2019 Publications

Welty R., Rau M., Pabit S., Dunstan M.S., Conn G.L., Pollack L., & Hall K.B. (2019). “Ribosomal Protein L11 Selectively Stabilizes a Tertiary Structure of the GTPase Center rRNA Domain.” J Mol Biol. 2019 Dec 24. pii: S0022-2836(19)30710-7. doi: 10.1016/j.jmb.2019.12.010. [Epub ahead of print] (Abstract)

Maybruck B.T., Lam W.C., Specht C.A., Ilagan M.X.G., Donlin M.J., & Lodge J.K. (2019). “The Aminoalkylindole BML-190 Negatively Regulates Chitosan Synthesis via the Cyclic AMP/Protein Kinase A1 Pathway in Cryptococcus neoformans.” mBio. 2019 Dec 17;10(6). pii: e02264-19. doi: 10.1128/mBio.02264-19. (Abstract)

Singh S.P., Soranno A., Sparks M.A., & Galletto R. (2019). “Branched unwinding mechanism of the Pif1 family of DNA helicases.” Proc Natl Acad Sci U S A. 2019 Nov 19. pii: 201915654. doi: 10.1073/pnas.1915654116. [Epub ahead of print] (Abstract)

Jordan E Ezekian, Sarah R Clippinger, Jackie Garcia, Susan W Denfield, Aamir Jeewa, William Dreyer, Wenxin Zou, Yuxin Fan, Hugh D Allen, Jeffrey Kim, Michael Greenberg, & Andrew P Landstrom (2019). “The Mutation R94C InTNNT2-encoded Troponin T Predisposes to Restrictive Cardiomyopathy and Pediatric Sudden Death Through Impaired Thin Filament Relaxation Resulting in Myocardial Diastolic Dysfunction” American Heart Association, Inc. 11 Nov 2019, Circulation. 2019;140:A12139 (Abstract)

Yates L.A., Williams R.M., Hailemariam S., Ayala R., Burgers P., & Zhang X. (2019). “Cryo-EM Structure of Nucleotide-Bound Tel1ATM Unravels the Molecular Basis of Inhibition and Structural Rationale for Disease-Associated Mutations.” Structure. 2019 Nov 4. pii: S0969-2126(19)30353-3. doi: 10.1016/j.str.2019.10.012. [Epub ahead of print] (Abstract)

Sparks J.L., Gerik K.J., Stith C.M., Yoder B.L., & Burgers P.M. (2019). “The roles of fission yeast exonuclease 5 in nuclear and mitochondrial genome stability.” DNA Repair (Amst). 2019 Nov;83:102720. doi: 10.1016/j.dnarep.2019.102720. Epub 2019 Sep 21. (Abstract)

Alexander G. Kozlov, Min Kyung Shinn, & Timothy M. Lohman (2019). “Regulation of Nearest-neighbor cooperative binding of E. coli SSB protein to DNA” Biophysical Journal. 28 October 2019. doi.org/10.1016/j.bpj.2019.09.047 (Abstract)

Meisheng Ma, Mihaela Stoyanova, Griffin Rademacher, Susan K. Dutcher, Alan Brown, & Rui Zhang (2019). “Structure of the Decorated Ciliary Doublet Microtubule” Cell. Volume 179, Issue 4, 31 October 2019, Pages 909-922.e12. doi: 10.1016/j.cell.2019.09.030 (Abstract)

Weisz D.A., Johnson V.M., Niedzwiedzki D.M., Shinn M.K., Liu H., Klitzke C.F., Gross M.L., Blankenship R.E., Lohman T.M., & Pakrasi H.B. (2019). “A novel chlorophyll protein complex in the repair cycle of photosystem II.” Proc Natl Acad Sci U S A. 2019 Oct 22;116(43):21907-21913. doi: 10.1073/pnas.1909644116. Epub 2019 Oct 8. (Abstract)

