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Analysis of biological structure at the atomic and molecular level
COMPUTER PHYSICS COMMUNICATIONS 3, S~UPPL. ! 1972"1 137-- 138. NORTIt-IIOLLAND PUBLISHING t'OMPAN$'
A N A L Y S I S OF BIOLOGICAL S T R I U C T U R E A T T H E A T O M I C A N D M O L E C U L A R
LEVEL
R.A. CROWTHER Medical Research Council's Labora.'ory o./Mo, ecutar Biology, tlills Road. Cambridge ~112 2QII. UK
In recer~t years X-ray crystallography has provided detailed pictures of the arrangement of atoms ill a number of different pro~.ein molecules and electron microscopy has permitted the analysis at the Ino[ecular level of ~arious biological aszemblies such as viruses and muscle fibres. In both fields computers play an essential role in collecting and processing the large amounts ol data involved and also in presenting the results in pictorial form. ' Measurement of the X-ray diffraction pattern of a crystal yields the amplitudes of the diffracted beams but not their relative phases. The latter can however be determined indirectly by the method of iso. morphous replacement, in which the diffraction pattern is modified by addition of heavy atoms to the protein. The electron density within the crystal n`1ay then be calculated from the amplitudes and phases of tlte diffracted beam by Fourier synthesis. In cer~:~in circumstances it may be possible to derive phases ~ ing not isomorphous replacement but rather the constraints which are placed on the diffraction pattern, if the repeating unit of the crystai contains multiple copies of a given structure, a si',:aation frequently obtaining in pr,)tein crystals. In electr~ n microscopy the difficulties of interpretation are r', ther different. Here there is no phase problem, since tl ~e microscope forms an image of the specimen. However, because the depth of focus is much greater than the thickness of the specimen, features at different levels are viperimposed, so that the final image is essentially a projection of the specimen in the direction of view. The image ten.'s, moreover, to be of rather poor quality. Irt order to e,dract the maximum amount of reliable structural inforntation, it is therefore necessary to perfi~rm various ty pes of processing including spatial filtering and three-dimensional image reconstruction. Most of these processes involve the extensive use of computers.
The subject of biological stJ'uctt.re determination has been thoroughly covered by ~ nunlber of recent synlposia, technical reviews and ,u,~re general articles, As most of these are readily avaiiaLle art addition to their number seems superfluous. A list o~ some oI the more recent publications follows.
Protein structure determination Technical articles
II I D.M. Bh)w and T.A. Sleitz, X,ray diffraction studies ~1 enzymes, Ann, Rev. Biochem. 39 t 197(t`163. 121 Structure and function of proteins at tile three-dimensional level, Cold Spring Ilarbor Synrposium on ()uantv tative Biology 36 t 1971 ). I31 D. Eisenberg, X-ray crystallography and enzyme structure. in: The enzymes, Vol. I. 3rd ed., ed. P.D. Bo.'.cr (Academic Press, New York, 1971`1). [41 M, Levitt, Cont~ormation analysis of proteins. Ph.D. Thesis, Univeisit',' of Cambridge t 1971 `1. 151 A.C.T. North and D.C. Phillips, X-ray studies of t'ry,:talline proteins, in: Progress in biophysics and molecular biology, Vol. 19, eds. J.A.V. Butler ~nd I). Noble (Pergamon Press, Oxford. 1969"1p.5. 161 M.F. Perutz, X-ray analysis, structure and function of enzymes. European .I. Biochem. 8 (19691 455. 171 M.G. Rossmann, ed.. The molecular replacement method: a collection of papers on the use of non-crystallographic symmetry (Gordon and Breach, New York, 19721. More general artich,s
18] R. Diamond, Some contemporary deveh pments in the techniques of protein crystallography, Cmtemp. Ph],s. 13 (1972} 23. [9] R.E. Dickerson and I. Gets, Structure and action or proteins (Harper and Row, New York, 1969). It0] J.T. Finch, The study of virus structures by X-ray diffraction. Contemp. Phys. 13 t1972) I, [I I ] C. Levimhal, Molecular building by computer, Sci. Am. 214 {6) {t966)42.
138
R.A, C.owther. Anal~,sis o f biological smteture
[ 121 D.C. Phillips. The threc-dimensional structule of an enzyme molecule, Sci. Am. 215 ~5) ~1966) 78. Image analysis o f electron micrographs I13[ R.A. Ctowther. Three-dimensional image recortstrtiction and tilt: architecture of spherical viruses. Endeavour 30 ll971) 124. 1141 R.A. Orowther and L.A. Amos. Harmonic anah,sis of electron microscope images v.'ith rotational sytr,metry. J. Mol. Biol. 60 II971) 123.
1151 D.J. DeRosier, The reconstruction of three-dimensional images from electron micrographs. Contemp. Phys. 12 ~1971) 437. [16] D.J. DeRosier and A, Klug. Reconstruction of three-dimensional structures from electron micrographs, Nature 217 (1968) 130. [17[ A. Klug and R.A. Crowther, Three-dimensional image reconstruction from the viewpoint of information theory, Nature to be published. [I 8[ C. Levinthal and R. Ware, ThKee-dimensiunal recon~truo tion from ~rial sections, Nature 236 [1972) 207.
