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Biochemical Spectroscopy PDF

851 Pages·1995·17.293 MB·English
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Contributors to Volume 246 elcitrA srebmun era ni parentheses gniwollof the seman of .srotubirtnoc snoitailiffA listed era .tnerruc ROBERT H. AUSTIN (7), Department of DANIEL R. GAMELIN (5), Department of Physics, Princeton University, Princeton, Chemistry, Stanford University, Stan- New Jersey 44580 ford, California 50349 GARY W. BRUDVlG (22), Department of ELLEN GOLDMAN (29), Curagen Corpora- Chemistry, Yale University, New Haven, tion, Branford, Connecticut 50460 Connecticut 11560 DONALD M. GRAY (3), Department of Mo- PETER S. BRZOVI~ (8), Department of Bio- lecular and Cell Biology, University of chemistry, University of Washington, Se- Texas at Dallas, Richardson, Texas 38057 attle, Washington 59189 BRIAN M. HOFFMANN (23), Department of THERESE M. COTTON (28), Department of Chemistry, Northwestern University, Chemistry, Iowa State University, Ames, Evanston, Illinois 80206 Iowa 11005 ROMAN S. CZERNUSZEWlCZ (18), Depart- ALFRED R. HOLZWARTH (14), Max-Planck- Institut for Radiation Chemistry, 07454-D ment of Chemistry, University of Hous- Miilheim/Ruhr, Germany ton, Houston, Texas 40277 VICTORIA J. DEROSE (23), Department of Su-Hwl HUNG (3), Department of Molecu- Chemistry, Northwestern University, lar and Cell Biology, University of Texas Evanston, Illinois 80206 at Dallas, Richardson, Texas 38057 SIMON DELAGRAVE (29), Department of Bi- DAVID M. JAMESON (12), Department of ology, Brandeis University, Waltham, Biochemistry and Biophysics, University Massachusetts 43220 of Hawaii, John A. Burns School of Medi- SHAOJUN DONG (28), Laboratory of Electro- cine, Honolulu, Hawaii 22869 analytical Chemistry, Changchun Insti- KENNETH H. JOHNSON (3), Baylor College tute of Applied Chemistry, Chinese Acad- of Medicine, Center for Biotechnology, emy of Sciences, Changchun ,220031 The Woodlands, Texas 18377 China JAMES R. KINCAID (19), Department of MICHAEL F. DUNN (8), Department of -DiB Chemistry, Marquette University, Mil- chemistry, University of California, Riv- waukee, Wisconsin 33235 erside, Riverside, California 12529 MARTIN L. KIRK (5), Department of Chem- SHYAMSUNDER ERRAMILLI (7), Department istry, Stanford University, Stanford, Cali- of Physics, Princeton University, Prince- fornia 50349 ton, New Jersey 44580 WAYNE R. FIORI (24), Department of Chem- MELVIN P. KLEIN (21), Structural Biology istry, Sinsheimer Laboratories, Univer- Division, Lawrence Berkeley Laboratory, sity of California, Santa Cruz, Santa University of California, Berkeley, Berke- Cruz, California 46059 ley, California 02749 JOSEF FRIEDRICH (10), Physikalisches Insti- SUE LEURGANS (27), Department of Preven- rut, Universitdt Bayreuth, D-95440 Bay- tive Medicine, Rush Medical College, reuth, Germany Chicago, Illinois 21606 ix X CONTRIBUTORS TO VOLUME 246 AUGUST H. MAKI (25), Department of Radiation Biology, University of Frei- Chemistry, University of California, burg, D-7800 Freiburg, Germany Davis, Davis, California 61659 DRAWDE .1 NOMOLOS (5), Department of DRAHCIR A. MATHIES (16), Department of Chemistry, Stanford University, Stan- Chemistry, University of California, ford, California 50349 Berkeley, Berkeley, California 94720 SAMOHT G. SPIRO (18), Department of NAHBOIS M. MIICK (24), Department of Chemistry, Princeton