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Karanicolas, John
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Karanicolas, John

Graduate Student
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Positions

  • 2016 - Faculty Member, Fox Chase Cancer Center
  • 2008 - 2016 Faculty Member, The University of Kansas

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Publications

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    • Reilly, S. W., Riad, A. A., Hsieh, C. J., Sahlholm, K., Jacome, D. A., Griffin, S., Taylor, M., Weng, C. C., Xu, K., Kirschner, N., Luedtke, R. R., Parry, C., et al. Leveraging a low-affinity diazaspiro orthosteric fragment to reduce dopamine D3 receptor (D3R) ligand promiscuity across highly conserved aminergic G-protein-coupled receptors (GPCRs) Journal of Medicinal Chemistry  2019 62:5132-5147  DOI:10.1021/acs.jmedchem.9b00412  PMID:31021617
    • Van Tyne, D., Manson, A. L., Huycke, M. M., Karanicolas, J., Earl, A. M., Gilmore, M. S. Impact of antibiotic treatment and host innate immune pressure on enterococcal adaptation in the human bloodstream Science Translational Medicine  2019 11  DOI:10.1126/scitranslmed.aat8418  PMID:30971455
    • Wodak, S. J., Paci, E., Dokholyan, N. V., Berezovsky, I. N., Horovitz, A., Li, J., Hilser, V. J., Behar, I., Karanicolas, J., Stock, G., Hamm, P., Stote, R. H., et al. Allostery in its many disguises: from theory to applications Structure  2019 27:566-578  DOI:10.1016/j.str.2019.01.003  PMID:30744993
    • Bai, N., Roder, H., Dickson, A., Karanicolas, J. Isothermal analysis of ThermoFluor Data can readily provide quantitative binding affinities Scientific Reports  2019 9  DOI:10.1038/s41598-018-37072-x  PMID:30804351  PMCID:PMC6389909
    • Zhang, H., Pandey, S., Travers, M., Sun, H., Morton, G., Madzo, J., Chung, W., Khowsathit, J., Perez-Leal, O., Barrero, C. A., Merali, C., Okamoto, Y., et al. Targeting CDK9 reactivates epigenetically silenced genes in cancer Cell  2018 175:1244-1258  DOI:10.1016/j.cell.2018.09.051  PMID:30454645  PMCID:PMC6247954
    • Lan, L., Liu, H., Smith, A. R., Appelman, C., Yu, J., Larsen, S., Marquez, R. T., Wu, X., Liu, F. Y., Gao, P., Gowthaman, R., Karanicolas, J., et al. Natural product derivative Gossypolone inhibits Musashi family of RNA-binding proteins BMC Cancer  2018 18  DOI:10.1186/s12885-018-4704-z  PMID:30097032  PMCID:PMC6086024
    • Rudolph, M. J., Vance, D. J., Kelow, S., Angalakurthi, S. K., Nguyen, S., Davis, S. A., Rong, Y., Middaugh, C. R., Weis, D. D., Dunbrack Jr., R., Karanicolas, J., Mantis, N. J. Contribution of an unusual CDR2 element of a single domain antibody in ricin toxin binding affinity and neutralizing activity Protein Engineering Design & Selection  2018 31:277-287  DOI:10.1093/protein/gzy022  PMID:30265352  PMCID:PMC6277176
    • Kaiser, C. E., Pabon, J. P. R., Khowsathit, J., Castaldi, M. P., Kazmirski, S. L., Weis, D. D., Zhang, A. X., Karanicolas, J. Modulating antibody structure and function through directed mutations and chemical rescue ACS Synthetic Biology  2018 7:1152-1162  DOI:10.1021/acssynbio.8b00124  PMID:29609459  PMCID:PMC5910032
    • Keohane, C. E., Steele, A. D., Fetzer, C., Khowsathit, J., Van Tyne, D., Maynie, L., Gilmore, M. S., Karanicolas, J., Sieber, S. A., Wuest, W. M. Promysalin elicits species-selective inhibition of pseudomonas aeruginosa by targeting succinate dehydrogenase Journal of the American Chemical Society  2018 140:1774-1782  DOI:10.1021/jacs.7b11212  PMID:29300464  PMCID:PMC5869686
