Selected Publications

Ahmed, S., D. G. Brickner, W. H. Light, M. McDonough, I. Cajigas, A. Froyshteter, T. Volpe and J.H. Brickner (2010).  DNA zip codes control an ancient mechanism for gene targeting to the nuclear periphery.  Nat. Cell Biol. 12 (2): 111-118.

Light, W., D. G. Brickner, V. Brand and J.H. Brickner (2010).  Interaction of a DNA zip code with the nuclear pore complex promotes H2A.Z incorporation and INO1 transcriptional memory.  Mol. Cell 40: 112-125.

Brickner, D. G. and J.H. Brickner (2010).  Cdk phosphorylation of a nucleoporin controls gene localization through the cell cycle.  Mol. Biol. Cell 21:3421-3432.

Structural basis of transcription promoter opening using single particle cryo-EM. He Y, Yan C, Inouye C, Fang J, Tjian R, Ivanov I, and Nogales E. 2015 Manuscript in preparation

Structural visualization of key steps in human transcription initiation. He Y, Fang J, Taatjes DJ, and Nogales E. 2013 Nature 495, 481-6.

Structure of the 30 kDa Sin3-Associated Protein (SAP30) in Complex with the Mammalian Sin3A Corepressor and its Role in Nucleic Acid Binding. Xie T, He Y, Korkeamaki H, Zhang Y, Imhoff R, Lohi O, Radhakrishnan I. 2011 J. Biol. Chem. 286, 27814–24.

Kay, J.E. and Jewett, M.C. 2015. Lysate of engineered Escherichia coli supports high-level conversion of glucose to 2,3-butanediol. Metabolic Engineering. In press.

Orelle C., Carlson, E.D., Szal, T., Florin, T., Jewett, M.C., and Mankin, A.S. 2015. Protein synthesis by ribosomes with tethered subunits. Nature. 524, 119–124.

Oza, J.P., Aerni, H.R., Pirman, N.L., Barber, K.W., ter Haar, C.M., Rogulina, S., Amrofell, M.B., Isaacs, F.J., Rinehart, J., and Jewett, M.C. 2015. Robust production of recombinant phosphoproteins using cell-free protein synthesis. Nature Communications. 6: 8168.

Daringer NM, Schwarz KA, Leonard JN (2015). Contributions of Unique Intracellular Domains to Switch-Like Biosensing by Toll-like Receptor 4. Journal of Biological Chemistry. 290 (14): 8764-8777.

Hung ME, Leonard JN (2015). Stabilization of exosome targeting peptides via engineered glycosylation. Journal of Biological Chemistry. 109 (13):8166-72.

Pitner RA, Scarpelli AH, Leonard JN (2015). Regulation of bacterial gene expression by protease-alleviated spatial sequestration (PASS). ACS Synthetic Biology. 4 (9), pp 966–974.

DNA-segment-facilitated dissociation of Fis and NHP6A from DNA detected
via single-molecule mechanical response
R.D. Giuntoli, N.B. Linzer, E.J. Banigan, C.E. Sing, M. Olvera de la Cruz,
J.S. Graham, R.C. Johnson, J.F. Marko
J. Mol. Biol. 427, 3123-36 (2015) [14 pages].

Age-associated alterations in the micromechanical properties of
chromosomes in the mammalian egg
J.E. Hornick, F.E. Duncan, M. Sun, R. Kawamura, J.F. Marko, T.K. Woodruff
J. Assist. Reprod. Genet. 32, 765-769 (2015) [5 pages].

Biophysics of protein-DNA interactions and chromosome organization
J.F. Marko
Physica A 418, 126-153 (2015) [28 pages].

Terekhova K., Gunn K.H., Marko J.F., and Mondragón, A. Bacterial topoisomerase I and topoisomerase III relax supercoiled DNA via distinct pathways. Nucleic Acids Res. 40, 10432-110440, 2012.

Rajan R., Prasad R., Taneja B., Wilson S.H., and Mondragón, A. Identification of one of the apurinic/apyrimidinic lyase active sites of topoisomerase V by structural and functional studies. Nucleic Acids Res. 41, 657-666, 2013.

Philips, S.J., Canalizo-Hernandez, M., Yildirim, I., Schatz, G.C., Mondragón, A., and O'Halloran, T.V., Allosteric transcriptional regulation via changes in the overall topology of the core promoter, Science, 349, 877-881, 2015.

D.K. Wells, W.L. Kath, and A.E. Motter,  
Control of stochastic and induced switching in biophysical networks,  
Phys. Rev. X 5, 031036 (2015). 
doi:10.1103/PhysRevX.5.031036

A.E. Motter
Networkcontrology, 
Chaos 25, 097621 (2015). 
doi: 10.1063/1.4931570

P. Gawand, F.S. Abukar, N. Venayak, S. Partow, A.E. Motter, and R. Mahadevan,  
Sub-optimal phenotypes of double-knockout mutants of Escherichia coli depend on the order of gene deletions,  
Integr. Biol., Advance Article (2015). 
doi:10.1039/C5IB00096C

Ahn, R.W., Chen, F., Chen, H., Stern, S.T., Clogston, J.D., Patri, A.K., Raja, M.R., Cryns, V.L., O’Halloran, T.V. “A Novel Nanoparticulate Formulation of Arsenic Trioxide with Enhanced Therapeutic Efficacy in a Murine Model of Breast Cancer” Clinical Cancer Research 2010 Jul 15;16(14):3607-17. PMCID: PMC2943376

