Canales M. Taking care of self: Health care decision making of American Indian women. Health Care Women Int. 2004a;25(5):411-35.
Canales MK, Geller BM. Moving in between mammography: screening decisions of American Indian women in Vermont. Qual Health Res. 2004b;14(6):836-57.
Carpenter MJ, Hughes JR, Solomon LJ, Callas PW. Both smoking reduction with nicotine replacement therapy and motivational advice increase future cessation among smokers unmotivated to quit. J Consult Clin Psychol. 2004;72(3):371-81.
Geller BM, Oppenheimer RG, Mickey RM, Worden JK. Patient perceptions of breast biopsy procedures for screen-detected lesions. Am J Obstet Gynecol. 2004;190(4):1063-9.
Graham WG, Costello J, Vacek PM. Vermont granite mortality study: an update with an emphasis on lung cancer. J Occup Environ Med. 2004;46(5):459-66.
Kaminsky DA, Marcy TW. COPD and smoking cessation motivation. Chest. 2004;125(5):1958.
Miglioretti DL, Rutter CM, Geller BM, Cutter G, Barlow WE, Rosenberg R, Weaver DL, Taplin SH, Ballard-Barbash R, Carney PA, Yankaskas BC, Kerlikowske K. Effect of breast augmentation on the accuracy of mammography and cancer characteristics. JAMA. 2004;291(4):442-50.
Solomon L, Quinn V. Spontaneous quitting: self-initiated smoking cessation in early pregnancy. Nicotine Tob Res. 2004;6 Suppl 2:S203-16.
Trumbo CW. Mass-mediated information effects on testicular self-examination among college students. J Am Coll Health. 2004a;52(6):257-61.
Trumbo CW. Cancer information on the World Wide Web: gross characteristics. J Natl Cancer Inst. 2004b;96(4):332-3.
Vacek PM, Geller BM. A prospective study of breast cancer risk using routine mammographic breast density measurements. Cancer Epidemiol Biomarkers Prev. 2004;13(5):715-22.
Borowsky AD, Munn RJ, Galvez JJ, Cardiff RD, Ward JM, Morse HC 3rd, Kogan SC, Aldape KD, Louis DN, Bosenberg MW. (2004) Mouse models of human cancers. Comp Med 54, 258-270.
Burch PM, Yuan Z, Loonen A, Heintz NH. (2004) An extracellular signal-regulated kinase 1- and 2-dependent program of chromatin trafficking of c-Fos and Fra-1 is required for cyclin D1 expression during cell cycle reentry. Mol Cell Biol 24, 4696-4709.
Carey KL, Westwood NJ, Mitchison TJ, Ward GE. (2004) A small-molecule approach to studying invasive mechanisms of Toxoplasma gondii. Proc Natl Acad Sci U S A 101, 7433-7438.
Ckless K, Reynaert NL, Taatjes DJ, Lounsbury KM, Van der Vliet A, Janssen-Heininger Y. (2004). In situ detection and visualization of S-nitrosylated proteins following chemical derivatization: identification of Ran GTPase as a target for S-nitrosylation. Nitric Oxide, in press.
Diehl S, Krahl T, Rinaldi L, Norton R, Irvin CG, Rincón M. (2004). Inhibition of NFAT specifically in T cells prevents allergic pulmonary inflammation. J Immunol 172, 3597-3603.
Ding H, Friestad GK. (2004) Trifluoroacetyl-activated nitrogen-nitrogen bond cleavage of hydrazines by samarium(II) iodide. Org Lett 6, 637-640.
Ding H, Friestad GK. (2004) Allyltrimethoxysilane addition to N-Acylhydrazones: two catalytic methods employing CuC1 and fluoride. Synthesis, in press.
Friestad GK, Massari, SE. (2004) A silicon tether approach for addition of functionalized radicals to chiral alpha-hydroxyhydrazones: diastereoselective additions of hydroxymethyl and vinyl synthons. J Org Chem 69, 863-875.
Friestad GK, Deveau AM; Jean-Charles M. (2004).Stereoselective Mn-Mediated Coupling of Functionalized Iodides and Hydrazones: A Synthetic Entry to the Tubulysin gamma-Amino Acids. Organic Letters, 6, 3249-3252.