    • Bazzoli, A., Vance, D. J., Rudolph, M. J., Rong, Y. H., Angalakurthi, S. K., Toth, R. T., Middaugh, C. R., Volkin, D. B., Weis, D. D., Karanicolas, J., Mantis, N. J. Using homology modeling to interrogate binding affinity in neutralization of ricin toxin by a family of single domain antibodies Proteins-Structure Function and Bioinformatics  2017 85:1994-2008  DOI:10.1002/prot.25353  PMID:28718923  PMCID:PMC5754017
    • Yu, J., Lan, L., Lewin, S. J., Rogers, S. A., Roy, A., Wu, X., Gao, P., Karanicolas, J., Aube, J., Sun, B., Xu, L. Identification of novel small molecule Beclin 1 mimetics activating autophagy Oncotarget  2017 8:51355-51369  DOI:10.18632/oncotarget.17977  PMID:28881653  PMCID:PMC5584254
    • Bazzoli, A., Karanicolas, J. "Solvent hydrogen-bond occlusion": A new model of polar desolvation for biomolecular energetics Journal of Computational Chemistry  2017 38:1321-1331  DOI:10.1002/jcc.24740  PMID:28318014  PMCID:PMC5407913
    • Dickson, A., Bailey, C. T., Karanicolas, J. Optimal allosteric stabilization sites using contact stabilization analysis Journal of Computational Chemistry  2017 38:1138-1146  DOI:10.1002/jcc.24517  PMID:27774625  PMCID:PMC5403592
    • Kudinov, A. E., Karanicolas, J., Golemis, E. A., Boumber, Y. Musashi RNA-binding proteins as cancer drivers and novel therapeutic targets Clinical Cancer Research  2017 23:2143-2153  DOI:10.1158/1078-0432.ccr-16-2728  PMID:28143872  PMCID:PMC5413399
    • Kaur, K., Wu, X., Fields, J. K., Johnson, D. K., Lan, L., Pratt, M., Somoza, A. D., Wang, C. C. C., Karanicolas, J., Oakley, B. R., Xu, L., De Guzman, R. N. The fungal natural product azaphilone-9 binds to HuR and inhibits HuR-RNA interaction in vitro PLoS One  2017 12  DOI:10.1371/journal.pone.0175471  PMID:28414767  PMCID:PMC5393604
    • Malhotra, S., Karanicolas, J. When does chemical elaboration induce a ligand to change its binding mode? Journal of Medicinal Chemistry  2017 60:128-145  DOI:10.1021/acs.jmedchem.6b00725  PMID:27982595  PMCID:PMC5525026
    • Johnson, D. K., Karanicolas, J. Computational screening and design for compounds that disrupt protein-protein interactions Current Topics in Medicinal Chemistry  2017 17:2703-2714  DOI:10.2174/1568026617666170508153904  PMID:28482793
    • Budiardjo, S. J., Licknack, T. J., Cory, M. B., Kapros, D., Roy, A., Lovell, S., Douglas, J., Karanicolas, J. Full and partial agonism of a designed enzyme switch ACS Synthetic Biology  2016 5:1475-1484  DOI:10.1021/acssynbio.6b00097  PMID:27389009  PMCID:PMC5161622
    • Lea, W. A., O'Neil, P. T., Machen, A. J., Naik, S., Chaudhri, T., McGinn-Straub, W., Tischer, A., Auton, M. T., Burns, J. R., Baldwin, M. R., Khar, K. R., Karanicolas, J., et al. Chaperonin-based biolayer interferometry to assess the kinetic stability of metastable, aggregation-prone proteins Biochemistry  2016 55:4885-4908  DOI:10.1021/acs.biochem.6b00293  PMID:27505032
    • Gowthaman, R., Miller, S. A., Rogers, S., Khowsathit, J., Lan, L., Bai, N., Johnson, D. K., Liu, C., Xu, L., Anbanandam, A., Aube, J., Roy, A., et al. DARC: Mapping surface topography by ray-casting for effective virtual screening at protein interaction sites Journal of Medicinal Chemistry  2016 59:4152-4170  DOI:10.1021/acs.jmedchem.5b00150  PMID:26126123  PMCID:PMC4707132
