Publications


Selected and most recent publications (out of 78)

  • Collagen degradation Advanced Visualization Techniques

    1. Fragai, M., Luchinat, C., Martelli, T., Ravera, E., Sagi, I., Solomonov, I., Udi, Y. (2014).
      SSNMR of biosilica-entrapped enzymes permits an easy assessment of preservation of native conformation at atomic detail.
      Chem. Commun. 50, 421-423.
    2. Grossman, M., Sagi, I. (2012).
      Application of Stopped-Flow and Time-Resolved X-Ray Absorption Spectroscopy to the Study of Metalloproteins Molecular Mechanisms.
      X-Ray Spectroscopy , ISBN 978-953-307-967-7, edited by Shatendra K. Sharma.
    3. Kaminker, I., Sushenko, A., Potapov, A., Daube, S., Akabayov, B., Sagi, I., Goldfarb, D. (2011).
      Probing Conformational Variations at the ATPase Site of the RNA Helicase DbpA by High-Field Electron-Nuclear Double Resonance Spectroscopy.
      J. Am. Chem. Soc. 133(39), 15514-15523.
    4. Rosenblum, G., Van Den Steen, P.E., Cohen, S.R., Bitler, A., Brand, D.D., Opdenakker, G., Sagi, I. (2010).
      Direct Visualization of Protease Action on Collagen Triple Helical Structure.
      PLoS ONE 5, e11043.
    5. Frenkel, A., Kleifeld, O., Wasserman, S.R., Sagi, I. (2002).
      Phase speciation by extended X-ray-absorption fine structure spectroscopy.
      J. Chem. Phys. 116, 9449-9456.
    6. Federman, S., Miller, L., Sagi, I. (2002).
      Following Matrix Metalloproteinases Activity Near the Cell Boundary by Infrared Micro-spectroscopy.
      Matrix Biol. 21, 567-577.
    7. Levi-Kalisman, Y., Raz, S., Weiner, S., Addadi, L., Sagi, I. (2002).
      Structural differences between biogenic amorphous calcium carbonate phases using X-ray absorption spectroscopy.
      Adv. Funct. Mat. 12, 43-48.
    8. Henn, A., Medalia, O., Shi, S., Steinberg, M., Franceschi, F., Sagi, I. (2001).
      Visualization of unwinding activity of duplex RNA by dbpA, a DEAD Box helicase, at single molecule resolution by atomic force microscopy.
      Proc. Natl. Acad. Sci. USA 98, 5007-5012.
    9. Kleifeld, O., Kotra, L.P., Gervasi, D.C., Brown, S. Bernardo, M.M., Fridman, R., Mobashery, S., Sagi, I. (2001).
      X-Ray absorption studies of human matrix metalloproteinase-2 (MMP-2) bound to a highly selective mechanism-based inhibitor: comparison to the latent and active forms of the enzyme.
      J. Biol. Chem. 276, 17125-17131
  • Water dynamics Molecular Control

    1. Sharabi, O., Shirian, J., Grossman, M., Lebendiker, M., Sagi, I., Shifman, J. (2014).
      Affinity- and Specificity-Enhancing Mutations Are Frequent in Multispecific Interactions between TIMP2 and MMPs.
      PLoS ONE 9(4), e93712.

    2. Ogata, H., Decaneto, E., Grossman, M., Havenith, M., Sagi, I., Lubitz, W., Knipp, M. (2014).
      Crystallization and preliminary X-ray crystallographic analysis of the catalytic domain of membrane type 1 matrix metalloproteinase.
      Acta Cryst. F70, 232-235.
    3. Solomonov, I.#, Korkotian, E.#, Born, B., Feldman, Y., Bitler, A., Rahimi, F., Li, H., Bitan, G., Sagi, I. (2012).
      Zn2+-Aβ40 complexes form metastable quasi-spherical oligomers that are cytotoxic to cultured hippocampal neurons.
      J. Biol. Chem. 287 (24), 20555-64.
        # equal contributors
    4. Grossman, M.#, Born, B.#, Heyden, M.#, Tworowski, D., Fields, G.B., Sagi, I.*, Havenith, M.* (2011).
      Correlated structural kinetics and retarded solvent dynamics at the metalloprotease active site.
      Nature Structural & Molecular Biology 18(10), 1102-1108.

