Publications

See PubMed for a recent list of publications.

2014

  1. Vlasblom, J., Zuberi, K., Rodriguez, H., Arnold, R., Gagarinova, A., Deineko, V., Leung, E., Samanfar, B., Chang, L., Phanse, S., Golshani, A., Greenblatt, J., Houry, W. A., Emili, A., Morris, Q., Bader, G., & Babu, M. “Novel function discovery with GeneMANIA: a new integrated resource for gene function prediction in Escherichia coli” accepted in Bioinformatics (2014).
  2. Goodreid, J. D., Wong, K., Leung, E., McCaw, S. E., Gray-Owen, S. D., Lough, A., Houry, W. A., & Batey, R. A. “Total Synthesis and Antibacterial Testing of the A54556 Cyclic Acyldepsipeptides Isolated from Streptomyces hawaiiensis” Journal of Natural Products 77(10), 2170−2181 (2014).
  3. Malet, H., Liu, K., El Bakkouri, M., Chan, S. W. S., Effantin, G., Bacia, M., Houry*, W. A., & Gutsche*, I. “Assembly Principles of a Unique Cage Formed by Hexameric and Decameric E. coli Proteins” eLife 3: e03653, 1-11. doi: 10.7554/eLife.03653 (2014). *Co-corresponding authors.
  4. Kakihara, Y., Makhnevych, T., Zhao, L., Tang, W., & Houry, W. A. “Nutritional Status Modulates Box C/D snoRNP Biogenesis by Regulated Subcellular Relocalization of the R2TP Complex” Genome Biology 15(7): 404, 1-20 (2014).
  5. Babu, M, Arnold, R., Bundalovic-Torma, C., Gagarinova, A., Wong, K. S., Kumar, A., Stewart, G., Samanfar, B., Aoki, H., Wagih, O., Vlasblom, J., Phanse, S., Lad, K., Yu, A. Y. H., Graham, C., Jin, K., Brown, E., Golshani, A., Kim, P., Moreno-Hagelsieb, G., Greenblatt, J., Houry, W. A., Parkinson, J., & Emili, A. “Quantitative Genome-Wide Genetic Interaction Screens Reveal Global Epistatic Relationships of Protein Complexes in Escherichia coli” PLOS Genetics 10(2): e1004120, 1-15. doi: 10.1371/journal.pgen.1004120 (2014).
  6. Wong, K. S., Snider, J. D., Graham, C., Greenblatt, J. F., Emili, A., Babu, M., & Houry, W. A. “The MoxR ATPase RavA and its Cofactor ViaA Interact with the NADH:Ubiquinone Oxidoreductase I in Escherichia coli” PLOS ONE 9(1): e85529, 1-15. doi:10.1371/journal.pone.0085529 (2014).
  7. Liu, K., Ologbenla, A., & Houry, W. A. “Dynamics of the ClpP Serine Protease: A Model for Self-Compartmentalized Proteases” Critical Reviews in Biochemistry and Molecular Biology 49(5), 400-412 (2014).
  8. Rizzolo, K., Wong, P., Tillier, E. R. M., & Houry, W. A. “The Interaction Network of the Hsp90 Molecular Chaperone” in the book Interactomics & Systems Biology: The Molecular Chaperones Interaction Networks in Protein Folding and Degradation, Walid A. Houry (Editor). Springer Science + Business Media New York (2014). DOI 10.1007/978-1-4939-1130-1_5.
  9. Liu, K. & Houry, W. A. “Chaperones and Proteases of Plasmodium falciparum” in the book Heat Shock Proteins of Malaria, Addmore Shonhai and Gregory L. Blatch (Editors). Springer Science + Business Media Dordrecht (2014).

