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Biochemical Spectroscopy PDF

814 Pages·1995·13.968 MB·English
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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 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 1 NOITCUDORTNI 1 1 Why Spectroscopy? Which Spectroscopy? yB KENNETH SAUER Biochemists and scientists in related fields have a "need to know" about information covering an enormous range of disciplines. They are interested in the involvement and fates of very small molecules like 02, CO2, n20, and N 2, as well as those of the largest proteins and nucleic acids. Scientists also want to know about the interactions of the small molecules with the large ones: not only to view the needle in the hay- stack, but to determine whether "it is threaded and ready to use." These studies may involve "simple" reactions like the interchange between dissolved CO2 gas and bicarbonate ion in aqueous solution, as well as the role of enzymes that can speed up such processes by orders of magni- tude. The context in which biochemical processes occur is essential to defin- ing mechanisms and functions. The component proteins and nucleic acids exhibit dramatic changes in properties when they are incorporated into ribosomes or chromosomes or functional membranes. Even then, it is not sufficient to determine a static or average structure of the components in such complex assemblies, because the function typically depends on essential structural fluctuations or driven conformational changes. In this way time enters as a significant variable. Short-term events (picosecond time scale and shorter) can involve vibrational motion to dissipate heat energy or to initiate conformational events that trigger vision processes or start the electron transfer reactions of photosynthesis. Diffusion of small substrate molecules is a few orders of magnitude slower. The motion of major portions of proteins may require only microseconds, whereas the complex decision-making required for enzymes to function selectively may require times in the range of seconds. Such an enormous range of conditions and interests places enormous demands on the panoply of experimental approaches needed to address the related issues. In a recent single issue of the American Chemical Society journal yrtsimehcoiB there were 25 articles, of which all but 4 explicitly involved some form of spectroscopy among the methods that were cited. In many cases two or three spectroscopic methods were used in the same study, and none of these entailed simply using absorbance at a particular wavelength to monitor the concentration of a particular component. Even the other 4 articles, which included one study involving X-ray crystallography and another that followed the course of a radioiso- Copyright © 1995 by Academic Press, Inc. METHODS IN ENZYMOLOGY, VOL. 246 All rights of reproduction in any form reserved. 2 INTRODUCTION 1 tope, contained procedures that implied the application of spectroscopic methods in the preparation and purification of materials. Numerous, wide-ranging spectroscopic techniques will be presented in this volume, with the exception of nuclear magnetic resonance 1,)RMN( which was the subject of Volumes 176, 177, and 932 of Methods ni Enzy- mology, and mass spectrometry,: which was the subject of Volume .391 Examples of techniques from each of three major areas, ultraviolet/visible spectroscopy, vibrational spectroscopy, and electron or electron/nuclear magnetic resonance, are presented in this volume. Also included are special topics like rapid-scan diode-array spectroscopy, terbium labeling ofchromopeptides, and deconvolution of complex spectra that are covered in chapters in Section IV of this volume. Why Spectroscopy? The range of areas of scientific interest represented in the Biochemistry issue mentioned above was extremely broad. A sampling includes the following: the interaction with DNA of a cobalt probe that resulted in shifts in the electron paramagnetic resonance (EPR) spectrum as well as changes in the circular dichroism, a study of protein oligomerization, premelting flexibility of a synthetic oligonucleotide, the formation of cross- links between DNA and protein using platinum and ruthenium compounds, enzyme-substrate interactions, the structure and dynamics of channel- forming membrane proteins, the dynamics of unfolding and refolding of a redoxactive protein, and the use of a fluorescent amino acid reporter to send signals from the channel of a transporter protein. Spectroscopic methods can be used to examine the behavior of cell organelles or macro- scopic assemblies that are not yet amenable to interpretation at the molecu- lar level. One of the virtues of spectroscopic approaches is that they are com- monly nondestructive and noninvasive, although some procedures involve the attachment of labels chemically at specific sites. The former ap- proaches are particularly valuable for ni uivo studies. In laboratory experi- ments, the amounts of materials required range from the femtomole (I0-,5 tool) level for some particularly sensitive fluorescence approaches to milli- grams or more for typical EPR, infrared, or X-ray spectroscopy. Ongoing requirements in instrumentation and techniques are continually whittling away at the limits to the amount of material required. t N. J. Oppenheimer and T. L. James (eds.), this series, Vols. 176, 177, and 239: Nuclear Magnetic Resonance. 