    • Wahome, N., Sully, E., Singer, C., Thomas, J. C., Hu, L., Joshi, S. B., Volkin, D. B., Fang, J. W., Karanicolas, J., Jacobs, D. J., Mantis, N. J., Middaugh, C. R. Novel ricin subunit antigens with enhanced capacity to elicit toxin-neutralizing antibody responses in mice Journal of Pharmaceutical Sciences  2016 105:1603-1613  DOI:10.1016/j.xphs.2016.02.009  PMID:26987947  PMCID:PMC4846473
    • Johnson, D. K., Karanicolas, J. Ultra-high-throughput structure-based virtual screening for small molecule inhibitors of protein-protein interactions Journal of Chemical Information and Modeling  2016 56:399-411  DOI:10.1021/acs.jcim.5b00572  PMID:26726827  PMCID:PMC4765363
    • Ali, A. M., Reis, J. M., Xia, Y., Rashid, A. J., Mercaldo, V., Walters, B. J., Brechun, K. E., Borisenko, V., Josselyn, S. A., Karanicolas, J., Woolley, G. A. Optogenetic inhibitor of the transcription factor CREB Chemistry & Biology  2015 22:1531-1539  DOI:10.1016/j.chembiol.2015.09.018  PMID:26590638  PMCID:PMC4656143
    • Bazzoli, A., Kelow, S. P., Karanicolas, J. Enhancements to the Rosetta energy function enable improved identification of small molecules that inhibit protein-protein interactions PLoS One  2015 10  DOI:10.1371/journal.pone.0140359  PMID:26484863  PMCID:PMC4617380
    • Lan, L., Appelman, C., Smith, A. R., Yu, J., Larsen, S., Marquez, R. T., Liu, H., Wu, X., Gao, P., Roy, A., Anbanandam, A., Gowthaman, R., et al. Natural product (-)-gossypol inhibits colon cancer cell growth by targeting RNA-binding protein Musashi-1 Molecular Oncology  2015 9:1406-1420  DOI:10.1016/j.molonc.2015.03.014  PMID:25933687  PMCID:PMC4523432
    • Gowthaman, R., Lyskov, S., Karanicolas, J. DARC 2.0: Improved docking and virtual screening at protein interaction sites PLoS One  2015 10  DOI:10.1371/journal.pone.0131612  PMID:26181386  PMCID:PMC4504481
    • Johnson, D. K., Karanicolas, J. Selectivity by small-molecule inhibitors of protein interactions can be driven by protein surface fluctuations PLoS Computational Biology  2015 11  DOI:10.1371/journal.pcbi.1004081  PMID:25706586  PMCID:PMC4338137
    • Xia, Y., DiPrimio, N., Keppel, T. R., Vo, B., Fraser, K., Battaiei, K. P., Egan, C., Bystroff, C., Lovell, S., Weis, D. D., Anderson, J. C., Karanicolas, J. The designability of protein switches by chemical rescue of structure: mechanisms of inactivation and reactivation Journal of the American Chemical Society  2013 135:18840-18849  DOI:10.1021/ja407644b  PMID:24313858  PMCID:PMC3919134
    • Khar, K. R., Goldschmidt, L., Karanicolas, J. Fast docking on graphics processing units via Ray-Casting PLoS One  2013 8  DOI:10.1371/journal.pone.0070661  PMID:23976948  PMCID:PMC3745428
    • Gowthaman, R., Deeds, E. J., Karanicolas, J. Structural properties of non-traditional drug targets present new challenges for virtual screening Journal of Chemical Information and Modeling  2013 53:2073-2081  DOI:10.1021/ci4002316  PMID:23879197  PMCID:PMC3819422
    • Thomas, J. C., O'Hara, J. M., Hu, L., Gao, F. P., Joshi, S. B., Volkin, D. B., Brey, R. N., Fang, J., Karanicolas, J., Mantis, N. J., Middaugh, C. R. Effect of single-point mutations on the stability and immunogenicity of a recombinant ricin A chain subunit vaccine antigen Human Vaccines & Immunotherapeutics  2013 9:744-752  DOI:10.4161/hv.22998  PMID:23563512  PMCID:PMC3903890