 

2013

  1. Kamano, Y., Saeki, M., Egusa, H., Kakihara, Y., Houry, W. A., Yatani, H., & Kamisaki, Y. “PIH1D1 Interacts with mTOR Complex 1 and Enhances Ribosome RNA Transcription” FEBS Letters 587(20), 3303-3308 (2013).
  2. Saeki, M., Egusa, H., Kamano, Y., Kakihara, Y., Houry, W. A., Yatani, H., Noguchi, S., & Kamisaki, Y. “Exosome-Bound WD Repeat Protein Monad Inhibits Breast Cancer Cell Invasion by Degrading Amphiregulin mRNA” PLOS ONE 8(7): e67326, 1-11. doi:10.1371/journal.pone.0067326 (2013).
  3. El Bakkouri, M., Rathore, S., Calmettes, C., Wernimont, A. K., Liu, K., Sinha, D., Asad, M., Jung, P., Hui, R., Mohmmed, A., & Houry, W. A. “Structural Insights into the Inactive Subunit of the Apicoplast-Localized Caseinolytic Protease Complex of Plasmodium falciparum” The Journal of Biological Chemistry 288(2), 1022-1031 (2013).
  4. Kanjee, U. & Houry, W. A. “Mechanisms of Acid Resistance in Escherichia coli” Annual Review of Microbiology 67, 65-81 (2013).
  5. Makhnevych, T. & Houry, W. A. “The Control of Spindle Length by Hsp70 and Hsp110 Molecular Chaperones” FEBS Letters 587(8), 1067-1072 (2013).
  6. Nano, N. & Houry, W. A. “Chaperone-Like Activity of the AAA+ Proteins Rvb1 and Rvb2 in the Assembly of Various Complexes” Philosophical Transactions of the Royal Society B 368(1617):20110399, 1-12. doi: 10.1098/rstb.2011.0399 (2013).
  7. Rosenbaum, J., Baek, S. H., Dutta, A., Houry, W. A., Huber, O., Hupp, T. R., & Matias, P. M. “The Emergence of the Conserved AAA+ ATPases Pontin and Reptin on the Signaling Landscape” Science Signaling 6(266) mr1, 1-6 (2013).

 

2012

  1. Paci, A., Liu, X. H., Huang, H., Lim, A., Houry, W. A., & Zhao, R. “The Stability of the Small Nucleolar Ribonucleoprotein (snoRNP) Assembly Protein Pih1 in Saccharomyces cerevisiae is Modulated by its C-Terminus” The Journal of Biological Chemistry 287(52), 43205–43214 (2012).
  2. Makhnevych, T., Wong, P., Pogoutse, O., Vizeacoumar, F. J., Greenblatt, J. F., Emili, A., & Houry, W. A. “Hsp110 is Required for Spindle Length Control” Journal of Cell Biology 198(4), 623-636 (2012).
  3. Thibault, G. & Houry, W. A. “The Role of the N-Terminal Domain of the Chaperone ClpX in the Recognition and Degradation of Lambda Phage Protein O” The Journal of Physical Chemistry B 6(23), 6717-6724 (2012).
  4. Jiméneza, B., Ugwu, F., Zhao, R., Ortía, L., Makhnevych, T., Pineda-Lucena, A., & Houry, W. A. “The Structure of the Minimal TPR Domain Protein Tah1 Reveals the Mechanism of Its Interaction with Pih1 and Hsp90″ The Journal of Biological Chemistry 287(8), 5698-5709 (2012).
  5. Kanjee, U., Ogata, K., & Houry, W. A. “Direct Binding Targets of the Stringent Response Alarmone (p)ppGpp” Molecular Microbiology 85(6), 1029-1043 (2012).
  6. Wong, K. S. & Houry, W. A. “Novel Structural and Functional Insights into the MoxR Family of AAA+ ATPases” Journal of Structural Biology 179(2), 211-221 (2012).
  7. Makhnevych, T. & Houry, W. A. “The Role of Hsp90 in Protein Complex Assembly” Biochimica et Biophysica Acta – Molecular Cell Research 1823(3), 674-682 (2012).
  8. Kakihara, Y. & Houry, W. A. “The R2TP Complex: Discovery and Functions” Biochimica et Biophysica Acta – Molecular Cell Research 1823(1), 101-107 (2012).
  9. Houry, W. A. “Mapping the Molecular Chaperone Interaction Network in Yeast” (http://hstalks.com/lib.php?t=HST142.3170_1_2&c=252), in The Biomedical & Life Sciences Collection, Henry Stewart Talks Series on “Protein Homeostasis” (http://hstalks.com/main/browse_talks.php?father_id=641&c=252). Walid A. Houry, Editor (2012). Henry Stewart Talks Ltd, London.