University, Prince- Chemistry, Sinsheimer Laboratories, ton, New Jersey 08544 University of California, Santa Cruz, WALTER S. STRUVE (11), Ames Labora- Santa Cruz, California 95064 tory-United States Department of En- GLENN L. MILLHAUSER (24), Department of ergy, and Department of Chemistry, Iowa Chemistry, Sinsheimer Laboratories, State University, Ames, Iowa 11005 University of California, Santa Cruz, JOHN C. SUTHERLAND (6), Department of Santa Cruz, California 95064 Biology, Brookhaven National Labora- JIANJUN NIU (28), Laboratory of Electroan- tory, Upton, New York 37911 alytical Chemistry, Changchun Institute OICANGI TINOCO, JR. (2), Department of of Applied Chemistry, Chinese Academy Chemistry and Chemical Biodynamics of Sciences, Changchun 130022, China Laboratory, University of California, RENRAW L. SALOCITEP (17), Department of Berkeley, Berkeley, California 02749 Chemistry, University of Oregon, TREBREH NAV NEGNOREMA (9, 11), Depart- Eugene, Oregon 30479 ment of Physics and Astronomy, Free ENIBAS PULVER (5), Department of Chemis- University of Amsterdam, 1081 HV Am- try, Stanford University, Stanford, Cali- sterdam, The Netherlands fornia 50349 RIENK NAV ELLEDNORG (9), Department of TREBOR T. ROSS (27), Department of -DiB Physics and Astronomy, Free University chemistry, Ohio State University, Colum- of Amsterdam, 1081 HV Amsterdam, The bus, Ohio 43210 Netherlands KENNETH SAUER (1), Department of Chem- ALAN RENOGGAW (15), Department of Bio- istry, and Structural Biology Division, La- logical Sciences, and Center for Light Mi- wrence Berkeley Laboratory, University croscope Imaging and Biotechnology, of California, Berkeley, Berkeley, Califor- Carnegie Mellon University, Pittsburgh, nia 02749 Pennsylvania 31251 MAILLIW H. SAWYER (12), Russell TREBOR W. YDOOW (4), Department of Bio- Grimwade School of Biochemistry, Uni- chemistry and Molecular Biology, Colo- versity of Melbourne, Parkville, Victoria rado State University, Fort Collins, Colo- 3052, Australia rado 80523 HUGO SCHEER (30), Botanisches Institut der VITTAL K. ARDNAHCAY (26), Structural Bi- Universitiit Miinchen, D-80683 Miinchen, ology Division, Lawrence Berkeley Labo- Germany ratory, University of California, Berkeley, PAUL R. SELVIN (13), StructuralBiology Di- Berkeley, California 94720 vision, Calvin Laboratory, Lawrence MARY M. YANG (29), KAIROS Inc., San Berkeley Laboratory, and Department of Jose, California 63159 Chemistry, University of California, SALGUOD C. YOUVAN (29), PaiD Alto Insti- Berkeley, Berkeley, California 94720 tute of Molecular Medicine, Mountain F. SIEBERT (20), Institute of Biophysics and View, California 34049 Preface The use of spectroscopic methods to examine biomolecules has a long and rich history. Such methods have the virtue of being largely noninva- sive and capable of probing living materials as well as subcellular prepara- tions and isolated biomolecules. The information gained is interpretable in terms of structural parameters and intramolecular interactions. Using time-resolved approaches, dynamics can be explored readily over a time range from less than a picosecond to seconds and longer. This permits ready exploration of intermolecular interactions and intramolecular mo- tion relevant to biological processes. Advances in technology and methodology in spectroscopy have moved the field forward at a breathtaking pace in recent years. We have come a long way from the era when cytochrome