Biophysical Methods in Virus Research

All viruses are composed at least of protein and nucleic acid, and certain viruses contain other biochemical constituents as integral parts of their structure. Thus the biophysical methods used in the isolation and characterization of viruses are the same as those used by biochemists generally. It would be impossible in a chapter of reasonable length to deal with all such methods exhaustively. For that reason, an attempt will be made to limit this discussion to those most extensively used by virologists. The approach will be to explain the underlying principles involved in each method and to illustrate its use by citing examples drawn more or less randomly from the literature, including previous volumes of Comprehensive Virology. The purpose of the present effort is to provide readers not familiar with these methods a basis for understanding them, and perhaps some appreciation of which methods are best adapted to the solution of specific problems. However, anyone desiring to make use of any of the methods must consult more detailed specific treatments available in the literature. Certain methods, like electron microscopy and X-ray crystallography, are either so widely used or so highly technical that they deserve chapters in their own right, written by experts in the particular field. These methods are dealt with in Chapters 2 and 3 of this volume.

[1]  P. Grabar,et al.  Immunoelectrophoretic Studies on Serum Proteins , 1955, The Journal of Immunology.

[2]  O OUCHTERLONY,et al.  Diffusion-in-gel methods for immunological analysis. , 1958, Progress in allergy.

[3]  Bruno H. Zimm,et al.  Apparatus and Methods for Measurement and Interpretation of the Angular Variation of Light Scattering; Preliminary Results on Polystyrene Solutions , 1948 .

[4]  G. Cooper,et al.  The diffusion constant of Tomato bushy stunt virus. , 1940 .

[5]  H. Boedtker,et al.  The Preparation and Characterization of Essentially Uniform Tobacco Mosaic Virus Particles , 1958 .

[6]  M. A. Lauffer,et al.  Chromatographic purification of Southern bean mosaic virus. , 1956, Archives of biochemistry and biophysics.

[7]  F. Loeffler,et al.  Berichte der Kommission zur Erforschung der Maul- und Klauenseuche bei dem Institut für Infektionskrankheiten in Berlin , 1898 .

[8]  C. Mcewen Tables for estimating sedimentation through linear concentration gradients of sucrose solution. , 1967, Analytical biochemistry.

[9]  A. Allison Molecular Studies in Viral Neoplasia , 1975, British Journal of Cancer.

[10]  F. D. Carlson,et al.  Translational and rotational diffusion constants of tobacco mosaic virus from Rayleigh linewidths. , 1969, Biophysical journal.

[11]  C. A. Knight,et al.  THE COMPLETE AMINO ACID SEQUENCE OF THE PROTEIN OF TOBACCO MOSAIC VIRUS. , 1960, Proceedings of the National Academy of Sciences of the United States of America.

[12]  M. A. Lauffer,et al.  The effect of ionic strength on the entropy-driven polymerization of tobacco mosaic virus protein. Contributions of electrical work and salting-out. , 1980, Archives of biochemistry and biophysics.

[13]  A. Guinier,et al.  La diffraction des rayons X aux très petits angles : application à l'étude de phénomènes ultramicroscopiques , 1939 .

[14]  K. Richards,et al.  Assembly of tobacco mosaic virus rods in vitro. Elongation of partially assembled rods. , 1973, Biochemistry.

[15]  David E. Green,et al.  Currents in biochemical research. , 1946 .

[16]  E. G. Pickels SEDIMENTATION IN THE ANGLE CENTRIFUGE , 1943, The Journal of general physiology.

[17]  C. J. Davisson,et al.  Diffraction of Electrons by a Crystal of Nickel , 1927 .

[18]  P. Kaesberg,et al.  An x-ray scattering investigation of wild cucumber mosaic virus and a related protein. , 1961, Biophysical journal.

[19]  M. A. Lauffer,et al.  Native Tobacco Mosaic Virus Protein of Molecular Weight 18,000 , 1959, Nature.

[20]  J. Craigie The Nature of the Vaccinia Flocculation Reaction, and Observations on the Elementary Bodies of Vaccinia. , 1932 .

[21]  M. A. Lauffer Theory of diffusion in gels. , 1961, Biophysical journal.

[22]  A. Klug,et al.  Assembly of the particle of tobacco mosaic virus from RNA and disks of protein. , 1971, Nature: New biology.

[23]  Miller Gl,et al.  Physical and chemical studies on Southern bean mosaic virus; size, shape, hydration and elementary composition. , 1946, Archives of biochemistry.

[24]  M. A. Lauffer,et al.  Structure of the tobacco mosaic virus particle; polymerization of tobacco mosaic virus protein. , 1968, Advances in virus research.

[25]  M. A. Lauffer The Size and Shape of Tobacco Mosaic Virus Particles1 , 1944 .