 

2011

  1. Kanjee, U., Gutsche, I., Ramachandran, S., & Houry, W. A. “Regulation of the activity of the Escherichia coli basic aliphatic amino acid decarboxylases by nucleotides and oligomerization reveals the presence of a pH zone of inhibition” Biochemistry 50(43), 9388-9398 (2011).
  2. Leung, E., Datti, A., Cossette, M., Goodreid, J., McCaw, S. E., Mah, M., Nakhamchik, A., Ogata, K., El Bakkouri, M., Cheng, Y.-Q., Wodak, S. J., Eger, B. T., Pai, E. F., Liu, J., Gray-Owen, S., Batey, R. A., & Houry, W. A. “Activators of Cylindrical Proteases as Antimicrobials: Identification and Development of Novel Small Molecule Activators of the ClpP Protease” Chemistry & Biology 18(9), 1167–1178 (2011).
  3. Kanjee, U., Gutsche, I., Alexopoulos, E., Zhao, B., El Bakkouri, M., Thibault, G., Liu, K., Ramachandran, S., Snider, J., Pai, E. F., & Houry, W. A. “Linkage between the Bacterial Acid Stress and Stringent Responses Revealed by the Structure of the Inducible Lysine Decarboxylase” The EMBO Journal 30(5), 931-944 (2011).
  4. Gong, Y, Zhang, Z., & Houry. W. A. “Bioinformatic Approach to Identify Chaperone Pathway Relationship from Large-Scale Interaction Networks” Methods in Molecular Biology 787, 189-203 (2011).