Hailemariam S., De Bona P., Galletto R., Hohl M., Petrini J.H., & Burgers P.M. (2019). “The telomere-binding protein Rif2 and ATP-bound Rad50 have opposing roles in the activation of yeast Tel1^ATM kinase.” J Biol Chem. 2019 Oct 22. pii: jbc.RA119.011077. doi: 10.1074/jbc.RA119.011077. [Epub ahead of print] (Abstract)

Clippinger S.R., Cloonan P.E., Greenberg L., Ernst M., Stump W.T., & Greenberg M.J. (2019). “Disrupted mechanobiology links the molecular and cellular phenotypes in familial dilated cardiomyopathy” Proc Natl Acad Sci U S A. 2019 Aug 19. pii: 201910962. doi: 10.1073/pnas.1910962116. [Epub ahead of print] (Abstract)

Ordabayev Y.A., Nguyen B., Kozlov A.G., Jia H., & Lohman T.M. (2019). “UvrD helicase activation by MutL involves rotation of its 2B subdomain.” Proc Natl Acad Sci U S A. 2019 Jul 30. pii: 201905513. doi: 10.1073/pnas.1905513116. [Epub ahead of print] (Abstract)

Sparks M.A., Singh S.P, Burgers P.M., & Galletto R. (2019). “Complementary roles of Pif1 helicase and single stranded DNA binding proteins in stimulating DNA replication through G-quadruplexes.” Nucleic Acids Res. 2019 Jul 24. pii: gkz608. doi: 10.1093/nar/gkz608. [Epub ahead of print] (Abstract)

Shinn M.K., Kozlov A.G., Nguyen B., Bujalowski W.M., & Lohman T.M. (2019). “Are the intrinsically disordered linkers involved in SSB binding to accessory proteins?” Nucleic Acids Res. 2019 Jul 22. pii: gkz606. doi: 10.1093/nar/gkz606. [Epub ahead of print] (Abstract)

Vishnu C. Damalanka, Scott A. Wildman, & James W. Janetka (2019). “Piperidine carbamate peptidomimetic inhibitors of the serine proteases HGFA, matriptase and hepsin” MedChemComm. 18 Jul 2019, doi: 10.1039/C9MD00234K (Abstract)

Boyle, S., D’Eustachio, P., Egan, S.E., Haw, R., Ilagan, M.X.G., Jassal, B., Joutel, A., & Orlic-Milacic, M. (2019). “Signaling by NOTCH” Reactome. R-HSA-157118 (Abstract)

Tyagi R., Elfawal M.A., Wildman S.A., Helander J., Bulman C.A., Sakanari J., Rosa B.A., Brindley P.J., Janetka J.W., Aroian R.V., & Mitreva M. (2019). “Identification of small molecule enzyme inhibitors as broad-spectrum anthelmintics.” Sci Rep. 2019 Jun 24;9(1):9085. doi: 10.1038/s41598-019-45548-7. (Abstract)

Zhu D.X., Garner A.L., Galburt E.A., & Stallings C.L. (2019). “CarD contributes to diverse gene expression outcomes throughout the genome of Mycobacterium tuberculosis” Proc Natl Acad Sci U S A. 2019 Jul 2;116(27):13573-13581. doi: 10.1073/pnas.1900176116. Epub 2019 Jun 19. (Abstract)

Nguyen B., Ciuba M.A., Kozlov A.G., Levitus M., & Lohman T.M. (2019). “Protein Environment and DNA Orientation Affect Protein-Induced Cy3 Fluorescence Enhancement.” Biophys J. 2019 Jun 7. pii: S0006-3495(19)30448-5. doi: 10.1016/j.bpj.2019.05.026. [Epub ahead of print] (Abstract)

Jensen D., Ruiz Manzano A., Rammohan J., Stallings C.L., & Galburt E.A. (2019). “CarD and RbpA modify the kinetics of initial transcription and slow promoter escape of the Mycobacterium tuberculosis RNA polymerase.” Nucleic Acids Res. 2019 May 25. pii: gkz449. doi: 10.1093/nar/gkz449. [Epub ahead of print] (Abstract)