[26]  W. M. Stanley,et al.  ISOLATION OF A CRYSTALLINE PROTEIN POSSESSING THE PROPERTIES OF TOBACCO-MOSAIC VIRUS. , 1935, Science.

[27]  B. Roizman,et al.  The Replication of Herpesviruses , 1974 .

[28]  B. R. Leonard,et al.  On the Size, Shape, and Hydration of Southern Bean Mosaic Virus and Tobacco Necrosis Virus in Solution , 1951 .

[29]  B. Roizman,et al.  Proteins Specified by Herpes Simplex Virus XII. The Virion Polypeptides of Type 1 Strains , 1974, Journal of virology.

[30]  M. A. Lauffer The Influence of Concentration upon the Sedimentation Rate of Tobacco Mosaic Virus , 1944 .

[31]  K. Saigo Isolation of high-density mutants and identification of nonessential structural proteins in bacteriophage T5; dispensability of L-shaped tail fibers and a secondary major head protein. , 1978, Virology.

[32]  R. Zeiger,et al.  Role of base composition in the electrophoresis of microbial and crab DNA in polyacrylamide gels. , 1972, Nature: New biology.

[33]  P. O’Farrell High resolution two-dimensional electrophoresis of proteins. , 1975, The Journal of biological chemistry.

[34]  D. Gish,et al.  Studies on the amino acid sequence of tobacco mosaic virus (TMV) protein. I. Fractionation of products of tryptic hydrolysis by countercurrent distribution. , 1958, Archives of biochemistry and biophysics.

[35]  M. A. Lauffer,et al.  Comments on the structure of myosin. , 1955, Archives of biochemistry and biophysics.

[36]  Howard M. Goodman,et al.  Resolution of simian virus 40 proteins in whole cell extracts by two-dimensional electrophoresis: Heterogeneity of the major capsid protein , 1976, Cell.

[37]  H. Neurath The Investigation of Proteins by Diffusion Measurements. , 1942 .

[38]  M. A. Lauffer,et al.  The protein subunit of cucumber virus 4; degradation of viruses by succinylation. , 1965, Virology.

[39]  M. L. Anson,et al.  A METHOD FOR THE DETERMINATION OF DIFFUSION CONSTANTS AND THE CALCULATION OF THE RADIUS AND WEIGHT OF THE HEMOGLOBIN MOLECULE , 1929, The Journal of general physiology.

[40]  F. E. Karasz,et al.  Rotational Diffusion of Tobacco Mosaic Virus , 1971 .

[41]  H. Ozeki,et al.  Clustering of transfer RNA genes in bacteriophage BF23. , 1978, Virology.

[42]  P. Kallós Progress in Allergy. , 1949 .

[43]  D. Caspar,et al.  ASSEMBLY AND STABILITY OF THE TOBACCO MOSAIC VIRUS PARTICLE. , 1963, Advances in protein chemistry.

[44]  G. Scatchard,et al.  Physical chemistry of protein solutions; derivation of the equations for the osmotic pressure. , 1946, Journal of the American Chemical Society.

[45]  R. Oppermann Proteins, amino acids and peptides , 1943 .

[46]  M. A. Lauffer THE MOLECULAR WEIGHT AND SHAPE OF TOBACCO MOSAIC VIRUS PROTEIN. , 1938, Science.

[47]  T. P. Hughes,et al.  IMMUNOLOGICAL AND CHEMICAL INVESTIGATIONS OF VACCINE VIRUS : II. CHEMICAL ANALYSIS OF ELEMENTARY BODIES OF VACCINIA. , 1935 .

[48]  R. D. Dyson,et al.  SEDIMENTATION EQUILIBRIUM OF LOW‐MOLECULARWEIGHT ASSOCIATING SOLUTES , 1969, Annals of the New York Academy of Sciences.

[49]  M. Meselson,et al.  EQUILIBRIUM SEDIMENTATION OF MACROMOLECULES IN DENSITY GRADIENTS. , 1957, Proceedings of the National Academy of Sciences of the United States of America.

[50]  H. K. Schachman Ultracentrifugation in biochemistry , 1959 .

[51]  A. Haschemeyer,et al.  Proteins: A guide to study by physical and chemical methods , 1973 .

[52]  H. Neurath,et al.  THE DIFFUSION OF TOBACCO MOSAIC VIRUS PROTEIN IN AQUEOUS SOLUTION , 1938 .

[53]  E. Oppenheimer,et al.  Differential Centrifugalization : A Method for the Study of Filtrable Viruses, as applied to Vaccinia. , 1922 .

[54]  M. A. Lauffer,et al.  Role of cation and anion in the polymerization and depolymerization of tobacco mosaic virus protein. , 1971, Biochemistry.

[55]  H. Wittmann,et al.  Weitere Untersuchungen zur Aminosäuresequenz des Proteins im Tabakmosaikvirus , 1965 .

