Penny J. Beuning - Publications

Affiliations: 
Chemistry Northeastern University, Boston, MA, United States 
Area:
Physical Chemistry, Biochemistry, Bioinformatics Biology

61 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2020 Ngu L, Winters JN, Nguyen K, Ramos KE, DeLateur NA, Makowski L, Whitford PC, Ondrechen MJ, Beuning PJ. Probing remote residues important for catalysis in Escherichia coli ornithine transcarbamoylase. Plos One. 15: e0228487. PMID 32027716 DOI: 10.1371/journal.pone.0228487  0.6
2019 Muenter MM, Aiken A, Akanji JO, Baig S, Bellou S, Carlson A, Conway C, Cowell CM, DeLateur NA, Hester A, Joshi C, Kramer C, Leifer BS, Nash E, Qi MH, ... ... Beuning PJ, et al. The response of Escherichia coli to the alkylating agents chloroacetaldehyde and styrene oxide. Mutation Research. 840: 1-10. PMID 30857727 DOI: 10.1016/j.mrgentox.2019.02.001  0.4
2018 Mills CL, Garg R, Lee JS, Tian L, Suciu A, Cooperman G, Beuning PJ, Jo Ondrechen M. Functional classification of protein structures by local structure matching in graph representation. Protein Science : a Publication of the Protein Society. PMID 29604149 DOI: 10.1002/pro.3416  0.4
2018 Parasuram R, Coulther TA, Hollander JM, Keston-Smith E, Ondrechen MJ, Beuning PJ. Prediction of active site and distal residues in E. coli DNA polymerase III alpha polymerase activity. Biochemistry. PMID 29341605 DOI: 10.1021/acs.biochem.7b01004  0.6
2017 Murison DA, Ollivierre JN, Huang Q, Budil DE, Beuning PJ. Altering the N-terminal arms of the polymerase manager protein UmuD modulates protein interactions. Plos One. 12: e0173388. PMID 28273172 DOI: 10.1371/journal.pone.0173388  0.8
2016 Fornander LH, Frykholm K, Fritzsche J, Araya J, Nevin P, Werner E, Cakir A, Persson F, Garcin EB, Beuning PJ, Mehlig B, Modesti M, Westerlund F. Visualizing the non-homogeneous structure of RAD51 filaments using nanofluidic channels. Langmuir : the Acs Journal of Surfaces and Colloids. PMID 27479732 DOI: 10.1021/acs.langmuir.6b01877  1
2015 Parasuram R, Mills CL, Wang Z, Somasundaram S, Beuning PJ, Ondrechen MJ. Local structure based method for prediction of the biochemical function of proteins: Applications to glycoside hydrolases. Methods (San Diego, Calif.). PMID 26564235 DOI: 10.1016/j.ymeth.2015.11.010  1
2015 Hawver LA, Tehrani M, Antczak NM, Kania D, Muser S, Sefcikova J, Beuning PJ. Point mutations in Escherichia coli DNA pol V that confer resistance to non-cognate DNA damage also alter protein-protein interactions. Mutation Research. 780: 1-14. PMID 26218456 DOI: 10.1016/j.mrfmmm.2015.07.003  1
2015 Nevin P, Lu X, Zhang K, Engen JR, Beuning PJ. Noncognate DNA damage prevents the formation of the active conformation of the Y-family DNA polymerases DinB and DNA polymerase κ. The Febs Journal. 282: 2646-60. PMID 25899385 DOI: 10.1111/febs.13304  1
2015 Mills CL, Beuning PJ, Ondrechen MJ. Biochemical functional predictions for protein structures of unknown or uncertain function. Computational and Structural Biotechnology Journal. 13: 182-91. PMID 25848497 DOI: 10.1016/j.csbj.2015.02.003  1
2015 Nevin P, Engen JR, Beuning PJ. Steric gate residues of Y-family DNA polymerases DinB and pol kappa are crucial for dNTP-induced conformational change. Dna Repair. 29: 65-73. PMID 25684709 DOI: 10.1016/j.dnarep.2015.01.012  1
2015 Brodkin HR, DeLateur NA, Somarowthu S, Mills CL, Novak WR, Beuning PJ, Ringe D, Ondrechen MJ. Prediction of distal residue participation in enzyme catalysis. Protein Science : a Publication of the Protein Society. 24: 762-78. PMID 25627867 DOI: 10.1002/pro.2648  1
2014 Bajaj SO, Shi P, Beuning PJ, O'Doherty GA. Structure activity relationship study of Mezzettiasides natural products and their four new disaccharide analogues for anticancer/antibacterial activity. Medchemcomm. 5: 1138-1142. PMID 25729554 DOI: 10.1039/C4MD00095A  1