2 j. A. McCloskey (ed.), this series, Vol. 193: Mass Spectrometry. 1 NOITCUDORTNI 3 Which Spectroscopy? One of the most important questions facing an experimentalist at the outset of a research project is the decision about which of the available (or potentially available) spectroscopic methods is most suitable to a par- ticular problem or investigation. The decision is complex, in that it in- volves consideration of the nature of the biological or chemical materials being investigated, the particular goals of the research, the availability of suitable spectroscopic tools, and the ability to interpret the results in a meaningful way. The latter requirement implies the need for at least a vestige of a theoretical framework in which to formulate the interpretation and, in many cases, access to an "expert" who is knowledgeable about the relation between the experimentally observed quantities and their origin at the molecular or electronic level. One important source of such expertise is a suitable text or reference book that describes the underlying principles in terms that are both informative and understandable. Although the relation between underlying principles and spectroscopic measure- ments properly involves subjects such as quantum mechanics, statistical mechanics, and molecular dynamics, one does not necessarily need to be an authority in these fields to be sufficiently conversant to make intelligent use of the spectroscopic observables. Each of the individual chapters in this volume presents references to authoritative monographs or compendia of relevant information on the main topic covered. There are, in addition, introductory books that de- scribe a broad range of relevant methods; these books are particularly helpful in making the initial decision as to which spectroscopic methods to choose for a particular problem. 4,3 Sections that involve spectroscopy are included in a variety of texts in biochemistry, 5 physical chemistry for biological scientists, 6-1° or biophysics. At a somewhat more advanced 3 ,R E. Hester dna .R .B Stirling, "Spectroscopy of lacigoloiB Molecules." CRC Press, Boca Raton, Florida, .1991 4 I. .D Campbell and .R .A Dwek, "Biological Spectroscopy." ,sgnimmuC/nimajneB Menlo Park, California, .4891 L. Stryer, "Biochemistry," dr3 Ed. Freeman, naS Francisco, California, .8891 6 I. Tinoco, Jr., K. Sauer, and J. C. Wang, "Physical Chemistry--Principles dna -acilppA tions ni lacigoloiB Sciences," dr3 Ed. Prentice-Hall, Englewood Cliffs, New Jersey, .5991 7 .D Eisenberg and .D Crothers, "Physical Chemistry, with Applications to the Life Sci- ences." ,sgnimmuC/nimajneB Menlo Park, California, ,9791 8 .A G. Marshall, "Biophysical Chemistry--Principles, Techniques dna Applications." Wiley, weN York, .8791 9 .D Freifelder, "Physical Biochemistry--Applications to Biochemistry dna Molecular -loiB ogy," dn2 Ed. Freeman, naS Francisco, California, .2891 0~ K. E. naV Holde, "Physical Biochemistry," dn2 Ed. Prentice-Hall, Englewood ,sffilC weN Jersey, .5891 4 NOITCUDORTNI ll level, the monograph by Cantor and Schimme111 is a particularly valuable resource for this purpose. Greater detail in the theoretical underpinnings of many of the types of spectroscopy used by biochemists is covered in an excellent book by Struve. 21 Nevertheless, it is inevitable that some of the topics covered in the present volume are not to be found or are only briefly mentioned in the broader surveys. This occurs either because the fields, or the applications to biological problems, are relatively new X-ray spectroscopy, hole burning, Fourier transform infrared spectroscopy (FTIR) or because until recently the applications to biology were con- strued to be highly specialized electron nuclear double resonance spec- troscopy (ENDOR), spin labels, digital imaging spectroscopy. Several of these methods have sufficient potential that they should be considered to be a part of the reserve toolkit of experimental biochemists and biolo- gists. Spectrometric methods rely on the availability of reference data or relevant properties of well-examined biochemical materials. Such data are abundant and widespread in the literature, but compilations of such spectrometric data are not nearly so available as are those in the areas of chemistry or physics. Even the few compilations that exist 4a31 are not particularly recent or up-to-date. This is a shortcoming that the leaders of the discipline should endeavor to remedy. To aid the reader in the process of choosing suitable tools from the toolkit, the following paragraphs focus on a variety of objectives that are typical of biochemical and biological investigations and how each of the objectives may be productively illuminated by the methods described in detail in the subsequent chapters. Structure of Biomolecules The distinction between monomer, duplex, and triplex helices of DNA or RNA can be established by a comparison of absorption and circular dichroism (CD) spectroscopy. A clear difference in the CD is seen that distinguishes triplexes of RNA from those of DNA. 6A51 The CD spectra II C. R. Cantor and P. R. Schimmel, "Biophysical Chemistry--Part II: Techniques for the Study of Biological Structure and Function." Freeman, San Francisco, California, 1980. 21 W. S. Struve, "Fundamentals of Molecular Spectroscopy." Wiley (Interscience), New York, 1989. 31 G. D. Fasman (ed.), "Handbook of Biochemistry and Molecular Biology, Vol. :1 Physical and Chemical Data," 3rd Ed. CRC Press, Cleveland, Ohio, 1976. 