Skip to main content

Structure Determination of Biomolecules by Physical Methods

  • Chapter
Biophysics

Abstract

Proteins and nucleic acids are macromolecules, with dimensions up to some 102 nm and molecular weights up to 108. To determine their idealized global structural parameters, physical methods as developed for polymer analytics are especially useful. Whereas even large biomolecules have well-defined molecular weights, correlated with their specialized function, synthetic polymers have not but instead are characterized by a molecular weight distribution. Depending on the measuring method used, different average values may thus result. The following types of means have been introduced in polymer chemistry, defining

$$ {{\bar{M}}_{x}} = \frac{{\sum {{{N}_{i}} \cdot {\text{M}}_{i}^{x}} }}{{\sum {{{N}_{i}} \cdot {\text{M}}_{i}^{{x - 1}}} }} $$

N i , number of molecules with molecular weight M i .

This is a preview of subscription content, log in via an institution to check access.

Access this chapter

Chapter
USD 29.95
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
eBook
USD 74.99
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever

Tax calculation will be finalised at checkout

Purchases are for personal use only

Institutional subscriptions

Selected References

  • Beeman, W., Kaesberg, P., Anderegg, J.W., Webb, M.B.: Size of particles and lattice defects. Handb. Phys. 32, 322–389 (1957).

    Google Scholar 

  • Brumberger, H.: Proceedings of the Conference held at Syracuse University, June 1965, on “Small-Angle X-Ray Scattering”. New York, London, Paris: Gordon and Breach 1967.

    Google Scholar 

  • Glatter, O. and Kratky, O. (Editors): Small Angle X-ray Scattering. Academic Press London 1982.

    Google Scholar 

  • Guinier, A., Fournet, G.: Small Angle Scattering of X-Rays. New York: J. Wiley Sons Inc. and London: Chapmann & Hall 1955.

    Google Scholar 

  • Kratky, O.: X-ray small angle scattering with substances of biological interest in diluted solution. Prog. Biophys. 13, 105–173 (1963).

    Article  Google Scholar 

  • Kratky, O., Pilz, I.: Recent advances and applications of diffuse X-ray small-angle scattering on biopolymers in dilute solutions. Q. Rev. Biophys. 5, 481–537 (1972).

    Article  Google Scholar 

  • Kratky, O., Pilz, I.: A Comparison of X-ray small-angle scattering results to crystal structure analysis and other physical techniques in the field of biological macromolecules. Q. Rev. Biophys. 2, 39–70 (1978).

    Article  Google Scholar 

  • Pessen, H., Kumosinsky, T.F., Timasheff, S.N.: Small-angle X-ray scattering. Methods Enzymol. Academic Press New York 27, 151–209 (1973).

    Google Scholar 

  • Pilz, I.: Small-Angle X-Ray Scattering. In: Physical Principles and Techniques of Protein Chemistry, Part C London, New York: Academic Press 1973, pp. 141–243.

    Google Scholar 

  • Pilz, I., Glatter, O., Kratky, O.: Small-angle X-ray scattering. Methods Enzymol. Academic Press New York 61, 148–249 (1979).

    Google Scholar 

  • Cummins, H., Swinney, H.: In: E. Wolf (Ed.): Progress in Optics, p. 135. Amsterdam: North Holland Pubi. 1970.

    Google Scholar 

  • Debye, P.: J. Phys. Chem. 51, 18 (1951).

    Article  Google Scholar 

  • Mie, G.: Ann. Physik 25, 37 (1908).

    Google Scholar 

  • Lord Rayleigh: Phil. Mag. 41, 107 (1871).

    Google Scholar 

  • Tanford, C.: Physical Chemistry of Macromolecules, Chap. 5. New York: Wiley 1961.

    Google Scholar 

  • Zimm, B.: J. Chem. Phys. 16, 1100 (1948).

    ADS  Google Scholar 

  • Jaffe, H.H., Orchin, M.: Theory and Application of Ultraviolet Spectroscopy. New York: Wiley 1962

    Google Scholar 

  • Korte, F. (Ed.): Methodicum Chimicum. Stuttgart: Thieme; New York-London: Academic Press 1973

    Google Scholar 

  • Kortüm, G.: Kolorimetrie, Photometrie und Spektroskopie. Berlin-Göttingen-Heidelberg: Springer 1962

    Google Scholar 

  • Murrel, J.N.: Elektronenspektren organischer Moleküle. Mannheim: Bibliographisches Institut 1967

    Google Scholar 

  • Schläfer, H.L., Gliemann, G.: Einführung in die Ligandenfeldtheorie, Frankfurt/Main, Akademische Verlagsgesellschaft 1967

