Biopolymer synthesis and analysis related articles from Microchemical Facility organized by topics

Proteomics, complete or partial protein covalent sequences, disulphide bridges, protein assemblies

Wilkinson, K. D., Lee, J., Desphande, S., Duerkensen-Hughes, P., Boss, J. and Pohl, J.: The neuronal-specific protein PGP9.5 is a ubiquitin carboxyl-terminal hydrolase. Science 240, 670-673, 1989.

Pereira, H. A., Spitznagel, J. K., Pohl, J., Wilson, D. E., Morgan, J., Palings, I. and Larrick, J. W.: CAP37, a 37 kD human neutrophil granule cationic protein shares homology with inflammatory proteinases. Life Sci. 46, 189-196, 1990.

Pohl, J., Pereira, H. A., Martin, N. M. and Spitznagel, J. K.: Amino acid sequence of CAP37, a human neutrophil granule-derived antibacterial and monocyte-specific chemotactic glycoprotein structurally similar to neutrophil elastase. FEBS Lett. 272, 200-204, 1990.

Pereira, H. A., Shafer, W. M., Pohl, J., Martin, L. E. and Spitznagel, J. K.: CAP37, a human neutrophil-derived chemotactic factor with monocyte specific activity. J. Clin. Invest. 85, 1468-1476, 1990.

Pereira, H. A., Spitznagel, J. K., Winton, E. F., Shafer, W. M., Martin, L. E., Guzman, G. S., Pohl, J. and Kinkade, J. M.: The ontogeny of a 57 kD cationic antimicrobial protein of human polymorphonuclear leukocytes. Localization to a novel granule population. Blood 76, 825-834, 1990.

Taylor, K. L., Guzman, G. S., Pohl, J. and Kinkade, J. K.: Distinct chromatographic forms of human hemimyeloperoxidase obtained by reductive cleavage of the dimeric enzyme: evidence for subunit heterogeneity. J. Biol. Chem. 265, 15938-15946, 1990.

Bonkovsky, H. L., Healey, J. and Pohl, J.: Purification and characterization of hepatic heme oxygenase from chicken liver. Comparison of the avian and mammalian enzymes. Eur. J. Biochem. 189, 155-166, 1990.

Baudys, M., Meloun, B., Gan-Erdene, T., Pohl, J. and Kostka, V.: Disulfide bridges of bovine cathepsin B. Biol. Chem. Hoppe-Seyler 371, 485-491, 1990.

Baudys, M., Meloun, B., Gan-Erdene, T., Fusek, M., Mares, M., Kostka, V., Pohl, J. and Blake, C. C. F.: SS bridges of cathepsin B and H from bovine spleen: a basis for cathepsin B model building and possible functional implications for discrimination between exo- and endopeptidase activities among cathepsins B, H and L. Biomed. Biochim. Acta 50, 569-577, 1991.

Taylor, K. L., Pohl, J. and Kinkade, J. M.: A unique autolytic cleavage of human myeloperoxidase: Implications for the involvement of active site Met409. J. Biol. Chem. 267, 25282-25288, 1992.

Kumar, A., Pei-Shen, S., Descoteaux, S., Pohl, J., Bailey, G. and Samuelson, J.: Cloning and expression of an NADP+-dependent alcohol dehydrogenase gene of Entamoeba histolytica. Proc. Natl. Acad. Sci. USA 89, 10188-10192, 1992.

Pohl, J.: Sequence analysis of peptide resins from Boc/benzyl solid-phase synthesis. Methods Mol. Biol. 36, 107-129, 1994.

Pohl, J., Hubalek, F., Byrnes, M. E., Nielsen, K. R., Woods, A. and Pennington, M. W.: Assignment of the three disulfide bonds in ShK toxin: A potent potassium channel inhibitor from the sea anemone Stichodactyla heliathus. Lett. Peptide Sci. 2, 291-297, 1995.

Taylor, K. L., Strobel, F., Yue, K. T., Ram, P., Pohl, J., Woods, A. and Kinkade, J. M. Jr.: Isolation and identification of a protoheme IX derivative released during autolytic cleavage of human myeloperoxidase. Arch. Biochem. Biophys. 316, 635-642, 1995.