    • Johnson, D. K., Karanicolas, J. Druggable protein interaction sites are more predisposed to surface pocket formation than the rest of the protein surface PLoS Computational Biology  2013 9  DOI:10.1371/journal.pcbi.1002951  PMID:23505360  PMCID:PMC3591273
    • Deckert, K., Budiardjo, S. J., Brunner, L. C., Lovell, S., Karanicolas, J. Designing allosteric control into enzymes by chemical rescue of structure Journal of the American Chemical Society  2012 134:10055-10060  DOI:10.1021/ja301409g  PMID:22655749  PMCID:PMC3381609
    • Karanicolas, J. Designing orthogonal signaling pathways: How to fit in with the surroundings Proceedings of the National Academy of Sciences of the United States of America  2012 109:5140-5141  DOI:10.1073/pnas.1202624109  PMID:22451928  PMCID:PMC3325707
    • Fleishman, S. J., Corn, J. E., Strauch, E. M., Whitehead, T. A., Karanicolas, J., Baker, D. Hotspot-centric de novo design of protein binders Journal of Molecular Biology  2011 413:1047-1062  DOI:10.1016/j.jmb.2011.09.001  PMID:21945116  PMCID:PMC4144197
    • Sievers, S. A., Karanicolas, J., Chang, H. W., Zhao, A., Jiang, L., Zirafi, O., Stevens, J. T., Munch, J., Baker, D., Eisenberg, D. Structure-based design of non-natural amino-acid inhibitors of amyloid fibril formation Nature  2011 475:96-100  DOI:10.1038/nature10154  PMID:21677644  PMCID:PMC4073670
    • Karanicolas, J., Com, J. E., Chen, I., Joachimiak, L. A., Dym, O., Peck, S. H., Albeck, S., Unger, T., Hu, W., Liu, G., Delbecq, S., Montelione, G. T., et al. A de novo protein binding pair by computational design and directed evolution Molecular Cell  2011 42:250-260  DOI:10.1016/j.molcel.2011.03.010  PMID:21458342  PMCID:PMC3102007
    • Hofmann, F. T., Lindemann, C., Salia, H., Adamitzki, P., Karanicolas, J., Seebeck, F. P. A phosphoarginine containing peptide as an artificial SH2 ligand Chemical Communications  2011 47:10335-10337  DOI:10.1039/c1cc13341a  PMID:21853174
    • Leaver-Fay, A., Tyka, M., Lewis, S. M., Lange, O. F., Thompson, J., Jacak, R., Kaufman, K., Renfrew, P. D., Smith, C. A., Sheffler, W., Davis, I. W., Cooper, S., et al. ROSETTA3: an object-oriented software suite for the simulation and design of macromolecules Methods in Enzymology  2011 545-574  DOI:10.1016/s0076-6879(11)87019-9  PMID:21187238  PMCID:PMC4083816
    • Das, R., Karanicolas, J., Baker, D. Atomic accuracy in predicting and designing noncanonical RNA structure Nature Methods  2010 7:291-294  DOI:10.1038/nmeth.1433  PMID:20190761  PMCID:PMC2854559
    • Karanicolas, J., Kuhlman, B. Computational design of affinity and specificity at protein-protein interfaces Current Opinion in Structural Biology  2009 19:458-463  DOI:10.1016/j.sbi.2009.07.005  PMID:19646858  PMCID:PMC2882636
    • Luo, B. H., Karanicolas, J., Harmacek, L. D., Baker, D., Springer, T. A. Rationally designed integrin beta3 mutants stabilized in the high affinity conformation Journal of Biological Chemistry  2009 284:3917-3924  DOI:10.1074/jbc.M806312200
    • Thompson, M. J., Sievers, S. A., Karanicolas, J., Ivanova, M. I., Baker, D., Eisenberg, D. The 3D profile method for identifying fibril-forming segments of proteins Proceedings of the National Academy of Sciences of the United States of America  2006 103:4074-4078  DOI:10.1073/pnas.0511295103  PMID:16537487  PMCID:PMC1449648