Abstract: Synthesis of gamma-amino acids, important building blocks in bioorganic and natural product chemistry, is accomplished using a stereoselective carbon-carbon bond construction of the chiral amine. Alkyl iodides and chiral hydrazones with protected alcohol functionality are coupled via highly diastereoselective photolytic Mn-mediated addition to the C=N bond, providing access to enantiomerically pure multifunctional chiral alpha-branched amines. Reductive N-N bond cleavage and alcohol oxidation provides alpha-substituted gamma-amino acid building blocks for tubulysin D.
Hovey RC, Trott JF. (2004) Morphogenesis of mammary gland development. In: Protecting infants through human milk. Eds. Pickering, L.K., Morrow, A.L., Ruiz-Palacios, G.M., and Schanler, R.J. pp 219-228.
Howe AK. (2004) Regulation of actin-based cell migration by cAMP/PKA. Biochim Biophys Acta 1692, 159-174.
Abstract: A wide variety of soluble signaling substances utilize the cyclic AMP-dependent protein kinase (PKA) pathway to regulate cellular behaviors including intermediary metabolism, ion channel conductivity, and transcription. A growing literature suggests that integrin-mediated cell adhesion may also utilize PKA to modulate adhesion-associated events such as actin cytoskeletal dynamics and migration. PKA is dynamically regulated by integrin-mediated cell adhesion to extracellular matrix (ECM). Furthermore, while some hallmarks of cell migration and cytoskeletal organization require PKA activity (e.g. activation of Rac and Cdc42; actin filament assembly), others are inhibited by it (e.g. activation of Rho and PAK; interaction of VASP with the c-Abl tyrosine kinase). Also, cell migration and invasion can be impeded by either inhibition or hyper-activation of PKA. Finally, a number of A-kinase anchoring proteins (AKAPs) serve to associate PKA with various components of the actin cytoskeleton, thereby enhancing and/or specifying cAMP/PKA signaling in those regions. This review discusses the growing literature that supports the hypothesis that PKA plays a central role in cytoskeletal regulation and cell migration.
Illenye S, Heintz NH. (2004) Functional analysis of bacterial artificial chromosomes in mammalian cells: mouse Cdc6 is associated with the mitotic spindle apparatus. Genomics 83, 66-75.
Jung M, Grunberg S, Timblin C, Buder-Hoffman S, Vacek P, Taatjes DJ, Mossman BT. (2004) Paclitaxel and vinorelbine cause synergistic increases in apoptosis but not in microtubular disruption in human lung adenocarcinoma cells (A-549). Histochem Cell Biol 121, 115-121.
Langen RC, Van Der Velden JL, Schols AM, Kelders MC, Wouters EF, Janssen-Heininger YM. (2004) Tumor necrosis factor-alpha inhibits myogenic differentiation through MyoD protein destabilization. Faseb J 18, 227-237.
Langevin HM, Cornbrooks CJ, Taatjes DJ. (2004). Fibroblasts form a body-wide cellular network. Histochem Cell Biol 122, (1):7-15.
Mossman BT, Klein G, zurHausen H. (2004) Modern criteria to determine the etiology of human carcinogens. Seminars Cancer Biol. Dec;14(6): 449-52.
Okamoto T, Gohil K, Finkelstein EI, Bove P, Akaike T, Van der Vliet A. (2004) Multiple contributing roles for NOS2 in LPS-induced acute airway inflammation in mice. Am J Physiol Lung Cell Mol Physiol 286, L198-209.
Pepe J, Rincón M, Wu J. (2004 in press) Experimental comparison of sonoporation and electroporation in cell transfection applications. ARLO. 5, 62-67.
Puranik M, Nielsen SB, Youn H, Hvitved AN, Bourassa JL, Case MA, Tengroth C, Balakrishnan G, Thorsteinsson MV, Groves JT, et al. (2004) Dynamics of carbon monoxide binding to CooA. J Biol Chem 279, 21096-21108.
Ramos-Ninos ME, Martinelli M, Scapoli L, Mossman BT. (2004) Asbestos-induced mesothelioma. In: Pass, Vogelzang and Carbone, eds. Malignant Mesothelioma: Advances in Pathogenesis, Diagnosis, and Translational Therapies. Springer-Verlag. in press.
Ranjan P, Shrivastava P, Singh SM, Sodhi A, Heintz NH. (2004). Baculovirus P35 inhibits NO-induced apoptosis in activated macrophages by inhibiting cytochrome c release. J Cell Sci 117, 3031-3039.
