Robert Polakowski - Academia.edu (original) (raw)

Papers by Robert Polakowski

CardioVascular and Interventional Radiology, Jul 6, 2011

Introduction This study evaluated the safety, effectiveness, and biodegradation of a new embolic ... more Introduction This study evaluated the safety, effectiveness, and biodegradation of a new embolic agent, Occlusin TM 503 Artificial Embolization Device (OCL 503). The agent consists of biodegradable poly-lactic-co-glycolic acid microspheres (150-212 lm) coated with type I bovine collagen and was compared with Embosphere Ò Microspheres (300-500 lm) in this controlled study of uterine artery embolization (UAE) in sheep. Methods Unilateral UAE was performed in 32 adult ewes randomly assigned. Vessels were embolized to effective stasis. The cohort was divided into four groups, which were sacrificed at 1, 3, 6, and 12 months. Results Both agents were 100% effective in achieving stasis. At 6 months, all OCL 503-treated arteries were occluded, the microspheres degraded with time, and at 12 months all four animals examined demonstrated recanalization. OCL 503 was found in the untreated uterine artery in one animal with no other evidence of non target embolization. In the Embosphere-treated group, all vessels remained occluded and microspheres were detected in the contralateral uterine artery in 6 of 15 examined vessels and in 10 vaginal, 2 ovarian, and 1 vesical artery. No procedural-related complications were seen in either group. Conclusions OCL 503 is as effective an embolic agent as Embosphere Ò Microspheres when embolizing ovine uterine arteries and resorbs with time, allowing recanalization of the treated arteries. No device-related issues or adverse events were observed.

Glycobiology, Jun 20, 2018

Homologous glycosyltransferases GTA and GTB perform the final step in human ABO(H) blood group A ... more Homologous glycosyltransferases GTA and GTB perform the final step in human ABO(H) blood group A and B antigen synthesis by transferring the sugar moiety from donor UDP-GalNAc/UDP-Gal to the terminal H antigen disaccharide acceptor. Like other GT-A fold family 6 glycosyltransferases, GTA and GTB undergo major conformational changes in two mobile regions, the C-terminal tail and internal loop, to achieve the closed, catalytic state. These changes are known to establish a salt bridge network among conserved active site residues Arg188, Asp211 and Asp302, which move to accommodate a series of discrete donor conformations while promoting loop ordering and formation of the closed enzyme state. However, the individual significance of these residues in linking these processes remains unclear. Here, we report the kinetics and high-resolution structures of GTA/GTB mutants of residues 188 and 302. The structural data support a conserved salt bridge network critical to mobile polypeptide loop organization and stabilization of the catalytically competent donor conformation. Consistent with the X-ray crystal structures, the kinetic data suggest that disruption of this salt bridge network has a destabilizing effect on the transition state, emphasizing the importance of Arg188 and Asp302 in the glycosyltransfer reaction mechanism. The salt bridge network observed in GTA/GTB structures during substrate binding appears to be conserved not only among other Carbohydrate Active EnZyme family 6 glycosyltransferases but also within both retaining and inverting GT-A fold glycosyltransferases. Our findings augment recently published crystal structures, which have identified a correlation between donor substrate conformational changes and mobile loop ordering.

Analytical Chemistry, Dec 11, 1999

A single HT29 human colon adenocarcinoma cell was introduced into a fused-silica capillary and ly... more A single HT29 human colon adenocarcinoma cell was introduced into a fused-silica capillary and lysed, and the protein content was fluorescently labeled with the fluorogenic reagent 3-(2-furoyl)quinoline-2-carboxaldehyde. The labeled proteins were separated by capillary electrophoresis in a submicellar buffer and detected by laser-induced fluorescence in a postcolumn sheath-flow cuvette. Several dozen components were resolved. A number of experiments were done to verify that these components were proteins. Most components of the single-cell electropherogram had the same mobility as components present in the 30-100 kDa fraction of a protein extract prepared from the cell culture. One component was identified as a ∼100 kDa protein by co-injecting the sample with purified protein obtained from an SDS-PAGE gel. Protein expression varied significantly between cells, but the average expression was consistent with that observed from a protein extract prepared from 10 6 cells.

