New Insights into Active Site Conformation Dynamics of E. coli PNP Revealed by Combined H/D Exchange Approach and Molecular Dynamics Simulations

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• 作者：Saša Kazazić ; Branimir Bertoša ; Marija Luić…
• 关键词：Allostery ; Negative cooperativity ; Phosphate binding site ; Purine metabolism ; Purine nucleoside phosphorylase
• 刊名：Journal of The American Society for Mass Spectrometry
• 出版年：2016
• 出版时间：January 2016
• 年：2016
• 卷：27
• 期：1
• 页码：73-82
• 全文大小：1,623 KB
• 参考文献：1.Peracchi, A., Mozzarelli, A.: Exploring and exploiting allostery: models, evolution, and drug targeting. Biochim. Biophys. Acta – Proteins Proteomics 1814, 922–933 (2011)CrossRef
  2.Changeux, J.-P.: Fifty years of allosteric interactions: the twists and turns of the models. Nat. Rev. Mol. Cell Biol. 14, 819–829 (2013)CrossRef
  3.Cornish-Bowden, A.: Understanding allosteric and cooperative interactions in enzymes. FEBS J. 281, 621–632 (2014)CrossRef
  4.Motlagh, H.N., Wrabl, J.O., Li, J., Hilser, V.J.: The ensemble nature of allostery. Nature 508, 331–339 (2014)CrossRef
  5.Brunori, M.: Variations on the theme: allosteric control in hemoglobin. FEBS J. 281, 633–643 (2014)CrossRef
  6.Yuan, Y., Tam, M.F., Simplaceanu, V., Ho, C.: New look at hemoglobin allostery. Chem. Rev. 115, 1702–1724 (2015)CrossRef
  7.Levantino, M., Schirò, G., Lemke, H.T., Cottone, G., Glownia, J.M., Zhu, D., Chollet, M., Ihee, H., Cupane, A.: Cammarata M: Ultrafast myoglobin structural dynamics observed with an X-ray free-electron laser. Nat. Commun. 6, 1–6 (2015)
  8.Kern, D., Zuiderweg, E.R.P.: The role of dynamics in allosteric regulation. Curr. Opin. Struct. Biol. 13, 748–757 (2003)CrossRef
  9.Goodey, N.M., Benkovic, S.J.: Allosteric regulation and catalysis emerge via a common route. Nat. Chem. Biol. 4, 474–482 (2008)CrossRef
  10.Laskowski, R.A., Gerick, F., Thornton, J.M.: The structural basis of allosteric regulation in proteins. FEBS Lett. 583, 1692–1698 (2009)CrossRef
  11.Koshland Jr., D.E.: The structural basis of negative cooperativity: receptors and enzymes. Curr. Opin. Struct. Biol. 6, 757–761 (1996)CrossRef
  12.Stevens, S.Y., Sanker, S., Kent, C., Zuiderweg, E.R.P.: Delineation of the allosteric mechanism of a cytidylyltransferase exhibiting negative cooperativity. Nat. Struct. Mol. Biol. 8, 947–952 (2001)CrossRef
  13.Nørager, S., Arent, S., Björnberg, O., Ottosen, M., Leggio, L.L., Jensen, K.F., Larsen, S.: Lactococcus lactis dihydroorotate dehydrogenase A mutants reveal important facets of the enzymatic function. J. Biol. Chem. 278, 28812–28822 (2003)
  14.Cornish-Bowden, A.: The physiological significance of negative cooperativity revisited. J. Theor. Biol. 319, 144–147 (2013)CrossRef
  15.Carreras, C.W., Santi, D.V.: The Catalytic mechanism and structure of thymidylate synthase. Annu. Rev. Biochem. 64, 721–762 (1995)CrossRef
  16.Anderson, A.C., O'Neil, R.H., DeLano, W.L., Stroud, R.M.: The structural mechanism for half-the-sites reactivity in an enzyme, thymidylate synthase, involves a relay of changes between subunits. Biochemistry 38, 13829–13836 (1999)CrossRef
  17.Sidhu, R.S., Lee, J.Y., Yuan, C., Smith, W.L.: Comparison of cyclooxygenase-1 crystal structures: cross-talk between monomers comprising cyclooxygenase-1 homodimers. Biochemistry 49, 7069–7079 (2010)CrossRef
  18.Buddha, M.R., Crane, B.R.: Structures of tryptophanyl-tRNA synthetase II from Deinococcus radiodurans bound to ATP and tryptophan: insight into subunit cooperativity and domain motions linked to catalysis. J. Biol. Chem. 280, 31965–31973 (2005)CrossRef