Reynaert NL, Ckless K, Korn SH, Vos N, Guala AS, Wouters EF, Van der Vliet A, Janssen-Heininger YM. (2004) Nitric oxide represses inhibitory kappaB kinase through S-nitrosylation. Proc Natl Acad Sci U S A 101, 8945-8950.
Richman TJ, Toenjes KA, Morales SE, Cole KC, Wasserman BT, Taylor CM, Koster JA, Whelihan MF, Johnson DI. (2004) Analysis of cell-cycle specific localization of the Rdi1p RhoGDI and the structural determinants required for Cdc42p membrane localization and clustering at sites of polarized growth. Curr Genet 45, 339-349.
Scapoli L, Ramos-Nino ME, Martinelli M, Mossman BT. (2004) Src-dependent ERK5 and Src/EGFR-dependent ERK1/2 activation is required for cell proliferation by asbestos. Oncogene 23, 805-813.
Schock BC, Van der Vliet A, Corbacho AM, Leonard SW, Finkelstein E, Valacchi G, Obermueller-Jevic U, Cross CE, Traber MG. (2004) Enhanced inflammatory responses in alpha-tocopherol transfer protein null mice. Arch Biochem Biophys 423, 162-169.
Schroll AL, Heintz NH. (2004) Chemical footprinting of structural and functional elements of dhfr oribeta during the CHOC 400 cell cycle. Gene 332, 139-147.
Shrivastava P, Pantano C, Watkin R, McElhinney B, Guala A, Poynter ML, Persinger RL, Budd R, Janssen-Heininger Y. (2004) Reactive nitrogen species-induced cell death requires Fas-dependent activation of c-Jun N-terminal kinase. Mol Cell Biol 24, 6763-6772.
Stahl JM, Sharma A, Cheung M, Zimmerman M, Cheng JQ, Bosenberg MW, Kester M, Sandirasegarane L, Robertson GP. (2004) Deregulated Akt3 promotes development of malignant melanoma. Cancer Res. Oct 1; 64(19): 7002-10.
Taylor MS, Okwuchukwuasanya C, Nickl CK, Tegge W, Brayden JE, Dostmann WR. (2004) Inhibition of cGMP-dependent protein kinase by the cell-permeable peptide DT-2 reveals a novel mechanism of vasoregulation. Mol Pharmacol 65, 1111-1119.
Teuscher C, Poynter ME, Offner H, Zamora A, Watanabe T, Fillmore PD, Zachary JF, Blankenhorn, EP. (2004) Attenuation of Th1 effector cell responses and susceptibility to experimental allergic encephalomyelitis in histamine H2 receptor knockout mice is due to dysregulation of cytokine production by antigen-presenting cells. Am J Pathol 164, 883-892.
Toenjes KA, Simpson D, Johnson DI. (2004) Separate membrane targeting and anchoring domains function in the localization of the S. cerevisiae Cdc24p guanine nucleotide exchange factor. Curr Genet 45, 257-264.
VandenBerg AL, Ibrahim AS, Edwards JE Jr, Toenjes KA, Johnson DI. (2004) Cdc42p GTPase regulates the budded-to-hyphal-form transition and expression of hypha-specific transcripts in Candida albicans. Eukaryot Cell 3, 724-734.
Wellman TL, Jenkins J, Penar PL, Tranmer B, Zahr R, Lounsbury KM. (2004) Nitric oxide and reactive oxygen species exert opposing effects on the stability of hypoxia-inducible factor-1alpha (HIF-1alpha) in explants of human pial arteries. Faseb J 18, 379-381.
Wesley UV, Tiwari S, Houghton AN. (2004) Role for dipeptidyl peptidase IV in tumor suppression of human non small cell lung carcinoma cells. Int J Cancer 109, 855-866.