Liu, X., Kim, C. N., Pohl, J. and Wang, X.: Purification and characterization of an interleukin-1b converting enzyme family protease that activates cysteine protease P32 (CPP32). J. Biol. Chem. 271, 13371-13376, 1996.

Ahmed, H., Pohl, J., Fink, N. E., Strobel, F. and Vasta, G.: The primary structure and carbohydrate specificity of a b-galactosyl-binding lectin from toad (Bufo arenarum Hensel) ovary reveal closer similarities to the mammalian galectin-1 than to the galectin from the clawed frog Xenopus laevis. J. Biol. Chem. 271, 33083-33094, 1996.

Ahmed, H., Fink, N. E., Pohl, J. and Vasta, G. R.: Galectin-1 from bovine spleen: biochemical characterization, carbohydrate specificity and tissue-specific isoform profiles. J. Biochem. (Tokyo) 120, 1007-1019, 1996.

Parker, E. T., Pohl, J., Blackburn, M. N. and Lollar, P.: Subunit Structure and function of porcine factor Xa-activated factor VIII. Biochemistry, 36, 9365-9373, 1997.

Gernert, K., Pohl, J. and Wohlhueter, R. (1998) "The Nature of Proteins", a post-graduate course (http://sleepy.bimcore.emory.edu/home/Tutorials/proteins98).

Schaffhauser, H., Cai, Z., Hubalek, F., Macek, T. A., Pohl, J., Murphy, T. J. and Conn, J. P.: CAMP protein kinase inhibits mGluR2 coupling to G-proteins by direct receptor phosphorylation. J. Neuroscience, 20, 5663-5670, 2000.

Ono, S., McGough, A., Pope, A. J., Tolbert, V. T., Bui, A., Pohl, J., Benian, G. B., Gernert, K. M. Amd Weeds, A. G.: The C-terminal tail of UNC-60B (ADF/Cofilin) is critical for maintaining its stableassociation with F-actin and is implicated in the second actin-binding site. J. Biol. Chem., 276, 5952-5958, 2001.

Remgarajan, K., Pohl, J. and Nickerson, J.: Photoaffinity labeling of human IRBP with all-trans-retinoic acid. Biochem. Biophys. Res. Commun. 284, 268-274, 2001.

Cai, Z., Saugstad, J. A., Sorenses, S. D., Ciombor, K. J., Schaffhauser, H., Hubalek, F., Pohl, J., Zhang, C., Duvoisin, R. M. And Conn, J.: Cyclic AMP-dependent protein kinase phosphorylates group III metabotropic glutamate receptors and inhibits their function as presynaptic receptors. J. Neurochemistry, 781, 756-766, 2001.

Cole, A. M., Liao, H.-I., Stuchlik, O., Tilan, J., Pohl, J. and Ganz, T.: Cationic peptides are required for antimicrobial activity of human airway fluid. J. Immunol., 169 , 6985-6991, 2002.

Saugstad, J. A., Yang, S., Pohl, J., Hall, R. A. and Conn, P.J.: Interation between metabotropic glutamate receptor 7 and alpha tubulin. J. Neurochemistry, 80, 980-988, 2002.

Rumlova, M., Ruml, T., Pohl, J. and Pichova, I.: Specific in vitro cleavage of Mason-Pfizer monkey virus capsid protein: Evidence for a potential role of retroviral protease in early stages of infection. Virology, 310, 310-318, 2003.

Hubalek, F., Pohl, J. and Edmondson, D. E.: Structural comparison of human MAO A and human MAO B. Mass spectrometry monitoring of cysteine reactivities. J. Biol. Chem. 278, 28612-28618, 2003.

Watson, W. H., Pohl, J., Montfort, W. R., Stuchlik, O., Reed, M. S., Powis, G. and Jones, D. P.: Redox potential of human thioredoxin 1 and identification of a second dithiol/disulfide motif. J. Biol. Chem. 278, 33408-33415, 2003.