2014 Cuccarese MF, Wang Y, Beuning PJ, O'Doherty GA. Cryptocaryol Structure-Activity Relationship Study of Cancer Cell Cytotoxicity and Ability to Stabilize PDCD4. Acs Medicinal Chemistry Letters. 5: 522-6. PMID 24900873 DOI: 10.1021/ml4005039  1
2014 Fang J, Nevin P, Kairys V, Venclovas C, Engen JR, Beuning PJ. Conformational analysis of processivity clamps in solution demonstrates that tertiary structure does not correlate with protein dynamics. Structure (London, England : 1993). 22: 572-81. PMID 24613485 DOI: 10.1016/j.str.2014.02.001  1
2013 Chaurasiya KR, Ruslie C, Silva MC, Voortman L, Nevin P, Lone S, Beuning PJ, Williams MC. Polymerase manager protein UmuD directly regulates Escherichia coli DNA polymerase III α binding to ssDNA. Nucleic Acids Research. 41: 8959-68. PMID 23901012 DOI: 10.1093/nar/gkt648  1
2013 Walsh JM, Ippoliti PJ, Ronayne EA, Rozners E, Beuning PJ. Discrimination against major groove adducts by Y-family polymerases of the DinB subfamily. Dna Repair. 12: 713-22. PMID 23791649 DOI: 10.1016/j.dnarep.2013.05.006  1
2013 Ollivierre JN, Sikora JL, Beuning PJ. Dimer exchange and cleavage specificity of the DNA damage response protein UmuD. Biochimica Et Biophysica Acta. 1834: 611-20. PMID 23220418 DOI: 10.1016/j.bbapap.2012.11.008  1
2012 Ippoliti PJ, Delateur NA, Jones KM, Beuning PJ. Multiple strategies for translesion synthesis in bacteria. Cells. 1: 799-831. PMID 24710531 DOI: 10.3390/cells1040799  0.4
2012 Shi P, Silva MC, Wang HY, Wu B, Akhmedov NG, Li M, Beuning PJ, O'Doherty GA. Structure Activity Relationship Study of the Cleistriosides and Cleistetrosides for Antibacterial/Anticancer Activity. Acs Medicinal Chemistry Letters. 3: 1086-1090. PMID 23543830 DOI: 10.1021/ml300303g  1
2012 Walsh JM, Parasuram R, Rajput PR, Rozners E, Ondrechen MJ, Beuning PJ. Effects of non-catalytic, distal amino acid residues on activity of E. coli DinB (DNA polymerase IV). Environmental and Molecular Mutagenesis. 53: 766-76. PMID 23034734 DOI: 10.1002/em.21730  1
2012 Walsh JM, Beuning PJ. Synthetic nucleotides as probes of DNA polymerase specificity. Journal of Nucleic Acids. 2012: 530963. PMID 22720133 DOI: 10.1155/2012/530963  1
2012 Silva MC, Nevin P, Ronayne EA, Beuning PJ. Selective disruption of the DNA polymerase III α-β complex by the umuD gene products. Nucleic Acids Research. 40: 5511-22. PMID 22406830 DOI: 10.1093/nar/gks229  1
2011 Chen Q, Mulzer M, Shi P, Beuning PJ, Coates GW, O'Doherty GA. De novo asymmetric synthesis of fridamycin E. Organic Letters. 13: 6592-5. PMID 22107019 DOI: 10.1021/ol203041b  1
2011 Ollivierre JN, Budil DE, Beuning PJ. Electron spin labeling reveals the highly dynamic N-terminal arms of the SOS mutagenesis protein UmuD. Molecular Biosystems. 7: 3183-6. PMID 21975937 DOI: 10.1039/c1mb05334e  1
2011 Somarowthu S, Brodkin HR, DAquino JA, Ringe D, Ondrechen MJ, Beuning PJ. A tale of two isomerases: Compact versus extended active sites in ketosteroid isomerase and phosphoglucose isomerase Biochemistry. 50: 9283-9295. PMID 21970785 DOI: 10.1021/bi201089v  1
2011 Hawver LA, Gillooly CA, Beuning PJ. Characterization of Escherichia coli UmuC active-site loops identifies variants that confer UV hypersensitivity. Journal of Bacteriology. 193: 5400-11. PMID 21784925 DOI: 10.1128/JB.05301-11  1
2011 Fang J, Engen JR, Beuning PJ. Escherichia coli processivity clamp β from DNA polymerase III is dynamic in solution. Biochemistry. 50: 5958-68. PMID 21657794 DOI: 10.1021/bi200580b  1
2011 Fang J, Rand KD, Beuning PJ, Engen JR. False EX1 signatures caused by sample carryover during HX MS analyses. International Journal of Mass Spectrometry. 302: 19-25. PMID 21643454 DOI: 10.1016/j.ijms.2010.06.039  1