  19.Koellner, G., Luić, M., Shugar, D., Saenger, W., Bzowska, A.: Crystal structure of the ternary complex of E. coli purine nucleoside phosphorylase with formycin B, a structural analogue of the substrate inosine, and phosphate (sulphate) at 2.1 Å resolution. J. Mol. Biol. 280, 153–166 (1998)CrossRef
  20.Koellner, G., Bzowska, A., Wielgus-Kutrowska, B., Luić, M., Steiner, T., Saenger, W., Stȩpiński, J.: Open and closed conformation of the E. coli purine nucleoside phosphorylase active center and implications for the catalytic mechanism. J. Mol. Biol. 315, 351–371 (2002)
  21.Mikleušević, G., Štefanić, Z., Narczyk, M., Wielgus-Kutrowska, B., Bzowska, A., Luić, M.: Validation of the catalytic mechanism of Escherichia coli purine nucleoside phosphorylase by structural and kinetic studies. Biochimie 93, 1610–1622 (2011)CrossRef
  22.Štefanić, Z., Mikleušević, G., Narczyk, M., Wielgus-Kutrowska, B., Bzowska, A., Luić, M.: Still a long way to fully understanding the molecular mechanism of Escherichia coli purine nucleoside phosphorylase. Croat. Chem. Acta 86, 117–127 (2013)CrossRef
  23.Štefanić, Z., Narczyk, M., Mikleušević, G., Wielgus-Kutrowska, B., Bzowska, A., Luić, M.: New phosphate binding sites in the crystal structure of Escherichia coli purine nucleoside phosphorylase complexed with phosphate and formycin A. FEBS Lett. 586, 967–971 (2012)CrossRef
  24.Bertoša, B., Mikleušević, G., Wielgus-Kutrowska, B., Narczyk, M., Hajnić, M., Leščić Ašler, I., Tomić, S., Luić, M., Bzowska, A.: Homooligomerization is needed for stability: a molecular modelling and solution study of Escherichia coli purine nucleoside phosphorylase. FEBS J. 281, 1860–1871 (2014)
  25.Pugmire, M.J., Ealick, S.E.: Structural analyses reveal two distinct families of nucleoside phosphorylases. Biochem. J. 361, 1–25 (2002)CrossRef
  26.Bzowska, A., Kulikowska, E., Shugar, D.: Purine nucleoside phosphorylases: properties, functions, and clinical aspects. Pharmacol. Ther 88, 349–425 (2000)CrossRef
  27.Condezo, L.A., Fernandez-Lucas, J., Garcia-Burgos, C.A., Alcántara, A.R., Sinisterra, J.V.: In: Patel, R.N. (ed.) Enzymatic Synthesis of Modified Nucleosides. CRC Press, Boca Raton (2006)
  28.Zhang, Y., Parker, W.B., Sorscher, E.J., Ealick, S.E.: PNP Anticancer Gene Therapy. Curr. Top. Med. Chem. 5, 1259–1274 (2005)CrossRef
  29.Basso, L.A., Santos, D.S., Shi, W., Furneaux, R.H., Tyler, P.C., Schramm, V.L., Blanchard, J.S.: Purine nucleoside phosphorylase from Mycobacterium tuberculosis. Analysis of inhibition by a transition-state analogue and dissection by parts. Biochemistry 40, 8196–8203 (2001)
  30.Lewandowicz, A., Schramm, V.L.: Transition state analysis for human and Plasmodium falciparum purine nucleoside phosphorylases. Biochemistry 43, 1458–1468 (2004)CrossRef
  31.Munagala, N., Wang, C.C.: The purine nucleoside phosphorylase from Trichomonas vaginalis is a homologue of the bacterial enzyme. Biochemistry 41, 10382–10389 (2002)CrossRef
  32.Pereira, H.D.M., Franco, G.R., Cleasby, A., Garratt, R.C.: Structures for the potential drug target purine nucleoside phosphorylase from Schistosoma mansoni causal agent of schistosomiasis. J. Mol. Biol. 353, 584–599 (2005)CrossRef
  33.Wales, T.E., Fadgen, K.E., Gerhardt, G.C., Engen, J.R.: High-speed and high-resolution UPLC separation at zero degrees celsius. Anal. Chem. 80, 6815–6820 (2008)CrossRef
  34.Karplus, M., Kuriyan, J.: Molecular dynamics and protein function. Proc. Natl. Acad. Sci. U. S. A. 102, 6679–6685 (2005)CrossRef