Dyson H.J., Hall K.B., & Piston D.W. (2019). “Economics and Politics of Publishing in Our Mission-Driven Society.” Biophys J. 2019 May 21;116(10):E1-E2. doi: 10.1016/j.bpj.2019.04.019. Epub 2019 May 1. (Abstract)

Sarem Hailemariam, Sandeep Kumar, & Peter M. Burgers (2019). “Activation of Tel1^ATM kinase requires Rad50 ATPase and long nucleosome-free DNA, but no DNA ends.” J Biol Chem. 2019 Jun 28;294(26):10120-10130. doi: 10.1074/jbc.RA119.008410. Epub 2019 May 9. (Abstract)

Heitmeier M.R., Hresko R.C., Edwards R.L., Prinsen M.J., Ilagan M.X.G., Odom John A.R, & Hruz P.W. (2019). “Identification of druggable small molecule antagonists of the Plasmodium falciparum hexose transporter PfHT and assessment of ligand access to the glucose permeation pathway via FLAG-mediated protein engineering.” PLoS One. 2019 May 9;14(5):e0216457. doi: 10.1371/journal.pone.0216457. eCollection 2019. (Abstract)

Barrick S.K., Clippinger S.R., Greenberg L., & Greenberg M.J. (2019). “Computational Tool to Study Perturbations in Muscle Regulation and Its Application to Heart Disease.” Biophys J. 2019 May 7. pii: S0006-3495(19)30379-0. doi: 10.1016/j.bpj.2019.05.002. [Epub ahead of print] (Abstract)

Harding R.J., Loppnau P., Ackloo S., Lemak A., Hutchinson A., Hunt B., Holehouse A.S., Ho J.C., Fan L., Toledo-Sherman L., Seitova A., & Arrowsmith C.H. (2019). “Design and characterization of mutant and wildtype huntingtin proteins produced from a toolkit of scalable eukaryotic expression systems.” J Biol Chem. 2019 Apr 26;294(17):6986-7001. doi: 10.1074/jbc.RA118.007204. Epub 2019 Mar 6. (Abstract)

Yang Z., Yan H., Dai W., Jing J., Yang Y., Mahajan S., Zhou Y., Li W., Macaubas C., Mellins E.D., Shih C.C., Fitzpatrick J.A.J., & Faccio R. (2019). “Tmem178 negatively regulates store-operated calcium entry in myeloid cells via association with STIM1.” J Autoimmun. 2019 Jul;101:94-108. doi: 10.1016/j.jaut.2019.04.015. Epub 2019 Apr 22. (Abstract)

Damalanka V.C. & Janetka J.W. (2019). “Recent progress on inhibitors of the type II transmembrane serine proteases, hepsin, matriptase and matriptase-2.” Future Med Chem. 2019 Apr;11(7):743-769. doi: 10.4155/fmc-2018-0446. Epub 2019 Apr 4. (Abstract)

Heffern E.F., Ramani R., Marshall G., Kyei G.B. (2019). “Identification of isoform-selective hydroxamic acid derivatives that potently reactivate HIV from latency.” J Virus Erad. 2019 Apr 1;5(2):84-91. (Abstract)

Michael Kinch (2019). “The End of the Beginning: Cancer, Immunity, and the Future of a Cure” ISBN-13: 978-1643130255, ISBN-10: 1643130250

Wang H., Eschweiler J., Cui W., Zhang H., Frieden C., Ruotolo B.T., & Gross M.L. (2019) “Native Mass Spectrometry, Ion Mobility, Electron-Capture Dissociation, and Modeling Provide Structural Information for Gas-Phase Apolipoprotein E Oligomers.” J Am Soc Mass Spectrom. 2019 Mar 18. doi: 10.1007/s13361-019-02148-z. [Epub ahead of print] (Abstract)