Abstract: Lung cancer is one of the most frequent causes of cancer deaths worldwide. Non-small cell lung cancer (NSCLC) accounts for approximately 80% of the cases and curative treatments are not available for advanced stages of the disease. Therefore, a better understanding of the molecular mechanisms leading to development of NSCLC is of great therapeutic importance. Lung cancer development in general is facilitated by unregulated expression of growth factors and neuropeptides. The cell surface protease, dipeptidyl peptidase IV (DPPIV) inactivates many of these mitogenic peptides. DPPIV is expressed in various normal tissues including, lung epithelial and endothelial cells. Its expression is lost in many types of cancers including lung cancer. DPPIV enzyme activities are found in the serum of healthy individuals but its levels are greatly reduced in patients with many cancer types. These limited observations indicate an important role for DPPIV in regulating the development of cancer. Little is known about the biological role of DPPIV in lung cancer development. We have shown that DPPIV expression is lost in NSCLC cells and restoration of its expression leads to the reversal of cancer phenotype characterized by suppression of tumor growth in nude mice, morphological changes, inhibition of cell proliferation, anchorage independent growth, and in vitro cell migration. DPPIV also increases the sensitivity of NSCLC cells to apoptosis and cell cycle arrest. These data suggest that DPPIV functions as tumor suppressor gene in NSCLC cells and its expression may not only have prognostic significance but also be a potential therapeutic target to block the growth factor signaling involved in lung cancer progression.
Wu W, Rinaldi L, Fortner KA, Russell JQ, Tschopp J, Irvin C, Budd RC. (2004) Cellular FLIP long form-transgenic mice manifest a Th2 cytokine bias and enhanced allergic airway inflammation. J Immunol 172, 4724-4732.
Zhao FQ, Miller PJ, Wall EH, Zheng Y-C, Dong B, Neville MC, McFadden TB. (2004) Bovine glucose transporter GLUT8: cloning, expression, and developmental regulation in mammary gland. Biochim. Biophys. Acta, 1680, 103-113.
Zhao FQ, Zheng Y-C, Dong B, Oka T. (2004) Molecular cloning and genomic organization of a new mouse Oct-1 isoform. Gene 326, 175-187.
Abstract: The ubiquitously expressed transcription factor Oct-1, a member of the POU domain factors, is involved in the regulation of expression of many tissue-specific and house-keeping genes. Multiple alternatively spliced isoforms of Oct-1 have been identified in human and mouse cells. The expression patterns of these isoforms and the analysis of their genomic organization and structure have suggested that the structural variation of Oct-1 isoforms may be important in conferring target and tissue specificity to its transcriptional activity. In this study, we have cloned and sequenced a new mouse Oct-1 isoform, named mOct-1Z. This novel isoform differs markedly at the C-terminus from the previously identified Oct-1 isoforms A, B, and C. It is generated by alternative splicing from the Oct-1 gene and its transcript exhibits a frameshift followed by an early stop codon, thus, its predicted protein has a distinct, much shorter C-terminal tail. However, this truncated isoform could still effectively bind to a consensus Oct-1 motif oligonucleotide and, like Oct-1B, activated the basal promoter activity of the mouse beta-casein gene. Oct-1Z is another ubiquitously expressed Oct-1 isoform, its transcript being detected in all mouse tissues examined, including the mammary gland, liver, lung, kidney, spleen, small intestine mucosa, uterus, and ovary.
Anthony T, Simmang C, Hyman N, Buie D, Kim D, Cataldo P, Orsay C, Church J, Otchy D, Cohen J, Perry WB, Dunn G, Rafferty J, Ellis CN, Rakinic J, Fleshner P, Stahl T, Gregorcyk S, Ternent C, Kilkenny JW 3rd, Whiteford M. Standards Practice Task Force, The American Society of Colon and Rectal Surgeons. Practice parameters for the surveillance and follow-up of patients with colon and rectal cancer. Diseases of the Colon & Rectum. 47(6):807-17, 2004.
Branda RF, Naud SJ, Brooks EM, Chen Z, Muss H. Effect of vitamin B12, folate and dietary supplements on breast carcinoma chemotherapy-induced mucositis and neutropenia. Cancer 101(5):1058-64, 2004.
Hornick JL, Bosenberg MW, Mentzel T, McMenamin ME, Oliveira AM, Fletcher CDM. Pleomorphic liposarcoma: clinicopathologic analysis of 57 cases. Am J Surg Pathol 2004; 28:1257-1267.
McCahill LE. Methodology for scientific evaluation of palliative surgery. Surgical Oncology Clinics of North America. 13(3):413-27,vii, 2004.
Pero SC, Shukla GS, Armstrong AL, Peterson D, Fuller SP, Godin K, Kingsley-Richards SL, Weaver DL, Bond J, Krag DN. Identification of a small peptide that inhibits the phosphorylation of ErbB2 and proliferation of ErbB2 overexpressing breast cancer cells. Int. J of Cancer. Oct 10; 111(6); 951-60, 2004.
