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Yan, C.; Dodd, T.; Tainer, J.A.; He, Y.; Tsutakawa, S.E.; & Ivanov, I.* Transcription preinitiation complex structure and dynamics provide insight into genetic diseases Nature Structural & Molecular Biology (2019) in press; doi:10.1038/s41594-019-0220-3
Zhang, J., Qian, K., Yan, C., He, M., Jassim, B., Ivanov, I. & Zheng, Y. Discovery of decamidine as a new and potent PRMT1 inhibitor . Medicinal Chemistry Communications (2017) 8, 440-444, doi:10.1039/C6MD00573J
He, Y., Yan, C., Inouye, C., Fang, J., Tjian, R., Ivanov, I. & Nogales E. Near-atomic resolution visualization of human transcription promoter opening . Nature (2016) 533 , 359–365, doi:10.1038/nature17970
Turaga, R.C., Yin, L., Yang, J.J., Lee, H., Ivanov, I. , Yan, C., Grossniklaus, H.E., Wang, S., Ma, C., Sun, L. & Liu, Z. Development of protein drug targeting integrin αvβ3 at a novel site by rational protein design. Nature Communications (2016), 7 , e11675 doi:10.1038/ncomms11675.
Hudson, W.H., Kossmann, B., de Vera, I.M., Chuo, S.W., Weikum, E.A., Eick G., Thornton, J., Ivanov, I. , Kojetin, D.J., & Ortlund, E.A Distal substitutions drive divergent DNA specificity among paralogous transcription factors through a subdivision of conformational space. Proceedings of the National Academy of Sciences USA (2016) 113 , 326-331, doi:10.1073/pnas.1518960113
Musille, P. M., Kossmann, B., Kohn, J. A., Ivanov, I. , & Ortlund E. A. Unexpected allosteric network contributes to LRH-1 co-regulator selectivity. Journal of Biological Chemistry (2016) 291 , 1411-1426, doi:10.1074/jbc.M115.662874
Brosey, C.A., Soss, S.E., Brooks, S., Yan, C., Ivanov, I. , Dorai, K., & Chazin, W.J. Functional dynamics in RPA DNA binding and protein recruitment domains. Structure (2015) 23 , 1028–1038, doi:10.1016/j.str.2015.04.008
Tsutakawa, S.E., Yan, C., Xu, X., Weinacht, C., Frudental, B., Zhuang, Z., Washington, M.T., Tainer, J.A. & Ivanov, I. * Structurally distinct ubiquitin- and SUMO-modified PCNA: Implications for their distinct roles in the DNA Damage response. Structure (2015) 23 , 724–733, doi:10.1016/j.str.2015.02.008
Yan, L., Yan, C., Su, H., Qian, K., Wofford, S., Zhao, X., Ivanov, I.* & Zheng Y.G. Diamidine compounds as selective inhibitors of protein arginine methyltransferase 1. Journal of Medicinal Chemistry (2014) 57 , 2611–2622, doi:10.1021/jm401884z
Wang, L., Xu, X., Kumar, R., Maiti, B., Liu, C. T., Ivanov, I. *, Lee, T.-H. & Benkovic, S. J. Probing DNA clamps with single-molecule force spectroscopy. Nucleic Acids Research (2013) 41 , 7804-7814, doi:10.1093/nar/gkt487.
Brosey, C. A., Yan, C., Tsutakawa, S. E., Heller, W. T., Rambo, R. P., Tainer, J. A., Ivanov, I. * & Chazin, W. J. A new structural framework for integrating replication protein A into DNA processing machinery. Nucleic Acids Research (2013) 41 , 2313-2327, doi:10.1093/nar/gks1332. (selected as a featured paper in the top 5% of NAR submissions)
Tsutakawa, S. E., Shin, D. S., Mol, C. D., Izumi, T., Arvai, A. S., Mantha, A. K., Szczesny, B., Ivanov, I. N., Hosfield, D. J., Maiti, B., Pique, M. E., Frankel, K. A., Hitomi, K., Cunningham, R. P., Mitra, S. & Tainer, J. A. Conserved structural chemistry for incision activity in structurally non-homologous apurinic/apyrimidinic endonuclease APE1 and endonuclease IV DNA repair enzymes. Journal of Biological Chemistry (2013) 288 , 8445-8455, doi:10.1074/jbc.M112.422774.
Querol-Audi, J., Yan, C., Xu, X., Tsutakawa, S. E., Tsai, M.S., Tainer, J. A., Cooper, P. K., Nogales, E. & Ivanov, I. * Repair complexes of FEN1, DNA and Rad9-Hus1-Rad1 are distinguished from their PCNA counterparts by functionally important stability. Proceedings of the National Academy of Sciences USA (2012) 109 , 8528-8533, doi:10.1073/pnas.1121116109.
