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Williamson, James
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Williamson, James

Vice President for Academic Affairs
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Positions

  • 2015 - Vice President for Academic Affairs, Scripps Research
  • 2013 - Professor, Integrative Structural and Computational Biology (ISCB) , Scripps Research
  • 2001 - Professor (Joint Appointment), Chemistry , Scripps Research
  • 1998 - Faculty Member, Skaggs Graduate School of Chemical and Biological Sciences , Scripps Research
  • 1998 - Member, The Skaggs Institute for Chemical Biology , Scripps Research
  • 2008 - 2017 Dean, Graduate & Postdoctoral Studies, Skaggs Graduate School of Chemical and Biological Sciences , Scripps Research
  • 1998 - 2012 Professor, Molecular Biology , Scripps Research
  • 2001 - 2008 Associate Dean, Chemistry Program, Skaggs Graduate School of Chemical and Biological Sciences , Scripps Research
  • 1995 - 1997 Associate Professor, Department of Chemistry, Massachusetts Institute of Technology
  • 1990 - 1995 Assistant Professor, Department of Chemistry, Massachusetts Institute of Technology
  • 1988 - 1990 Postdoctoral Fellow with Dr. Thomas R. Cech, University of Colorado Boulder
Dr. Jamie Williamson studies the structure and dynamics of RNA molecules and RNA-protein complexes involved in the regulation of gene expression by employing NMR spectroscopy and X-ray crystallography for solving high-resolution three-dimensional structures and examining the mechanism of assembly of multiprotein-RNA complexes.

Research Areas research areas

  • HIV (UMLS)
  • T-cell activation (UMLS)
  • helicase (UMLS)
  • ribosome assembly (UMLS)

Contact

  • jrwill@scripps.edu

Websites

  • James R. Williamson, Ph.D.
  • Laboratory Website
  • ORCID
  • ResearcherID
  • Publications
  • Research
  • Teaching
  • Background
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  • Identity
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Publications