2010

  1. El Bakkouri, M., Gutsche, I., Kanjee, U., Zhao, B., Yu, M., Goret, G., Schoehn, G., Burmeister, W. P., & Houry, W. A. “Structure of RavA MoxR AAA+ Protein Reveals the Design Principles of a Molecular Cage Modulating the Inducible Lysine Decarboxylase Activity” Proceedings of the National Academy of Sciences 107(52), 22499-22504 (2010).
  2. Cheung, K. L. Y., Huen, J., Kakihara, Y., Houry, W. A., & Ortega, J. “Alternative Oligomeric States of the Yeast Rvb1/Rvb2 Complex Induced by Histidine Tags” Journal of Molecular Biology 404(3), 478-492 (2010).
  3. El Bakkouri, M., Pow, A., Mulichak, A., Cheung, K. L. Y., Artz, J. D., Amani, M., Fell, S., de Koning-Ward, T. F., Goodman, C. D., McFadden, G. I., Ortega, J., Hui, R., & Houry, W. A. “The Clp Chaperones and Proteases of the Human Malaria Parasite Plasmodium falciparum” Journal of Molecular Biology 404(3), 456-477 (2010).
  4. Kimber, M. S., Yu, A. Y. H., Borg, M., Chan, H. S., & Houry, W. A. “The Structure of a Disulfide Cross-Linked ClpP Protease: Implications for ClpP Dynamics” Structure 18(7), 798-808 (2010).
  5. Zhao, R., Leung, E., Gruener, S., Schapira, M., & Houry, W. A. “Tamoxifen Enhances the Hsp90 Molecular Chaperone ATPase Activity” PLoS ONE 5(4):e9934, 1-8 (2010).
  6. Costanzo, M., Baryshnikova, A., Bellay, J., Kim, Y., Spear, E. D., Sevier, C. S., Ding, H., Koh, J. L. Y., Toufighi, K., Mostafavi, S., Prinz, J., St. Onge, R. P., VanderSluis, B., Makhnevych, T., Vizeacoumar, F. J., Alizadeh, S., Bahr, S., Brost, R. L., Chen, Y., Cokol, M., Deshpande, R., Li, Z., Li, Z.-Y., Liang, W., Marback, M., Paw, J., San Luis, B.-J., Shuteriqi, E., Tong, A. H. Y., van Dyk, N., Wallace, I. M., Whitney, J. A., Weirauch, M. T., Zhong, G., Zhu, H., Houry, W. A., Brudno, M., Ragibizadeh, S., Papp, B., Pál, C., Roth, F. P., Giaever, G., Nislow, C., Troyanskaya, O. G., Bussey, H., Bader, G. D., Gingras, A.-C., Morris, Q. D., Kim, P. M., Kaiser, C. A., Myers, C. L., Andrews, B. J., & Boone, C. “The Genetic Landscape of a Cell” Science 327(5964), 425-431 (2010).
  7. Kanjee, U. & Houry, W. A. “An Assay for Measuring the Activity of Escherichia coli Inducible Lysine Decarboxyase” http://www.jove.com/details.stp?id=2094 doi: 10.3791/2094 Journal of Visualized Experiments 46 (2010).
  8. Zhao, B. & Houry, W. A. “Acid Stress Response in Enteropathogenic Gammaproteobacteria: An Aptitude for Survival” Biochemistry and Cell Biology 88(2), 301–314 (2010).
  9. Cheung, K., Huen, J., Houry, W. A., & Ortega, J. “Comparison of the Multiple Oligomeric Structures Observed for the Rvb1 and Rvb2 Proteins” Biochemistry and Cell Biology 88(1), 77-88 (2010).
  10. Huen, J., Kakihara, Y., Ugwu, F., Cheung, K. L. Y., Ortega, J., & Houry, W. A. “Rvb1-Rvb2: Essential ATP-Dependent Helicases for Critical Complexes” Biochemistry and Cell Biology 88(1), 29-40 (2010).
  11. Houry, W. A. & Ortega, J. “AAA Proteins: Movers and Shakers” (2010) Biochemistry and Cell Biology 88(1), i-iv (2010).

 

2009

  1. Gong, Y., Kakihara, Y., Krogan, N., Greenblatt, J., Emili, A., Zhang, Z., & Houry, W. A. “An atlas of Chaperone-Protein Interactions in Saccharomyces cerevisiae: Implications to Protein Folding Pathways in the Cell” Molecular Systems Biology 5:275, 1-14 (2009).

 

2008

  1. Alexopoulos, E., Kanjee, U., Snider, J., Houry, W. A., & Pai, E. F. “Crystallization and Preliminary X-ray Analysis of the Inducible Lysine Decarboxylase from Escherichia coli” Acta Crystallographica Section F: Structural Biology and Crystallization Communications 64(8),700-706 (2008).
  2. Gribun, A., Cheung, K. L. Y., Huen, J., Ortega, J., & Houry, W. A. “Yeast Rvb1 and Rvb2 are ATP-Dependent DNA Helicases that Form a Heterohexameric Complex” Journal of Molecular Biology 376(5), 1320-1333 (2008).
  3. Zhao, R., Kakihara, Y., Gribun, A., Huen, J., Yang, G., Khanna, M., Costanzo, M., Brost, R. L., Boone, C., Hughes, T. R., Yip, C. M., & Houry, W. A. “Molecular Chaperone Hsp90 Stabilizes Pih1/Nop17 to Maintain R2TP Complex Activity that Regulates snoRNA Accumulation” Journal of Cell Biology 180(3), 563-578 (2008).
  4. Snider, J., Thibault, G., & Houry, W. A. “The AAA+ superfamily of Functionally Diverse Proteins”, Genome Biology 9(4), article 216, 1-8 (2008).
  5. Snider, J. & Houry, W. A. “AAA+ Proteins: Diversity in Function Similarity in Structure”, Biochemical Society Transactions 36(1), 72-77 (2008).

