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1

NMR resonance assignments for the N-terminal domain of the δ subunit of the E. coli γ clamp loader complex

Alyami, Esmael M., Rizzo, Alessandro A., Beuning, Penny J., Korzhnev, Dmitry M.

Journal:

Biomolecular NMR Assignments

Year:

2017

Language:

english

File:

PDF, 1.38 MB

english, 2017

2

Transfer RNA recognition by aminoacyl-tRNA synthetases

Penny J. Beuning, Karin Musier-Forsyth

Journal:

Year:

1999

Language:

english

File:

PDF, 296 KB

english, 1999

3

Song: SOS (To the Tune of ABBA's “SOS”)

Sharotka M. Simon, Lauren S. Waters, Daniel F. Jarosz, Penny J. Beuning

Journal:

Biochemistry and Molecular Biology Education

Year:

2009

Language:

english

File:

PDF, 29 KB

english, 2009

4

Sequence-Dependent Conformational Differences of Small RNAs Revealed by Native Gel Electrophoresis

Penny J. Beuning, Michael R. Tessmer, Christoph G. Baumann, Deborah A. Kallick, Karin Musier-Forsyth

Journal:

Analytical Biochemistry

Year:

1999

Language:

english

File:

PDF, 159 KB

english, 1999

5

False EX1 signatures caused by sample carryover during HX MS analyses

Jing Fang, Kasper D. Rand, Penny J. Beuning, John R. Engen

Journal:

International Journal of Mass Spectrometry

Year:

2011

Language:

english

File:

PDF, 857 KB

english, 2011

6

Single DNA molecule stretching measures the activity of chemicals that target the HIV-1 nucleocapsid protein

Margareta Cruceanu, Andrew G. Stephen, Penny J. Beuning, Robert J. Gorelick, Robert J. Fisher, Mark C. Williams

Journal:

Analytical Biochemistry

Year:

2006

Language:

english

File:

PDF, 326 KB

english, 2006

7

Crystal structure of a metal-dependent phosphoesterase (YP_910028.1) from Bifidobacterium adolescentis: Computational prediction and experimental validation of phosphoesterase activity

Gye Won Han, Jaeju Ko, Carol L. Farr, Marc C. Deller, Qingping Xu, Hsiu-Ju Chiu, Mitchell D. Miller, Jana Sefcikova, Srinivas Somarowthu, Penny J. Beuning, Marc-André Elsliger, Ashley M. Deacon, Adam

Journal:

Proteins: Structure, Function, and Bioinformatics

Year:

2011

Language:

english

File:

PDF, 2.20 MB

english, 2011

8

Two processivity clamp interactions differentially alter the dual activities of UmuC

Penny J. Beuning, Dorota Sawicka, Daniel Barsky, Graham C. Walker

Journal:

Molecular Microbiology

Year:

2006

Language:

english

File:

PDF, 402 KB

english, 2006

9

Functional Role of the Prokaryotic Proline-tRNA Synthetase Insertion Domain in Amino Acid Editing†

Wong, Fai-Chu, Beuning, Penny J., Nagan, Maria, Shiba, Kiyotaka, Musier-Forsyth, Karin

Journal:

Year:

2002

Language:

english

File:

PDF, 120 KB

english, 2002

10

Amino acid activation of a dual-specificity tRNA synthetase is independent of tRNA

Richard S.A Lipman, Penny J Beuning, Karin Musier-Forsyth, Ya-Ming Hou

Journal:

Journal of Molecular Biology

Year:

2002

Language:

english

File:

PDF, 157 KB

english, 2002

11

Conformational Dynamics of the Escherichia coli DNA Polymerase Manager Proteins UmuD and UmuD′

Jing Fang, Kasper D. Rand, Michelle C. Silva, Thomas E. Wales, John R. Engen, Penny J. Beuning

Journal:

Journal of Molecular Biology

Year:

2010

Language:

english

File:

PDF, 1.51 MB

english, 2010

12

Discrimination against the Cytosine Analog tC by Escherichia coli DNA Polymerase IV DinB

Jason M. Walsh, Imenne Bouamaied, Tom Brown, L. Marcus Wilhelmsson, Penny J. Beuning

Journal:

Journal of Molecular Biology

Year:

2011

Language:

english

File:

PDF, 1.21 MB

english, 2011

13

Y-family DNA polymerases in Escherichia coli

Daniel F. Jarosz, Penny J. Beuning, Susan E. Cohen, Graham C. Walker

Journal:

Trends in Microbiology

Year:

2007

Language:

english

File:

PDF, 776 KB

english, 2007

14

Structure–Activity Relationship Study of the Cleistriosides and Cleistetrosides for Antibacterial/Anticancer Activity

Shi, Pei, Silva, Michelle C., Wang, Hua-Yu Leo, Wu, Bulan, Akhmedov, Novruz G., Li, Miaosheng, Beuning, Penny J., O’Doherty, George A.