h-index

  • 59

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    • Basan, M., Honda, T., Christodoulou, D., Horl, M., Chang, Y. F., Leoncini, E., Mukherjee, A., Okano, H., Taylor, B. R., Silverman, J. M., Sanchez, C., Williamson, J. R., et al. A universal trade-off between growth and lag in fluctuating environments Nature  2020 584:470-474  DOI:10.1038/s41586-020-2505-4  PMID:32669712  PMCID:PMC7442741
    • Rabuck-Gibbons, J. N., Popova, A. M., Greene, E. M., Cervantes, C. F., Lyumkis, D., Williamson, J. R. SrmB rescues trapped ribosome assembly intermediates Journal of Molecular Biology  2020 432:978-990  DOI:10.1016/j.jmb.2019.12.013  PMID:31877323  PMCID:PMC7106940
    • Duss, O., Stepanyuk, G. A., Puglisi, J. D., Williamson, J. R. Transient protein-RNA interactions guide nascent ribosomal RNA folding Cell  2019 179:1357-+  DOI:10.1016/j.cell.2019.10.035  PMID:31761533
    • Razi, A., Davis, J. H., Hao, Y., Jahagirdar, D., Thurlow, B., Basu, K., Jain, N., Gomez-Blanco, J., Britton, R. A., Vargas, J., Guarne, A., Woodson, S. A., et al. Role of Era in assembly and homeostasis of the ribosomal small subunit Nucleic Acids Research  2019 47:8301-8317  DOI:10.1093/nar/gkz571  PMID:31265110  PMCID:PMC6736133
    • Craveur, P., Gres, A. T., Kirby, K. A., Liu, D., Hammond, J. A., Deng, Y., Forli, S., Goodsell, D. S., Williamson, J. R., Sarafianos, S. G., Olson, A. J. Novel Intersubunit Interaction Critical for HIV-1 Core Assembly Defines a Potentially Targetable Inhibitor Binding Pocket MBio  2019 10:e02858-18  DOI:10.1128/mBio.02858-18  PMID:30862755  PMCID:PMC6414707
    • Duss, O., Stepanyuk, G. A., Grot, A., O'Leary, S. E., Puglisi, J. D., Williamson, J. R. Real-time assembly of ribonucleoprotein complexes on nascent RNA transcripts Nature Communications  2018 9  DOI:10.1038/s41467-018-07423-3  PMID:30504830  PMCID:PMC6269517
    • Solis, G. M., Kardakaris, R., Valentine, E. R., Bar-Peled, L., Chen, A. L., Blewett, M. M., McCormick, M. A., Williamson, J. R., Kennedy, B., Cravatt, B. F., Petrascheck, M. Translation attenuation by minocycline enhances longevity and proteostasis in old post-stress-responsive organisms Elife  2018 7  DOI:10.7554/eLife.40314  PMID:30479271  PMCID:PMC6257811
    • Hammond, J. A., Zhou, L., Lamichhane, R., Chu, H. Y., Millar, D. P., Gerace, L., Williamson, J. R. A survey of DDX21 activity during Rev/RRE complex formation Journal of Molecular Biology  2018 430:537-553  DOI:10.1016/j.jmb.2017.06.023  PMID:28705764  PMCID:PMC5762417
    • Dai, X., Zhu, M., Warren, M., Balakrishnan, R., Okano, H., Williamson, J. R., Fredrick, K., Hwa, T. Slowdown of translational elongation in Escherichia coli under hyperosmotic stress MBio  2018 9:e02375-17  DOI:10.1128/mBio.02375-17  PMID:29440576  PMCID:PMC5821080
    • Erickson, D. W., Schink, S. J., Patsalo, V., Williamson, J. R., Gerland, U., Hwa, T. A global resource allocation strategy governs growth transition kinetics of Escherichia coli Nature  2017 551:119-123  DOI:10.1038/nature24299  PMID:29072300
    • Basan, M., Hui, S., Williamson, J. R. ArcA overexpression induces fermentation and results in enhanced growth rates of E-coli Scientific Reports  2017 7  DOI:10.1038/s41598-017-12144-6  PMID:28928483  PMCID:PMC5605494
    • Tan, Y. Z., Baldwin, P. R., Davis, J. H., Williamson, J. R., Potter, C. S., Carragher, B., Lyumkis, D. Addressing preferred specimen orientation in single-particle cryo-EM through tilting Nature Methods  2017 14:793-796  DOI:10.1038/nmeth.4347  PMID:28671674  PMCID:PMC5533649
    • Lamichhane, R., Hammond, J. A., Pauszek, R. F., Anderson, R. M., Pedron, I., van der Schans, E., Williamson, J. R., Millar, D. P. A DEAD-box protein acts through RNA to promote HIV-1 Rev-RRE assembly Nucleic Acids Research  2017 45:4632-4641  DOI:10.1093/nar/gkx206  PMID:28379444  PMCID:PMC5416872
    • Davis, J. H., Williamson, J. R. Structure and dynamics of bacterial ribosome biogenesis Philosophical Transactions of the Royal Society B-Biological Sciences  2017 372  DOI:10.1098/rstb.2016.0181  PMID:28138067  PMCID:PMC5311925
    • Hammond, J. A., Lamichhane, R., Millar, D. P., Williamson, J. R. A DEAD-box helicase mediates an RNA structural transition in the HIV-1 Rev response element Journal of Molecular Biology  2017 429:697-714  DOI:10.1016/j.jmb.2017.01.018  PMID:28153748
    • Dai, X., Zhu, M., Warren, M., Balakrishnan, R., Patsalo, V., Okano, H., Williamson, J. R., Fredrick, K., Wang, Y. P., Hwa, T. Reduction of translating ribosomes enables Escherichia coli to maintain elongation rates during slow growth Nature Microbiology  2017 2  DOI:10.1038/nmicrobiol.2016.231  PMID:27941827  PMCID:PMC5346290
    • Jin, H. Y., Oda, H., Chen, P., Yang, C., Zhou, X., Kang, S. G., Valentine, E., Kefauver, J. M., Liao, L., Zhang, Y., Gonzalez-Martin, A., Shepherd, J., et al. Differential sensitivity of target genes to translational repression by miR-17~92 PLoS Genetics  2017 13  DOI:10.1371/journal.pgen.1006623  PMID:28241004  PMCID:PMC5348049
    • Davis, J. H., Tan, Y. Z., Carragher, B., Potter, C. S., Lyumkis, D., Williamson, J. R. Modular assembly of the bacterial large ribosomal subunit Cell  2016 167:1610-1622  DOI:10.1016/j.cell.2016.11.020  PMID:27912064  PMCID:PMC5145266
    • Thurlow, B., Davis, J. H., Leong, V., Moraes, T. F., Williamson, J. R., Ortega, J. Binding properties of YjeQ (RsgA), RbfA, RimM and Era to assembly intermediates of the 30S subunit Nucleic Acids Research  2016 44:9918-9932  DOI:10.1093/nar/gkw613  PMID:27382067  PMCID:PMC5175332
    • Ni, X., Davis, J. H., Jain, N., Razi, A., Benlekbir, S., McArthur, A. G., Rubinstein, J. L., Britton, R. A., Williamson, J. R., Ortega, J. YphC and YsxC GTPases assist the maturation of the central protuberance, GTPase associated region and functional core of the 50S ribosomal subunit Nucleic Acids Research  2016 44:8442-8455  DOI:10.1093/nar/gkw678  PMID:27484475  PMCID:PMC5041480
    • Beuck, C., Williamson, J. R., Wuthrich, K., Serrano, P. The acidic domain is a unique structural feature of the splicing factor SYNCRIP Protein Science  2016 25:1545-1550  DOI:10.1002/pro.2935  PMID:27081926  PMCID:PMC4972210
    • Lavergne, T., Lamichhane, R., Malyshey, D. A., Li, Z., Li, L., Sperling, E., Williamson, J. R., Millar, D. P., Romesberg, F. E. FRET characterization of complex conformational changes in a large 165 ribosomal RNA fragment site-specifically labeled using unnatural base pairs ACS Chemical Biology  2016 11:1347-1353  DOI:10.1021/acschembio.5b00952  PMID:26942998  PMCID:PMC4874843
    • Stepanyuk, G. A., Serrano, P., Peralta, E., Farr, C. L., Axelrod, H. L., Geralt, M., Das, D., Chiu, H. J., Jaroszewski, L., Deacon, A. M., Lesley, S. A., Elsliger, M. A., et al. UHM-ULM interactions in the RBM39-U2AF65 splicing-factor complex Acta Crystallographica Section D-Structural Biology  2016 72:497-511  DOI:10.1107/s2059798316001248  PMID:27050129  PMCID:PMC4822562
    • Whisenant, T. C., Peralta, E. R., Aarreberg, L. D., Gao, N. J., Head, S. R., Ordoukhanian, P., Williamson, J. R., Salomon, D. R. The activation-induced assembly of an RNA/protein interactome centered on the splicing factor U2AF2 regulates gene expression in human CD4 T cells PLoS One  2015 10:e0144409  DOI:10.1371/journal.pone.0144409  PMID:26641092  PMCID:PMC4671683
    • Basan, M., Hui, S., Okano, H., Zhang, Z., Shen, Y., Williamson, J. R., Hwa, T. Overflow metabolism in Escherichia coli results from efficient proteome allocation Nature  2015 528:99-104  DOI:10.1038/nature15765  PMID:26632588  PMCID:PMC4843128