Shern, J. F., Sharer, J. D., Pallas, D., Bartolini, F., Cowan, N. J., Reed, M. S., Pohl, J. and Kahn, R. A.: Cytosolic Arl2 is complexed with cofactor D and PP2A. J. Biol. Chem. 278, 40829-40836, 2003.

Tseung, C. W., McMahon, L. G., Vazquez, J., Pohl, J. and Gregory, J. F.: Partial amino acid sequence and mRNA analysis of cytosolic pyridoxamine-beta-D glucoside hydrolase from porcine intestinal mucosa: proposed derivation from the lactase-phlorizin hydrolase gene. Biochemical J., 380, 211-218, 2004.

Puchart, V., Vrsanska, M., Svoboda, P., Pohl, J., Ogel, Z.B. and Biely, P.:Purification and characterization of two forms of endo-ß-1,4-mannanase from a thermotolerand fungus, Aspergillus fumigatus IMI 385708 (formerly Thermomyces lanuginosus IMI 158749). Biochim. Biophys. Acta 1674, 239-250, 2004.

Freeman, W.M., Brebner, K., Amara, S.G., Reed, M.S., Pohl, J. and Phillips, A.G.: Distinct proteomic profiles of amphetamine self-administration transitional states. Pharmacogenomics. J., 5, 203-214, 2005.

Mendrinos, S., Nolen, J.D., Styblo, T., Carlson, G., Pohl, J., Lewis, M. and Ritchie, J.: Cytologic findings and protein expression profiles associated with ductal carcinoma of the breast in ductal lavage specimens using surface-enhanced laser desorption and ionization-time of flight mass spectrometry. Cancer Cytopathology, 105, 178-183, 2005.

Khwaja, F. W., Nolen, J. D. L., Mendrinos, S. E., Lewis, M. M., Olson, J. J., Pohl, J., Van Meir, E. G., Ritchie, J. C., Brat, D. J.:  Proteomic analysis of cerebrospinal fluid discriminates malignant and non-malignant disease of the central nervous system and identifies specific protein markers.  Proteomics 6, 6277-6287, 2006.

Khwaja, F. W., Svoboda, P., Reed. M. S., Pohl, J. and Van Meir, E. G.: Proteomic identification of the wt-p53-regulated tumor cell secretome.  Oncogene, advance online publication, doi:10.1038/sj.onc.1209969, 2006.

Brune, D., Denslow, N. D., Kobayashi, R., Lane, W. S., Leone, J. W., Madden, B. J., Neveu, J. M. and Pohl, J.:  ABRF ESRG 2005 Study: Identification of seven modified amino acids by Edman sequencing.  J. Biomolecular. Techniques 17, 308-326, 2006.

Khwaja, F. W., Reed, M. S., Olson, J. J., Schmotzer, B. J., Gillespie, G. Y., Guha, A., Groves, M. D., Pohl, J. and Van Meir, E. G.: Proteomic identification of biomarkers in the cerebrospinal fluid (CSF) of astrocytoma patients. J. Proteome Res. 6, 559-570, 2007.

Gabr, A. A., Reed, M., Khosla, J., Pohl, J., Newman, D. R. and Sannes, P. L.: Alterations in cytoskeletal and immune function-related proteome profiles in whole rat lung following intratracheal instillation of heparin. Respiratory Research, 8:36 doi:10.1186/1465-9921-8-36, 2007.

Thoma, R.S., Leone, J.W., Pohl, J., Kobayashi, R., Linse, K.D., Hampton, B., Brune, D.C. and Denslow, N.D.: ABRF ESRG 2006 study: Edman sequencing as a method for polypeptide quantitation. J. Biomolecular Techniques 18, in press, 2007.

Go, Y.M., Halvey, P.J., Hansen J.M., Reed, M., Pohl, J., and Jones, D.P.: Reactive aldehyde modification of thioredoxin-1 activates early steps of inflammation and cell adhesion. Am. J. Pathol. 171, in press, 2007.

Go, Y.M., Pohl, J., and Jones, D.P. Quantification of redox conditions in the nucleus. In Methods in Molecular Biology: The Nucleus (Ronald Hancock, Editor), Humana Press, Totawa, New Jersey; in press, 2007.