Journal:

ACS Medicinal Chemistry Letters

Year:

2012

Language:

english

File:

PDF, 575 KB

english, 2012

15

Effects of non-catalytic, distal amino acid residues on activity of E. coli DinB (DNA polymerase IV)

Walsh, Jason M., Parasuram, Ramya, Rajput, Pradyumna R., Rozners, Eriks, Ondrechen, Mary Jo, Beuning, Penny J.

Journal:

Environmental and Molecular Mutagenesis

Year:

2012

Language:

english

File:

PDF, 999 KB

english, 2012

16

The Dynamic DNA Damage Inducible Protein UmuD Inhibits Replication

Beuning, Penny J., Fang, Jing, Sefcikova, Jana, Silva, Michelle C., Engen, John R.

Journal:

Biophysical Journal

Year:

2010

Language:

english

File:

PDF, 34 KB

english, 2010

17

Dimer exchange and cleavage specificity of the DNA damage response protein UmuD

Ollivierre, Jaylene N., Sikora, Jacquelyn L., Beuning, Penny J.

Journal:

Biochimica et Biophysica Acta (BBA) - Proteins and Proteomics

Year:

2013

Language:

english

File:

PDF, 1.46 MB

english, 2013

18

Discrimination against major groove adducts by Y-family polymerases of the DinB subfamily

Walsh, Jason M., Ippoliti, Paul J., Ronayne, Erin A., Rozners, Eriks, Beuning, Penny J.

Journal:

Year:

2013

Language:

english

File:

PDF, 2.57 MB

english, 2013

19

[Methods in Enzymology] DNA Repair, Part A Volume 408 || Characterization of Escherichia coli Translesion Synthesis Polymerases and Their Accessory Factors

Beuning, Penny J.

Year:

2006

Language:

english

File:

PDF, 295 KB

english, 2006

20

Conformational Analysis of Processivity Clamps in Solution Demonstrates that Tertiary Structure Does Not Correlate with Protein Dynamics

Fang, Jing, Nevin, Philip, Kairys, Visvaldas, Venclovas, Česlovas, Engen, John R., Beuning, Penny J.

Journal:

Year:

2014

Language:

english

File:

PDF, 2.39 MB

english, 2014

21

Quantitative Characterization of Interactions of the Escherichia Coli SOS DNA Damage Response Proteins UmuD and UmuD' with the Replicative DNA Polymerase

Sefcikova, Jana, Malcho, Jade, Foley, Kelly, Beuning, Penny

Journal:

Biophysical Journal

Year:

2009

Language:

english

File:

PDF, 120 KB

english, 2009

22

Conformational Dynamics of the E. Coli SOS Mutagenesis Protein UmuD

Beuning, Penny, Ollivierre, Jaylene, Sikora, Jacquelyn

Journal:

Biophysical Journal

Year:

2012

Language:

english

File:

PDF, 40 KB

english, 2012

23

Obituary

Beuning, Penny, Ollivierre, Jaylene, Sikora, Jacquelyn

Journal:

Year:

1971

Language:

english

File:

PDF, 566 KB

english, 1971

24

Multple Active Forms of UmuD Protein that Regulates Bacterial Mutagenesis

Beuning, Penny, Ollivierre, Jaylene N., Sikora, Jacquelyn

Journal:

Biophysical Journal

Year:

2011

Language:

english

File:

PDF, 39 KB

english, 2011

25

Simultaneous Interaction of E. Coli Single Stranded DNA Binding Protein and Replicativedna Polymerase III Alpha Subunit with Single-Stranded DNA Molecules

Pant, Kiran, Nimitpattana, Susie, Silva, Michelle C., Sefcikova, Jana, Beuning, Penny J., Williams, Mark C.

Journal:

Biophysical Journal

Year:

2013

Language:

english

File:

PDF, 41 KB

english, 2013

26

Editorial Board

Pant, Kiran, Nimitpattana, Susie, Silva, Michelle C., Sefcikova, Jana, Beuning, Penny J., Williams, Mark C.

Journal:

Journal of Vascular and Interventional Radiology

Year:

2009

Language:

english

File:

PDF, 50 KB

english, 2009

27

Regulation Of The DNA Damage Response By The DNA Polymerase Manager Protein UmuD

Beuning, Penny J., Fang, Jing Susan, Sefcikova, Jana, Engen, John R.