    • Earnest, T. M., Lai, J., Chen, K., Hallock, M. J., Williamson, J. R., Luthey-Schulten, Z. Toward a whole-cell model of ribosome biogenesis: kinetic modeling of SSU assembly Biophysical Journal  2015 109:1117-1135  DOI:10.1016/j.bpj.2015.07.030  PMID:26333594  PMCID:PMC4576174
    • Gomez-Amaro, R. L., Valentine, E. R., Carretero, M., LeBoeuf, S. E., Rangaraju, S., Broaddus, C. D., Solis, G. M., Williamson, J. R., Petrascheck, M. Measuring food intake and nutrient absorption in Caenorhabditis elegans Genetics  2015 200:443-454  DOI:10.1534/genetics.115.175851  PMID:25903497  PMCID:PMC4492371
    • Hui, S., Chen, S. S., Erickson, D. W., Basan, M., Wang, J., Hwa, T., Williamson, J. R. Quantitative proteomic analysis reveals a simple strategy of global resource allocation in bacteria Molecular Systems Biology  2015 11:784  DOI:10.15252/msb.20145697  PMID:25678603  PMCID:PMC4358657
    • Williamson, J. R. Really exasperating viral protein from HIV Elife  2015 4:e05169  DOI:10.7554/eLife.05169  PMID:25574642  PMCID:PMC4337408
    • Sashital, D. G., Greeman, C. A., Lyumkis, D., Potter, C. S., Carragher, B., Williamson, J. R. A combined quantitative mass spectrometry and electron microscopy analysis of ribosomal 30S subunit assembly in E. coli Elife  2014 3  DOI:10.7554/eLife.04491  PMID:25313868  PMCID:PMC4371863
    • Gulati, M., Jain, N., Davis, J. H., Williamson, J. R., Britton, R. A. Functional interaction between ribosomal protein L6 and RbgA during ribosome assembly PLoS Genetics  2014 10:e1004694  DOI:10.1371/journal.pgen.1004694  PMID:25330043  PMCID:PMC4199504
    • Stokes, J. M., Davis, J. H., Mangat, C. S., Williamson, J. R., Brown, E. D. Discovery of a small molecule that inhibits bacterial ribosome biogenesis Elife  2014 3:03574  DOI:10.7554/eLife.03574  PMID:25233066  PMCID:PMC4371806
    • Jomaa, A., Jain, N., Davis, J. H., Williamson, J. R., Britton, R. A., Ortega, J. Functional domains of the 50S subunit mature late in the assembly process Nucleic Acids Research  2014 42:3419-3435  DOI:10.1093/nar/gkt1295  PMID:24335279  PMCID:PMC3950693
    • Popova, A. M., Williamson, J. R. Quantitative analysis of rRNA modifications using stable isotope labeling and mass spectrometry Journal of the American Chemical Society  2014 136:2058-2069  DOI:10.1021/ja412084b  PMID:24422502  PMCID:PMC3985470
    • Ban, N., Beckmann, R., Cate, J. H. D., Dinman, J. D., Dragon, F., Ellis, S. R., Lafontaine, D. L. J., Lindahl, L., Liljas, A., Lipton, J. M., McAlear, M. A., Moore, P. B., et al. A new system for naming ribosomal proteins Current Opinion in Structural Biology  2014 24:165-169  DOI:10.1016/j.sbi.2014.91.002  PMID:24524803
    • Ridgeway, W. K., Millar, D. P., Williamson, J. R. Vectorized data acquisition and fast triple-correlation integrals for Fluorescence Triple Correlation Spectroscopy Computer Physics Communications  2013 184:1322-1332  DOI:10.1016/j.cpc.2012.12.022  PMID:23525193  PMCID:PMC3601675
    • Wu, J. A., Campbell, Z. T., Menichelli, E., Wickens, M., Williamson, J. R. A protein.protein interaction platform involved in recruitment of GLD-3 to the FBF.Fem-3 mRNA complex Journal of Molecular Biology  2013 425:738-754  DOI:10.1016/j.jmb.2012.11.013  PMID:23159559  PMCID:PMC3568228
    • Menichelli, E., Wu, J., Campbell, Z. T., Wickens, M., Williamson, J. R. Biochemical characterization of the Caenorhabditis elegans FBF. CPB-1 translational regulation complex identifies conserved protein interaction hotspots Journal of Molecular Biology  2013 425:725-737  DOI:10.1016/j.jmb.2012.11.012  PMID:23159558  PMCID:PMC3568192
    • Chen, S. S., Williamson, J. R. Characterization of the ribosome biogenesis landscape in E. coli using quantitative mass spectrometry Journal of Molecular Biology  2013 425:767-779  DOI:10.1016/j.jmb.2012.11.040  PMID:23228329  PMCID:PMC3568210
    • Beuck, C., Qu, S., Fagg, W. S., Ares, M., Williamson, J. R. Structural analysis of the quaking homodimerization interface Journal of Molecular Biology  2012 423:766-781  DOI:10.1016/j.jmb.2012.08.027  PMID:22982292  PMCID:PMC3472039
    • Ridgeway, W. K., Millar, D. P., Williamson, J. R. Quantitation of ten 30S ribosomal assembly intermediates using fluorescence triple correlation spectroscopy Proceedings of the National Academy of Sciences of the United States of America  2012 109:13614-13619  DOI:10.1073/pnas.1204620109  PMID:22869699  PMCID:PMC3427059
    • Puglisi, J. D., Williamson, J. R. Digging deep into nucleic acid structure and nucleic acid protein recognition Current Opinion in Structural Biology  2012 22:249-250  DOI:10.1016/j.sbi.012.05.003  PMID:22632873
    • Campbell, Z. T., Menichelli, E., Friend, K., Wu, J., Kimble, J., Williamson, J. R., Wickens, M. Identification of a conserved interface between PUF and CPEB proteins Journal of Biological Chemistry  2012 287:18854-18862  DOI:10.1074/jbc.M112.352815  PMID:22496444  PMCID:PMC3365739
    • Campbell, Z. T., Bhimsaria, D., Valley, C. T., Rodriguez-Martinez, J. A., Menichelli, E., Williamson, J. R., Ansari, A. Z., Wickens, M. Cooperativity in RNA-protein interactions: Global analysis of RNA binding specificity Cell Reports  2012 1:570-581  DOI:10.1016/j.celrep.2012.04.003  PMID:22708079  PMCID:PMC3375920
    • Ridgeway, W. K., Millar, D. P., Williamson, J. R. The spectroscopic basis of fluorescence triple correlation spectroscopy Journal of Physical Chemistry B  2012 116:1908-1919  DOI:10.1021/jp208605z  PMID:22229664  PMCID:PMC3293655
    • Kerkow, D. E., Carmel, A. B., Menichelli, E., Ambrus, G., Hills, R. D., Gerace, L., Williamson, J. R. The structure of the NXF2/NXT1 heterodimeric complex reveals the combined specificity and versatility of the NTF2-like fold Journal of Molecular Biology  2012 415:649-665  DOI:10.1016/j.jmb.2011.11.027  PMID:22123199  PMCID:PMC3265607
    • Menichelli, E., Edgcomb, S. P., Recht, M. I., Williamson, J. R. The structure of Aquifex aeolicus ribosomal protein S8 reveals a unique subdomain that contributes to an extremely tight association with 16S rRNA Journal of Molecular Biology  2012 415:489-502  DOI:10.1016/j.jmb.2011.10.046  PMID:22079365  PMCID:PMC3259246
    • Edgcomb, S. P., Carmel, A. B., Naji, S., Ambrus-Aikelin, G., Reyes, J. R., Saphire, A. C. S., Gerace, L., Williamson, J. R. DDX1 is an RNA-dependent ATPase involved in HIV-1 Rev function and virus replication Journal of Molecular Biology  2012 415:61-74  DOI:10.1016/j.jmb.2011.10.032  PMID:22051512  PMCID:PMC3249508
    • Chen, S. S., Sperling, E., Davis, J. H., Williamson, J. R. Measuring the dynamics of E. coli ribosome biogenesis using pulse-labeling and quantitative mass spectrometry Molecular Biosystems  2012 8:3325-3334  DOI:10.1039/c2mb25310k  PMID:23090316  PMCID:PMC3501348
    • Shoji, S., Dambacher, C. M., Shajani, Z., Williamson, J. R., Schultz, P. G. Systematic chromosomal deletion of bacterial ribosomal protein genes Journal of Molecular Biology  2011 413:751-761  DOI:10.1016/j.jmb.2011.09.004  PMID:21945294  PMCID:PMC3694390
    • Robertson-Anderson, R. M., Wang, J., Edgcomb, S. P., Carmel, A. B., Williamson, J. R., Millar, D. P. Single-molecule studies reveal that dead box protein DDX1 promotes oligomerization of HIV-1 Rev on the Rev response element Journal of Molecular Biology  2011 410:959-971  DOI:10.1016/j.jmb.2011.04.026  PMID:21763499  PMCID:PMC3140434