Journal of Food Composition and Analysis, Dec 1, 2015

Abstract Gangliosides are an important class of glycosphingolipids involved in numerous biologica... more Abstract Gangliosides are an important class of glycosphingolipids involved in numerous biological processes such as neuronal development, host–pathogen interactions and gastrointestinal health. Due to the highly heterogeneous nature and relatively low abundance of gangliosides, characterization of gangliosides in biological membranes is challenging. Existing methods for ganglioside analysis are quite time consuming and require expensive high resolution mass spectrometers. A rapid method combining reversed phase chromatography and mass spectrometry was developed using a triple-quadrupole mass spectrometer operating in multiple reaction monitoring mode. The ganglioside species were separated with a Poroshell 120 EC-C18 column and analysed under the negative ion mode. This method allows a sensitive, specific, and quantitative assay for profiling gangliosides. The method is developed for analysis of gangliosides in the milk fat globule membrane of whole milk and applied to other biological membranes. Application includes the cellular membrane of prostate cancer cells. In summary, the method allows various biological membranes to be screened for over 600 gangliosides from 12 classes (GM1, GM2, GM3, GM4, GD1, GD2, GD3, GD4, GT1, GT2, GT3, and GT4) in less than three hours. In summary, expressed as % of relative amounts: 1.5% GM3, 80.2% GD3, 14.4% GT3, 1.5% GM1, 2.4% GD1 were observed in whole milk; 2.5% GD1, 88.2% GD3, 2.5% GM1, 2.2% GM3, 0.2% GT2, 4.2% GT3 were observed in buttermilk and 10.6% GD1, 55.6% GD3, 1.6% GM1, 12.2% GM3, 19.2% GT3, 0.9% GT4 were observed in colostrum.

Electrophoresis, Sep 1, 1998

Journal of Biological Chemistry, Apr 1, 2008

The final step in the enzymatic synthesis of the ABO(H) blood group A and B antigens is catalyzed... more The final step in the enzymatic synthesis of the ABO(H) blood group A and B antigens is catalyzed by two closely related glycosyltransferases, an ␣-(133)-N-acetylgalactosaminyltransferase (GTA) and an ␣-(133)-galactosyltransferase (GTB). Of their 354 amino acid residues, GTA and GTB differ by only four "critical" residues. High resolution structures for GTB and the GTA/GTB chimeric enzymes GTB/G176R and GTB/G176R/ G235S bound to a panel of donor and acceptor analog substrates reveal "open," "semi-closed," and "closed" conformations as the enzymes go from the unliganded to the liganded states. In the open form the internal polypeptide loop (amino acid residues 177-195) adjacent to the active site in the unliganded or H antigen-bound enzymes is composed of two ␣-helices spanning Arg 180-Met 186 and Arg 188-Asp 194 , respectively. The semiclosed and closed forms of the enzymes are generated by binding of UDP or of UDP and H antigen analogs, respectively, and show that these helices merge to form a single distorted helical structure with alternating ␣-3 10-␣ character that partially occludes the active site. The closed form is distinguished from the semiclosed form by the ordering of the final nine C-terminal residues through the formation of hydrogen bonds to both UDP and H antigen analogs. The semi-closed forms for various mutants generally show significantly more disorder than the open forms, whereas the closed forms display little or no disorder depending strongly on the identity of residue 176. Finally, the use of synthetic analogs reveals how H antigen acceptor binding can be critical in stabilizing the closed conformation. These structures demonstrate a delicately balanced substrate recognition mechanism and give insight on critical aspects of donor and acceptor specificity, on the order of substrate binding, and on the requirements for catalysis.

Journal of Molecular Biology, Sep 1, 2010

A common feature in the structures of GT-A-fold-type glycosyltransferases is a mobile polypeptide... more A common feature in the structures of GT-A-fold-type glycosyltransferases is a mobile polypeptide loop that has been observed to participate in substrate recognition and enclose the active site upon substrate binding. This is the case for the human ABO(H) blood group B glycosyltransferase GTB, where amino acid residues 177-195 display significantly higher levels of disorder in the unliganded state than in the fully liganded state. Structural studies of mutant enzymes GTB/C80S/C196S and GTB/C80S/C196S/C209S at resolutions ranging from 1.93 to 1.40 Å display the opposite trend, where the unliganded structures show nearly complete ordering of the mobile loop residues that is lost upon substrate binding. In the liganded states of the mutant structures, while the UDP moiety of the donor molecule is observed to bind in the expected location, the galactose moiety is observed to bind in a conformation significantly different from that observed for the wild-type chimeric structures. Although this would be expected to impede catalytic turnover, the kinetics of the transfer reaction are largely unaffected. These structures demonstrate that the enzymes bind the donor in a conformation more similar to the dominant solution rotamer and facilitate its gyration into the catalytically competent form. Further, by preventing active-site closure, these structures provide a basis for recently observed cooperativity in substrate binding. Finally, the mutation of C80S introduces a fully occupied UDP binding site at the enzyme dimer interface that is observed to be dependent on the binding of H antigen acceptor analog.