        Highlighted as news & views in Nature.
        # equal contributors (first authors); * equal contributors (corresponding authors)
    5. Grossman, M., Sela-Passwel, N., Sagi, I. (2011).
      Achieving broad molecular insights into dynamic protein interactions by integrated structural-kinetic approaches.
      Curr. Opin. Struct. Biol. 21(5), 678-685.
    6. Orgel, J.P., Antipova, O., Sagi, I., Bitler, A., Qiu, D., Wang, R., Xu, Y., San Antonio, J.D. (2011).
      Collagen fibril surface displays a constellation of sites capable of promoting fibril assembly, stability, and hemostasis.
      Connect. Tissue Res. 52(1), 18-24.
    7. Politi, Y., Batchelor, D.R., Zaslansky, P., Chmelka, B.F., Weaver, J.C., Sagi, I., Weiner, S., Addadi, L. (2010).
      Role of Magnesium Ion in the Stabilization of Biogenic Amorphous Calcium Carbonate: A Structure-Function Investigation.
      Chem. Mater. 22, 161-166.
    8. Grossman, M., Tworowski, D., Dym, O., Lee, M.H., Levy, Y., Murphy, G., Sagi, I. (2010).
      The Intrinsic Protein Flexibility of Endogenous Protease Inhibitor TIMP-1 Controls Its Binding Interface and Affects Its Function.
      Biochemistry 49, 6184-6192.
    9. Politi, Y., Metzler, R.A., Abrecht, M., Gilbert, B., Wilt, F.H., Sagi, I., Addadi, L., Weiner, S., Gilbert, P.U. (2008).
      Transformation mechanism of amorphous calcium carbonate into calcite in the sea urchin larval spicule.
      Proc. Natl. Acad. Sci. USA 105, 17362-17366.
    10. Noy, D., Solomonov, I., Sinkevich, O., Arad, T., Kjaer, K., Sagi I. (2008).
      Zinc-amyloid beta interactions on a millisecond time-scale stabilize non-fibrillar Alzheimer-related species.
      J. Am. Chem. Soc. 130, 1376-1383.
    11. Sagi, I., Milla., M. (2008).
      Application of structural-dynamic approaches provide novel insights into the enzymatic mechanism of the tumor necrosis factor-α converting enzyme (TACE).
      Anal. Biochem. 372, 1-10.
    12. Lewis, K.C., Selzer, T., Shahar, C., Udi, Y., Tworowski, D., Sagi, I. (2008).
      Inhibition of pectin methyl esterase activity by green tea catechins.
      Phytochem. 69, 2586-2592.
    13. Rosenblum, G., Meroueh, S., Toth, M., Fisher, J., Fridman, R., Mobashery, S, Sagi, I. (2007).
      Molecular structures and dynamics of the stepwise activation mechanism of a matrix metalloproteinase zymogen: challenging the cysteine switch dogma.
      J. Am. Chem. Soc. 129, 13566-13574.
    14. Rosenblum, G., Van den Steen, P., Cohen, S.R., Grossmann, G.J., Frenkel, J., Sertchook, R., Slack, N., Strange, R.W., Opdenakker, G., Sagi, I. (2007).
      Insights into the structure and domain flexibility of full-length pro-matrix metalloproteinase-9/gelatinase B.
      Structure 15, 1227-1236.
    15. Solomon, A., Akabayov, B., Milla, M., Sagi, I. (2007).
      Key feature of the catalytic cycle of TNF-α converting enzyme involves communication between distal protein sites and the enzyme catalytic core.
      Proc. Natl. Acad. Sci. USA 104, 4931-4936.
    16. Politi, Y., Levi-Kalisman, Y., Raz, S., Wilt, F., Addadi, L.,Weiner, S., Sagi, I. (2006).
      The Transient Amorphous Calcium Carbonate Precursor Phase in Developing Sea Urchin Larval Spicules has Short range Order Similar to Calcite.
      Adv. Funct. Mat. 16, 1289-1298.
    17. Weiner, S., Sagi, I., Addadi, L. (2005).
      Choosing the crystallization path less traveled.
      Science 309, 1027-1028.
    18. Solomon, A., Rosenblum, G., Gonzales, P.E., Leonard, J.D., Mobashery, S., Milla, M.E., Sagi, I. (2004).
      Pronounced Diversity in Electronic and Chemical Properties between the Catalytic Zinc Sites of TACE and MMPs Despite their High Structural Similarity.
      J. Biol. Chem. 279, 31646-31654.
    19. Gonzales, P.E., Solomon, A., Sagi, I., Milla, M.E. (2004).
      Inhibition of the TNF-α-converting enzyme (TACE) by its pro domain.
      J. Biol. Chem. 279, 31638-31645.
    20. Kleifeld, O., Frenkel, A., Martin, J.M.L., Sagi, I. (2003).
      Active Site Electronic Structure and Dynamics during Metalloenzyme Catalysis.
      Nature Structural Biology 10, 98-103.