 

2007

  1. Houry, W. A. “Overview of Prokaryotic Molecular Chaperones” in Henry Stewart Talks Series on “Molecular Chaperones: Principles and Diseases”, http://www.hstalks.com/molchap/index.htm, Walid A. Houry, Editor (2007).
  2. Yu, A. Y.-H., & Houry, W. A. “ClpP: A Distinctive Family of Cylindrical Energy-Dependent Serine Proteases” FEBS Letters 581(19), 3749-3757 (2007).
  3. Zhao, R., & Houry, W. A. “Molecular Interaction Network of the Hsp90 Chaperone System” in Molecular Aspects of the Stress Response: Chaperones, Membranes, and Networks, Peter Csermely and Laszlo Vigh, eds. (Landes Bioscience) – part of the series Advances in Experimental Medicine and Biology, Vol 594 (2007).

 

2006

  1. Thibault, G., Yudin, J., Wong, P., Tsitrin, V., Sprangers, R., Zhao, R., & Houry, W. A. “Specificity in Substrate and Cofactor Recognition by the N-Terminal Domain of the Chaperone ClpX” Proceedings of the National Academy of Sciences 103 (47), 17724-17729 (2006).
  2. Thibault, G., Tsitrin, Y., Davidson, T., Gribun, A., & Houry, W. A. “Large Nucleotide-Dependent Movement of the N-Terminal Domain of the ClpX Chaperone” The EMBO Journal 25 (14), 3367-3376 (2006).
  3. Snider, J., & Houry, W. A. “MoxR AAA+ ATPases: A Novel Family of Molecular Chaperones?” Journal of Structural Biology 156 (1), 200–209 (2006).
  4. Snider, J., Gutsche, I. , Lin, M., Baby, S., Cox, B., Butland, G., Greenblatt, J., Emili, A., & Houry, W. A. “Formation of a Distinctive Complex Between the Inducible Bacterial Lysine Decarboxylase and a Novel AAA+ ATPase” Journal of Biological Chemistry 281(3), 1532-1546 (2006).
  5. Wong, K. S. K., & Houry, W. A. “Hsp90 at the Crossroads of Genetics and Epigenetics” Cell Research 16 (9), 742-749 (2006).

 

2005

  1. Sprangers, R., Gribun, A., Hwang, P. M., Houry, W. A., & Kay , L. E. “Quantitative NMR Spectroscopy of Supramolecular Complexes: Dynamic Side Pores in ClpP are Important for Product Release” Proceedings of the National Academy of Sciences 102(46), 16678-16683 (2005).
  2. Gribun, A., Kimber, M. S., Ching, R., Spranger, R., Fiebig, K. M., & Houry, W. A. “The ClpP Double-Ring Tetradecameric Protease Exhibits Plastic Ring-Ring Interactions and the N-Termini of Its Subunits Form Flexible Loops that are Essential for ClpXP and ClpAP Complex Formation” Journal of Biological Chemistry 280 (16), 16185-16196 (2005).
  3. Zhao, R., & Houry, W. A. “Hsp90: A Chaperone for Protein Folding and Gene Regulation” Biochemistry and Cell Biology 83 (6), 703-710 (2005).
  4. Zhao , R., Davey, M., Hsu , Y.-C., Kaplanek , P., Tong, A., Parsons, A., Cagney, G., Mai, D., Krogan, N., Greenblatt, J., Boone, C., Emili, A., & Houry, W. A. “Navigating the Chaperone Network: An Integrative Map of Physical and Genetic Interactions Mediated by the Hsp90 Chaperone” Cell 120 (5), 715-727 (2005).

 

2004

  1. Wong, P., & Houry, W. A. “Chaperone Networks in Bacteria: Analysis of Protein Homeostasis in Minimal Cells” Journal of Structural Biology 146 (1-2), 79-89 (2004).