    Google Scholar 

  • Thiessen, H., Thiessen, G.: Microspectrophotometric Cell Analysis, Stuttgart, Gustav Fischer Verlag 1977

    Google Scholar 

  • Rosencwaig, A., Gersho, A.: J. Appi. Phys. 47, 64, 1976

    Article  ADS  Google Scholar 

  • McDonald, F.A., Wetsel, G.C., Jr.: J. Appi. Phys. 49, 2313, 1978

    Article  ADS  Google Scholar 

  • Wetsel, G.C., McDonald, F. A.: Appi. Phys. Lett. 30, 252, 1977

    Article  ADS  Google Scholar 

  • Roark, J.C., Palmer, R. A., Hutchinson, J. S.: Chem. Phys. Lett. 60, 112, 1978

    Article  ADS  Google Scholar 

  • Pao, Y.-H. (Ed.): Optoacoustic Spectroscopy and Detection, Academic Press, New York, San Francisco, London 1977

    Google Scholar 

  • Albrecht, H. et al.: Optische Strahlungsquellen. Grafenau/Württ.: Lexika-Verlag 1977.

    Google Scholar 

  • Björn, L.O.: Simple Methods for the Calibration of Light Measuring Equipment. Physiol. Plant. 25, 300–307 (1971).

    Article  Google Scholar 

  • Flügge, J.: Studienbuch zur technischen Optik. Hrsg. G. Hartwig. Göttingen: Vandenhoeck & Ruprecht 1976.

    Google Scholar 

  • Gerlach, D.: Das Lichtmikroskop. Stuttgart: G. Thieme 1976.

    Google Scholar 

  • Kiefer, J., Hrsg.: Ultraviolette Strahlen. Berlin, New York: de Gruyter 1977.

    Google Scholar 

  • Kortüm, G.: Reflexionsspektroskopie. Berlin, Heidelberg, New York: Springer 1969.

    Google Scholar 

  • Mielenz, K. D., Velapoldi, R. A., Mavrodineanu, R.: Standardization in Spectrophotometry and Luminescence Measurements. Washington: U.S. Government Printing Office 1977.

    Google Scholar 

  • Schäfer, E., Fukshansky, L., Shropshire, W.: Action spectroscopy. In: Photomorphogenesis. Encyclopedia of Plant Physiology, N.S. Vol. 18. Berlin Heidelberg, New York: Springer 1983.

    Google Scholar 

  • Scheuner, G., Hutschenreiter, J.: Polarisationsmikroskopie in der Histophysik. Leipzig: Thieme 1972.

    Google Scholar 

  • Senger, H. Hrsg.: The Blue Light Syndrome. Berlin, Heidelberg, New York: Springer 1980.

    Google Scholar 

  • Setlow, R. B., Pollard, E. C.: Action Spectra and Quantum Yields. In: Molecular Biophysics pp. 267–305. Oxford, London, New York, Paris: Pergamon Press 1962.

    Google Scholar 

  • Zimmer, K.G.: Zur Berücksichtigung der biologischen Variabilität bei der Treffertheorie der biologischen Strahlenwirkung. Bial. Zbl. 61, 208 (1941).

    Google Scholar 

  • Brahms, J., Brahms, S.: Circular Dichroism of Nucleic Acids. In Fasman, G.D., Timasheff, S.N. (Eds.): Fine Structure of Proteins and Nucleic Acids, Biological Macromolecules Series Vol. 4. Marcel Dekker, New York, 1970.

    Google Scholar 

  • Caldwell, D.J., Eyring, H.: The Theory of Optical Activity. Wiley-Interscience, New York, 1971.

    Google Scholar 

  • Hsu, M.-C., Woody, R. W.: J. Am. Chem. Soc. 93, 3515–3525 (1971).

    Article  Google Scholar 

  • Imahori, K., Nicola, N.A.: Optical Rotatory Dispersion and the Main Chain Conformation of Proteins. In S. J. Leach (Ed.): Physical Principles and Techniques of Protein Chemistry, Part C, Academic Press, New York, 1973.

    Google Scholar 

  • Sears, D.W., Beychok, S.: Circular Dichroism. In S. J. Leach (Ed.): Physical Principles and Techniques of Protein Chemistry, de Gruyter, Academic Press, New York, 1973.

    Google Scholar 

  • Strickland, E.H.: CRC Crit. Rev. Biochem. 2, 113–175 (1974).