[56]  M. K. Brakke Density Gradient Centrifugation And its Application to Plant Viruses , 1961 .

[57]  A. Durham Structures and roles of the polymorphic forms of tobacco mosaic virus protein. I. Sedimentation studies. , 1972, Journal of molecular biology.

[58]  Robert L. Baldwin,et al.  Rapid Attainment of Sedimentation Equilibrium , 1958 .

[59]  G. Logrippo Partial Purification of Viruses with an Anion Exchange Resin.∗ , 1950, Proceedings of the Society for Experimental Biology and Medicine. Society for Experimental Biology and Medicine.

[60]  R. Simha,et al.  The Influence of Brownian Movement on the Viscosity of Solutions. , 1940 .

[61]  L. G. Longsworth THE DIFFUSION OF ELECTROLYTES AND MACROMOLECULES IN SOLUTION: A HISTORICAL SURVEY , 1945, Annals of the New York Academy of Sciences.

[62]  C. Randall,et al.  Sedimentation characteristics and molecular weights of three poxvirus DNAs. , 1978, Virology.

[63]  U. K. Laemmli,et al.  Cleavage of Structural Proteins during the Assembly of the Head of Bacteriophage T4 , 1970, Nature.

[64]  L. Craig,et al.  Partition Chromatography and Countercurrent Distribution , 1950 .

[65]  J. Oudin B. Specific precipitation in gels and its application to immunochemical analysis. , 1952, Methods in medical research.

[66]  C. Scholtissek,et al.  Biochemical studies on influenza viruses. II. Assignment of gene functions to RNA segments 5, 7, and 8 of fowl plague virus and virus N. , 1978, Virology.

[67]  M. A. Lauffer Entropy-driven processes in biology. , 1975, Molecular biology, biochemistry, and biophysics.

[68]  E. Winocour Further studies on the incorporation of cell DNA into polyoma-related particles. , 1968, Virology.

[69]  T. Rivers,et al.  IMMUNOLOGICAL AND CHEMICAL INVESTIGATIONS OF VACCINE VIRUS VI. ISOLATION OF A HEAT-STABLE, SEROLOGICALLY ACTIVE SUBSTANCE FROM TISSUES INFECTED WITH VACCINE VIRUS , 1937 .

[70]  P. Spear,et al.  Proteins spcified by herpes simplex virus. II. Viral glycoprotins associated with cellular membranes. , 1970, Journal of virology.

[71]  L. Harper,et al.  Identification of orthopoxviruses by polyacrylamide gel electrophoresis of intracellular polypeptides. I. Four major groupings. , 1979, Virology.

[72]  M. A. Lauffer,et al.  Pollymerization–Depolymerizatic Tobacco Mosaic Virus Protein , 1958, Nature.

[73]  J. Ledingham THE ÆTIOLOGICAL IMPORTANCE OF THE ELEMENTARY BODIES IN VACCINIA AND FOWL-POX. , 1931 .

[74]  Myron K. Brakke,et al.  Density Gradient Centrifugation: A New Separation Technique1 , 1951 .

[75]  A. Klug,et al.  Structures and roles of the polymorphic forms of tobacco mosaic virus protein. IV. Control of mode of aggregation of tobacco mosaic virus protein by proton binding. , 1972, Journal of molecular biology.

[76]  A. J. Martin,et al.  A new form of chromatogram employing two liquid phases: A theory of chromatography. 2. Application to the micro-determination of the higher monoamino-acids in proteins. , 1941, The Biochemical journal.

[77]  C. Hutchison,et al.  The Process of Infection with Bacteriophage øX174 XII. Phenotypic Mixing between Electrophoretic Mutants of øX174 , 1967 .

[78]  P. Cooper,et al.  Poliovirus polypeptides examined in more detail. , 1975, The Journal of general virology.

[79]  G. Schramm,et al.  Über das Molekulargewicht des Tabakmosaikvirus , 1947 .

[80]  M. A. Lauffer Motion in viscous liquids: Simplified derivations of the Stokes and Einstein equations , 1981 .

[81]  T. Rivers,et al.  IMMUNOLOGICAL AND CHEMICAL INVESTIGATIONS OF VACCINE VIRUS : I. PREPARATION OF ELEMENTARY BODIES OF VACCINIA. , 1935 .

[82]  M. A. Lauffer,et al.  Diffusion measurements in agar gel. , 1962, Biochemistry.

[83]  P. Pusey,et al.  Intensity fluctuation spectroscopy of laser light scattered by solutions of spherical viruses: R17, Q beta, BSV, PM2, and T7. I. Light-scattering technique. , 1974, Biochemistry.

[84]  M. A. Lauffer,et al.  The hydration of viruses. , 1954, Advances in virus research.

[85]  R. Hamilton Properties of brome mosaic virus and its related antigens. , 1961, Virology.