Phosphorylation sites in proteins and peptides

Chambers, T. C., Pohl, J., Raynor, R. L. and Kuo, J. F.: Identification of specific sites in human P-glycoprotein phosphorylated by protein kinase C. J. Biol. Chem. 268, 4592-4595, 1993.

Chambers, T. C., Pohl, J., Glass, D. B. and Kuo, J. F.: Phosphorylation by protein kinase C and cyclic AMP-dependent protein kinase A of synthetic peptides derived from the linker region of human P-glycoprotein. Biochem. J. (London) 299, 309-315, 1994.

Lei, J., Tang, X., Chambers, T. C., Pohl, J., and Benian, G. M.: The protein kinase domain of twitchin has protein kinase activity and an autoinhibitory region. J. Biol. Chem. 269, 21078-21985, 1994.

Petosa, C., Masters, S. C., Bankston, L. A., Pohl, J., Wang, B., Fu, H. and Liddington, R. C.: 14-3-3 binds a phosphorylated Raf peptide and an non-phosphorylated peptide via its conserved amphipathic groove. J. Biol.Chem. 273, 16305-16310, 1998.

Cai, Z., Saugstad, J. A., Sorenses, S. D., Ciombor, K. J., Schaffhauser, H., Hubalek, F., Pohl, J., Zhang, C., Duvoisin, R. M. And Conn, J.: Cyclic AMP-dependent protein kinase phosphorylates group III metabotropic glutamate receptors and inhibits their function as presynaptic receptors. J. Neurochemistry, in press, 2001.54.

Hubalek, F., Edmondson, D. E. and Pohl, J.: Chemical synthesis and characterization of a model O phosphohydroxylysine-containing peptide. Anal. Biochem., 306, 124-134, 2002.

Ceman, S., ODonnell, W. T., Reed, M., Patton, S., Pohl, J. and Warren, S. T.: Phosphorylation influences the translation state of FMRP-associated polyribosomes. Hum. Mol. Genet. 12, 3295-3305, 2003.

Ogbi, M., Chew, C.S., Pohl, J., Stuchlik, O., Obgi, S. and Johnson, J.: Cytochrome c oxidase subunit IV as a marker of protein kinase Ce function in neonatal cardiac myocytes: implications for cytochrome c oxidase activity. Biochem. J. 382, 1-10, 2004.

Durkin, J. T., Holskin, B. P., Kopec, K. K., Reed, M. S., Spais, C. M., Steffy, B. M., Gessner, G., Angeles, T. S., Pohl, J., Ator, M. A. and Meyer, S. L.: Phosphoregulation of Mixed-Lineage Kinase 1 Activity by Multiple Phosphorylation in the Activation Loop. Biochemistry, 43, 16348-16355, 2004.

Roberts, B., Pohl, J. and Gooch, J.L.: A fluorimetric assay for determination of calcineurin activity. Cell Calcium, in press, 2007.

New peptide structures, MHC peptides, peptide libraries

Pohl, J. and Dunn, B. M.: Secondary enzyme-substrate interactions: Kinetic evidence for ionic interactions between substrate side chains and the pepsin active site. Biochemistry 27, 4827-4833, 1988.

Pohl, J.: Action of pepsin on peptide substrates containing N-methylamino acids. In: Peptides: Chemistry and Biology (Rivier, J. E. and Marshall, G. R., Eds.) pp. 365-366. ESCOM Science Publishers, Leiden, 1990.

Flynn, G. C., Pohl, J., Flocco, M. T. and Rothmann, J. E.: Peptide binding specificity of the molecular shaperone BiP. Nature 353, 726-730, 1991.

Evans, B. D., Pohl, J., Kartsonis, N. A. and Calabrese, R. L.: Identification of RF- amide neuropeptides in the medicinal leech. Peptides 12, 897-908, 1991.

Kraft, J. R., Vance, R. E., Pohl, J., Martin, A. M., Raulet, D. H. and Jensen, P. E.: Analysis of Qa1b peptide binding specificity and the capacity of CD94/NKG2A to discriminate between Qa-1-peptide complexes. J. Exp. Med., 192, 613-624, 2000.