    Article  Google Scholar 

  • Tinoco, J., Jr.: Advan. Chem. Phys. 4, 113–160 (1962).

    Article  Google Scholar 

  • Weissberger, A., Rossiter, B. (Eds.): Techniques of Chemistry, Vol. I, Part III C, Polarimetry. Wiley & Sons, New York, 1972.

    Google Scholar 

  • Bade, D., Parak, F.: Biophys. Struc. Mech. 2, 219–231 (1976).

    Article  Google Scholar 

  • Bade, D., Parak, F.: Z. Naturforsch. 33c, 488–494 (1978).

    Google Scholar 

  • Bearden, A., Dunham, W.R.: Struct. Bond. 8, 1–52 (1970).

    Google Scholar 

  • Braunitzer, G., Buse, G., Gersonde, K.: Structure and function of hemoglobins. In: Hayaishi, D. (Ed.). Molecular Oxigen in Biology, Chap. 6. Series: Frontiers of Biology, Holland.

    Google Scholar 

  • Eicher, H., Bade, D., Parak, F.: J. Chem. Phys. 64, 1446–1455 (1976).

    Article  ADS  Google Scholar 

  • Eicher, H., Parak, F., Bogner, L., Gersonde, K.: Z. Naturforsch. 29c, 683–691 (1974).

    Google Scholar 

  • Gersonde, K., Schlaak, H.I., Breitenbach, M., Parak, F., Eicher, H., Zgorzalla, W., Kalvius, G.M., Mayer, A.: Eur. J. Biochem. 43, 307–317 (1974).

    Article  Google Scholar 

  • Goldanskii, V.I., Herber, R.H.: Chemical Applications of Mossbauer Spectroscopy. London, New York: Academic Press 1968.

    Google Scholar 

  • Gonser, U., Maeda, Y., Trautwein, A., Parak, F., Formanek, H.: Z. Naturforsch. 29b, 241–244 (1974).

    Google Scholar 

  • Greenwood, N.N., Gibb, T.C.: Mossbauer Spectroscopy. London: Chapman and Hall 1971.

    Book  Google Scholar 

  • Kalvius, G.M., Kankeleit, E.: Mossbauer Spectroscopy and its Application. International Atomic Energy Agency, p. 9, Vienna 1972.

    Google Scholar 

  • Mossbauer, R.L.: Annu. Rev. Nucl. Sci. 12, 123–152 (1962).

    Article  ADS  Google Scholar 

  • Mossbauer, R.L.: Naturwissenschaften 60, 493 (1973).

    Article  ADS  Google Scholar 

  • Parak, F., Formanek, H.: Acta Cryst. A27, 573–578 (1971).

    Google Scholar 

  • Parak, F.: Proc. Int. Conf. On Mossbauer Spectroscopy, Vol. 1. Hrynkiewicz, A.Z., Sawicki, J.A. (Eds.), pp. 439–440 (1975).

    Google Scholar 

  • Parak, F., Mossbauer, R.L., Hoppe, W., Thomanek, U.F., Bade, D.: J. Phys. Coll. C6 37, C6 703–706 (1976).

    Google Scholar 

  • Parak, F., Knapp, E.W., Kucheida, D.: J. Mol. Biol. 161, 177–194 (1982).

    Article  Google Scholar 

  • Perutz, M.F.: Nature (London) 228, 726–739 (1970)

    Article  ADS  Google Scholar 

  • Phillips, D.C.: In: Brill, R., Mason, R. (Eds.). Advances in Structure Research by Diffraction Methods, Vol. 2. Braunschweig: Vieweg 1966, pp. 75–140.

    Google Scholar 

  • Stevens, J.G., Stevens, V.E.: Mossbauer Effect Data Index. New York: IFI Plenum Press (annual since 1965).

    Google Scholar 

  • Thomanek, U.F., Parak, F., Mossbauer, R.L., Formanek, H., Schwager, P., Hoppe, W.: Acta Cryst. A29, 263–265 (1973).

    Google Scholar 

  • Bernasconi, C. F.: Relaxation Kinetics, New York, San Francisco, London: Academic Press 1976.

    Google Scholar 

  • Eigen, M., de Mayer, L.: Theoretical Basis of Relaxation Spectroscopy, Chapt. Ill in: Techniques of Chemistry (A. Weisberger, Ed.) Vol. VI, Part II, New York, London, Toronto; Wiley 1973; s. other chapters in part II: Investigation in Elementary Reaction Steps in Solution and Very Fast Reactions (G. G. Hammes, Ed.).