Vasilkoski Z, Weaver DL. Diffusion-collision model algorithms for protein folding kinetics. Journal of Computational Chemistry. 25(8):1101-7, 2004.
Albertini RJ. (2004) Mechanistic insights from biomarker studies: somatic mutations and rodent/human comparisons following exposure to a potential carcinogen. IARC Sci Publ, 153-177.
Bandaru V, Cooper W, Wallace SS, Doublié S. (2004) Overproduction, crystallization and preliminary crystallographic analysis of a novel human DNA-repair enzyme that recognizes oxidative DNA damage. Acta Crystallogr D Biol Crystallogr. 2004 Jun;60(Pt 6):1142-4.
Abstract: DNA glycosylases repair oxidative DNA damage caused by free radicals. Recently, NEIL1, a human homolog of Escherichia coli DNA glycosylase endonuclease VIII, has been identified and shown to exhibit broad substrate specificity for a variety of types of pyrimidine-base damage. An active C-terminal deletion construct of NEIL1 was overexpressed in E. coli and crystallized. The unliganded NEIL1 crystallizes in space group R3, with unit-cell parameters a = b = 132.2, c = 51.1 A. Complete data sets were collected from native, selenomethionyl and iodinated NEIL1 to 2.1, 2.3 and 2.4 angstroms, respectively.
Argilla D, Bosenberg MW, Singh M, Hodgson M, Greider C, Gray J, DePinho R, Hanahan D. (2004) Absence of telomerase has minimal effects in mouse models of skin and pancreatic carcinogenesis elicited by viral oncogenes. Cancer Cell, Oct; 6(4): 373-85.
Abstract: Telomeres act as caps on the ends of chromosomes that shorten a bit with each cell division. Once telomeres have shortened to a critical length, normal and cancerous cell division is typically impaired. Cancers bypass this restriction by turning the enzyme telomerase back on, resulting in the maintenance of chromosomal caps. In the study by Argilla et al in Cancer Cell this month, tumor formation in mice lacking the enzyme telomerase was examined in the skin and in the pancreas. Unexpectedly and in contrast to other mouse tumor models, tumor formation was not significantly affected in these particular models. These findings suggest that some tumors are not critically dependent on telomerase activity and have implications for chemotherapeutic strategies aimed at inhibiting telomerase in certain human cancer types.
Bleuit JS, Ma Y, Munro J, Morrical SW. (2004) Mutations in a conserved motif inhibit single-stranded DNA binding and recombination mediator activities of bacteriophage T4 UvsY protein. J Biol Chem. 279, 6077-6086.
Brieba LG, Eichman BF, Kokoska RG, Doublié S, Kunkel TA, Ellenberger T. (2004) Structural basis for the dual coding potential of 8-oxoguanosine by a high fidelity DNA polymerase. EMBO J.
Abstract: Accurate DNA replication involves polymerases with high nucleotide selectivity and proofreading activity. We show here why both fidelity mechanisms fail when normally accurate T7 DNA polymerase bypasses the common oxidative lesion 8-oxo-7, 8-dihydro-2'-deoxyguanosine (8oG). The crystal structure of the polymerase with 8oG templating dC insertion shows that the O8 oxygen is tolerated by strong kinking of the DNA template. A model of a corresponding structure with dATP predicts steric and electrostatic clashes that would reduce but not eliminate insertion of dA. The structure of a postinsertional complex shows 8oG(syn).dA (anti) in a Hoogsteen-like base pair at the 3' terminus, and polymerase interactions with the minor groove surface of the mismatch that mimic those with undamaged, matched base pairs. This explains why translesion synthesis is permitted without proofreading of an 8oG.dA mismatch, thus providing insight into the high mutagenic potential of 8oG.
Chen L, Peng Z, Bateman E. (2004) In vivo interactions of the Acanthamoeba TBP gene promoter. Nucleic Acids Res 32:1251-1260.
Chen L, Orfeo T, Gilmartin G, Bateman E. (2004). Mechanism of cyst specific protein 21 mRNA induction during Acanthamoeba differentiation. Biochimica et Biophysica Acta. 1691(1):23-31.
Connolly SA, Rosen AE, Musier-Forsyth K, Francklyn CS. (2004) G-1:C73 Recognition by an arginine cluster in the active site of Escherichia coli histidyl-tRNA synthetase. Biochemistry 43:962-969.