Ruef, J., Kacharava, A., Pohl, J. , Bode, C. and Runge, M. S.: Indications for the presence of an atypical protease-activated receptor on rat platelets. Annals of Hematology. 79, 604-11, 2000.

Stanek, D., Pohl, J., Crim, J. W. and Brown, M. J.: Neuropeptide F and its expression in the yellow fever mosquito, Aedes aegypti. Peptides, 23, 1367-1378, 2002.

Weber, D. A., Attinger, A., Kemball, C. C., Wigal, J. L., Pohl, J., Cheroutre, H., Kronenberg, M. and Jensen, P. E.: Peptide-independent folding and CD8aa binding by the non-classical class I molecule, TL. J. Immunol., 169 , 5708-5714, 2002.

Miller, J. D., Weber, D. A., Ibegbu, C., Pohl, J., Altman, J. D. and Jensen, P. E.: Analysis of HLA-E peptide-binding specificity and contact residues in bound peptide required for recognition by CD94/NKG2. J. Immunol. 171, 1369-1375, 2003.

Stodulkova, E., Man, P., Pohl, J., Van Nguyen, D., Vaingatova, S., Ivaskova, E., Pla, M., Capkova, J., Sedlackova, M., Ivanyi, P. and Flieger, M.: Peptides eluted from HLA-B27 of human splenocytes and blood cells reveal a similar but partially different profile compared to in vitro grown cell lines. Immunol. Lett., 94, 261-265, 2004.

Caro-Aguilar, I., Lapp, S., Pohl, J., Galinski, M. and Moreno, A.: Chimeric epitopes delivered by polymeric synthetic linear peptides induces protective immunity to malaria. Microbes and Infection, 7, 1324-1337, 2005.

Venkataraman, N., Cole, A. S., Svoboda, P., Pohl, J. and Cole, A. M.: Cationic polypeptides are required for anti-HIV-1 activity of human vaginal fluid, J. Immuno., 175, 7560–7567, 2005.

Stodulkova, E., Pohl, J., Man, P., Votruba, J., Capkova, J., Sedlackova, M., Ivaskova, E., Ivanyi, P. and Flieger, M.: Comparison of amino acid compositions of peptides eluted from HLA-B27 molecules of healthy individuals and patients with ankylosing spondylitis.  Immunol. Lett. 103, 135-141, 2006.

Alonso-Echanove, J., Sippy, B. D., Chin, A. E., Cairns, L., Haley, R., Epstein, J. S., Richards, M. J., Edelhauser, H., Hedberg, K., Kuehnert, M. J., Jarvis, W. R., Pearson, M. L., and the Transfusion-Associated Red Eye Syndrome Study Group: Kobayashi, J., Grossniklaus, H., Veprek, P., Holley, G., Pohl, J. and Lundstrom, T.: Nationwide outbreak of the red eye syndrome associated with transfusion of leukocyte-reduced red blood cell units. Infect. Control Hosp. Epidemiol. 27, 1146-1152, 2006.

Cerovsky, V., Pohl, J., Yang, Z., Alam, N. and Attygale, A. B.: Identification of three novel peptides isolated from the venom of the neutropical social wasp Polistes major major. J. Peptide Sci. 13, 445-450, 2007.

Antimicrobial peptides, naturally occuring and synthetic

Bangalore, N., Travis, J., Onunka, V. C., Pohl, J. and Shafer, W. M.: Digestion of human lysosomal cathepsin G with clostripain yields antimicrobial peptides. J. Biol. Chem. 265, 13584-13588, 1990.

Shafer, W. M., Pohl, J., Onunka, V. C., Bangalore, N. and Travis, J.: Human lysosomal cathepsin G and granzyme B share a functionally conserved broad spectrum antibacterial peptide. J. Biol. Chem. 266, 112-116, 1991.

Shafer, W. M., Shepherd, M. E., Boltin, B. C., Wells, R. L. and Pohl, J.: Synthetic peptides of human lysosomal cathepsin G having potent antipseudomonal activity. Infect. Immun. 61, 1900-1908, 1993.