Tsutakawa, S. E., Van Wynsberghe, A. W., Freudenthal, B. D., Weinacht, C. P., Gakhar, L., Washington, M. T., Zhuang, Z., Tainer, J. A. & Ivanov, I. * Solution X-ray scattering combined with computational modeling reveals multiple conformations of covalently-bound ubiquitin on PCNA. Proceedings of the National Academy of Sciences USA (2011) 108 , 17672-17677, doi:10.1073/pnas.1110480108. (Faculty of 1000 recommended Factor 8.0 ; highlighted by the Oak Ridge Leadership Computing Facility at https://www.olcf.ornl.gov/2011/11/09/researchers-show-how-proteins-help-dna-replicate-past-a-damaged-site/)
Cheng, X. & Ivanov, I. Molecular dynamics. Methods in Molecular Biology (Clifton, N.J.) (2012) 929 , 243-285. (Springer Protocols Series; ISBN 978-1-62703-049-6)
Feng, Y., Wang, J., Asher, S., Hoang, L., Guardiani, C., Ivanov, I. * & Zheng, Y. G. Histone H4 acetylation differentially modulates arginine methylation by an in Cis mechanism. Journal of Biological Chemistry (2011) 286 , 20323-20334, doi:10.1074/jbc.M110.207258.
Sander, T., Frolund, B., Bruun, A. T., Ivanov, I. , McCammon, J. A. & Balle, T. New insights into the GABA(a) receptor structure and orthosteric ligand binding: Receptor modeling guided by experimental data. Proteins: Structure Function and Bioinformatics (2011) 79 , 1458-1477, doi:10.1002/prot.22975.
Cheng, X., Ivanov, I. , Wang, H., Sine, S. M. & McCammon, J. A. Molecular dynamics simulations of ELIC – a prokaryotic homologue of the nicotinic acetylcholine receptor. Biophysical Journal (2009) 96 , 4502-4513, doi:10.1016/j.bpj.2009.03.018.
Amaro, R. E., Cheng, X., Ivanov, I. , Xu, D. & McCammon, J. A. Characterizing loop dynamics and ligand recognition in human- and avian-type influenza neuraminidases via Generalized Born molecular dynamics and end-point free energy calculations. Journal of the American Chemical Society (2009) 131 , 4702-4709, doi:10.1021/ja8085643.
Cheng, X., Ivanov, I. *, Wang, H., Sine, S. M. & McCammon, J. A. Nanosecond time scale conformational dynamics of the human alpha7 nicotinic acetylcholine receptor. Biophysical Journal (2007) 93 , 2622-2634, doi:10.1529/biophysj.107.109843.
Ivanov, I. *, Vemparala, S., Pophristic, V., Kuroda, K., DeGrado, W. F., McCammon, J. A. & Klein, M. L. Characterization of non-biological antimicrobial polymers in aqueous solution and at water-lipid interfaces. Journal of the American Chemical Society (2006) 128 , 1778-1779, doi:10.1021/ja0564665.
Vemparala, S., Ivanov, I. , Pophristic, V., Spiegel, K. & Klein, M. L. Ab initio calculations of intra bond parameters for a class of arylamide polymers. Journal of Computational Chemistry (2006) 27 , 693-700, doi:10.1002/jcc.20382.
Pophristic, V., Vemparala, S., Ivanov, I. , Liu, Z. W., Klein, M. L. & DeGrado, W. F. Controlling the shape and flexibility of arylamides: a combined ab initio, ab initio molecular dynamics and classical molecular dynamics study. Journal of Physical Chemistry B (2006) 110 , 3517-3526, doi:10.1021/jp054306.
Choi, S., Clements, D. J., Pophristic, V., Ivanov, I. , Vemparala, S., Bennett, J. S., Klein, M. L., Winkler, J. D. & DeGrado, W. E. The design and evaluation of heparin-binding foldamers. Angewandte Chemie-International Edition (2005) 44 , 6685-6689, doi:10.1002/anie.200501279. (featured on the cover of Angewandte Chemie )
Nielsen, S. O., Lopez, C. F., Ivanov, I. , Moore, P. B., Shelley, J. C. & Klein, M. L. Transmembrane peptide induced lipid sorting and mechanism of L- alpha to inverted phase transition using coarse grain molecular dynamics. Biophysical Journal (2004) 87 , 2107-2115, doi:10.1529/biophysj.104.040311.
Chen, B., Ivanov, I. , Klein, M. L. & Parrinello, M. Hydrogen bonding in water. Physical Review Letters (2003) 91 , doi:10.1103/PhysRevLett.91.215503. (cited over 250 times )
Min, G., Savin, D., Gu, Z., Patterson, G. D., Kim, S. H., Ramsay, D. J., Fishman, D., Ivanov, I. , Sheina, E., Slaby, E. & Oliver, J. Solution characterization of monodisperse atactic polystyrenes by static and dynamic light scattering. International Journal of Polymer Analysis and Characterization (2003) 8 , 187-207, doi:10.1080/10236660304875.
Chen, B., Ivanov, I. , Park, J. M., Parrinello, M. & Klein, M. L. Solvation structure and mobility mechanism of OH-: A Car- Parrinello molecular dynamics investigation of alkaline solution. Journal of Physical Chemistry B 2002 106 , 12006-12016, doi:10.1021/jp026504w.
Chen, B., Park, J. M., Ivanov, I. , Tabacchi, G., Klein, M. L. & Parrinello, M. First-principles study of aqueous hydroxide solutions. Journal of the American Chemical Society 2002 124 , 8534-8535, doi:10.1021/ja020350g.