oxidation state changes were monitored visually using a hand spectroscope or when absorption spectrometry was done using photographic detection. In this volume the reader can learn about instrumentation that uses diode array detectors to monitor absorption or emission spectral properties with great precision at hundreds of wavelengths simultaneously or Fourier transform methods that provide a significant increase in the efficiency of collecting and ana- lyzing spectroscopic information distributed over a wide wavelength band. Mode-locked lasers and associated pulse-compression and contin- uum-generation techniques allow pulse-probe measurements of fast (to l0 fsec = l0 4~- sec) absorption changes or fluorescence relaxation in the picosecond regime. Single-photon counting methods have greatly im- proved the signal-to-noise of optical detection systems for steady-state spectroscopy and especially for time-resolved fluorescence measure- ments. Pulsed lasers have advanced the application of time-resolved Ra- man spectroscopy and the ability to discriminate between Raman and fluorescence signals. In combination with the use of ultralow tempera- tures, intense monochromatic laser sources can be used in hole-burning experiments to probe chromophore local environments and the modes by which the chromophores interact with their surroundings. Computation intensive methods, such as Fourier transform infrared, electron spin echo (ESE), pulsed electron nuclear doable resonance (ENDOR), and digital imaging optical spectroscopy, have provided entirely new approaches to data collection and processing. Major developments in radiation sources, such as synchrotrons, have opened entirely new areas of investigation, including X-ray absorption spectroscopy (XAS) and extended X-ray ab- sorption fine structure (EXAFS). The reader will find descriptions and examples of each of these new methodologies in the chapters that follow, ix xii ECAFERP The audience for this volume includes the current generation of gradu- ate students and professional scientists involved in biological or biochem- ical studies seeking an introduction to modern spectroscopic methods and instrumentation. To help the interested reader develop a deeper back- ground and understanding of these methodologies and approaches, the authors of the individual chapters have cited general references and pub- lished reviews of the individual topics. The chapters fall into major sections covering optical spectroscopy, vibrational spectroscopy, electron paramagnetic resonance, and X-ray spectroscopy. Areas such as nuclear magnetic resonance which have been described extensively in recent volumes of this series have not been included. A general overview of the contents of this volume and examples of problems or situations to which the different approaches have been applied are described in the first chapter. I am indebted to many of my colleagues and students who have of- fered suggestions, have read and provided valuable comments on many of the contributed chapters, and have helped with the assembly of this vol- ume. In particular, I wish to thank several Berkeley colleagues, including Judith Klinman who was instrumental in initiating this project. Ignacio Tinoco, Richard Mathies, and Melvin P. Klein have not only written comprehensive overviews of the broader spectroscopic fields, but have also reviewed the contributed chapters included in each