Miyasaki, K. T., Bodeau, A. L., Pohl, J. and Shafer, W. M.: Bactericidal activities of synthetic human leukocyte cathepsin G-derived antibiotic peptides and congeners against Actinobacillus actinomycetemcomitans and Capnocytophaga sputigena. Antimicrob. Agents Chemother. 37, 2710-2715, 1993.

Pereira, H. A., Erdem, I., Pohl, J. and Spitznagel, J.: Identification of the bactericidal domain of CAP37, a human neutrophil granule protein with antibiotic and chemotactic properties. Proc. Natl. Acad. Sci. USA 90, 4733-4737, 1993.

Miyasaki, K. T., Bodeau, A. L., Shafer, W. M., Pohl, J., Murthy, A. R. and Lehrer, R. I.: New ideas about neutrophil antimicrobial mechanisms: antibiotic peptides, postphagocytic protein processing, and cytosolic defense factors. In: Molecular Pathogenesis of Periodontal Disease (R. Genco et al., Eds.) Amer. Soc. Microbiol., Washington, DC, pp. 321-336, 1994.

Shafer, W. M., Hubalek, F., Huang, M. and Pohl, J.: The bactericidal activity of a synthetic peptide (CG 117-136) of human lysosomal cathepsin G is dependent on arginine content. Infect. Immun. 64, 4842-4845, 1996.

Miyasaki, K. T., Bodeau, A. L., Pohl, J. and Shafer, W. M.: Activity of antibiotic domains of cathepsin G against periodontal disease-causing bacteria. Int. J. Oral Biology, 22, 191-197, 1997.

Shafer, W. M., Katzif, S., Bowers, S., Fallon, M., Hubalek, M., Reed, M. S. and Pohl, J.,: Tailoring an antibacterial peptide of human lysosomal cathepsin G to enhance its broad-spectrum action against antibiotic-resistant bacterial pathogens. Current Pharmacological Design, 8, 99-110, 2002.

Mak, P., Pohl, J., Dubin, A., Reed, M. S., Bowers, S. E., Fallon, M. T. and Shafer, W. M.: The increased bactericidal activity of a fatty acid-modified synthetic antimicrobial peptide of human cathepsin G correlates with its enhanced capacity to interact with model membranes. Int. J. Antimicrobial Agents 21, 13-19, 2003.

Sieprawska-Lupa, H., Mydel, P., Krawczyk, K., Wjcik, K., Puklo, M., Lupa, B., Suder, P., Silberring, J., Reed, M., Pohl, J., Shafer, W., McAleese, F., Foster, T., Travis, J. and Potempa, J.: Degradation of Human Antimicrobial Peptide LL-37 by Staphylococcus aureus-Derived Proteinases. Antimicrob. Agents Chemother., 2004 48: 4673-4679.

Sun, C. Q., Arnold, R. Fernandez-Golarz, C., Baumann, A., Almekinder, T., He, J., Ho, S., Svoboda, P., Pohl, J., Marshall, F. F. and Petros, J. A.:  Human beta defensins-1, a potential chromosome 8p tumor suppressor: control of transcription and induction of apoptosis in renal cell carcinoma.  Cancer Research 66, 8542-8549, 2006.

Mak, P., Pohl, J. and Dubin, A.: Menstrual hemocidin HbB115-146 is an acidophilic antibacterial peptide potentiating the activity of human defensins, cathelicidin and lysozyme.  Amer. J. Reproductive Immunol., in press, 2006.

Mak, P., Siwek, M., Pohl, J. and Dubin, A.: Menstrual hemocidin
HbB115-146 is an acidophilic antibacterial peptide potentiating the activity of human defensins, cathelicidin and lysozyme. Amer. J.
Reproductive Immunol. 57, 81-91, 2007.

Non-standard DNA synthesis

Villanueva, J. M., Pohl, J., Doetsch, P. W. and Marzilli, L. G.: The mutagenic damaged DNA base, 5,6-dihydrouracil (DHU), incorporated into a 14-mer duplex: NMR evidence that DHU is intrahelical and causes minimal DNA distortion. J. Amer. Chem. Soc., 121, 10652-10653, 1999.