Divi RL, Walker VE, Wade NA, Nagashima K, Seilkop SK, Adams ME, Nesel CJ, O'Neill JP, Abrams EJ, Poirier MC. (2004) Mitochondrial Damage and DNA Depletion in Cord Blood and Umbilical Cord from Infants Exposed In Utero to Combivir®, AIDS, 18:1013-1021.
Doublié S. Infidelity out in the open. (2004) Structure (Camb). Oct;12(10):1749-50.
Abstract: The crystal structures of DNA polymerase beta in complex with two different mispairs (A-C and T-C) reveal that the two bases stack partially, rather than engage in hydrogen bonding with each other. The N-domain of the polymerase, which is closed when the correct nucleotide pairs with the template base, adopts a partially open conformation suboptimal for catalysis.
Doublié S, Bandaru V, Bond JP, Wallace SS. (2004) The crystal structure of human NEIL1 reveals a novel DNA binding motif required for glycosylase activity. Proc. Natl. Acad. Sci. U.S.A. 101:10284-10289.
Abstract: In prokaryotes, two DNA glycosylases recognize and excise oxidized pyrimidines: endonuclease III (Nth) and endonuclease VIII (Nei). The oxidized purine 8-oxoguanine, on the other hand, is recognized by Fpg (also known as MutM), a glycosylase that belongs to the same family as Nei. The recent availability of the human genome sequence allowed the identification of three human homologs of Escherichia coli Nei. We report here the crystal structure of a human Nei-like (NEIL) enzyme, NEIL1. The structure of NEIL1 exhibits the same overall fold as E. coli Nei, albeit with an unexpected twist. Sequence alignments had predicted that NEIL1 would lack a zinc finger, and it was therefore expected to use a different DNA-binding motif instead. Our structure revealed that, to the contrary, NEIL1 contains a structural motif composed of two antiparallel beta-strands that mimics the antiparallel beta-hairpin zinc finger found in other Fpg/Nei family members but lacks the loops that harbor the zinc-binding residues and, therefore, does not coordinate zinc. This "zincless finger" appears to be required for NEIL1 activity, because mutating a very highly conserved arginine within this motif greatly reduces the glycosylase activity of the enzyme.
Garate M, Cao Z, Bateman E, Panjwani N. (2004) Cloning and characterization of a novel mannose-binding protein of Acanthamoeba. J Biol Chem 279:29849-29856.
Hogg M, Wallace SS, Doublié S. (2004) Crystallographic snapshots of a replicative DNA polymerase encountering an abasic site EMBO J. 23:1483-1493.
Ibba M, Francklyn C. (2004) Turning tRNA Upside down: When aminoacylation is not a prerequisite to protein synthesis. Proc. Natl. Acad. Sci. U.S.A. 101:7493-74942.
Illenye S, Heintz NH. (2004) Functional analysis of bacterial artificial chromosomes in mammalian cells: mouse Cdc6 is associated with the mitotic spindle apparatus. Genomics 83:66-75.
Inoue M, Shen GP, Chaudhry MA, Galick H, Blaisdell JO, Wallace SS. (2004) Expression of the oxidative base excision repair enzymes is not induced in TK6 human lymphoblastoid cells after low doses of ionizing radiation. Radiat Res. 161: 409-417.
Kathe SD, Shen G-P, Wallace SS. (2004) Single-strand breaks in DNA but not oxidative DNA base damages block transcriptional elongation by RNA polymerase II in HeLa cell nuclear extracts. J. Biol. Chem. 279:18511-18520.
Li Y, Dutta S, Doublié S, Moh'd Bdour H, Taylor J-S, Ellenberger T. (2004) Nucleotide insertion opposite a cis-syn thymine dimer by a replicative DNA polymerase from bacteriophage T7. Nature Structural and Molecular Biology 11:784-790.
Abstract: Ultraviolet-induced DNA damage poses a lethal block to replication. To understand the structural basis for this, we determined crystal structures of a replicative DNA polymerase from bacteriophage T7 in complex with nucleotide substrates and a DNA template containing a cis-syn cyclobutane pyrimidine dimer (CPD). When the 3' thymine is the templating base, the CPD is rotated out of the polymerase active site and the fingers subdomain adopts an open orientation. When the 5' thymine is the templating base, the CPD lies within the polymerase active site where it base-pairs with the incoming nucleotide and the 3' base of the primer, while the fingers are in a closed conformation. These structures reveal the basis for the strong block of DNA replication that is caused by this photolesion.