  35.Best, R.B., Vendruscolo, M.: Structural interpretation of hydrogen exchange protection factors in proteins: characterization of the native state fluctuations of CI2. Structure 14, 97–106 (2006)CrossRef
  36.Sljoka, A., Wilson, D.: Probing protein ensemble rigidity and hydrogen-deuterium exchange. Phys. Biol. 10, 1–26 (2013)
  37.Hilser, V.J., Freire, E.: Structure-based calculation of the equilibrium folding pathway of proteins. Correlation with hydrogen exchange protection factors. J. Mol. Biol. 262, 756–772 (1996)CrossRef
  38.Hilser, V., Whitten, S.: Using the COREX/BEST Server to Model the Native-State Ensemble. In: Livesay D.R. (ed.) Protein Dynamics. Springer Science+Business Media, New York Humana Press (2014)
  39.Liu, T., Pantazatos, D., Li, S., Hamuro, Y., Hilser, V.J., Woods, V.L.: Quantitative assessment of protein structural models by comparison of H/D exchange MS rata with exchange behavior accurately predicted by DXCOREX. J. Am. Soc. Mass Spectrom. 23, 43–56 (2012)CrossRef
  40.Petruk, A.A., Defelipe, L.A., Rodríguez Limardo, R.G., Bucci, H., Marti, M.A., Turjanski, A.G.: Molecular dynamics simulations provide atomistic insight into hydrogen exchange mass spectrometry experiments. J. Chem. Theory Comput. 9, 658–669 (2013)CrossRef
  41.Radou, G., Dreyer, F.N., Tuma, R., Paci, E.: Functional dynamics of hexameric helicase probed by hydrogen exchange and simulation. Biophys. J. 107, 983–990 (2014)CrossRef
  42.McAllister, R.G., Konermann, L.: Challenges in the interpretation of protein H/D exchange data: a molecular dynamics simulation perspective. Biochemistry 54, 2683–2692 (2015)CrossRef
  43.Skinner, J.J., Lim, W.K., Bédard, S., Black, B.E., Englander, S.W.: Protein hydrogen exchange: testing current models. Protein Sci. 21, 987–995 (2012)CrossRef
  44.Skinner, J.J., Lim, W.K., Bédard, S., Black, B.E., Englander, S.W.: Protein dynamics viewed by hydrogen exchange. Protein Sci. 21, 996–1005 (2012)CrossRef
  45.Bzowska, A., Kulikowska, E., Shugar, D.: Formycins A and B and some analogues: selective inhibitors of bacterial (Escherichia coli) purine nucleoside phosphorylase. Biochim. Biophys. Acta 1120, 239–247 (1992)CrossRef
  46.Shugar, D., Psoda, A.: In: Saenger, W. (ed.) 4.12.2 Predominant Tautomeric Species of Nucleic Acid Components. Springer, Berlin and Heidelberg (1990)
  47.Tarnowski, K., Fituch, K., Szczepanowski, R.H., Dadlez, M., Kaus-Drobek, M.: Patterns of structural dynamics in RACK1 protein retained throughout evolution: a hydrogen-deuterium exchange study of three orthologs. Protein Sci. 23, 639–651 (2014)CrossRef
  48.Kazazic, S., Zhang, H.-M., Schaub, T., Emmett, M., Hendrickson, C., Blakney, G., Marshall, A: Automated data reduction for hydrogen/deuterium exchange experiments, enabled by high-resolution fourier transform ion cyclotron resonance mass spectrometry. J. Am. Soc. Mass Spectrom. 21, 550–558 (2010)
  49.Houde, D., Berkowitz, S.A., Engen, J.R.: The utility of hydrogen/deuterium exchange mass spectrometry in biopharmaceutical comparability studies. J. Pharm. Sci. 100, 2071–2086 (2011)CrossRef
  50.Mao, C., Cook, W.J., Zhou, M., Koszalka, G.W., Krenitsky, T.A., Ealick, S.E.: The crystal structure of Escherichia coli purine nucleoside phosphorylase: a comparison with the human enzyme reveals a conserved topology. Structure 5, 1373–1383 (1997)CrossRef
  51.Vriend, G.: WHAT IF: A molecular modeling and drug design program. J. Mol. Graph. 8, 52–56 (1990)CrossRef
  52.Case, D., Darden, T., Cheatham III, T., Simmerling, C., Wang, J., Duke, R., Luo, R., Merz, K., Wang, B.,Pearlman, D.: AMBER 8, 5th edn, p. 39. University of California, San Francisco (2004)