Journal:

Biophysical Journal

Year:

2009

Language:

english

File:

PDF, 98 KB

english, 2009

28

Single Molecule DNA Interactions Between the E. Coli DNA Polymerase III α Subunit and the Polymerase Manager Protein UmuD

Ruslie, Clarissa, Chaurasiya, Kathy, Silva, Michelle C., Nevin, Philip, Beuning, Penny J., Williams, Mark C.

Journal:

Biophysical Journal

Year:

2012

Language:

english

File:

PDF, 70 KB

english, 2012

29

Conformational Analysis of Processivity Clamps Demonstrates that Protein Tertiary Structure Does Not Correlate with Dynamics

Beuning, Penny J., Fang, Jing, Nevin, Philip, Engen, John R.

Journal:

Biophysical Journal

Year:

2013

Language:

english

File:

PDF, 58 KB

english, 2013

30

Probing Physical Properties of a DNA-Protein Complex Using Nanofluidic Channels

Frykholm, Karolin, Alizadehheidari, Mohammadreza, Fritzsche, Joachim, Wigenius, Jens, Nevin, Philip, Araya, Joshua, Beuning, Penny, Modesti, Mauro, Persson, Fredrik, Westerlund, Fredrik

Journal:

Biophysical Journal

Year:

2014

Language:

english

File:

PDF, 113 KB

english, 2014

31

Using Nanofluidic Channels to Probe the Dynamics of Rad51-DNA Filaments

Fornander, Louise Helena, Persson, Fredrik, Fritzsche, Joachim, Araya, Joshua, Nevin, Philip, Beuning, Penny, Modesti, Mauro, Frykholm, Karolin, Westerlund, Fredrik

Journal:

Biophysical Journal

Year:

2014

Language:

english

File:

PDF, 67 KB

english, 2014

32

Interactions Between the E. Coli Sos Response Protein Umud and DNA Polymerase III Alpha Subunit Have Implications for Regulating Replication in Response to DNA Damage

Beuning, Penny, Silva, Michelle C., Nevin, Philip, Chaurasiya, Kathy R., Ruslie, Clarissa, Voortman, Lukas, Lone, Samer, Ronayne, Erin A., Williams, Mark C.

Journal:

Biophysical Journal

Year:

2014

Language:

english

File:

PDF, 64 KB

english, 2014

33

Specific Atomic Groups and RNA Helix Geometry in Acceptor Stem Recognition by a tRNA Synthetase

Penny J. Beuning, Fan Yang, Paul Schimmel and Karin Musier-Forsyth

Journal:

Proceedings of the National Academy of Sciences

Year:

1997

Language:

english

File:

PDF, 755 KB

english, 1997

34

Distinct Double- and Single-Stranded DNA Binding of E. coli Replicative DNA Polymerase III α Subunit

McCauley, Micah J., Shokri, Leila, Sefcikova, Jana, Venclovas, Česlovas, Beuning, Penny J., Williams, Mark C.

Journal:

ACS Chemical Biology

Year:

2008

Language:

english

File:

PDF, 1.75 MB

english, 2008

35

Escherichia coli Processivity Clamp β from DNA Polymerase III Is Dynamic in Solution

Fang, Jing, Engen, John R., Beuning, Penny J.

Journal:

Year:

2011

Language:

english

File:

PDF, 3.60 MB

english, 2011

36

A Tale of Two Isomerases: Compact versus Extended Active Sites in Ketosteroid Isomerase and Phosphoglucose Isomerase

Somarowthu, Srinivas, Brodkin, Heather R., D’Aquino, J. Alejandro, Ringe, Dagmar, Ondrechen, Mary Jo, Beuning, Penny J.

Journal:

Year:

2011

Language:

english

File:

PDF, 1.92 MB

english, 2011

37

De Novo Asymmetric Synthesis of Fridamycin E

Chen, Qian, Mulzer, Michael, Shi, Pei, Beuning, Penny J., Coates, Geoffrey W., O’Doherty, George A.

Journal:

Organic Letters

Year:

2011

Language:

english

File:

PDF, 1.07 MB

english, 2011

38

Cryptocaryol Structure–Activity Relationship Study of Cancer Cell Cytotoxicity and Ability to Stabilize PDCD4

Cuccarese, Michael F., Wang, Yanping, Beuning, Penny J., O’Doherty, George A.