 

2003

  1. Donaldson, L. W., Wojtyra, U., & Houry, W. A. “Solution Structure of the Dimeric Zinc Binding Domain of the Chaperone ClpX” Journal of Biological Chemistry 278 (49), 48991-48996 (2003).
  2. Wojtyra, U., Thibault, G., Tuite, A., & Houry, W. A. “The N-Terminal Zinc Binding Domain of ClpX is a Dimerization Domain that Modulates the Chaperone Function” Journal of Biological Chemistry 278 (49), 48981-48990 (2003).
  3. Wong, P., Kolesov, G., Frishman, D., & Houry, W. A. “Phylogenetic Web Profiler” Bioinformatics 19(6), 782-783 (2003).

 

2001

  1. Houry, W. A. “Mechanism of Substrate Recognition by the Chaperonin GroEL” Biochemistry and Cell Biology, 79(5) , 569-577 (2001).
  2. Houry, W. A. “Chaperone-Assisted Protein Folding in the Cell Cytoplasm” Current Protein and Peptide Science, 2(3), 227-244 (2001).

 

1999

  1. Houry, W. A., Frishman, D., Eckerskorn, C., Lottspeich, F., & Hartl, F. U. “Identification of the In Vivo Substrates of the Chaperonin GroEL” Nature 402(11), 147-154 (1999).
  2. Teter, S. A., Houry, W. A., Ang, D., Tradler, T., Rockabrand, D., Fischer, G., Blum, P., Georgopolous, C., & Hartl, F. U. “Polypeptide Flux through Bacterial Hsp70: DnaK Cooperates with Trigger Factor in Chaperoning Nascent Chains” Cell 97(6), 755-765 (1999).

 

1998

  1. Houry, W. A., Sauder, J. M., Roder, H., & Scheraga, H. A. “Definition of Amide Protection Factors for Early Kinetic Intermediates in Protein Folding” Proceedings of the National Academy of Sciences 95(8), 4299-4302 (1998).

 

1997

  1. Ewalt+, K. L., Hendrick+, J. P., Houry+, W. A., & Hartl, F. U. “In vivo Observation of Polypeptide Flux through the Bacterial Chaperonin System” Cell 90(3), 491-500 (1997).
    +These authors contributed equally to this work.

 

1996

  1. Sendak, R. A., Rothwarf, D. M., Wedemeyer, W. J., Houry, W. A., & Scheraga, H. A. “Kinetic and Thermodynamic Studies of the Folding/Unfolding of a Tryptophan-Containing Mutant of Ribonuclease A” Biochemistry 35(39), 12978-12992 (1996).
  2. Houry, W. A., & Scheraga, H. A. “Structure of a Hydrophobically Collapsed Intermediate on the Conformational Folding Pathway of Ribonuclease A Probed by Hydrogen-Deuterium Exchange” Biochemistry 35(36), 11734-11746 (1996).
  3. Houry, W. A., & Scheraga, H. A. “Nature of the Unfolded State of Ribonuclease A: Effect of Cis-Trans X-Pro Peptide Bond Isomerization” Biochemistry 35(36), 11719-11733 (1996).
  4. Houry, W. A., Rothwarf, D. M., & Scheraga, H. A. “Circular Dichroism Evidence for the Presence of Burst-Phase Intermediates on the Conformational Folding Pathway of Ribonuclease A” Biochemistry 35(31), 10125-10133 (1996).

 

1995

  1. Houry, W. A., Rothwarf, D. M., & Scheraga, H. A. “The Nature of the Initial Step in the Conformational Folding of Disulfide-Intact Ribonuclease A” Nature Structural Biology 2(6), 495-503 (1995).

 

1994

  1. Houry, W. A., Rothwarf, D. M., & Scheraga, H. A. “A Very Fast Phase in the Refolding of Disulfide-Intact Ribonuclease A: Implications for the Refolding and Unfolding Pathways” Biochemistry 33(9), 2516-2530 (1994).

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