    • Schultheisz, H. L., Szymczyna, B. R., Scott, L. G., Williamson, J. R. Enzymatic de novo pyrimidine nucleotide synthesis Journal of the American Chemical Society  2011 133:297-304  DOI:10.1021/ja1059685  PMID:21166398  PMCID:PMC3134529
    • Sykes, M. T., Shajani, Z., Sperling, E., Beck, A. H., Williamson, J. R. Quantitative proteomic analysis of ribosome assembly and turnover in vivo Journal of Molecular Biology  2010 403:331-345  DOI:10.1016/j.jmb.2010.08.005  PMID:20709079  PMCID:PMC2953596
    • Mulder, A. M., Yoshioka, C., Beck, A. H., Bunner, A. E., Milligan, R. A., Potter, C. S., Carragher, B., Williamson, J. R. Visualizing ribosome biogenesis: parallel assembly pathways for the 30S subunit Science  2010 330:673-677  DOI:10.1126/science.1193220  PMID:21030658  PMCID:PMC2990404
    • Carmel, A. B., Wu, J. A., Lehmann-Blount, K. A., Williamson, J. R. High-affinity consensus binding of target RNAs by the STAR/GSG proteins GLS-1, STAR-2 and quaking BMC Molecular Biology  2010 11:48  DOI:10.1186/1471-2199-11-48  PMID:20573244  PMCID:PMC2905418
    • Sykes, M. T., Sperling, E., Chen, S. S., Williamson, J. R. Quantitation of the ribosomal protein autoregulatory network using mass spectrometry Analytical Chemistry  2010 82:5038-5045  DOI:10.1021/ac9028664  PMID:20481440  PMCID:PMC2894367
    • Bunner, A. E., Nord, S., Wikstrom, M., Williamson, J. R. The effect of ribosome assembly cofactors on in vitro 30S subunit reconstitution Journal of Molecular Biology  2010 398:1-7  DOI:10.1016/j.jmb.2010.02.036  PMID:20188109  PMCID:PMC2866118
    • Bunner, A. E., Beck, A. H., Williamson, J. R. Kinetic cooperativity in Escherichia coli 30S ribosomal subunit reconstitution reveals additional complexity in the assembly landscape Proceedings of the National Academy of Sciences of the United States of America  2010 107:5417-5422  DOI:10.1073/pnas.0912007107  PMID:20207951  PMCID:PMC2851750
    • Beuck, C., Szymczyna, B. R., Kerkow, D. E., Carmel, A. B., Columbus, L., Stanfield, R. L., Williamson, J. R. Structure of the GLD-1 homodimerization domain: insights into STAR protein-mediated translational regulation Structure  2010 18:377-389  DOI:10.1016/j.str.2009.12.016  PMID:20223220  PMCID:PMC2837851
    • Ridgeway, W. K., Seitaridou, E., Phillips, R., Williamson, J. R. RNA-protein binding kinetics in an automated microfluidic reactor Nucleic Acids Research  2009 37:e142  DOI:10.1093/nar/gkp733  PMID:19759214  PMCID:PMC2790880
    • Schultheisz, H. L., Szymczyna, B. R., Williamson, J. R. Enzymatic synthesis and structural characterization of 13C, 15N-poly(ADP-ribose) Journal of the American Chemical Society  2009 131:14571-14578  DOI:10.1021/ja903155s  PMID:19757771  PMCID:PMC2758922
    • Elles, L. M. S., Sykes, M. T., Williamson, J. R., Uhlenbeck, O. C. A dominant negative mutant of the E. Coli RNA helicase DbpA blocks assembly of the 50S ribosomal subunit Nucleic Acids Research  2009 37:6503-6514  DOI:10.1093/nar/gkp711  PMID:19734347  PMCID:PMC2770675
    • Bunner, A. E., Williamson, J. R. Stable isotope pulse-chase monitored by quantitative mass spectrometry applied to E.coli 30S ribosome assembly kinetics Methods  2009 49:136-141  DOI:10.1016/j.ymeth.2009.06.002  PMID:19559090  PMCID:PMC2753762
    • Williamson, J. R. My h-index turns 40: my midlife crisis of impact ACS Chemical Biology  2009 4:311-313  DOI:10.1021/cb9001014  PMID:19441857
    • El Yacoubi, B., Lyons, B., Cruz, Y., Reddy, R., Nordin, B., Agnelli, F., Williamson, J. R., Schimmel, P., Swairjo, M. A., de Crecy-Lagard, V. The universal YrdC/Sua5 family is required for the formation of threonylcarbamoyladenosine in tRNA Nucleic Acids Research  2009 37:2894-2909  DOI:10.1093/nar/gkp152  PMID:19287007  PMCID:PMC2685093
    • Szymczyna, B. R., Taurog, R. E., Young, M. J., Snyder, J. C., Johnson, J. E., Williamson, J. R. Synergy of NMR, computation, and x-ray crystallography for structural biology Structure  2009 17:499-507  DOI:10.1016/j.str.2009.03.001  PMID:19368883  PMCID:PMC2705668
    • Sykes, M. T., Williamson, J. R. A complex assembly landscape for the 30S ribosomal subunit Annual Review of Biophysics  2009 38:197-215  DOI:10.1146/annurev.biophys.050708.133615  PMID:19416066
    • Bunner, A. E., Trauger, S. A., Siuzdak, G., Williamson, J. R. Quantitative ESI-TOF analysis of macromolecular assembly kinetics Analytical Chemistry  2008 80:9379-9386  DOI:10.1021/ac8020505  PMID:19007188  PMCID:PMC2735594
    • Carlomagno, T., Amata, I., Williamson, J. R., Hennig, M. NMR assignments of HIV-2 TAR RNA Biomolecular NMR Assignments  2008 2:167-169  DOI:10.1007/s12104-008-9112-x  PMID:19636896
    • Sykes, M. T., Williamson, J. R. Envelope: Interactive software for modeling and fitting complex isotope distributions BMC Bioinformatics  2008 9:446  DOI:10.1186/1471-2105-9-446  PMID:18937869  PMCID:PMC2605472
    • Williamson, J. R. Cooperativity in macromolecular assembly Nature Chemical Biology  2008 4:458-465  DOI:10.1038/nchembio.102  PMID:18641626
    • Schultheisz, H. L., Szymczyna, B. R., Scott, L. G., Williamson, J. R. Pathway engineered enzymatic de novo purine nucleotide synthesis ACS Chemical Biology  2008 3:499-511  DOI:10.1021/cb800066p  PMID:18707057  PMCID:PMC2746247
    • Sperling, E., Bunner, A. E., Sykes, M. T., Williamson, J. R. Quantitative analysis of isotope distributions in proteomic mass spectrometry using least-squares Fourier transform convolution Analytical Chemistry  2008 80:4906-4917  DOI:10.1021/ac800080v  PMID:18522437  PMCID:PMC2502059
    • Williamson, J. R. Biophysical studies of bacterial ribosome assembly Current Opinion in Structural Biology  2008 18:299-304  DOI:10.1016/j.sbi.2008.05.001  PMID:18541423  PMCID:PMC2494948
    • Naidoo, N., Harrop, S. J., Sobti, M., Haynes, P. A., Szymczyna, B. R., Williamson, J. R., Curmi, P. M. G., Mabbutt, B. C. Crystal structure of Lsm3 octamer from Saccharomyces cerevisiae: Implications for Lsm ring organisation and recruitment Journal of Molecular Biology  2008 377:1357-1371  DOI:10.1016/j.jmb.2008.01.007  PMID:18329667
    • Edgcomb, S. P., Aschrafi, A., Kompfner, E., Williamson, J. R., Gerace, L., Hennig, M. Protein structure and oligomerization are important for the formation of export-competent HIV-1 Rev-RRE complexes Protein Science  2008 17:420-430  DOI:10.1110/ps.073246608  PMID:18218716  PMCID:PMC2248316
    • Recht, M. I., Ryder, S. P., Williamson, J. R. Monitoring assembly of ribonucleoprotein complexes by isothermal titration calorimetry Methods in Molecular Biology  2008 488:117-127  DOI:10.1007/978-1-60327-475-3_8  PMID:18982287  PMCID:PMC2922068
    • Ryder, S. P., Recht, M. I., Williamson, J. R. Quantitative analysis of protein-RNA interactions by gel mobility shift Methods in Molecular Biology  2008 488:99-115  DOI:10.1007/978-1-60327-475-3_7  PMID:18982286  PMCID:PMC2928675
    • Hennig, M., Scott, L. G., Sperling, E., Bermel, W., Williamson, J. R. Synthesis of 5-fluoropyrimidine nucleotides as sensitive NMR probes of RNA structure Journal of the American Chemical Society  2007 129:14911-14921  DOI:10.1021/ja073825i  PMID:17990877
    • Szymczyna, B. R., Gan, L., Johnson, J. E., Williamson, J. R. Solution NMR studies of the maturation intermediates of a 13 MDa viral capsid Journal of the American Chemical Society  2007 129:7867-7876  DOI:10.1021/ja071118j  PMID:17536799