    Google Scholar 

  • Neumann, E.: Principles of Electric Field Effects in Chemical and Biological Systems, in Vol. 4 of Topics in Bioelectrochemistry and Bioenergetics, G. Milazzo, Ed., John Wiley and Sons, London, 1981, pp. 113–160.

    Google Scholar 

  • Rüppel, H., Witt, H. T.: Measurements of fast reactions by single and repetitive excitation with pulses of electromagnetic radiation, in: S. P. Colowick and N. O. Kaplan (Eds.): Vol. XVI: Fast reactions, Article 9, New York, London: Academic Press 1969.

    Google Scholar 

  • Winkler-Oswatitsch, R., Eigen, M.: “The Art of Titration”, Angew. Chem. Intern. Ed. (Engl.) 18, 20–49 (1979).

    Article  Google Scholar 

  • Abragam, A., Bleaney, B.: Electron Paramagnetic Resonance of Transition Ions. Oxford: Clarendon Press 1970.

    Google Scholar 

  • Carrington, A., McLachlan, A.D.: Introduction to Magnetic Resonance. London: Chapman & Hall 1979.

    Google Scholar 

  • Dorio, M.M., Freed, J.H. (Eds.): Multi Electron Resonance Spectroscopy. New York: Plenum Press 1979.

    Google Scholar 

  • Knowles, P.F., Marsh, D., Rattle, H.W.E.: Magnetic Resonance of Biomolecules. London: John Wiley & Sons 1976.

    Google Scholar 

  • Scheffler, K., Stegman, H.B.: Elektronenspinresonanz. Berlin, Heidelberg, New York: Springer 1970.

    Google Scholar 

  • Schneider, F., Plato, M.: Elektronenspinresonanz. München: Verlag Karl Thiemig 1971.

    Google Scholar 

  • Swartz, H.M., Bolton, J.R., Borg, D.C. (Eds.): Biological Applications of Electron Spin Resonance. New York: Wiley Interscience 1972.

    Google Scholar 

  • Wertz, J.B., Bolton, J.R.: Electron Spin Resonance, Elementary Theory and Practical Applications. New York: McGraw-Hill 1972.

    Google Scholar 

  • Berliner, L.J., Reuben, J.: Biological Magnetic Resonance, Bd. 1 u. 2. New York: Plenum Press 1978, 1980.

    Google Scholar 

  • Breitmaier, E., Voelter, W.: Carbon-13 NMR Spectroscopy, Monographs in Modern Chemistry, Vol. 5. Weinheim: Verlag Chemie 1978.

    Google Scholar 

  • Dwek, R. A.: Nuclear Magnetic Resonance in Biochemistry. Oxford: Clarendon Press 1973.

    Google Scholar 

  • Emsley, J.W., Feeney, J., Sutcliffe, L.H.: Progress in Nuclear Magnetic Resonance Spectroscopy. Oxford : Pergamon Press 1966.

    Google Scholar 

  • Günther, H. : NMR-Spektroskopie. Stuttgart : Thieme 1973

    Google Scholar 

  • Levy, G.C., Nelson, G.L. : Carbon-13 Nuclear Magnetic Resonance for Organic Chemists. New York: John Wiley & Sons 1972.

    Google Scholar 

  • Martin, M.L., Délpuech, J.J., Martin, G.J. : Practical NMR spectroscopy. London : Heydon & Son 1980.

    Google Scholar 

  • Shulman, R.G. : Biological Applications of Magnetic Resonance. New Yotk, San Francisco, London: Academic Press 1979.

    Google Scholar 

  • Slichter, C.P. : Principles of Magnetic Resonance. Berlin, Heidelberg, New York: Springer 1978.

    Google Scholar 

  • Stothers, J.B.: Carbon-13 nmr Spectroscopy. New York, London: Academic Press 1972.

    Google Scholar 

  • Suhr, H. : Anwendung der kernmagnetischen Resonanz in der organischen Chemie. Berlin, Heidelberg, New York: Springer 1965.

    Google Scholar 

  • Wehrli, F.W., Wirtlin, T. : Interpretation of Carbon-13 NMR Spectra. London, New York, Rheine : Heyden & Son 1976.

    Google Scholar 

  • Wüthrich, K. : NMR in Biological Research : Peptides and Proteins. Amsterdam, Oxford : North-Holland; New York : American Elsevier 1976.

    Google Scholar 

General

  • Author group: Strukturuntersuchungen an Biopolymeren mit spektroskopischen und hydrodynamischen Methoden. Akademie-Verlag, Berlin (DDR), 1976.