4i G. D. Fasman (ed.), "Practical Handbook of Biochemistry and Molecular Biology." CRC Press, Boca Raton, Florida, 1989. 51 D. M. Gray, S.-H. Hung, and K. H. Johnson, this volume 3. 61 R. W. Woody, this volume 4. ll NOITCUDORTNI 5 of proteins and polypeptides are also useful in determining the content of zc helix,/3 sheet, and/3 turns.~6 The coordination geometry and spin state of transition metal centers in biomolecules can be characterized using CD and magnetic circular dichroism (MCD) measurements.17 The conforma- tion of macromolecules in solution is sensitively measured by excitation transfer between fluorescence donor-acceptor molecular pairs that are covalently or noncovalently attached. 9~,8~ Detailed information about the backbone conformation of proteins or nucleic acid helices can be read from Raman °2 or infrared ~2 spectra. Resonance Raman spectra are useful in documenting the subtle distinction between the a- and/3-subunit hemes in hemoglobin. 22 Changes in the oxidation state of iron- or copper-contain- ing proteins allow ENDOR spectroscopy to elucidate the coordination environment of the redox-active cofactors. 32 Rotational diffusion con- stants that are sensitive to molecular extension can be determined using spin-labeled macromolecules. The difference between a peptide in the a helix or 0~3 helix configuration is readily seen in the EPR spectra of doubly spin-labeled molecules. 42 Changes in Structure or Conformation The transformation of polyproline from a right-handed to a left-handed 3-fold helix can be followed using CD.~6 MCD spectra are sensitive to the conformation of the heme-imidazole ligand interaction in cytochromes. 52 Hole-burning measurements provide sensitive tools for detecting differ- ences in structure produced on thermal cycling or as a consequence of increasing pressure on horseradish peroxidase solutions. 62 Attachment of a fluorescence label 72 provides a useful indicator of the loss of activity of human immunodeficiency virus (HIV) protease, 8~ and lifetime measure- ments can be used to determine the binding of ligands, of drugs to proteins, or the association of proteins with membranes. 91 Similarly, the decreasing content of free sulfhydryl groups that accompanies aging is detectable by Raman spectroscopy using deuterium exchange methods.2° Raman spectra 7I E. I. Solomon, .M L. Kirk, .D .R Gamelin, and .S Pulver, this volume .5 81 p. .R Selvin, this volume .31 91 .A .R Holzwarth, this volume .41 02 .W L. Peticolas, this volume .71 i2 F. Siebert, this volume .02 22 j. .R Kincaid, this volume .91 32 .V J. DeRose and .B .M Hoffman, this volume .32 42 .G L. Millhauser, .W .R Fiori, dna .S .M Miick, this volume .42 52 j. .C Sutherland, this volume .6 62 j. Friedrich, this volume .01 72 .A Waggoner, this volume .51 6 NOITCUDORTNI 1 also can be used to follow the course of DNA or RNA melting, °z The involvement of aspartate in the photocycling of bacteriorhodopsin can be followed using difference infrared studies of isotopically substituted molecules. 12 Electron spin-labeled proteins exhibit striking changes in EPR spectra on undergoing structural transformations, 4z noitisopmoC of sexelpmocoiB The stoichiometry of RNA in duplex or DNA in triplex complexes is discernible from CD spectra, as are hybrid complexes between RNA and DNA. 51 The amino acid content of proteins and polypeptides is reflected in the UV absorption and CD spectra, as is the presence of cofactors such as heme or flavin. The CD spectrum is also sensitive to interactions between proteins and nucleic acids. 61 In general, cofactors that involve transition metals with incomplete d electron shells exhibit characteristic features in absorption, CD, and MCD 52,71.artceps The presence of trypto- phan gives rise to a distinctive band in the MCD spectrum of any protein.25 The binding of substrate analogs like e-AMP to carbamoyl-phosphate synthase can be detected by the influence on the anisotropy of the fluores- cence. Protein-DNA interactions have been monitored using the anisot- ropy of fluorescence of Trp of the Ada protein and the cal promoter with cyclic AMP in the presence of receptor protein, 8z Added fluorescent dyes can be used to tag DNA molecules, even during electrophoresis.~8 FTIR spectra reflect the interaction between certain drugs and DNA, and they characterize caged Ca +z and caged ATP as well. ~2 Stacking interactions in protein-DNA complexes have been investigated using optically detected magnetic resonance (ODMR). 92 Photosynthetic complexes that contain antenna complexes and reaction centers exhibit complex fluorescence relaxation that reflects the spectroscopic heterogeneity of the complexes. 9~ The identity and integrity of photosynthetic reaction center complexes are readily determined using chromatography with a diode-array detector, as is the degradation of isolated photosynthetic pigments. °3 noitatneirO of Component Structures The orientation of structural components in proteins can be character- ized using polarized absorption or emission spectroscopy. Where single crystals are not available or convenient, anisotropic macromolecules may be oriented using gel compression, electric or magnetic fields, or stretched 82 D. M. Jameson and W. H. Sawyer, this volume 12. 92 A. H. Maki, this volume 25. o3 H. Scheer, this volume 30.

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