  53.Duan, Y., Wu, C., Chowdhury, S., Lee, M.C., Xiong, G., Zhang, W., Yang, R., Cieplak, P., Luo, R., Lee, T., Cladwell, J., Wang, J., Kollman, P.: A point-charge force field for molecular mechanics simulations of proteins based on condensed-phase quantum mechanical calculations. J. Comput. Chem. 24, 1999 III 2012 (2003)
  54.Jorgensen, W.L., Chandrasekhar, J., Madura, J.D., Impey, R.W., Klein, M.L.: Comparison of simple potential functions for simulating liquid water. J. Chem. Phys. 79, 926–935 (1983)CrossRef
  55.Aaqvist, J.: Ion-water interaction potentials derived from free energy perturbation simulations. J. Phys. Chem. 94, 8021–8024 (1990)CrossRef
  56.Berendsen, H.J.C., Postma, J.P.M., van Gunsteren, W.F., DiNola, A., Haak, J.R.: Molecular dynamics with coupling to an external bath. J. Chem. Phys. 81, 3684–3690 (1984)CrossRef
  57.Hess, B., Kutzner, C., van der Spoel, D., Lindahl, E.: GROMACS 4: algorithms for highly efficient, load-balanced, and scalable molecular simulation. J. Chem. Theory Comput. 4, 435–447 (2008)CrossRef
  58.Humphrey, W., Dalke, A., Schulten, K.: VMD—Visual Molecular Dynamics. J. Mol. Graph 14, 33–38 (1996)CrossRef
  59.Spence, J.: X-ray lasers and serial crystallography. IUCrJ. 2, 305–306 (2015)CrossRef
  
• 作者单位：Saša Kazazić (1)
  Branimir Bertoša (2)
  Marija Luić (1)
  Goran Mikleušević (1)
  Krzysztof Tarnowski (3)
  Michal Dadlez (3)
  Marta Narczyk (4)
  Agnieszka Bzowska (4)
  
  1. Division of Physical Chemistry, Ruđer Bošković Institute, Zagreb, Croatia
  2. Division of Physical Chemistry, Faculty of Science at University of Zagreb, Zagreb, Croatia
  3. Institute of Biochemistry and Biophysics Department, Polish Academy of Science, Warsaw, Poland
  4. Division of Biophysics, Institute of Experimental Physics, University of Warsaw, Warsaw, Poland
  
• 刊物主题：Analytical Chemistry; Biotechnology; Organic Chemistry; Proteomics; Bioinformatics;
• 出版者：Springer US
• ISSN：1879-1123

文摘

The biologically active form of purine nucleoside phosphorylase (PNP) from Escherichia coli (EC 2.4.2.1) is a homohexamer unit, assembled as a trimer of dimers. Upon binding of phosphate, neighboring monomers adopt different active site conformations, described as open and closed. To get insight into the functions of the two distinctive active site conformations, virtually inactive Arg24Ala mutant is complexed with phosphate; all active sites are found to be in the open conformation. To understand how the sites of neighboring monomers communicate with each other, we have combined H/D exchange (H/DX) experiments with molecular dynamics (MD) simulations. Both methods point to the mobility of the enzyme, associated with a few flexible regions situated at the surface and within the dimer interface. Although H/DX provides an average extent of deuterium uptake for all six hexamer active sites, it was able to indicate the dynamic mechanism of cross-talk between monomers, allostery. Using this technique, it was found that phosphate binding to the wild type (WT) causes arrest of the molecular motion in backbone fragments that are flexible in a ligand-free state. This was not the case for the Arg24Ala mutant. Upon nucleoside substrate/inhibitor binding, some release of the phosphate-induced arrest is observed for the WT, whereas the opposite effects occur for the Arg24Ala mutant. MD simulations confirmed that phosphate is bound tightly in the closed active sites of the WT; conversely, in the open conformation of the active site of the WT phosphate is bound loosely moving towards the exit of the active site. In Arg24Ala mutant binary complex P_i is bound loosely, too.