    • Karnaukhov, A. V., Karnaukhova, E. V., Williamson, J. R. Numerical Matrices Method for nonlinear system identification and description of dynamics of biochemical reaction networks Biophysical Journal  2007 92:3459-3473  DOI:10.1529/biophysj.106.093344  PMID:17350997  PMCID:PMC1853128
    • Vallurupalli, P., Scott, L., Williamson, J. R., Kay, L. E. Strong coupling effects during X-pulse CPMG experiments recorded on heteronuclear ABX spin systems: artifacts and a simple solution Journal of Biomolecular NMR  2007 38:41-46  DOI:10.1007/s10858-006-9139-1  PMID:17334825
    • Kiessling, L. L., Doudna, J. A., Johnsson, K., Mapp, A. K., Marletta, M. A., Seeberger, P. H., Williamson, J. R., Wedde, S. G. A higher degree of difficulty ACS Chemical Biology  2007 2:197-199  DOI:10.1021/cb7000846  PMID:17455890
    • Tahmassebi, D. C., Williamson, J. R. Balancing teaching and research in obtaining a faculty position at a predominantly undergraduate institution ACS Chemical Biology  2007 2:521-524  DOI:10.1021/cb700155d  PMID:17708667
    • Vallurupalli, P., Scott, L., Hennig, M., Williamson, J. R., Kay, L. E. New RNA labeling methods offer dramatic sensitivity enhancements in 2H NMR relaxation spectra Journal of the American Chemical Society  2006 128:9346-9347  DOI:10.1021/ja0632512  PMID:16848466
    • Hennig, M., Munzarovl, M. L., Bermel, W., Scott, L. G., Sklenar, V., Williamson, J. R. Measurement of long-range 1H-19F scalar coupling constants and their glycosidic torsion dependence in 5-fluoropyrimidine-substituted RNA Journal of the American Chemical Society  2006 128:5851-5858  DOI:10.1021/ja060165t  PMID:16637654  PMCID:PMC2556634
    • Leontis, N. B., Altman, R. B., Berman, H. M., Brenner, S. E., Brown, J. W., Engelke, D. R., Harvey, S. C., Holbrook, S. R., Jossinet, F., Lewis, S. E., Major, F., Mathews, D. H., et al. The RNA Ontology Consortium: an open invitation to the RNA community RNA-a Publication of the RNA Society  2006 12:533-541  DOI:10.1261/rna.2343206  PMID:16484377  PMCID:PMC1421088
    • Talkington, M. W. T., Siuzdak, G., Williamson, J. R. An assembly landscape for the 30S ribosomal subunit Nature  2005 438:628-632  DOI:10.1038/nature04261  PMID:16319883  PMCID:PMC1444899
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    • Chao, J. A., Lee, J. H., Chapados, B. R., Debler, E. W., Schneemann, A., Williamson, J. R. Dual modes of RNA-silencing suppression by Flock House virus protein B2 Nature Structural & Molecular Biology  2005 12:952-957  DOI:10.1038/nsmb1005  PMID:16228003
    • Davis, J. H., Tonelli, M., Scott, L. G., Jaeger, L., Williamson, J. R., Butcher, S. E. RNA helical packing in solution: NMR structure of a 30 kDa GAAA tetraloop-receptor complex Journal of Molecular Biology  2005 351:371-382  DOI:10.1016/j.jmb.2005.05.069  PMID:16002091
    • Scott, L. G., Williamson, J. R. The binding interface between Bacillus stearothermophilus ribosomal protein S15 and its 5 '-translational operator mRNA Journal of Molecular Biology  2005 351:280-290  DOI:10.1016/j.jmb.2005.06.030  PMID:16005889
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    • Lehmann-Blount, K. A., Williamson, J. R. Shape-specific nucleotide binding of single-stranded RNA by the GLD-1 STAR domain Journal of Molecular Biology  2005 346:91-104  DOI:10.1016/j.jmb.2004.11.049  PMID:15663930
    • Recht, M. I., Williamson, J. R. RNA tertiary structure and cooperative assembly of a large ribonucleoprotein complex Journal of Molecular Biology  2004 344:395-407  DOI:10.1016/j.jmb.2004.09.009  PMID:15522293
    • Scott, L. G., Geierstanger, B. H., Williamson, J. R., Hennig, M. Enzymatic synthesis and 19F NMR studies of 2-fluoroadenine-substituted RNA Journal of the American Chemical Society  2004 126:11776-11777  DOI:10.1021/ja047556x  PMID:15382896
    • Ryder, S. P., Williamson, J. R. Specificity of the STAR/GSG domain protein Qk1: implications for the regulation of myelination RNA-a Publication of the RNA Society  2004 10:1449-1458  DOI:10.1261/rna.7780504  PMID:15273320  PMCID:PMC1370631
    • Chao, J. A., Williamson, J. R. Joint X-ray and NMR refinement of the yeast L30e-mRNA complex Structure  2004 12:1165-1176  DOI:10.1016/j.str.2004.04.023  PMID:15242593
    • Torres, F. E., Kuhnt, P., De Bruyker, D., Bell, A. G., Wolkin, M. V., Peeters, E., Williamson, J. R., Anderson, G. B., Schmitz, G. P., Recht, M. I., Schweizer, S., Scott, L. G., et al. Enthalpy arrays Proceedings of the National Academy of Sciences of the United States of America  2004 101:9517-9522  DOI:10.1073/pnas.0403573101  PMID:15210951  PMCID:PMC470707
    • Klostermeier, D., Sears, P., Wong, C. H., Millar, D. P., Williamson, J. R. A three-fluorophore FRET assay for high-throughput screening of small-molecule inhibitors of ribosome assembly Nucleic Acids Research  2004 32:2707-2715  DOI:10.1093/nar/gkh588  PMID:15148358  PMCID:PMC419595
    • Ryder, S. P., Frater, L. A., Abramovitz, D. L., Goodwin, E. B., Williamson, J. R. RNA target specificity of the STAR/GSG domain post-transcriptional regulatory protein GLD-1 Nature Structural & Molecular Biology  2004 11:20-28  DOI:10.1038/nsmb706  PMID:14718919
    • Johnson, E. C., Feher, V. A., Peng, J. W., Moore, J. M., Williamson, J. R. Application of NMR SHAPES screening to an RNA target Journal of the American Chemical Society  2003 125:15724-15725  DOI:10.1021/ja037499s  PMID:14677945
    • Gonsalvez, G. B., Lehmann, K. A., Ho, D. K., Stanitsa, E. S., Williamson, J. R., Long, R. M. RNA-protein interactions promote asymmetric sorting of the ASH1 mRNA ribonucleoprotein complex RNA-a Publication of the RNA Society  2003 9:1383-1399  DOI:10.1261/rna.5120803  PMID:14561888  PMCID:PMC1287060
    • Cilley, C. D., Williamson, J. R. Structural mimicry in the phage phi 21 N peptide-boxB RNA complex RNA-a Publication of the RNA Society  2003 9:663-676  DOI:10.1261/rna.2189203  PMID:12756325  PMCID:PMC1370434
    • Hoggan, D. B., Chao, J. A., Prasad, G. S., Stout, C. D., Williamson, J. R. Combinatorial crystallization of an rna-protein complex Acta Crystallographica Section D-Biological Crystallography  2003 59:466-473  DOI:10.1107/s0907444902023399  PMID:12595703
    • Chao, J. A., Prasad, G. S., White, S. A., Stout, C. D., Williamson, J. R. Inherent protein structural flexibility at the RNA-binding interface of L30e Journal of Molecular Biology  2003 326:999-1004  DOI:10.1016/s0022-2836(02)01476-6  PMID:12589748
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    • Kim, H. D., Nienhaus, G. U., Ha, T., Orr, J. W., Williamson, J. R., Chu, S. Mg2+-dependent conformational change of RNA studied by fluorescence correlation and FRET on immobilized single molecules Proceedings of the National Academy of Sciences of the United States of America  2002 99:4284-4289  DOI:10.1073/pnas.032077799  PMID:11929999  PMCID:PMC123640
    • Dayie, K. T., Brodsky, A. S., Williamson, J. R. Base flexibility in HIV-2 TAR RNA mapped by solution (15)N, (13)C NMR relaxation Journal of Molecular Biology  2002 317:263-278  DOI:10.1006/jmbi.2001.5424  PMID:11902842
    • Carlomagno, T., Hennig, M., Williamson, J. R. A novel PH-cT-COSY methodology for measuring JPH coupling constants in unlabeled nucleic acids. Application to HIV-2 TAR RNA Journal of Biomolecular NMR  2002 22:65-81  DOI:10.1023/a:1013811631477  PMID:11885982
    • Tang, K., Shahgholi, M., Garcia, B. A., Heaney, P. J., Cantor, C., Scott, L. G., Williamson, J. R. Improvement in the apparent mass resolution of oligonucleotides by using 12C/14N-enriched samples Analytical Chemistry  2002 74:226-231  DOI:10.1021/ac010804c  PMID:11795798