section. Very helpful insights for several chapters were provided by Joy Andrews, Mar- tin Debreczeny, and Mary Talbot, based on their perspective as graduate students in my research group. It is my hope that this volume will be informative and beneficial to them and to their contemporaries and suc- cessors in research laboratories throughout the scientific community. HTENNEK REUAS METHODS IN ENZYMOLOGY EMULOV I. Preparation and Assay of Enzymes Edited by SIDNEY P. CoLowIcr DNA NATHAN O. KAPLAN EMULOV II. Preparation and Assay of Enzymes Edited by SIDNEY P. COLOWICK DNA NATHAN O. KAPLAN EMULOV III. Preparation and Assay of Substrates Edited by SIDNEY P. COLOWICK DNA NATHAN O. KAPLAN EMULOV IV. Special Techniques for the Enzymologist Edited by SIDNEY P. COLOWICK DNA NATHAN O. KAPLAN EMULOV V. Preparation and Assay of Enzymes Edited yb SIDNEY P. COLOWICK DNA NATHAN O. KAPLAN EMULOV VI. Preparation and Assay of Enzymes (Continued) Preparation and Assay of Substrates Special Techniques Edited yb SIDNEY P. COLOWICK DNA NATHAN O. KAPLAN EMULOV VII. Cumulative Subject Index Edited yb SIDNEY P. COLOWICK DNA NATHAN O. KAPLAN EMULOV VIII. Complex Carbohydrates Edited yb ELIZABETH F. NEUFELD DNA VICTOR GRUBSNIG VOLUME IX. Carbohydrate Metabolism Edited yb WILLIS A. WOOD EMULOV X. Oxidation and Phosphorylation Edited yb RONALD W. KOORBATSE DNA MAYNARD E. PULLMAN VOLUME XI. Enzyme Structure Edited yb C. H. W. HIRS EMULOV XII. Nucleic Acids (Parts A and B) Edited yb LAWRENCE GROSSMAN DNA KIVIE MOLDAVE EMULOV XIII. Citric Acid Cycle Edited yb J. M. NIETSNEWOL VOLUME XIV. Lipids Edited yb J. M. NIETSNEWOL EMULOV XV. Steroids and Terpenoids Edited yb DNOMYAR B. NOTYALC EMULOV XVI. Fast Reactions Edited yb KUSTIN KENNETH iiix xiv SDOHTEM NI YGOLOMYZNE EMULOV XVII. Metabolism of Amino Acids and Amines (Parts A and B) Edited by TREBREH ROBAT DNA WHITE CELIA ROBAT EMULOV XVIII. Vitamins and Coenzymes (Parts A, B, and C) Edited by DLANOD B. McCoRMICK DNA LEUMEL D. THGIRW EMULOV XIX. Proteolytic Enzymes Edited by EDURTREG E. NNAMLREP DNA OLZSAL DNAROL EMULOV XX. Nucleic Acids and Protein Synthesis (Part )C Edited by KIVIE EVADLOM DNA ECNERWAL NAMSSORG EMULOV XXI. Nucleic Acids (Part D) Edited by ECNERWAL NAMSSORG DNA KIVIE EVADLOM EMULOV XXII. Enzyme Purification and Related Techniques Edited by B. WILLIAM YBOKAJ EMULOV XXIII. Photosynthesis (Part A) Edited by YNOHTNA NAS ORTEIP EMULOV XXIV. Photosynthesis and Nitrogen Fixation (Part B) Edited by YNOHTNA NAS ORTEIP EMULOV XXV. Enzyme Structure (Part B) Edited by C. H. W. HIRS DNA EGRES N. FFEHSAMIT EMULOV XXVI. Enzyme Structure (Part C) Edited by C. H. W. Hms DNA EGRES N. FFEHSAMIT EMULOV XXVII. Enzyme Structure (Part D) Edited by C. H. W. HIRS DNA EGRES N. FFEHSAMIT EMULOV XXVIII. Complex Carbohydrates (Part B) Edited by ROTCIV GRUBSNIG EMULOV XXIX. Nucleic Acids and Protein Synthesis (Part E) Edited by ECNERWAL DNA NAMSSORG KIVIE EVADLOM EMULOV XXX. Nucleic Acids and Protein Synthesis (Part F) Edited by KIVIE EVADLOM DNA ECNERWAL NAMSSORG EMULOV XXXI. Biomembranes (Part A) Edited by SIDNEY REHCSIELF DNA RETSEL REKCAP EMULOV XXXII. Biomembranes (Part B) Edited by SIDNEY REHCSIELF DNA RETSEL REKCAP EMULOV XXXIII. Cumulative Subject Index Volumes I-XXX Edited by AHTRAM G. DENNIS DNA DRAWDE A. SINNED EMULOV XXXIV. Affinity Techniques (Enzyme Purification: Part B) Edited by WILLIAM B. YBOKAJ DNA MEIR KEHCLIW EMULOV XXXV. Lipids (Part B) Edited by