Tomko E.J. & Galburt E.A. (2019). “Single-molecule approach for studying RNAP II transcription initiation using magnetic tweezers.” Methods. 2019 Mar 18. pii: S1046-2023(18)30297-4. doi: 10.1016/j.ymeth.2019.03.010. [Epub ahead of print] (Abstract)

Singh S.P., Kukshal V., & Galletto R. (2019). “A stable tetramer is not the only oligomeric state that mitochondrial single-stranded DNA binding proteins can adopt.” J Biol Chem. 2019 Mar 15;294(11):4137-4144. doi: 10.1074/jbc.RA118.007048. Epub 2019 Jan 7. (Abstract)

Porter J.R., Moeder K.E., Sibbald C.A., Zimmerman M.I., Hart K.M., Greenberg M.J., & Bowman G.R. (2019). “Cooperative Changes in Solvent Exposure Identify Cryptic Pockets, Switches, and Allosteric Coupling.” Biophys J. 2019 Mar 5;116(5):818-830. doi: 10.1016/j.bpj.2018.11.3144. Epub 2019 Jan 25. (Abstract)

Mondol T., Stodola J.L., Galletto R., & Burgers P.M. (2019). “PCNA accelerates the nucleotide incorporation rate by DNA polymerase δ.” Nucleic Acids Res. 2019 Feb 28;47(4):1977-1986. doi: 10.1093/nar/gky1321. (Abstract)

Burgers, P.M. (2019). “Solution to the 50-year-old Okazaki-fragment problem.” Proc Natl Acad Sci U S A. 2019 Feb 26;116(9):3358-3360. doi: 10.1073/pnas.1900372116. Epub 2019 Feb 15. (Abstract)

Frieden, C. (2019). “Protein oligomerization as a metabolic control mechanism: Application to apoE.” Protein Sci. 2019 Apr;28(4):837-842. doi: 10.1002/pro.3583. Epub 2019 Feb 18. (Abstract)

Min Kyung Shinn, Alexander G. Kozlov, & Timothy M. Lohman. (2019). “Binding Specificity of E. coli SSB C-Terminal Tails to SIPs” Biophysical Journal. Volume 116, Issue 3, Supplement 1, 15 February 2019, Page 77a. (Abstract)

Drake Jensen, Ana Ruiz Manzano, Christina L. Stallings, & Eric A. Galburt. (2019). “Regulation of Mycobacterial RNA Polymerase Promoter Escape Kinetics by Transcription Factors Card and RbpA” Biophysical Journal. Volume 116, Issue 3, Supplement 1, 15 February 2019, Page 210a. (Abstract)

Eric A. Galburt, Eric J. Tomko, James Fishburn, & Steven Hahn. (2019). “Tfiih Generates a Six-Base-Pair Open Complex during Eukaryotic Transcription Initiation” Biophysical Journal. Volume 116, Issue 3, Supplement 1, 15 February 2019, Pages 209a-210a. (Abstract)

Sarah R. Clippinger, Paige E. Cloonan, Lina Greenberg, William Stump, & Michael J. Greenberg. (2019). “A Familial Dilated Cardiomyopathy Mutation Decreases Myosin Generated Tension at the Molecular Level and Alters Mechanosensing at the Cellular Level” Biophysical Journal. Volume 116, Issue 3, Supplement 1, 15 February 2019, Page 30a. (Abstract)

Samantha K. Barrick & Michael J. Greenberg. (2019). “Molecular Mechanism of a Mutation Implicated in Pediatric-Onset Heart Disesase” Biophysical Journal. Volume 116, Issue 3, Supplement 1, 15 February 2019, Page 115a. (Abstract)

Felicia Gibson, Andrea Soranno, Wenwei Zheng, & Sara M. Vaiana. (2019). “Extracting Sequence-Dependent Intra-Protein Interaction Parameters from Photo-Induced Electron Transfer Measurements of IDPs” Biophysical Journal. Volume 116, Issue 3, Supplement 1, 15 February 2019, Page 202a. (Abstract)