    • Scott, L. G., Williamson, J. R. Interaction of the Bacillus stearothermophilus ribosomal protein S15 with its 5 '-translational operator mRNA Journal of Molecular Biology  2001 314:413-422  DOI:10.1006/jmbi.2001.5165  PMID:11846555
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    • Treiber, D. K., Williamson, J. R. Beyond kinetic traps in RNA folding Current Opinion in Structural Biology  2001 11:309-314  DOI:10.1016/s0959-440x(00)00206-2  PMID:11406379
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    • Hennig, M., Carlomagno, T., Williamson, J. R. Residual dipolar coupling TOCSY for direct through space correlations of base protons and phosphorus nuclei in RNA Journal of the American Chemical Society  2001 123:3395-3396  DOI:10.1021/ja005835o  PMID:11457087
    • Treiber, D. K., Williamson, J. R. Concerted kinetic folding of a multidomain ribozyme with a disrupted loop-receptor interaction Journal of Molecular Biology  2001 305:11-21  DOI:10.1006/jmbi.2000.4253  PMID:11114243
    • Guo, Y. L., Kang, B. B., Han, J. H., Williamson, J. R. P38 beta MAP kinase protects rat mesangial cells from TNF-alpha-induced apoptosis Journal of Cellular Biochemistry  2001 82:556-565  DOI:10.1002/jcb.1180  PMID:11500933
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    • Williamson, J. R. Induced fit in RNA-protein recognition Nature Structural Biology  2000 7:834-837  DOI:10.1038/79575  PMID:11017187
    • Williamson, J. R. Molecular biology: Small subunit, big science Nature  2000 407:306-307  DOI:10.1038/35030271  PMID:11014170
    • Agalarov, S. C., Prasad, G. S., Funke, P. M., Stout, C. D., Williamson, J. R. Structure of the S15,S6,S18-rRNA complex: assembly of the 30S ribosome central domain Science  2000 288:107-112  DOI:10.1126/science.288.5463.107  PMID:10753109
    • Hennig, M., Williamson, J. R. Detection of N-H...N hydrogen bonding in RNA via scalar couplings in the absence of observable imino proton resonances Nucleic Acids Research  2000 28:1585-1593  DOI:10.1093/nar/28.7.1585  PMID:10710425  PMCID:PMC102791
    • Agalarov, S. C., Williamson, J. R. A hierarchy of RNA subdomains in assembly of the central domain of the 30 S ribosomal subunit RNA-a Publication of the RNA Society  2000 6:402-408  DOI:10.1017/s1355838200991945  PMID:10744024  PMCID:PMC1369922
    • Treiber, D. K., Williamson, J. R. Kinetic oligonucleotide hybridization for monitoring kinetic folding of large RNAs Methods in Enzymology  2000 317:330-353  DOI:10.1016/S0076-6879(00)17023-5  PMID:10829289
    • Scott, L. G., Tolbert, T. J., Williamson, J. R. Preparation of specifically 2H- and 13C-labeled ribonucleotides Methods in Enzymology  2000 317:18-38  DOI:10.1016/S0076-6879(00)17004-1  PMID:10829270
    • Mao, H. Y., White, S. A., Williamson, J. R. A novel loop-loop recognition motif in the yeast ribosomal protein L30 autoregulatory RNA complex Nature Structural Biology  1999 6:1139-1147  DOI:10.1038/70081  PMID:10581556
    • Rook, M. S., Treiber, D. K., Williamson, J. R. An optimal Mg(2+) concentration for kinetic folding of the tetrahymena ribozyme Proceedings of the National Academy of Sciences of the United States of America  1999 96:12471-12476  DOI:10.1073/pnas.96.22.12471  PMID:10535946
    • Mao, H. Y., Williamson, J. R. Assignment of the L30-mRNA complex using selective isotopic labeling and RNA mutants Nucleic Acids Research  1999 27:4059-4070  DOI:10.1093/nar/27.20.4059  PMID:10497271  PMCID:PMC148674
    • Mao, H. Y., Williamson, J. R. Local folding coupled to RNA binding in the yeast ribosomal protein L30 Journal of Molecular Biology  1999 292:345-359  DOI:10.1006/jmbi.1999.3044  PMID:10493880
    • Ha, T., Zhuang, X. W., Kim, H. D., Orr, J. W., Williamson, J. R., Chu, S. Ligand-induced conformational changes observed in single RNA molecules Proceedings of the National Academy of Sciences of the United States of America  1999 96:9077-9082  DOI:10.1073/pnas.96.16.9077  PMID:10430898  PMCID:PMC17735
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    • Zamore, P. D., Bartel, D. P., Lehmann, R., Williamson, J. R. The PUMILIO-RNA interaction: a single RNA-binding domain monomer recognizes a bipartite target sequence Biochemistry  1999 38:596-604  DOI:10.1021/bi982264s  PMID:9888799
    • Cilley, C. D., Williamson, J. R. PACE analysis of RNA-peptide interactions Methods in Molecular Biology  1999 118:129-141  DOI:10.1385/1-59259-676-2:129  PMID:10549520
    • Rook, M. S., Treiber, D. K., Williamson, J. R. Fast folding mutants of the Tetrahymena group I ribozyme reveal a rugged folding energy landscape Journal of Molecular Biology  1998 281:609-620  DOI:10.1006/jmbi.1998.1960  PMID:9710534
    • Batey, R. T., Williamson, J. R. Effects of polyvalent cations on the folding of an rRNA three-way junction and binding of ribosomal protein S15 RNA-a Publication of the RNA Society  1998 4:984-997  DOI:10.1017/s1355838298980426  PMID:9701289  PMCID:PMC1369675
    • Brodsky, A. S., Erlacher, H. A., Williamson, J. R. NMR evidence for a base triple in the HIV-2 TAR C-G.C+ mutant-argininamide complex Nucleic Acids Research  1998 26:1991-1995  DOI:10.1093/nar/26.8.1991  PMID:9518494  PMCID:PMC147484
    • Treiber, D. K., Rook, M. S., Zarrinkar, P. P., Williamson, J. R. Kinetic intermediates trapped by native interactions in RNA folding Science  1998 279:1943-1946  DOI:10.1126/science.279.5358.1943  PMID:9506945
    • Orr, J. W., Hagerman, P. J., Williamson, J. R. Protein and Mg(2+)-induced conformational changes in the S15 binding site of 16 S ribosomal RNA Journal of Molecular Biology  1998 275:453-464  DOI:10.1006/jmbi.1997.1489  PMID:9466923
    • Dayie, K. T., Tolbert, T. J., Williamson, J. R. 3D C(CC)H TOCSY experiment for assigning protons and carbons in uniformly 13C- and selectively 2H-labeled RNA Journal of Magnetic Resonance  1998 130:97-101  DOI:10.1006/jmre.1997.1286  PMID:9469903
    • Tolbert, T. J., Williamson, J. R. Preparation of specifically deuterated and 13C-labeled RNA for NMR studies using enzymatic synthesis Journal of the American Chemical Society  1997 119:12100-12108  DOI:10.1021/ja9725054
    • Zamore, P. D., Williamson, J. R., Lehmann, R. The Pumilio protein binds RNA through a conserved domain that defines a new class of RNA-binding proteins RNA-a Publication of the RNA Society  1997 3:1421-1433  PMID:9404893  PMCID:PMC1369583
    • Sun, B. Q., Rienstra, C. M., Costa, P. R., Williamson, J. R., Griffin, R. G. 3D 15N−13C−13C chemical shift correlation spectroscopy in rotating solids Journal of the American Chemical Society  1997 119:8540-8546  DOI:10.1021/ja970073r
    • Brodsky, A. S., Williamson, J. R. Solution structure of the HIV-2 TAR-argininamide complex Journal of Molecular Biology  1997 267:624-639  DOI:10.1006/jmbi.1996.0879  PMID:9126842
    • Curtis, D., Treiber, D. K., Tao, F., Zamore, P. D., Williamson, J. R., Lehmann, R. A CCHC metal-binding domain in Nanos is essential for translational regulation EMBO Journal  1997 16:834-843  DOI:10.1093/emboj/16.4.834  PMID:9049312  PMCID:PMC1169684
    • Cilley, C. D., Williamson, J. R. Analysis of bacteriophage N protein and peptide binding to boxB RNA using polyacrylamide gel coelectrophoresis (PACE) RNA-a Publication of the RNA Society  1997 3:57-67  PMID:8990399  PMCID:PMC1369462