Journal:

ACS Medicinal Chemistry Letters

Year:

2014

Language:

english

File:

PDF, 703 KB

english, 2014

39

Atomic Group “Mutagenesis” Reveals Major Groove Fine Interactions of a tRNA Synthetase with an RNA Helix

Beuning, Penny J., Gulotta, Miriam, Musier-Forsyth, Karin

Journal:

Journal of the American Chemical Society

Year:

1997

Language:

english

File:

PDF, 215 KB

english, 1997

40

Subtle Functional Interactions in the RNA Minor Groove at a Nonessential Base Pair

Henderson, Barry S., Beuning, Penny J., Shi, J.-P., Bald, Rolf, Fürste, Jens Peter, Erdmann, Volker A., Musier-Forsyth, Karin, Schimmel, Paul

Journal:

Journal of the American Chemical Society

Year:

1998

Language:

english

File:

PDF, 97 KB

english, 1998

41

Structure activity relationship study of mezzettiasides natural products and their four new disaccharide analogues for anticancer/antibacterial activity

Bajaj, Sumit O., Shi, Pei, Beuning, Penny J., O'Doherty, George A.

Journal:

Year:

2014

Language:

english

File:

PDF, 739 KB

english, 2014

42

Electron spin labeling reveals the highly dynamic N-terminal arms of the SOS mutagenesis protein UmuD

Ollivierre, Jaylene N., Budil, David E., Beuning, Penny J.

Journal:

Molecular BioSystems

Year:

2011

Language:

english

File:

PDF, 1.48 MB

english, 2011

43

Prediction of distal residue participation in enzyme catalysis

Brodkin, Heather R., DeLateur, Nicholas A., Somarowthu, Srinivas, Mills, Caitlyn L., Novak, Walter R., Beuning, Penny J., Ringe, Dagmar, Ondrechen, Mary Jo

Journal:

Protein Science

Year:

2015

Language:

english

File:

PDF, 1.64 MB

english, 2015

44

Biochemical functional predictions for protein structures of unknown or uncertain function

Mills, Caitlyn L., Beuning, Penny J., Ondrechen, Mary Jo

Journal:

Computational and Structural Biotechnology Journal

Year:

2015

Language:

english

File:

PDF, 1.87 MB

english, 2015

45

Steric gate residues of Y-family DNA polymerases DinB and pol kappa are crucial for dNTP-induced conformational change

Nevin, Philip, Engen, John R., Beuning, Penny J.

Journal:

Year:

2015

Language:

english

File:

PDF, 3.57 MB

english, 2015

46

10.1038/75816

Musier-Forsyth, Karin, Beuning, Penny J.

Journal:

Natural Structural Biology

Year:

2000

Language:

english

File:

PDF, 159 KB

english, 2000

47

Point mutations in Escherichia coli DNA pol V that confer resistance to non-cognate DNA damage also alter protein–protein interactions

Hawver, Lisa A., Tehrani, Mohammad, Antczak, Nicole M., Kania, Danielle, Muser, Stephanie, Sefcikova, Jana, Beuning, Penny J.

Journal:

Mutation Research/Fundamental and Molecular Mechanisms of Mutagenesis

Year:

2015

Language:

english

File:

PDF, 2.97 MB

english, 2015

48

Local structure based method for prediction of the biochemical function of proteins: Applications to glycoside hydrolases

Parasuram, Ramya, Mills, Caitlyn L., Wang, Zhouxi, Somasundaram, Saroja, Beuning, Penny J., Ondrechen, Mary Jo

Journal:

Year:

2015

Language:

english

File:

PDF, 2.73 MB

english, 2015

49

Discrimination of C1:G72 Microhelix Ala by AlaRS Is Based on Specific Atomic Groups Rather Than Conformational Effects: An NMR and MD Analysis

Kallick, Deborah A., Nagan, Maria C., Beuning, Penny J., Kerimo, Stephanie, Tessmer, Michael R., Cramer, Christopher J., Musier-Forsyth, Karin

Journal:

Journal of Physical Chemistry B

Year:

2002

Language:

english

File:

PDF, 146 KB

english, 2002

50

Progress against Escherichia coli with the Oxazolidinone Class of Antibacterials: Test Case for a General Approach To Improving Whole-Cell Gram-Negative Activity

Takrouri, Khuloud, Cooper, Harold D., Spaulding, Andrew, Zucchi, Paola, Koleva, Bilyana, Cleary, Dillon C., Tear, Westley, Beuning, Penny J., Hirsch, Elizabeth B., Aggen, James B.

Journal:

ACS Infectious Diseases

Year:

2016

Language:

english

File:

PDF, 3.50 MB

english, 2016