[86]  W. M. Stanley BIOCHEMICAL STUDIES ON INFLUENZA VIRUS , 1946 .

[87]  P. Grabar,et al.  The use of immunochemical methods in studies on proteins. , 1958, Advances in protein chemistry.

[88]  A. D. Hershey,et al.  A fractionating column for analysis of nucleic acids. , 1960, Analytical biochemistry.

[89]  M. A. Lauffer,et al.  Polymerization--depolymerization of tobacco mosaic virus protein. VI. Osmotic pressure studies of early stages of polymerization. , 1966, Biochemistry.

[90]  Barr Jb,et al.  HOME OR AWAY? , 1964, Lancet.

[91]  P. Pusey,et al.  Intensity fluctuation spectroscopy of laser light scattered by solutions of spherical viruses: R17, Q beta, BSV, PM2, and T7. II. Diffusion coefficients, molecular weights, solvation, and particle dimensions. , 1974, Biochemistry.

[92]  R. F. Parker,et al.  IMMUNOLOGICAL AND CHEMICAL INVESTIGATIONS OF VACCINE VIRUS : V. METABOLIC STUDIES OF ELEMENTARY BODIES OF VACCINIA. , 1937 .

[93]  B. R. Leonard,et al.  An x-ray investigation of the sizes and hydrations of three spherical virus macromolecules in solution. , 1953, Biochimica et biophysica acta.

[94]  P. Kaesberg,et al.  Small-angle x-ray scattering from turnip yellow mosaic virus. , 1954, Biochimica et biophysica acta.

[95]  C. A. Williams,et al.  Immunoelectrophoretic studies on serum proteins. I. The antigens of human serum. , 1955, Journal of immunology.

[96]  M. Meselson,et al.  The replication of DNA. , 1958, Cold Spring Harbor symposia on quantitative biology.

[97]  M Meselson,et al.  THE REPLICATION OF DNA IN ESCHERICHIA COLI. , 1958, Proceedings of the National Academy of Sciences of the United States of America.

[98]  S. Fujime Quasi-Elastic Light Scattering from Solutions of Macromolecules. I. Doppler Broadening of Light Scattered from Solutions of Tobacco Mosaic Virus Particles , 1970 .

[99]  A. Levine,et al.  Deoxyribonucleic Acid Replication in Simian Virus 40-Infected Cells , 1970, Journal of virology.

[100]  T. Rivers,et al.  IMMUNOLOGICAL AND CHEMICAL INVESTIGATIONS OF VACCINE VIRUS : III. RESPONSE OF RABBITS TO INACTIVE ELEMENTARY BODIES OF VACCINIA AND TO VIRUS-FREE EXTRACTS OF VACCINE VIRUS. , 1936, The Journal of experimental medicine.

[101]  R. W. Davis,et al.  Studies on the cleavage of bacteriophage lambda DNA with EcoRI Restriction endonuclease. , 1975, Journal of molecular biology.

[102]  D. Ivanowski Ueber die Mosaikkrankheit der Tabakspflanze , 1892 .

[103]  H. Aposhian Pseudovirions in Animals, Plants, and Bacteria , 1975 .

[104]  P. Cooper Genetics of Picornaviruses , 1977 .

[105]  M. A. Lauffer Polymerization--depolymerization of tobacco mosaic virus protein. V. Osmotic pressure theory for hydrated proteins. , 1966, Biochemistry.

[106]  M. A. Lauffer Entropy-Driven Processes in Biology: Polymerization of Tobacco Mosaic Virus Protein and Similar Reactions , 1975 .

[107]  R. Sinsheimer,et al.  The process of infection with bacteriophage φX174. XXVI. Transfer of the parental DNA of bacteriophage φX174 into progeny bacteriophage particles , 1969 .

[108]  W. Stanley AN EVALUATION OF METHODS FOR THE CONCENTRATION AND PURIFICATION OF INFLUENZA VIRUS , 1944, The Journal of experimental medicine.

[109]  J. Erickson,et al.  The self-assembly of papaya mosaic virus. , 1978, Virology.

[110]  B. Ames,et al.  A method for determining the sedimentation behavior of enzymes: application to protein mixtures. , 1961, The Journal of biological chemistry.

[111]  Charles Tanford,et al.  Physical Chemistry of Macromolecules , 1961 .

[112]  M. A. Lauffer,et al.  Polymerization-depolymerization of tobacco mosaic virus protein. 8. Light-scattering studies. , 1967, Biochemistry.

[113]  M. A. Lauffer,et al.  Ion binding by tobacco mosaic virus and its protein. , 1968, Biochemistry.

[114]  R. Francki,et al.  The chemical subunit of tobacco ringspot virus coat protein. , 1979, Virology.

[115]  W. J. Elford A new series of graded collodion membranes suitable for general bacteriological use, especially in filterable virus studies , 1931 .