    • Lee, S., Williamson, J., Lothman, E. W., Szele, F. G., Chesselet, M. F., VonHagen, S., Sapolsky, R. M., Mattson, M. P., Christakos, S. Early induction of mrna for calbindin-d-28k and bdnf but not nt-3 in rat hippocampus after kainic acid treatment Molecular Brain Research  1997 47:183-194  DOI:10.1016/s0169-328x(97)00043-0  PMID:9221916
    • Tan, R. Y., Brodsky, A., Williamson, J. R., Frankel, A. D. RNA recognition by HIV-1 Tat and Rev Seminars in Virology  1997 8:186-193  DOI:10.1006/smvy.1997.0121
    • Batey, R. T., Cloutier, N., Mao, H. Y., Williamson, J. R. Improved large scale culture of Methylophilus methylotrophus for 13C/15N labeling and random fractional deuteration of ribonucleotides Nucleic Acids Research  1996 24:4836-4837  DOI:10.1093/nar/24.23.4836  PMID:8972874  PMCID:PMC146305
    • Rao, N. S., Legault, P., Muhandiram, D. R., Greenblatt, J., Battiste, J. L., Williamson, J. R., Kay, L. E. NMR pulse schemes for the sequential assignment of arginine side-chain H-epsilon protons Journal of Magnetic Resonance Series B  1996 113:272-276  DOI:10.1006/jmrb.1996.0188  PMID:8995846
    • Battiste, J. L., Mao, H. Y., Rao, N. S., Tan, R. Y., Muhandiram, D. R., Kay, L. E., Frankel, A. D., Williamson, J. R. Alpha helix-RNA major groove recognition in an HIV-1 rev peptide-RRE RNA complex Science  1996 273:1547-1551  DOI:10.1126/science.273.5281.1547  PMID:8703216
    • Tolbert, T. J., Williamson, J. R. Preparation of specifically deuterated RNA for NMR studies using a combination of chemical and enzymatic synthesis Journal of the American Chemical Society  1996 118:7929-7940  DOI:10.1021/ja961274i
    • Williamson, J. R. Aptly named aptamers display their aptitude Nature  1996 382:112-113  DOI:10.1038/382112a0  PMID:8700196
    • Zarrinkar, P. P., Wang, J., Williamson, J. R. Slow folding kinetics of RNase P RNA RNA-a Publication of the RNA Society  1996 2:564-573  PMID:8718685  PMCID:PMC1369395
    • Zarrinkar, P. P., Williamson, J. R. The kinetic folding pathway of the Tetrahymena ribozyme reveals possible similarities between RNA and protein folding Nature Structural Biology  1996 3:432-438  DOI:10.1038/nsb0596-432  PMID:8612073
    • Zarrinkar, P. P., Williamson, J. R. The P9.1-P9.2 peripheral extension helps guide folding of the Tetrahymena ribozyme Nucleic Acids Research  1996 24:854-858  DOI:10.1093/nar/24.5.854  PMID:8600452  PMCID:PMC145724
    • Batey, R. T., Williamson, J. R. Interaction of the Bacillus stearothermophilus ribosomal protein S15 with 16 S rRNA: I. Defining the minimal RNA site Journal of Molecular Biology  1996 261:536-549  DOI:10.1006/jmbi.1996.0481  PMID:8794875
    • Batey, R. T., Williamson, J. R. Interaction of the Bacillus stearothermophilus ribosomal protein S15 with 16 S rRNA: II. Specificity determinants of RNA-protein recognition Journal of Molecular Biology  1996 261:550-567  DOI:10.1006/jmbi.1996.0482  PMID:8794876
    • Battiste, J. L., Tan, R. Y., Frankel, A. D., Williamson, J. R. Assignment and modeling of the Rev Response Element RNA bound to a Rev peptide using 13C-heteronuclear NMR Journal of Biomolecular NMR  1995 6:375-389  DOI:10.1007/BF00197637  PMID:8563466
    • Treiber, D. K., Williamson, J. R. A simple method for preparing pools of synthetic oligonucleotides with random point deletions Nucleic Acids Research  1995 23:3603-3604  DOI:10.1093/nar/23.17.3603  PMID:7567476  PMCID:PMC307244
    • Batey, R. T., Battiste, J. L., Williamson, J. R. Preparation of isotopically enriched RNAs for heteronuclear NMR Methods in Enzymology  1995 261:300-322  DOI:10.1016/S0076-6879(95)61015-4  PMID:8569501  PMCID:PMC8569501
    • Puglisi, E. V., Puglisi, J. D., Williamson, J. R., Rajbhandary, U. L. NMR analysis of tRNA acceptor stem microhelices: discriminator base change affects tRNA conformation at the 3' end Proceedings of the National Academy of Sciences of the United States of America  1994 91:11467-11471  DOI:10.1073/pnas.91.24.11467  PMID:7972085  PMCID:PMC45252
    • Zarrinkar, P. P., Williamson, J. R. Kinetic intermediates in RNA folding Science  1994 265:918-924  DOI:10.1126/science.8052848  PMID:8052848
    • Dias, E., Battiste, J. L., Williamson, J. R. Chemical probe for glycosidic conformation in telomeric DNAs Journal of the American Chemical Society  1994 116:4479-4480  DOI:10.1021/ja00089a048
    • Williamson, J. R. RNA origami Nature Structural Biology  1994 1:270-272  DOI:10.1038/nsb0594-270  PMID:7545071
    • Battiste, J. L., Tan, R. Y., Frankel, A. D., Williamson, J. R. Binding of an HIV Rev peptide to Rev responsive element RNA induces formation of purine-purine base pairs Biochemistry  1994 33:2741-2747  DOI:10.1021/bi00176a001  PMID:8130185
    • Williamson, J. R. G-quartet structures in telomeric DNA Annual Review of Biophysics and Biomolecular Structure  1994 23:703-730  DOI:10.1146/annurev.bb.23.060194.003415  PMID:7919797
    • Williamson, J. R. Guanine quartets Current Opinion in Structural Biology  1993 3:357-362  DOI:10.1016/s0959-440x(05)80106-x
    • Puglisi, J. D., Chen, L., Frankel, A. D., Williamson, J. R. Role of RNA structure in arginine recognition of TAR RNA Proceedings of the National Academy of Sciences of the United States of America  1993 90:3680-3684  DOI:10.1073/pnas.90.8.3680  PMID:7682716  PMCID:PMC46365
    • Batey, R. T., Inada, M., Kujawinski, E., Puglisi, J. D., Williamson, J. R. Preparation of isotopically labeled ribonucleotides for multidimensional NMR spectroscopy of RNA Nucleic Acids Research  1992 20:4515-4523  DOI:10.1093/nar/20.17.4515  PMID:1383928  PMCID:PMC334179
    • Puglisi, J. D., Tan, R. Y., Calnan, B. J., Frankel, A. D., Williamson, J. R. Conformation of the TAR RNA-arginine complex by NMR spectroscopy Science  1992 257:76-80  DOI:10.1126/science.1621097  PMID:1621097
    • Carey, G., Williamson, J. Linkage analysis of quantitative traits - increased power by using selected samples American Journal of Human Genetics  1991 49:786-796  PMID:1897525  PMCID:PMC1683186
    • Zahler, A. M., Williamson, J. R., Cech, T. R., Prescott, D. M. Inhibition of telomerase by G-quartet DNA structures Nature  1991 350:718-720  DOI:10.1038/350718a0  PMID:2023635
    • Williamson, J. R., Celander, D. W. Rapid procedure for chemical sequencing of small oligonucleotides without ethanol precipitation Nucleic Acids Research  1990 18:379-379  DOI:10.1093/nar/18.2.379  PMID:2183187  PMCID:PMC330294
    • Eimer, W., Williamson, J. R., Boxer, S. G., Pecora, R. Characterization of the overall and internal dynamics of short oligonucleotides by depolarized dynamic light scattering and NMR relaxation measurements Biochemistry  1990 29:799-811  DOI:10.1021/bi00455a030  PMID:2337597
    • Williamson, J. R., Raghuraman, M. K., Cech, T. R. Monovalent cation-induced structure of telomeric DNA: the G-quartet model Cell  1989 59:871-880  DOI:10.1016/0092-8674(89)90610-7  PMID:2590943
    • Williamson, J. R., Boxer, S. G. Multinuclear NMR studies of DNA hairpins. 1. Structure and dynamics of d(CGCGTTGTTCGCG) Biochemistry  1989 28:2819-2831  DOI:10.1021/bi00433a012  PMID:2742814
    • Williamson, J. R., Boxer, S. G. Multinuclear NMR studies of DNA hairpins. 2. Sequence-dependent structural variations Biochemistry  1989 28:2831-2836  DOI:10.1021/bi00433a013  PMID:2742815
    • Williamson, J. R., Boxer, S. G. Synthesis of a thymidine phosphoramidite labelled with 13C at C6: relaxation studies of the loop region in a 13C labelled DNA hairpin Nucleic Acids Research  1988 16:1529-1540  DOI:10.1093/nar/16.4.1529  PMID:3347496
  • thesis