Andrea Soranno, Jeremias Incicco, Paolo De Bona, Eric Tomko, Eric Galburt, & Roberto Galletto. (2019). “Shelterin Components Modulate the Phase-Separation Propensity of Telomeres” Biophysical Journal. Volume 116, Issue 3, Supplement 1, 15 February 2019, Pages 467a-468a. (Abstract)

Melissa D. Stuchell-Brereton, Berevan Baban, Greg DeKoster, Carl Frieden, & Andrea Soranno. (2019). “Single-Molecule Conformational Analysis of Apolipoprotein E” Biophysical Journal. Volume 116, Issue 3, Supplement 1, 15 February 2019, Page 167a. (Abstract)

Porter J.R., Zimmerman M.I., & Bowman G.R. (2019). “Enspara: Modeling molecular ensembles with scalable data structures and parallel computing.” J Chem Phys. 2019 Jan 28;150(4):044108. doi: 10.1063/1.5063794. (Abstract)

Griesenauer R.H., Schillebeeckx C., & Kinch M.S. (2019). “Assessing the public landscape of clinical-stage pharmaceuticals through freely available online databases.” Drug Discov Today. 2019 Jan 25. pii: S1359-6446(18)30258-7. doi: 10.1016/j.drudis.2019.01.010. [Epub ahead of print] (Abstract)

Maddirala A., Klein R.D., Pinkner J., Kalas V., Hultgren S.J., & Janetka J.W. (2019). “Biphenyl Gal and GalNAc FmlH Lectin Antagonists of Uropathogenic E. coli (UPEC): Optimization through iterative rational drug design.” J Med Chem. 2019 Jan 24;62(2):467-479. doi: 10.1021/acs.jmedchem.8b01561. Epub 2019 Jan 2. (Abstract)

Damalanka V.C., Han Z., Karmakar P., O’Donoghue A.J., La Greca F., Kim T., Pant S., Helander J., Klefström J., Craik C.S., & Janetka J.W. (2019). “Discovery of Selective Matriptase and Hepsin Serine Protease Inhibitors: Useful Chemical Tools for Cancer Cell Biology.” J Med Chem. 2019 Jan 24;62(2):480-490. doi: 10.1021/acs.jmedchem.8b01536. Epub 2019 Jan 4. (Abstract)

Makurath M.A., Whitley K.D., Nguyen B., Lohman T.M., & Chemla Y.R. (2019). “Regulation of Rep helicase unwinding by an auto-inhibitory subdomain.” Nucleic Acids Res. 2019 Mar 18;47(5):2523-2532. doi: 10.1093/nar/gkz023. (Abstract)

Katarzyna Dubiel, Angela R. Myers, Alexander G. Kozlov, Olivia Yang, Jichuan Zhang, Taekjip Ha, Timothy M. Lohman, & James L. Keck (2019). “Structural Mechanisms of Cooperative DNA Binding by Bacterial Single-Stranded DNA-Binding Proteins” J Mol Biol. 2019 Jan 18;431(2):178-195. doi: 10.1016/j.jmb.2018.11.019. Epub 2018 Nov 22. (Abstract)

Lisa Eshun-Wilson, Rui Zhang, Didier Portran, Maxence Nachury, Daniel Toso, Thomas Lohr, Michelle Vendruscolo, Massimiliano Bonomi, James Fraser, & Eva Nogales (2019). “Effects of α-tubulin acetylation on microtubule structure and stability” bioRxiv. January 09, 2019. doi.org/10.1101/516591. (Abstract)

Kawaguchi M., Yamamoto K., Takeda N., Fukushima T., Yamashita F., Sato K., Kitamura K., Hippo Y., Janetka J.W., & Kataoka H. (2019). “Hepatocyte growth factor activator inhibitor-2 stabilizes Epcam and maintains epithelial organization in the mouse intestine.” Commun Biol. 2019 Jan 4;2:11. doi: 10.1038/s42003-018-0255-8. eCollection 2019. (Abstract)