A N A L Y S I S OF BIOLOGICAL S T R I U C T U R E A T T H E A T O M I C A N D M O L E C U L A R
LEVEL
R.A. CROWTHER Medical Research Council's Labora.'ory o./Mo, ecutar Biology, tlills Road. Cambridge ~112 2QII. UK
In recer~t years X-ray crystallography has provided detailed pictures of the arrangement of atoms ill a number of different pro~.ein molecules and electron microscopy has permitted the analysis at the Ino[ecular level of ~arious biological aszemblies such as viruses and muscle fibres. In both fields computers play an essential role in collecting and processing the large amounts ol data involved and also in presenting the results in pictorial form. ' Measurement of the X-ray diffraction pattern of a crystal yields the amplitudes of the diffracted beams but not their relative phases. The latter can however be determined indirectly by the method of iso. morphous replacement, in which the diffraction pattern is modified by addition of heavy atoms to the protein. The electron density within the crystal n`1ay then be calculated from the amplitudes and phases of tlte diffracted beam by Fourier synthesis. In cer~:~in circumstances it may be possible to derive phases ~ ing not isomorphous replacement but rather the constraints which are placed on the diffraction pattern, if the repeating unit of the crystai contains multiple copies of a given structure, a si',:aation frequently obtaining in pr,)tein crystals. In electr~ n microscopy the difficulties of interpretation are r', ther different. Here there is no phase problem, since tl ~e microscope forms an image of the specimen. However, because the depth of focus is much greater than the thickness of the specimen, features at different levels are viperimposed, so that the final image is essentially a projection of the specimen in the direction of view. The image ten.'s, moreover, to be of rather poor quality. Irt order to e,dract the maximum amount of reliable structural inforntation, it is therefore necessary to perfi~rm various ty pes of processing including spatial filtering and three-dimensional image reconstruction. Most of these processes involve the extensive use of computers.
The subject of biological stJ'uctt.re determination has been thoroughly covered by ~ nunlber of recent synlposia, technical reviews and ,u,~re general articles, As most of these are readily avaiiaLle art addition to their number seems superfluous. A list o~ some oI the more recent publications follows.
Protein structure determination Technical articles
II I D.M. Bh)w and T.A. Sleitz, X,ray diffraction studies ~1 enzymes, Ann, Rev. Biochem. 39 t 197(t`163. 121 Structure and function of proteins at tile three-dimensional level, Cold Spring Ilarbor Synrposium on ()uantv tative Biology 36 t 1971 ). I31 D. Eisenberg, X-ray crystallography and enzyme structure. in: The enzymes, Vol. I. 3rd ed., ed. P.D. Bo.'.cr (Academic Press, New York, 1971`1). [41 M, Levitt, Cont~ormation analysis of proteins. Ph.D. Thesis, Univeisit',' of Cambridge t 1971 `1. 151 A.C.T. North and D.C. Phillips, X-ray studies of t'ry,:talline proteins, in: Progress in biophysics and molecular biology, Vol. 19, eds. J.A.V. Butler ~nd I). Noble (Pergamon Press, Oxford. 1969"1p.5. 161 M.F. Perutz, X-ray analysis, structure and function of enzymes. European .I. Biochem. 8 (19691 455. 171 M.G. Rossmann, ed.. The molecular replacement method: a collection of papers on the use of non-crystallographic symmetry (Gordon and Breach, New York, 19721. More general artich,s
18] R. Diamond, Some contemporary deveh pments in the techniques of protein crystallography, Cmtemp. Ph],s. 13 (1972} 23. [9] R.E. Dickerson and I. Gets, Structure and action or proteins (Harper and Row, New York, 1969). It0] J.T. Finch, The study of virus structures by X-ray diffraction. Contemp. Phys. 13 t1972) I, [I I ] C. Levimhal, Molecular building by computer, Sci. Am. 214 {6) {t966)42.
138
R.A, C.owther. Anal~,sis o f biological smteture
[ 121 D.C. Phillips. The threc-dimensional structule of an enzyme molecule, Sci. Am. 215 ~5) ~1966) 78. Image analysis o f electron micrographs I13[ R.A. Ctowther. Three-dimensional image recortstrtiction and tilt: architecture of spherical viruses. Endeavour 30 ll971) 124. 1141 R.A. Orowther and L.A. Amos. Harmonic anah,sis of electron microscope images v.'ith rotational sytr,metry. J. Mol. Biol. 60 II971) 123.
1151 D.J. DeRosier, The reconstruction of three-dimensional images from electron micrographs. Contemp. Phys. 12 ~1971) 437. [16] D.J. DeRosier and A, Klug. Reconstruction of three-dimensional structures from electron micrographs, Nature 217 (1968) 130. [17[ A. Klug and R.A. Crowther, Three-dimensional image reconstruction from the viewpoint of information theory, Nature to be published. [I 8[ C. Levinthal and R. Ware, ThKee-dimensiunal recon~truo tion from ~rial sections, Nature 236 [1972) 207.