    • Multinuclear NMR studies of the structure and dynamics of DNA hairpins 1988

featured in

  • James Williamson Elected to American Academy of Arts and Sciences  Newsletter
  • Jeffery Kelly, Jamie Williamson Assume New Leadership Roles  Newsletter
  • Scripps Research Scientists Win $65 Million in New Grants  Newsletter
  • Team "Watches" Formation of Cells' Protein Factories For First Time  Newsletter
  • The Scripps Research Institute Recruits Prominent Scientists to Join its Ranks  News Release
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Research

research overview

  • RNA Structure and RNP-Assembly

    The goal of my research program is to understand the structural role of RNA in mediating its many biological functions. We are interested in the 3-dimensional architecture of RNA, recognition of RNA by proteins, and the process by which RNAs fold into their complex structures. Experimentally, we apply a wide range of biochemical and biophysical methods to characterize specific model systems to obtain insights into how RNA structure contributes to RNA function.

    Ribosome Assembly.  We are using a multidisciplinary approach to study the dynamics of ribosome assembly, both in vitro and in cells.  In order to measure the kinetics of ribosomal protein binding in vitro, we developed an isotope pulse-chase method using quantitative mass spectrometry.  This approach allows us to measure the rate of ribosomal protein binding under a variety of conditions to interrogate the mechanism of assembly.  In addition, we are using single molecule fluoresence methods, in collaboration with David Millar's laboratory, to measure cooperativity in ribosome protein binding using Fluorescence Correlation Spectrocopy.  We are collaboratting with Clint Potter, Bridget Carragher and Ron Milligan's laboratory to determine the structure of ribosome assembly intermediates using time-resolved electron microscopy.  Finally, we are using isotope pulse experiments in conjunction with quantitative proteomic mass spectrometry to monitor the dynamics of ribosome assembly in cells.

    RNPs regulating C. elegans germline development.  We are using a biochemical and structural biology approach to determine the structure of RNA-protein complexes that regulate stem cell differentiation in the model organism C. elegans.  RNA binding proteins regulate many essential genes in this process by binding to 3'untranslated regions of the mRNA.  We are using X-ray crystallography to determine the structures of these multicomponent ribonucleoprotein complexes to learn how they regulate gene expression.

    Regulation of T-cell activation by RNA binding proteins.  We are collaborating with Dan Salomon's laboratory to study how RNA binding proteins regulation the activation of T-cells.  We are using a structural genomics approach to determine the structure of RNA binding proteins, protein-protein complexes, and RNA-protein complexes that are implicated in regulating T-cell activation. 

    Helicases involved in HIV Replication.  We are studying a set of helicases that are implicated in the function of the HIV Rev protein, which is important for transport of unspliced viral mRNAs from the nucleus to the cytoplasm.  Helicases are ATP-dependent RNA binding motors that are implicated in strand displacement and protein displacement reactions in many cellular processes, however, their specific role in HIV replication is not known.  We are taking a biochemical and X-ray crystallographic approach to understand how these helicases participate in key steps of the life cycle of HIV.

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Teaching

advisees

  • faculty mentoring relationship

    • Silverman, Joshua Max, Ph.D.  candidate, 2010 - 2016
  • graduate advising relationship

    • Deng, Yisong, Ph.D.  candidate, 2015 -
    • Chen, Stephen Suo, 2007 - 2012
    • Wu, Joann, Ph.D.  candidate, 2006 - 2012
    • Ridgeway, William, Ph.D.  candidate, 2004 - 2011
    • Bunner, Anne Elizabeth, Ph.D.  candidate, 2003 - 2009
    • Kerkow, Donald, Ph.D.  candidate, 2004 - 2009
    • Chao, Jeffrey Alan, Ph.D.  candidate, 2000 - 2005
    • Trevathan, Megan, Ph.D.  candidate, 1998 - 2004
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Background

education and training

  • Ph.D. in Organic Chemistry, Stanford University , with Dr. Steven G. Boxer 1981 - 1988
  • B.S. in Chemistry, Mount Union College 1977 - 1981

awards and honors

  • Fellow of the American Academy of Arts and Sciences, conferred by American Academy of Arts & Sciences, 2010
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Contact

full name

  • James R. Williamson

geographic location

  • Scripps California 
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Identity

ORCID iD

  • ORCID iD http://orcid.org/0000-0002-8772-468X

eRA Commons ID

  • jrwill

ResearcherID (Thomson Reuters)

  • B-2891-2009

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