Detection and characterization of xenon-binding sites in proteins by 129Xe NMR spectroscopy.

Xenon-binding sites in proteins have led to a number of applications of xenon in biochemical and structural studies. Here we further develop the utility of 129Xe NMR in characterizing specific xenon-protein interactions. The sensitivity of the 129Xe chemical shift to its local environment and the intense signals attainable by optical pumping make xenon a useful NMR reporter of its own interactions with proteins. A method for detecting specific xenon-binding interactions by analysis of 129Xe chemical shift data is illustrated using the maltose binding protein (MBP) from Escherichia coli as an example. The crystal structure of MBP in the presence of 8atm of xenon confirms the binding site determined from NMR data. Changes in the structure of the xenon-binding cavity upon the binding of maltose by the protein can account for the sensitivity of the 129Xe chemical shift to MBP conformation. 129Xe NMR data for xenon in solution with a number of cavity containing phage T4 lysozyme mutants show that xenon can report on cavity structure. In particular, a correlation exists between cavity size and the binding-induced 129Xe chemical shift. Further applications of 129Xe NMR to biochemical assays, including the screening of proteins for xenon binding for crystallography are considered.

[1]  S. Grzesiek,et al.  NMRPipe: A multidimensional spectral processing system based on UNIX pipes , 1995, Journal of biomolecular NMR.

[2]  B. Matthews,et al.  Specificity of ligand binding in a buried nonpolar cavity of T4 lysozyme: linkage of dynamics and structural plasticity. , 1995, Biochemistry.

[3]  Collaborative Computational,et al.  The CCP4 suite: programs for protein crystallography. , 1994, Acta crystallographica. Section D, Biological crystallography.

[4]  J. Thornton,et al.  PROCHECK: a program to check the stereochemical quality of protein structures , 1993 .

[5]  K. Miller,et al.  Xenon NMR: chemical shifts of a general anesthetic in common solvents, proteins, and membranes. , 1981, Proceedings of the National Academy of Sciences of the United States of America.

[6]  B. Matthews,et al.  Energetic origins of specificity of ligand binding in an interior nonpolar cavity of T4 lysozyme. , 1995, Biochemistry.

[7]  J. W. Peters,et al.  A simple device for studying macromolecular crystals under moderate gas pressures (0.1–10 MPa) , 1996 .

[8]  C. E. Webster,et al.  Exploring surfaces and cavities in lipoxygenase and other proteins by hyperpolarized xenon-129 NMR. , 1999, Journal of the American Chemical Society.

[9]  B. Matthews,et al.  Response of a protein structure to cavity-creating mutations and its relation to the hydrophobic effect. , 1992, Science.

[10]  Kalle Gehring,et al.  Solution NMR Studies of a 42 KDa Escherichia Coli Maltose Binding Protein/β-Cyclodextrin Complex: Chemical Shift Assignments and Analysis , 1998 .

[11]  Craig M. Ogata,et al.  MAD phasing grows up , 1998, Nature Structural Biology.

[12]  T. Prangé,et al.  On the Preparation and X-Ray Data-Collection of Isomorphous Xenon Derivatives , 1994 .

[13]  H. Desvaux,et al.  Magnetization transfer from laser‐polarized xenon to protons located in the hydrophobic cavity of the wheat nonspecific lipid transfer protein , 2001, Protein science : a publication of the Protein Society.

[14]  I. Kuntz,et al.  Nuclear magnetic resonance studies of xenon-129 with myoglobin and hemoglobin. , 1982, Biochemistry.

[15]  A. Pines,et al.  Detection of a conformational change in maltose binding protein by (129)Xe NMR spectroscopy. , 2001, Journal of the American Chemical Society.

[16]  A. Cherubini,et al.  Spin-lattice relaxation of laser-polarized xenon in human blood. , 1999, Proceedings of the National Academy of Sciences of the United States of America.

[17]  D. Rees,et al.  Successful flash‐cooling of xenon‐derivatized myoglobin crystals , 1997 .

[18]  L. Kay,et al.  Flexibility and ligand exchange in a buried cavity mutant of T4 lysozyme studied by multinuclear NMR. , 2000, Biochemistry.

[19]  Gil Navon,et al.  Enhancement of Solution NMR and MRI with Laser-Polarized Xenon , 1996, Science.

[20]  F. Quiocho,et al.  The 2.3-A resolution structure of the maltose- or maltodextrin-binding protein, a primary receptor of bacterial active transport and chemotaxis. , 1992 .

[21]  A. S. Kertes,et al.  SOLUBILITY DATA SERIES , 1985 .

[22]  J. Zou,et al.  Improved methods for building protein models in electron density maps and the location of errors in these models. , 1991, Acta crystallographica. Section A, Foundations of crystallography.