Gilston BA, Wang S, Marcus MD, Canalizo-Hernández MA, Swindell EP, Xue Y, Mondragón A, O'Halloran TV. Structural and mechanistic basis of zinc regulation across the E. coli Zur regulon. PLoS Biology. 2014 Nov 4;12(11):e1001987. doi:10.1371/journal.pbio.1001987. eCollection 2014. PMID: 25369000 PMCID: PMC4219657

Que EL, Bleher R, Duncan FE, Kong BY, Gleber SC, Vogt S, Chen S, Garwin SA, Bayer AR, Dravid V, Woodruff TK, O’Halloran TV. Quantitative mapping of zinc fluxes in the mammalian egg reveals the origin of fertilization-induced zinc sparks. Nature Chemistry (2015) Feb;7(2):130-9. doi: 10.1038/nchem.2133. Epub 2014 Dec 15. PMCID: PMC4315321

Prakriya M and Lewis RS (2015).  Store-operated calcium channels. Physiological Reviews. 95(4):1383-436.

Tirado-Lee L, Yamashita M, and Prakriya M (2015) Conformational changes in the Orai1 C-terminus evoked by STIM1 binding. PloS One 10(6):e0128622.

Jairaman A, Yamashita M, Schleimer RP and Prakriya M (2015) Store-operated CRAC channels regulate PAR2-activated Ca2+ signals and cytokine production in airway epithelial cells. J Immunology 195(5):2122-33.

Clark, M.D., Kumar, G.S., Marcum, R., Luo, Q., Zhang, Y., and Radhakrishnan, I. (2015). Molecular basis for the mechanism of constitutive CBP/p300 coactivator recruitment by CRTC1-MAML2 and its implications in cAMP signaling. Biochemistry 54, 5439-5446.

Clark, M.D., Marcum, R., Graveline, R., Chan, C.W., Xie, R. Chen, Z., Ding, Y., Zhang, Y., Mondragón, A., David, G., and Radhakrishnan, I. (2015). Structural insights into the assembly of the histone deacetylase-associated Sin3L/Rpd3L corepressor complex. Proc. Natl. Acad. Sci. USA 112, E3669-E3678.

Xie, T., Zmyslowski, M., Zhang, Y., and Radhakrishnan, I. (2015). Multi-specificity of MRG domains. Structure 23, 1049-1057.

Smith, A. T.; Barupala, D.; Stemmler, T. L.; Rosenzweig, A. C. Discovery and characterization of a novel metal binding domain involved in cadmium, cobalt, and zinc transport. Nat. Chem. Biol. 201511, 678-684.

Sirajuddin, S.; Rosenzweig, A. C. Enzymatic oxidation of methane. Biochemistry 201554, 2283-2294.

Culpepper, M. A.; Rosenzweig, A. C. Structure and protein-protein interactions of methanol dehydrogenase from Methylococcus capsulatus (Bath). Biochemistry 201453, 6211-6219.

Kang, S.; Li, H.; Tang, W.; Martásek, P.; Roman, L. J.; Poulos, T. L.; Silverman, R. B. 2-Aminopyridines with a truncated side chain to improve human neuronal nitric oxide synthase inhibitory potency and selectivity. J. Med. Chem. 201558, 5548-5560.

Holden, J. K.; Kang, S.; Beasley, F. C.; Cinelli, M. A.; Li, H.; Roy, S. G.; Dejam, D.; Edinger, A. L.; Nizet, V.; Silverman, R. B.; Poulos, T. L. Nitric oxide synthase as a target for methicillin resistant Staphylococcus aureusChem. Biol. 201522, 785-892.

Zigmond, E.; Ya'acov, A. B.; Lee, H.; Lichtenstein, Y.; Shalev, Z.; Smith, Y.; Zolotarov, L.; Ziv, E.; Kalman, R.; Le, H. V.; Lu, H.; Silverman, R. B.; Ilan, Y. Suppression of hepatocellular carcinoma by inhibition of overexpressed ornithine aminotransferase. ACS Med. Chem. Lett. 20156, 840-844.

Flores, A.G., and Unger, V.M. (2013). Atox1 Contains Positive Residues that Mediate Membrane Association and Aid Subsequent Copper Loading. J Membr Biol 246(12):903-913; PMC3827972

Pope, C.R., De Feo, C.J., and Unger, V.M. (2013). Cellular Distribution of Copper to Superoxide Dismutase Involves Scaffolding by Membranes. Proc Natl Acad Sci USA 110(51):20491-20496; PMC3870662

Cui, H., Mim, C., Vazquez, F.X., Lyman, E., Unger, V.M., and Voth, G.A. (2013) “Understanding the Role of Amphipathic Helices in N-BAR Domain Driven Membrane Remodeling”, Biophys J. 104(2): 404-411; PMC3552260

 

 


Areas of Research

Many of the research programs of Northwestern's Biophysics Faculty fall within the realms of Structural Biology, Drug Design, Quantitative and Mechanistic Biology, Computational Biology and Chemical Biology. With over 20 faculty involved in the program and mani inter-laboratory collaborations, a variety of fundamental biological questions are being studied, including:

  • Nucleic acid structure and function
  • Mechanisms of gene regulation
  • Protein and RNA processing in the cell
  • Intracellular metal trafficking
  • Molecular mechanisms of viral infection
  • Mechanisms of macromolecular machines
  • Membrane protein structure and function

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November 12, 2015