2011 Walsh JM, Hawver LA, Beuning PJ. Escherichia coli Y family DNA polymerases. Frontiers in Bioscience (Landmark Edition). 16: 3164-82. PMID 21622227  1
2011 Han GW, Ko J, Farr CL, Deller MC, Xu Q, Chiu HJ, Miller MD, Sefcikova J, Somarowthu S, Beuning PJ, Elsliger MA, Deacon AM, Godzik A, Lesley SA, Wilson IA, et al. Crystal structure of a metal-dependent phosphoesterase (YP_910028.1) from Bifidobacterium adolescentis: Computational prediction and experimental validation of phosphoesterase activity. Proteins. 79: 2146-60. PMID 21538547 DOI: 10.1002/prot.23035  1
2011 Walsh JM, Bouamaied I, Brown T, Wilhelmsson LM, Beuning PJ. Discrimination against the cytosine analog tC by Escherichia coli DNA polymerase IV DinB. Journal of Molecular Biology. 409: 89-100. PMID 21477595 DOI: 10.1016/j.jmb.2011.03.069  1
2011 Ollivierre JN, Sikora JL, Beuning PJ. The dimeric SOS mutagenesis protein UmuD is active as a monomer. The Journal of Biological Chemistry. 286: 3607-17. PMID 21118802 DOI: 10.1074/jbc.M110.167254  1
2011 Walsh JM, Hawver LA, Beuning PJ. Escherichia coli Y family DNA polymerases Frontiers in Bioscience. 16: 3164-3182. DOI: 10.2741/3904  1
2010 Ollivierre JN, Fang J, Beuning PJ. The Roles of UmuD in Regulating Mutagenesis. Journal of Nucleic Acids. 2010. PMID 20936072 DOI: 10.4061/2010/947680  1
2010 Fang J, Rand KD, Silva MC, Wales TE, Engen JR, Beuning PJ. Conformational dynamics of the Escherichia coli DNA polymerase manager proteins UmuD and UmuD'. Journal of Molecular Biology. 398: 40-53. PMID 20206636 DOI: 10.1016/j.jmb.2010.02.040  1
2010 Foti JJ, Simmons LA, Beuning PJ, Walker GC. Signal transduction in the escherichia coli sos response Handbook of Cell Signaling, 2/E. 3: 2127-2136. DOI: 10.1016/B978-0-12-374145-5.00258-8  1
2009 Beuning PJ, Chan S, Waters LS, Addepalli H, Ollivierre JN, Walker GC. Characterization of novel alleles of the Escherichia coli umuDC genes identifies additional interaction sites of UmuC with the beta clamp. Journal of Bacteriology. 191: 5910-20. PMID 19633075 DOI: 10.1128/JB.00292-09  1
2009 Shurtleff BW, Ollivierre JN, Tehrani M, Walker GC, Beuning PJ. Steric gate variants of UmuC confer UV hypersensitivity on Escherichia coli. Journal of Bacteriology. 191: 4815-23. PMID 19482923 DOI: 10.1128/JB.01742-08  1
2008 McCauley MJ, Shokri L, Sefcikova J, Venclovas C, Beuning PJ, Williams MC. Distinct double- and single-stranded DNA binding of E. coli replicative DNA polymerase III alpha subunit. Acs Chemical Biology. 3: 577-87. PMID 18652472 DOI: 10.1021/cb8001107  1
2007 Jarosz DF, Beuning PJ, Cohen SE, Walker GC. Y-family DNA polymerases in Escherichia coli. Trends in Microbiology. 15: 70-7. PMID 17207624 DOI: 10.1016/j.tim.2006.12.004  1
2006 Cruceanu M, Stephen AG, Beuning PJ, Gorelick RJ, Fisher RJ, Williams MC. Single DNA molecule stretching measures the activity of chemicals that target the HIV-1 nucleocapsid protein. Analytical Biochemistry. 358: 159-70. PMID 17034752 DOI: 10.1016/j.ab.2006.08.037  1
2006 Beuning PJ, Simon SM, Godoy VG, Jarosz DF, Walker GC. Characterization of Escherichia coli translesion synthesis polymerases and their accessory factors. Methods in Enzymology. 408: 318-40. PMID 16793378 DOI: 10.1016/S0076-6879(06)08020-7  1
2006 Beuning PJ, Simon SM, Zemla A, Barsky D, Walker GC. A non-cleavable UmuD variant that acts as a UmuD' mimic. The Journal of Biological Chemistry. 281: 9633-40. PMID 16464848 DOI: 10.1074/jbc.M511101200  1
2006 Beuning PJ, Sawicka D, Barsky D, Walker GC. Two processivity clamp interactions differentially alter the dual activities of UmuC. Molecular Microbiology. 59: 460-74. PMID 16390442 DOI: 10.1111/j.1365-2958.2005.04959.x  1