    • degree-related publication Feig, M., Karanicolas, J., Brooks III, C. L. MMTSB Tool Set: enhanced sampling and multiscale modeling methods for applications in structural biology Journal of Molecular Graphics & Modelling  2004 22:377-395  DOI:10.1016/j.jmgm.2003.12.005  PMID:15099834
    • degree-related publication Karanicolas, J., Brooks III, C. L. Integrating folding kinetics and protein function: biphasic kinetics and dual binding specificity in a WW domain Proceedings of the National Academy of Sciences of the United States of America  2004 101:3432-3437  DOI:10.1073/pnas.0304825101  PMID:14981252  PMCID:PMC373479
    • degree-related publication Karanicolas, J., Brooks III, C. L. An evolution of minimalist models for protein folding: from the behavior of protein-like polymers to protein function Drug Discovery Today: BIOSILICO  2004 2:127-133  DOI:10.1016/S1741-8364(04)02404-7
    • degree-related publication Karanicolas, J., Brooks III, C. L. Improved Gō-like models demonstrate the robustness of protein folding mechanisms towards non-native interactions Journal of Molecular Biology  2003 334:309-325  DOI:10.1016/j.jmb.2003.09.047  PMID:14607121
    • degree-related publication Karanicolas, J., Brooks III, C. L. The importance of explicit chain representation in protein folding models: an examination of Ising-like models Proteins-Structure Function and Genetics  2003 53:740-747  DOI:10.1002/prot.10459  PMID:14579364
    • degree-related publication Karanicolas, J., Brooks III, C. L. The structural basis for biphasic kinetics in the folding of the WW domain from a formin-binding protein: lessons for protein design? Proceedings of the National Academy of Sciences of the United States of America  2003 100:3954-3959  DOI:10.1073/pnas.0731771100  PMID:12655041  PMCID:PMC153029
    • degree-related publication Karanicolas, J., Brooks III, C. L. The origins of asymmetry in the folding transition states of protein L and protein G Protein Science  2002 11:2351-2361  DOI:10.1110/ps.0205402  PMID:12237457  PMCID:PMC2373711
    • Karanicolas, J., Fu, S., Power, J. F. Depth profiling the thermal reflection coefficient of an opaque solid via an inverse thermal wave scattering theory based on the Method of Images Applied Physics B-Lasers and Optics  2000 71:217-223
    • Power, J. F., Karanicolas, J., Fu, S. Method of Images direct mapping of one-dimensional heat flow patterns in an arbitrarily layered solid Applied Physics B-Lasers and Optics  2000 71:57-67
    • Woolley, G. A., Zunic, V., Karanicolas, J., Jaikaran, A. S. I., Starostin, A. V. Voltage-dependent behavior of a ''ball-and-chain'' gramicidin channel Biophysical Journal  1997 73:2465-2475  PMID:9370440  PMCID:PMC1181148
    • Liu, D., Karanicolas, J., Yu, C., Zhang, Z., Woolley, G. A. Site-specific incorporation of photoisomerizable azobenzene groups into ribonuclease S Bioorganic & Medicinal Chemistry Letters  1997 7:2677-2680  DOI:10.1016/s0960-894x(97)10044-0
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Background

education and training

  • Ph.D. in Biology, Scripps Research 1998 - 2003
  • B.S. in Biology, McGill University 1998

advisee of

  • graduate advising relationship

    • Brooks III, Charles L., Ph.D.  candidacy, 1999 - 2003
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Contact

full name

  • John Karanicolas

geographic location

  • Scripps California 

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