        Highlighted as news & views in Nature.
    21. Henn, A., Shu, S., Zarivach, R., Ben-Zeev, E., Sagi, I. (2002).
      The RNA helicase DbpA exhibits a markedly different conformation in the ADP-bound state compared with the ATP- or RNA-bound states.
      J. Biol. Chem. 277, 46559-46565.
    22. Kleifeld, O., Van den Steen, P., Frenkel, A., Jiang, H.L., Opdenakker, G., Sagi, I. (2000).
      Structural characterization of the catalytic active site in latent and active gelatinase B from human neutrophils.
      J. Biol. Chem. 275, 34335-34343.
  • MMP antibodies Drug Design

    1. Udi, Y., Fragai, M., Grossman, M., Mitternacht, M., Arad-Yellin, R., Calderone, V., Melikian,M., Toccafondi, M., Berezovsky, I. N., Luchinat, C. & Sagi, I. (2013)
      Unraveling Hidden Regulatory Sites in Structurally Homologous Metalloproteases.
      J. Mol. Biol., 425(13), 2330-2346.
    2. Sela-Passwell, N., Kikkeri, R., Dym, O., Rozenberg, H., Margalit, R., Arad-Yellin, R., Eisenstein, M., Brenner, O., Shoham, T., Danon, T., Shanzer, A., Sagi, I. (2012).
      Endogenous-like inhibitory antibodies targeting activated metalloproteinase motifs show therapeutic potential.
      Nature Medicine, 18, 143-147.

        Highlighted in a radio broadcast on "reshet bet", in press releases on the web site of the
        Weizmann Institute, on GEN News Highlights, on smartplanet, on "hayadan", and as one of
        the "Top ten" articles of Nature Medicine.
    3. Pradeep C.R., Zeisel A., Köstler W.J., Lauriola M., Jacob-Hirsch J., Haibe-Kains B., Amariglio N., Ben-Chetrit N., Emde A., Solomonov I., Neufeld G., Piccart M., Sagi I., Sotiriou C., Rechavi G., Domany E., Desmedt C., Yarden Y. (2012).
      Modeling invasive breast cancer: growth factors propel progression of HER2-positive premalignant lesions.
      Oncogene, 31, 3569-3583.
    4. Shechter, R., Raposo, C., London, A., Sagi, I., Schwartz, M. (2011).
      The Glial Scar-Monocyte Interplay: A Pivotal Resolution Phase in Spinal Cord Repair.
      PLoS ONE, 6(12), e27969.
    5. Sela-Passwel, N., Trahtenherts, A., Krüger, A., Sagi, I. (2011).
      New opportunities in drug design of metalloproteinase inhibitors: combination between structure-function experimental approaches and systems biology.
      Expert Opin. Drug Discov. 6(5), 527-542.
    6. Rouffet, M., Oliveira, C., Udi, Y., Agrawal, A., Sagi, I., McCammon, J.A., Cohen, S.M. (2010).
      From Sensors to Silencers: Quinoline- and Benzimidazole-Sulfonamides as Inhibitors for Zinc Proteases
      J. Am. Chem. Soc. 132, 8232-8233.
    7. Sela-Passwell, N., Rosenblum, G., Shoham, T., Sagi, I. (2010).
      Structural and functional bases for allosteric control of MMP activities: Can it pave the path for selective inhibition?
      Biochim. Biophys. Acta 1803, 29-38.
    8. Rosenblum, G., Meroueh, O.S., Kleifeld, O., Brown, S., Singson, S.P., Fridman, R., Mobashery, S., Sagi, I. (2003).
      Structural basis for potent slow-binding inhibition of human matrix metalloproteinase-2 (MMP-2).
      J. Biol. Chem. , 278, 27009-27015.