Analytical Chemistry, Aug 20, 1998

Capillary electrophoresis with laser-induced fluorescence detection was used to develop a univers... more Capillary electrophoresis with laser-induced fluorescence detection was used to develop a universal, highly specific protease assay. In this method, a peptide, biotinylated at the N-terminus, is labeled with fluorescein at a lysine residue near the C-terminus. Impurities are removed from the fluorescence labeling mixture by solid-phase extraction of the substrate on immobilized streptavidin, followed by extensive washing. The purified fluorescent substrate is dissociated from the streptavidin and incubated with the protease. The peptide sequence between the biotin and fluorescent label contains the cleavage sequence of the protease of interest. After cleavage, the fluorescent product does not contain a biotin group. A second solid-phase extraction is used to remove unreacted substrate to dramatically lower the background signal. The product is detected by capillary electrophoresis, which provides powerful discrimination against products generated by nonspecific proteases. With chymotrypsin as a test protease, product was detected with as little as 10 pg/mL (4.6 × 10-13 M) chymotrypsin, or 5 amol of enzyme in the 10-µL sample volume.

Journal of Biological Chemistry, Apr 1, 2003

Blood group A and B antigens are carbohydrate structures that are synthesized by glycosyltransfer... more Blood group A and B antigens are carbohydrate structures that are synthesized by glycosyltransferase enzymes. The final step in B antigen synthesis is carried out by an ␣1-3 galactosyltransferase (GTB) that transfers galactose from UDP-Gal to type 1 or type 2, ␣Fuc132␤Gal-R (H)-terminating acceptors. Similarly the A antigen is produced by an ␣1-3 N-acetylgalactosaminyltransferase that transfers N-acetylgalactosamine from UDP-GalNAc to H-acceptors. Human ␣1-3 N-acetylgalactosaminyltransferase and GTB are highly homologous enzymes differing in only four of 354 amino acids (R176G, G235S, L266M, and G268A). Single crystal x-ray diffraction studies have shown that the latter two of these amino acids are responsible for the difference in donor specificity, while the other residues have roles in acceptor binding and turnover. Recently a novel cis-AB allele was discovered that produced A and B cell surface structures. It had codons corresponding to GTB with a single point mutation that replaced the conserved amino acid proline 234 with serine. Active enzyme expressed from a synthetic gene corresponding to GTB with a P234S mutation shows a dramatic and complete reversal of donor specificity. Although this enzyme contains all four "critical" amino acids associated with the production of blood group B antigen, it preferentially utilizes the blood group A donor UDP-GalNAc and shows only marginal transfer of UDP-Gal. The crystal structure of the mutant reveals the basis for the shift in donor specificity.

BioProcessing Journal, Jun 30, 2006

Glycobiology, Aug 1, 2018

Glycobiology, Apr 22, 2016

The homologous glycosyltransferases α-1,3-N-acetylgalactosaminyltransferase (GTA) and α-1,3-galac... more The homologous glycosyltransferases α-1,3-N-acetylgalactosaminyltransferase (GTA) and α-1,3-galactosyltransferase (GTB) carry out the final synthetic step of the closely related human ABO(H) blood group A and B antigens. The catalytic mechanism of these model retaining enzymes remains under debate, where Glu303 has been suggested to act as a putative nucleophile in a double displacement mechanism, a local dipole stabilizing the intermediate in an orthogonal associative mechanism or a general base to stabilize the reactive oxocarbenium ion-like intermediate in an S N i-like mechanism. Kinetic analysis of GTA and GTB point mutants E303C, E303D, E303Q and E303A shows that despite the enzymes having nearly identical sequences, the corresponding mutants of GTA/GTB have up to a 13-fold difference in their residual activities relative to wild type. High-resolution single crystal X-ray diffraction studies reveal, surprisingly, that the mutated Cys, Asp and Gln functional groups are no more ...