[23]  F A Quiocho,et al.  Extensive features of tight oligosaccharide binding revealed in high-resolution structures of the maltodextrin transport/chemosensory receptor. , 1997, Structure.

[24]  A. Pines,et al.  Evidence of nonspecific surface interactions between laser-polarized xenon and myoglobin in solution. , 2000, Proceedings of the National Academy of Sciences of the United States of America.

[25]  P. Evans,et al.  A structural explanation for the recognition of tyrosine-based endocytotic signals. , 1998, Science.

[26]  J Hermans,et al.  Modeling protein-small molecule interactions: structure and thermodynamics of noble gases binding in a cavity in mutant phage T4 lysozyme L99A. , 2000, Journal of molecular biology.

[27]  P. Bjorkman,et al.  Crystal structure of invasin: a bacterial integrin-binding protein. , 1999, Science.

[28]  M. Anderson,et al.  Electron spin catalysis by xenon in an enzyme. , 2001, Journal of the American Chemical Society.

[29]  I. Kuntz,et al.  Cavities in proteins: structure of a metmyoglobin-xenon complex solved to 1.9 A. , 1984, Biochemistry.

[30]  Bruce A. Johnson,et al.  NMR View: A computer program for the visualization and analysis of NMR data , 1994, Journal of biomolecular NMR.

[31]  F A Quiocho,et al.  Refined 1.8-A structure reveals the mode of binding of beta-cyclodextrin to the maltodextrin binding protein. , 1993, Biochemistry.

[32]  Piero Sozzani,et al.  A Porous Crystalline Molecular Solid Explored by Hyperpolarized Xenon , 2000 .

[33]  M Schiltz,et al.  Exploring hydrophobic sites in proteins with xenon or krypton , 1998, Proteins.

[34]  J. Tse,et al.  The nuclear magnetic resonance of 129Xe trapped in clathrates and some other solids , 1988 .

[35]  G J Kleywegt,et al.  Detection, delineation, measurement and display of cavities in macromolecular structures. , 1994, Acta crystallographica. Section D, Biological crystallography.

[36]  I D Kuntz,et al.  Computational studies of the interaction of myoglobin and xenon. , 1986, Journal of molecular biology.

[37]  B. Matthews,et al.  Size versus polarizability in protein-ligand interactions: binding of noble gases within engineered cavities in phage T4 lysozyme. , 2000, Journal of molecular biology.

[38]  L. Kay.  Nuclear magnetic resonance methods for high molecular weight proteins: a study involving a complex of maltose binding protein and beta-cyclodextrin. , 2001, Methods in enzymology.

[39]  F. Quiocho,et al.  Crystallographic evidence of a large ligand-induced hinge-twist motion between the two domains of the maltodextrin binding protein involved in active transport and chemotaxis. , 1992, Biochemistry.

[40]  T. Walker,et al.  Spin-exchange optical pumping of noble-gas nuclei , 1997 .

[41]  S. Mowbray,et al.  Crystal structures and solution conformations of a dominant-negative mutant of Escherichia coli maltose-binding protein. , 1996, Journal of molecular biology.

[42]  A. Pines,et al.  Functionalized xenon as a biosensor , 2001, Proceedings of the National Academy of Sciences of the United States of America.

[43]  R J Read,et al.  Crystallography & NMR system: A new software suite for macromolecular structure determination. , 1998, Acta crystallographica. Section D, Biological crystallography.

[44]  M. Field,et al.  Gas access to the active site of Ni-Fe hydrogenases probed by X-ray crystallography and molecular dynamics , 1997, Nature Structural Biology.

[45]  M. Casu,et al.  Probing proteins in solution by (129)Xe NMR spectroscopy. , 2001, Journal of magnetic resonance.

[46]  J. Fraissard,et al.  Nuclear Magnetic Resonance of Physisorbed 129Xe Used as a Probe to Investigate Porous Solids , 1999 .

[47]  J. F. Hinton,et al.  Evidence of xenon transport through the gramicidin channel: a 129Xe-NMR study. , 1994, Biochimica et biophysica acta.

[48]  R. Lerner,et al.  Antibody Catalysis of the Oxidation of Water , 2001, Science.

[49]  A. Pines,et al.  Characterization of the effects of nonspecific xenon-protein interactions on (129)Xe chemical shifts in aqueous solution: further development of xenon as a biomolecular probe. , 2001, Journal of magnetic resonance.

[50]  Long,et al.  High-field NMR of adsorbed xenon polarized by laser pumping. , 1991, Physical review letters.

[51]  B. Schoenborn,et al.  Binding of Xenon to Sperm Whale Myoglobin , 1965, Nature.

[52]  S. Lippard,et al.  Xenon and halogenated alkanes track putative substrate binding cavities in the soluble methane monooxygenase hydroxylase. , 2001, Biochemistry.