    Google Scholar 

  • Williams, V. R., Williams, H. B.: Basic Physical Chemistry for the Life Sciences. W. H. Freeman, San Francisco, 1967.

    Google Scholar 

  • Haschemeyer, R.H., Haschemeyer, A.E.V.: Proteins: A Guide to Study by Physical and Chemical Methods. Wiley, New York, 1973.

    Google Scholar 

Special

  • Gosting, L.J.: Viscosity: Adv. Protein Chem. 11, 429 (1959).

    Google Scholar 

  • Schachman, H.K.: Ultracentrifugation in Biochemistry. Academic Press, New York, 1959.

    Google Scholar 

  • Weber, G.: Fluorescence Polarization: Adv. Protein Chem. 8, 415 (1953).

    Article  Google Scholar 

  • Hoppe, W.: Röntgenbeugung in: Ulimanns Encyklopädie der technischen Chemie, 3. Aufl., Bd. II/l (Methodenband), S. 529. München-Berlin: Urban & Schwarzenberg 1961. (Somewhat extended version of a theory which starts from the single molecule.)

    Google Scholar 

Textbooks of X-Ray Crystallography

  • The Crystalline State, Vol. I., II., III. London: G. Bell and Sons Ltd. 1968 (detailed treatment)

    Google Scholar 

  • Blundell, T.L., Cutfield, J.F.: X-ray Analysis of Protein. In: Molecular Structure by Diffraction Methods, Vol. 1, p. 384. London: Chemical Soc. 1973.

    Chapter  Google Scholar 

  • Phillips, D. C.: Advances in Protein Crystallography. In: Advances in Structure Research by Diffraction Methods, Vol. II, S. 75. Braunschweig: Vieweg & Sohn 1966.

    Google Scholar 

  • Anomalous Scattering, Chapter VII. Anomalous Scattering and Structure Analysis of Macromolecules, Copenhagen: International Union of Crystallography 1975. (Compare especially B. P. Schoenborn, p. 407; W. Hoppe and U. Jakubowski, p. 437; R. L. Mössbauer, p. 463.)

    Google Scholar 

General

  • Hall, C.D.: Introduction to Electron Microscopy, New York: McGraw-Hill 1966. (Introduction to conventional electron microscopy with an outline of the historical development.)

    Google Scholar 

  • Reimer, L.: Elektronenmikroskopische Untersuchungs- und Präparationsmethoden, Berlin-Heidelberg-New York: Springer 1967.

    Google Scholar 

  • Huxley, H.E., Klug, A. (Eds.): New Developments in Electron Microscopy, London: Royal Society 1971.

    Google Scholar 

Non-Conventional Electron Microscopy, Monographs

  • Hoppe, W., Mason, R. (Eds.): Advances in Structure Research by Diffraction Methods, Vol. 7. Braunschweig/Wiesbaden: Friedr. Vieweg & Sohn 1979.

    Google Scholar 

  • Hawkes, P.W. (Ed.): Computer Processing of Electron Microscope Images, Vol. 13. Berlin-Heidelberg-New York: Springer 1980.

    Google Scholar 

  • Kihlborg, L. (Ed.): Direct Imaging of Atoms in Crystals and Molecules. Stockholm: The Royal Swedish Academy of Sciences 1979 (Nobel Symposium 47).

    Google Scholar 

  • Baumeister, W., Vogell, W. (Eds.): Electron Microscopy at Molecular Dimensions, Berlin-Heidelberg-New York: Springer 1980.

    Google Scholar 

  • Crowther, R.A., Klug, A.: Structural analysis of macromolecular assemblies by image reconstruction from electron micrographs. Ann. Rev. Biochem. 44, 161–182 (1975).

    Article  Google Scholar 

  • Hoppe, W.: Three-Dimensional Electron Microscopy Ann. Rev. Biophys. 10, 563–92 (1981).

    Article  Google Scholar 

Download references

Authors

Editor information

Editors and Affiliations

Rights and permissions

Reprints and permissions

Copyright information

© 1983 Springer-Verlag Berlin Heidelberg

About this chapter

Cite this chapter

Dörr, F. (1983). Structure Determination of Biomolecules by Physical Methods. In: Hoppe, W., Lohmann, W., Markl, H., Ziegler, H. (eds) Biophysics. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-642-68877-5_3

Download citation

  • DOI: https://doi.org/10.1007/978-3-642-68877-5_3

  • Publisher Name: Springer, Berlin, Heidelberg

  • Print ISBN: 978-3-642-68879-9

  • Online ISBN: 978-3-642-68877-5

  • eBook Packages: Springer Book Archive

Publish with us

Policies and ethics