JOHN i. NIETSNEWOL SDOHTEM NI YGOLOMYZNE VX EMULOV XXXVI. Hormone Action (Part A: Steroid Hormones) Edited by BERT W. O'MALLEY DNA JOEL G. NAMDRAH EMULOV XXXVII. Hormone Action (Part B: Peptide Hormones) Edited yb BERT W. O'MALLEY DNA JOEL G. NAMDRAH EMULOV XXXVIII. Hormone Action (Part C: Cyclic Nucleotides) Edited yb JOEL G. NAMDRAH DNA BERT W. O'MALLEY EMULOV XXXlX. Hormone Action (Part D: Isolated Cells, Tissues, and Organ Systems) Edited yb JOEL G. NAMDRAH DNA BERT W. O'MALLEY EMULOV XL. Hormone Action (Part E: Nuclear Structure and Function) Edited yb BERT W. O'MALLEY DNA JOEL G. NAMDRAH EMULOV XLI. Carbohydrate Metabolism (Part B) Edited by W. A. DOOW EMULOV XLII. Carbohydrate Metabolism (Part C) Edited yb W. A. DOOW EMULOV XLIII. Antibiotics Edited yb JOHN H. HSAH EMULOV XLIV. Immobilized Enzymes Edited by KLAUS HCABSOM EMULOV XLV. Proteolytic Enzymes (Part B) Edited yb OLZSAL DNAROL EMULOV XLVI. Affinity Labeling Edited yb WILLIAM B. YBOKAJ DNA MEIR KEHCLIW EMULOV XLVII. Enzyme Structure (Part E) Edited yb C. H. W. HIRS DNA EGRES N. EEEHSAMIT EMULOV XLVIII. Enzyme Structure (Part F) Edited yb C. H. W. HIas DNA EGRES N. EEEHSAMIT EMULOV XLIX. Enzyme Structure (Part G) Edited by C. H. W. HIRS DNA EGRES N. FEEHSAMIT EMULOV L. Complex Carbohydrates (Part C) Edited yb ROTCIV GRUBSNIG EMULOV LI. Purine and Pyrimidine Nucleotide Metabolism Edited by AICIRTAP A. HOFFEE DNA YRAM ELLEN SENOJ EMULOV LII. Biomembranes (Part C: Biological Oxidations) Edited by SIDNEY REHCSIELF DNA RETSEL REKCAP EMULOV LIII. Biomembranes (Part D: Biological Oxidations) Edited yb SIDNEY REHCSIELF DNA RETSEL REKCAP EMULOV LIV. Biomembranes (Part E: Biological Oxidations) Edited by SIDNEY REHCSIELF DNA RETSEL REKCAP xvi SDOHTEM IN YGOLOMYZNE EMULOV LV. Biomembranes (Part F: Bioenergetics) Edited yb SIDNEY FLEISCHER DNA LESTER PACKER EMULOV LVI. Biomembranes (Part G: Bioenergetics) Edited yb SIDNEY FLEISCHER DNA LESTER REKCAP EMULOV LVII. Bioluminescence and Chemiluminescence Edited yb ENELRAM A. DELUCA EMULOV LVIII. Cell Culture Edited yb WILLIAM B. JAKOBY DNA ARI PASTAN EMULOV LIX. Nucleic Acids and Protein Synthesis (Part G) Edited yb KIVlE EVADLOM DNA ECNERWAL NAMSSORG EMULOV LX. Nucleic Acids and Protein Synthesis (Part H) Edited yb KIVlE EVADLOM DNA ECNERWAL NAMSSORG EMULOV 61. Enzyme Structure (Part H) Edited yb C. H. W. HIRS DNA EGRES N. FFEHSAMIT EMULOV 62. Vitamins and Coenzymes (Part D) Edited yb DONALD B. KCIMROCCM DNA LEMUEL D. WRIGHT EMULOV 63. Enzyme Kinetics and Mechanism (Part A: Initial Rate and Inhibi- tor Methods) Edited yb DANIEL L. PURICH EMULOV 64. Enzyme Kinetics and Mechanism (Part B: Isotopic Probes and Complex Enzyme Systems) Edited yb DANIEL L. PURICH EMULOV 65. Nucleic Acids (Part I) Edited yb ECNERWAL NAMSSORG DNA KIVlE EVADLOM EMULOV 66. Vitamins and Coenzymes (Part E) Edited yb DONALD B. KCIMROCCM DNA LEMUEL D. WRIGHT EMULOV 67. Vitamins and Coenzymes (Part F) Edited by DONALD B. McCoRMICK DNA LEMUEL D. WRIGHT EMULOV 68. Recombinant DNA Edited yb YAR Wu EMULOV 69. Photosynthesis and Nitrogen Fixation (Part C) Edited yb ANTHONY NAS ORTEIP EMULOV 70. Immunochemical Techniques (Part A) Edited by HELEN NAV VUNAKIS DNA JOHN J. ENOGNAL EMULOV 71. Lipids (Part C) Edited yb JOHN M. NIETSNEWOL EMULOV 72. Lipids (Part D) Edited yb JOHN M. NIETSNEWOL xvii METHODS IN ENZYMOLOGY EMULOV 73. Immunochemical Techniques (Part B) Edited by JOHN J. ENOGNAL DNA HELEN NAV SIKANUV EMULOV 