2003 Wong FC, Beuning PJ, Silvers C, Musier-Forsyth K. An Isolated Class II Aminoacyl-tRNA Synthetase Insertion Domain Is Functional in Amino Acid Editing Journal of Biological Chemistry. 278: 52857-52864. PMID 14530268 DOI: 10.1074/jbc.M309627200  1
2003 Beuning PJ, Walker GC. Signal Transduction in the Escherichia coli SOS Response Handbook of Cell Signaling. 3: 185-189. DOI: 10.1016/B978-012124546-7/50661-6  1
2002 Wong FC, Beuning PJ, Nagan M, Shiba K, Musier-Forsyth K. Functional role of the prokaryotic proline-tRNA synthetase insertion domain in amino acid editing. Biochemistry. 41: 7108-15. PMID 12033945 DOI: 10.1021/bi012178j  1
2002 Beuning PJ, Nagan MC, Cramer CJ, Musier-Forsyth K, Gelpí JL, Bashford D. Efficient aminoacylation of the tRNA(Ala) acceptor stem: dependence on the 2:71 base pair. Rna (New York, N.Y.). 8: 659-70. PMID 12022232 DOI: 10.1017/S1355838202020277  1
2002 Lipman RS, Beuning PJ, Musier-Forsyth K, Hou YM. Amino acid activation of a dual-specificity tRNA synthetase is independent of tRNA. Journal of Molecular Biology. 316: 421-7. PMID 11866507 DOI: 10.1006/jmbi.2001.5373  1
2002 Kallick DA, Nagan MC, Beuning PJ, Kerimo S, Tessmer MR, Cramer CJ, Musier-Forsyth K. Discrimination of C1:G72 microhelixAla by AlaRS is based on specific atomic groups rather than conformational effects: An NMR and MD analysis Journal of Physical Chemistry B. 106: 8878-8884. DOI: 10.1021/jp020956r  1
2001 Beuning PJ, Musier-Forsyth K. Species-specific Differences in Amino Acid Editing by Class II Prolyl-tRNA Synthetase Journal of Biological Chemistry. 276: 30779-30785. PMID 11408489 DOI: 10.1074/jbc.M104761200  1
2000 Beuning PJ, Musier-Forsyth K. Hydrolytic editing by a class II aminoacyl-tRNA synthetase Proceedings of the National Academy of Sciences of the United States of America. 97: 8916-8920. PMID 10922054 DOI: 10.1073/pnas.97.16.8916  1
2000 Musier-Forsyth K, Beuning PJ. Role of zinc ion in translational accuracy becomes crystal clear Nature Structural Biology. 7: 435-436. PMID 10881182 DOI: 10.1038/75816  1
2000 Nagan MC, Beuning P, Musier-Forsyth K, Cramer CJ. Importance of discriminator base stacking interactions: molecular dynamics analysis of A73 microhelix(Ala) variants. Nucleic Acids Research. 28: 2527-34. PMID 10871402  1
1999 Beuning PJ, Musier-Forsyth K. Transfer RNA recognition by aminoacyl-tRNA synthetases Biopolymers. 52: 1-28. PMID 10737860  1
1999 Fischer AE, Beuning PJ, Musier-Forsyth K. Identification of discriminator base atomic groups that modulate the alanine aminoacylation reaction. The Journal of Biological Chemistry. 274: 37093-6. PMID 10601268 DOI: 10.1074/jbc.274.52.37093  1
1999 Beuning PJ, Tessmer MR, Baumann CG, Kallick DA, Musier-Forsyth K. Sequence-dependent conformational differences of small RNAs revealed by native gel electrophoresis Analytical Biochemistry. 273: 284-290. PMID 10469499 DOI: 10.1006/abio.1999.4223  1
1998 Henderson BS, Beuning PJ, Shi JP, Bald R, Furste JP, Erdmann VA, Musier-Forsyth K, Schimmel P. Subtle functional interactions in the RNA minor groove at a nonessential base pair [21] Journal of the American Chemical Society. 120: 9110-9111. DOI: 10.1021/ja9809152  1
1997 Beuning PJ, Yang F, Schimmel P, Musier-Forsyth K. Specific atomic groups and RNA helix geometry in acceptor stem recognition by a tRNA synthetase Proceedings of the National Academy of Sciences of the United States of America. 94: 10150-10154. PMID 9294178 DOI: 10.1073/pnas.94.19.10150  1
1997 Beuning PJ, Gulotta M, Musier-Forsyth K. Atomic group 'mutagenesis' reveals major groove fine interactions of a tRNA synthetase with an RNA helix Journal of the American Chemical Society. 119: 8397-8402. DOI: 10.1021/ja971020c  1
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