Crystallization, Structural Determination and Structure Modeling Publications

  1. Suzumoto Y., Dym O., Roviello G. N., Worek F., Sussman J. L. & Manco G. (2020). Structural and functional characterization of new ssopox variant points to the dimer interface as a driver for the increase in promiscuous paraoxonase activity.  International Journal of Molecular Sciences. 2020 Mar 1 , 21 (5).
  2. Warszawski S., Katz A. B., Lipsh R., Khmelnitsky L., Nissan G. B., Javitt G., Dym O., Unger T., Knop O., Albeck S., Diskin R., Fass D., Sharon M. & Fleishman S. J. (2020). Erratum: Optimizing antibody affinity and stability by the automated design of the variable light-heavy chain interfaces (PLoS Computational Biology(2019)15: 8(e1007207)Doi: 10.1371/journal.pcbi.1007207).  PLoS Computational Biology. 2020 Oct 21 , 16 (10).
  3. Ben-David M., Soskine M., Dubovetskyi A., Cherukuri K., Dym O., Sussman J. L., Liao Q., Szeler K., Kamerlin S. C. L. & Tawfik D. S. (2020). Enzyme Evolution: An Epistatic Ratchet versus a Smooth Reversible Transition.  Molecular Biology and Evolution. 2020 Apr , 37 (4):1133-1147.
  4. Arafeh R., Di Pizio A., Elkahloun A. G., Dym O., Niv M. Y. & Samuels Y. (2019). RASA2 and NF1; two-negative regulators of Ras with complementary functions in melanoma.  Oncogene. 2019 Mar 28 , 38 (13):2432-2434.
  5. Warszawski S., Katz A. B., Lipsh R., Khmelnitsky L., Ben Nissan G., Javitt G., Dym O., Unger T., Knop O., Albeck S., Diskin R., Fass D., Sharon M. & Fleishman S. J. (2019). Optimizing antibody affinity and stability by the automated design of the variable light-heavy chain interfaces.  PLoS Computational Biology. 2019 Aug 23 , 15 (8).
  6. Karbat I., Altman-Gueta H., Fine S., Szanto T., Hamer-Rogotner S., Dym O., Frolow F., Gordon D., Panyi G., Gurevitz M. & Reuveny E. (2019). Pore-modulating toxins exploit inherent slow inactivation to block K+ channels.  Proceedings of the National Academy of Sciences of the United States of America. 2019 Sept 10 , 116 (37):18700-18709.
  7. Novichkova D. A., Lushchekina S., Dym O., Masson P., Silman I. & Sussman J. L. (2019). The four-helix bundle in cholinesterase dimers: Structural and energetic determinants of stability.  Chemico-Biological Interactions. 2019 Aug 25 , 309 .
  8. Kantaev R., Riven I., Goldenzweig A., Barak Y., Dym O., Peleg Y., Albeck S., Fleishman S. J. & Haran G. (2018). Manipulating the Folding Landscape of a Multi-Domain Protein.  Journal of Physical Chemistry B. 2018 Dec 13 , 122 (49):11030-11038.
  9. Khersonsky O., Lipsh R., Avizemer Z., Ashani Y., Goldsmith M., Leader H., Dym O., Rogotner S., Trudeau D. L., Prilusky J., Amengual-Rigo P., Guallar V., Tawfik D. S. & Fleishman S. J. (2018). Automated Design of Efficient and Functionally Diverse Enzyme Repertoires.  Molecular Cell. 2018 Oct 4 , 72 (1):178-186.e5.
  10. Karniel A., Mrusek D., Steinchen W., Dym O., Bange G. & Bibi E. (2018). Co-translational folding intermediate dictates membrane targeting of the signal recognition particle-receptor.  Journal of Molecular Biology. 2018 May 25 , 430 (11):1607-1620.
  11. Netzer R., Listov D., Lipsh R., Dym O., Albeck S., Knop O., Kleanthous C. & Fleishman S. J. (2018). Ultrahigh specificity in a network of computationally designed protein-interaction pairs.  Nature Communications. 2018 Dec 11 , 9 (1).
  12. Lapidoth G., Khersonsky O., Lipsh R., Dym O., Albeck S., Rogotner S. & Fleishman S. J. (2018). Highly active enzymes by automated combinatorial backbone assembly and sequence design.  Nature Communications. 2018 Jul 17 , 9 .
  13. Baran D., Pszolla M. G., Lapidoth G. D., Norn C., Dym O., Unger T., Albeck S., Tyka M. D. & Fleishman S. J. (2017). Principles for computational design of binding antibodies.  Proceedings of the National Academy of Sciences of the United States of America. 2017 Oct 10 , 114 (41):10900-10905.
  14. Ben-Nissan G., Belov M. E., Morgenstern D., Levin Y., Dym O., Arkind G., Lipson G., Makarov A. A. & Sharon M. (2017). Triple-Stage Mass Spectrometry Unravels the Heterogeneity of an Endogenous Protein Complex.  Analytical Chemistry. 2017 Apr 18 , 89 (8):4708-4715.
  15. Cohen-Khait R., Dym O., Hamer-Rogotner S. & Schreiber G. (2017). Promiscuous Protein Binding as a Function of Protein Stability.  Structure (London, England : 1993). 2017 Dec 5 , 25 (12):1867-1874.e3.
  16. Smock R. G., Yadid I., Dym O., Clarke J. & Tawfik D. (2016). De Novo Evolutionary Emergence of a Symmetrical Protein Is Shaped by Folding Constraints.  Cell. 2016 Jan 28 , 164 (3):476-486.
  17. Dym O., Song W., Felder C., Roth E., Shnyrov V., Ashani Y., Xu Y., Joosten R. P., Weiner L., Sussman J. & Silman I. (2016). The impact of crystallization conditions on structure-based drug design: A case study on the methylene blue/acetylcholinesterase complex.  Protein Science. 2016 Jun 1 , 25 (6):1096-1114.
  18. Bednarczyk D., Dym O., Prabahar V., Peleg Y., Pike D. H. & Noy D. (2016). Fine Tuning of Chlorophyll Spectra by Protein-Induced Ring Deformation.  ANGEWANDTE CHEMIE-INTERNATIONAL EDITION. 2016 Jun 6 , 55 (24):6901-6905.
  19. Goldenzweig A., Goldsmith M., Hill S. E., Gertman O., Laurino P., Ashani Y., Dym O., Unger T., Albeck S., Prilusky J., Lieberman R. L., Aharoni A., Silman I., Sussman J., Tawfik D. & Fleishman S. J. (2016). Automated Structure- and Sequence-Based Design of Proteins for High Bacterial Expression and Stability.  Molecular Cell. 2016 Jul 21 , 63 (2):337-346.
  20. Zimhony O., Schwarz A., Raitses-Gurevich M., Peleg Y., Dym O., Albeck S., Burstein Y. & Shakked Z. (2015). AcpM, the meromycolate extension Acyl carrier protein of mycobacterium tuberculosis, is activated by the 4\u2032-phosphopantetheinyl transferase PptT, a potential target of the multistep mycolic acid biosynthesis.  Biochemistry. 2015 Apr 14 , 54 (14):2360-2371.