Ma Y, Wang T, Villemain JL, Giedroc DP, Morrical SW. (2004) Dual functions of single-stranded DNA-binding protein in helicase loading at the bacteriophage T4 DNA replication fork. J Biol Chem. 279:19035-19045.
Martin G, Möglich A, Keller W, Doublié S. (2004) Biochemical and Structural Insights into Substrate Binding and Catalytic Mechanism of Mammalian Poly(A) Polymerase. J. Mol. Biol. 341(4):911-925.
Abstract: Polyadenylation of messenger RNA precursors is an essential process in eukaryotes. Poly(A) polymerase (PAP), a member of the nucleotidyltransferase family that includes DNA polymerase beta, incorporates ATP at the 3' end of mRNAs in a template-independent manner. Although the structures of mammalian and yeast PAPs are known, their mechanism of ATP selection has remained elusive. In a recent bovine PAP structure complexed with an analog of ATP and Mn2+, strictly conserved residues interact selectively with the adenine base, but the nucleotide was found in a "non-productive" conformation. Here we report a second bovine crystal structure, obtained in the presence of Mg2+, where 3'-dATP adopts a "productive" conformation similar to that seen in yeast PAP or DNA polymerase beta. Mutational analysis and activity assays with ATP analogs suggest a role in catalysis for one of the two adenine-binding sites revealed by our structural data. The other site might function to prevent futile hydrolysis of ATP. In order to investigate the role of metals in catalysis we performed steady state kinetics experiments under distributive polymerization conditions. These tests suggest a sequential random mechanism in vitro in the presence of ATP and RNA, without preference for a particular order of binding of the two substrates. In vivo, however, where polyadenylation is processive and the primer does not dissociate from the enzyme, an ordered mechanism with the primer as the leading substrate is more likely.
Murphy JA, Barrantes-Reynolds R, Kocherlakota R, Bond JP, Greenblatt MS. (2004) The CDKN2A Database: Integrating Allelic Variants with Evolution, Structure, Function, and Disease Association, Human Mutation 24:296-304.
Nicklas JA, Brooks EM, Hunter TC, Single R, Branda RF. (2004) Development of a quantitative PCR (TaqMan) assay for mitochondrial DNA copy number and the common mitochondrial DNA deletion in the rat. Environ. Mol. Mutagen. 44:313-320, 2004.
Parkash J, Chaudhry MA, Rhoten WB. (2004) Ca(2+) sensing receptor activation by CaCl(2) increases [Ca2+]i resulting in enhanced spatial interactions with calbindin-D28k protein. International Journal of Molecular Medicine. 13(1):3-11, Jan.
Peng Z, Bateman E. (2004) Analysis of the 5S rRNA gene promoter from Acanthamoeba castellanii. Mol Microbiol 52, 1123-1132.
Pinard R, Lambert D, Pothiawala G, Major F, Burke JM. (2004) Modifications and deletions of helices within the hairpin ribozyme-substrate complex: An active ribozyme lacking helix 1. RNA 10, 395-402.
Rice SC, Vacek P, Homans AH, Messier T, Rivers J, Kendall H, Finette BA. (2004) Genotoxicity of therapeutic intervention in children with acute lymphocytic leukemia. Cancer Res 64, 4464-4471.
Schroll A, Heintz NH. (2004) Chemical footprinting of structural and functional elements of dhfr orib during the CHOC 400 cell cycle. Gene 332:139-147.
Toraason M, Albertini RJ, et al. (2004) Applying new technologies to the study of occupational cancer: a workshop summary. Environ Health Perspect 112, 413-416.
Yang N, Galick H, Wallace SS. (2004) Attempted base excision repair of ionizing radiation damage in human lymphoblastoid cells produces lethal and mutagenic double strand breaks. DNA Repair 3(10):1323-1334.
Zhang L, Hayes RB, Guo W, McHale C, Yin S, Wiencke JK, O'Neill JP, Rothman N, Li G-L, Smith MT. (2004) Lack of increased genetic damage in 1,3-butadiene-exposed Chinese workers studied in relation to EPHX1 and GST genotypes. Mutation Res. 558:63-74.