74. Immunochemical Techniques (Part C) Edited yb JOHN J. ENOGNAL DNA HELEN NAV SIKANUV EMULOV .57 Cumulative Subject Index Volumes XXXI, XXXII, XXXIV-LX Edited by DRAWDE A. DENNIS DNA AHTRAM G. SINNED EMULOV .67 Hemoglobins Edited yb ODLARE ANTONINI, LUIGI ,IDRANREB-IsSOR DNA EMILIA -NAIHC ENOC EMULOV .77 Detoxication and Drug Metabolism Edited by WILLIAM B. YBOKAJ EMULOV .87 Interferons (Part A) Edited by YENDIS AKTSEP EMULOV .97 Interferons (Part B) Edited yb YENDIS AKTSEP EMULOV 80. Proteolytic Enzymes (Part C) Edited by OLZSAL DNAROL EMULOV .18 Biomembranes (Part H: Visual Pigments and Purple Mem- branes, I) Edited by RETSEL REKCAP EMULOV .28 Structural and Contractile Proteins (Part A: Extracellular Matrix) Edited yb LEON W. MAHGNINNUC DNA DIXIE W. NESKIREDERF EMULOV .38 Complex Carbohydrates (Part D) Edited by ROTCIV GRUBSNIG EMULOV .48 Immunochemical Techniques (Part D: Selected Immunoassays) Edited by JOHN J. ENOGNAL DNA HELEN NAV SIKANUV EMULOV .58 Structural and Contractile Proteins (Part B: The Contractile Appa- ratus and the Cytoskeleton) Edited by DIXIE W. NESKIREDERF DNA LEON W. MAHGNINNUC EMULOV 86. Prostaglandins and Arachidonate Metabolites Edited by WILLIAM E. M. LANDS DNA WILLIAM L. HTIMS EMULOV .78 Enzyme Kinetics and Mechanism (Part C: Intermediates, Stereo- chemistry, and Rate Studies) Edited yb DANIEL L. HCIRUP EMULOV .88 Biomembranes (Part I: Visual Pigments and Purple Mem- branes, II) Edited yb RETSEL REKCAP EMULOV .98 Carbohydrate Metabolism (Part D) Edited yb WILLIS A. DOOW IIIVX °°° SDOHTEM NI YGOLOMYZNE EMULOV 90. Carbohydrate Metabolism (Part E) Edited by WILLIS A. DOOW EMULOV .19 Enzyme Structure (Part I) Edited by C. H. W. HIRS DNA EGRES N. FFEHSAMIT EMULOV .29 Immunochemical Techniques (Part E: Monoclonal Antibodies and General Immunoassay Methods) Edited by JOHN J. ENOGNAL DNA HELEN NAV SIKANUV EMULOV .39 Immunochemical Techniques (Part F: Conventional Antibodies, Fc Receptors, and Cytotoxicity) Edited by JOHN J. ENOGNAL DNA HELEN NAV SIKANUV EMULOV 94. Polyamines Edited by TREBREH ROBAT DNA CELIA WHITE ROBAT EMULOV 95, Cumulative Subject Index Volumes 61-74, 76-80 Edited by DRAWDE A. DENNIS DNA AHTRAM G. SINNED EMULOV .69 Biomembranes Part J: Membrane Biogenesis: Assembly and Targeting (General Methods; Eukaryotes) Edited by SIDNEY REHCSIELF DNA ACCEB REHCSIELF EMULOV .79 Biomembranes Part K: Membrane Biogenesis: Assembly and Targeting (Prokaryotes, Mitochondria, and Chloroplasts) Edited by SIDNEY REHCSIELF DNA ACCEB REHCSIELF EMULOV .89 Biomembranes (Part L: Membrane Biogenesis: Processing and Recycling) Edited by SIDNEY REHCSIELF DNA ACCEB REHCSIELF EMULOV 99. Hormone Action (Part "F Protein Kinases) Edited by EIKCAJ D. NIBROC DNA JOEL G. NAMDRAH EMULOV 100. Recombinant DNA (Part B) Edited by YAR Wu, ECNERWAL ,NAMSSORG DNA KIVIE EVADLOM EMULOV I01. Recombinant DNA (Part C) Edited by YAR Wu, ECNERWAL ,NAMSSORG DNA KIVIE EVADLOM EMULOV 102. Hormone Action (Part G: Calmodulin and Calcium-Binding Pro- teins) Edited by YNOHTNA R. SNAEM DNA BERT W. O'MALLEY EMULOV 103. Hormone Action (Part H: Neuroendocrine Peptides) Edited by P. LEAHCIM NNOC EMULOV 104. Enzyme Purification and Related Techniques (Part C) Edited by WILLIAM B. YBOKAJ EMULOV 105. Oxygen Radicals in Biological Systems Edited by RETSEL REKCAP EMULOV 106. Posttranslational Modifications (Part A) Edited by FINN WOLD DNA KIVIE EVADLOM

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