with atherosclerotic renal artery stenosis (RAS) better than regionally selected region of interest-based methods.Materials and methodsThe study was approved by the institutional review board according to a HIPAA-compliant protocol, with written informed consent. BOLD MR imaging was performed in 40 patients with atherosclerotic RAS (age range, 51-83 years; 22 men, 18 women) and 32 patients with essential hypertension (EH) (age range, 26-85 years; 19 men, 13 women) during sodium intake and renin-angiotensin blockade. Fractional kidney hypoxia (percentage of entire axial image section with R2* above 30 sec(-1)) and conventional regional estimates of cortical and medullary R2* levels were measured. Stenotic and nonstenotic contralateral kidneys were compared for volume, tissue perfusion, and blood flow measured with multidetector computed tomography. Statistical analysis was performed (paired and nonpaired t tests, linear regression analysis).ResultsStenotic RBF was reduced compared with RBF of contralateral kidneys (225.2 mL/min vs 348 mL/min, P = .0003). Medullary perfusion in atherosclerotic RAS patients was lower than in EH patients (1.07 mL/min per milliliter of tissue vs 1.3 mL/min per milliliter of tissue, P = .009). While observer-selected cortical R2* (18.9 sec(-1) [stenosis] vs 18.5 sec(-1) [EH], P = .07) did not differ, fractional kidney hypoxia was higher in stenotic kidneys compared with kidneys with EH (17.4% vs 9.6%, P < .0001) and contralateral kidneys (7.2%, P < .0001). Fractional hypoxia correlated inversely with blood flow (r = -0.34), perfusion (r = -0.3), and GFR (r = -0.32).ConclusionFractional tissue hypoxia rather than cortical or medullary R2* values used to assess renal BOLD MR imaging demonstrated a direct relationship to chronically reduced blood flow and GFR.

Dataset Information

Differences in the fractional abundances of carbohydrates of natural and recombinant human tissue factor.

Publications

Differences in the fractional abundances of carbohydrates of natural and recombinant human tissue factor.

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