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The use of graph theoretical methods for the comparison of the structures of biological macromolecules

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Molecular Similarity II

Part of the book series: Topics in Current Chemistry ((TOPCURRCHEM,volume 174))

Abstract

The use of graph-theoretical algorithms in the similarity searching of databases of 3-dimensional structures of macromolecules is discussed. The emphasis is on the structures of protein molecules, for which the vast majority of 3-dimensional information is available. An initial survey is made of the types of information available on macromolecular structure, and of the methods conventionally used to compare them. Next the use of graph theoretical algorithms to identify previously unrecognized similarities between the overall folds of proteins is described, using the structure of the HIV reverse transcriptase enzyme as an example. The further application of these methods to the problem of searching for three-dimensional patterns of sidechain functional groups is then considered, using the active site of influenza sialidase as an example.

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Abbreviations

3-D:

three-dimensional

AIDS:

acquired immune deficiency syndrome

ASCII:

American Standard Code for Information Interchange

ATP:

adenosine triphosphate

CPU:

central processor unit

CSD:

Cambridge Structural Database

DNA:

2′-deoxy-ribonucleic acid

HIV:

Human Immunodeficiency Virus

ICDH:

isocitrate dehydrogenase

NMR:

nuclear magnetic resonance spectroscopy

PDB:

Protein Data Bank

RDBMS:

relational database management system

RNA:

ribonucleic acid

RNAase:

ribonuclease

RT:

reverse transcriptase

SSE:

secondary structure element

UMP:

uracil monophosphate

7 References

  1. Ash JE, Warr WA, Willett P (eds) (1991) Chemical Structure Systems. Ellis Horwood, Chichester

    Google Scholar 

  2. Watson JD, Crick FHC (1953) Nature 171: 371

    Google Scholar 

  3. Hunkerpillar MW, Strickler JE, Wilson KJ (1984) Science 226: 304

    Google Scholar 

  4. Nirenberg M (1973). In: Nobel Lectures: Physiology or Medicine. American Elsevier, pp, 272–395

    Google Scholar 

  5. Sanger F, Nicklen S, Coulson AR (1977) Proc Natl Acad Sci USA 7: 5463

    Google Scholar 

  6. Maxam A, Gilbert W (1977) Proc Natl Acad Sci USA 74: 560

    PubMed  Google Scholar 

  7. Sweeley CC, Nunez H (1985) Ann. Rev, Biochem. 54: 765

    Google Scholar 

  8. Bleasby AJ, Wooton JC, Akrigg, D, Dix NIM, Findlay JBC, North ACT, Parry-Smith D, Islam S, Gardner SP, Thornton JM, Sternberg MJE, Blundell TL, Hayes FRF & Tickle IJ (1988) ISIS. Integrated Sequence/Integrated Structure Resource, British Biotechnology Group

    Google Scholar 

  9. Lesk, AM (1988) in: Lesk AM (ed) The EMBL Data Library” in Computational Molecular Biology, Oxford University Press, Oxford, pp 55–65

    Google Scholar 

  10. Watson JD (1990) Science 44: 44

    Google Scholar 

  11. Cantor CR (1990) Science 44: 49

    Google Scholar 

  12. Lesk AM (ed) (1988) Computational Molecular Biology Oxford University Press, Oxford

    Google Scholar 

  13. Dayhoff MM (1978) in: Atlas of Protein Sequence and Structure, National Biomedical Research Foundation, vol 5, suppl 3

    Google Scholar 

  14. Needleman SB, Wunsch CD (1970) J Mol Biol 48 443

    Google Scholar 

  15. Staden R (1982) Nucleic Acids Res 10: 2951

    Google Scholar 

  16. Maizel JV and Lenk RP (1981) Proc Natl Acad Sci USA 78: 7665

    Google Scholar 

  17. Unger R, Harel D, Sussman JL, (1986) Comp Appl Biosci 2: 283

    Google Scholar 

  18. Smith TF and Waterman MS (1981) Adv Appl Math 2: 482

    Google Scholar 

  19. Lipman DJ, Pearson WR (1985) Science 227: 1435

    PubMed  Google Scholar 

  20. Wilbur WJ, Lipman DJ (1983) Proc Natl Acad Sci USA 80: 726

    Google Scholar 

  21. Deisenhofer J, Epp O, Miki K, Huber R, Michel H (1985) Nature 318: 618

    Google Scholar 

  22. Jurnak FA, McPherson A (eds) (1984) “Biological macromolecule and assemblies. Volume 1: Virus Structure”, Wiley.

    Google Scholar 

  23. Blundell TL, Johnson LN (1976) “Protein Crystallography”, Academic Press, London

    Google Scholar 

  24. Glusker JP, Trueblook KN (1972) “Crystal structure analysis: A primer”, Oxford University Press, Oxford

    Google Scholar 

  25. Wüthrich K (1986) “NMR of Proteins and Nucleic Acids”, Wiley, New York

    Google Scholar 

  26. Henderson R, Baldwin JM, Ceska TA, Zemlin F, Beckmann E, Downing KH (1990) J. Molec. Biol. 213: 899

    Google Scholar 

  27. Kühlbrandt W, Wang DA, Fujiyoshi Y (1994) Nature 367: 614

    Google Scholar 

  28. Bernstein FC, Koetzle TF, Williams GJB, Meyer EF Jnr., Brice MD, Rodgers JR, Kennard O, Shimanouchi M, Tasumi M (1977) J Molec Biol 112: 535

    Google Scholar 

  29. Abola EE, Bernstein FC, Bryant SH, Koetzle TF, Weng J (1987) in: Allen FH, Bergeroff G, Sievers R (eds) Crystallographic Databases-Information Content, Software Systems, Scientific Applications pp 107–132, Data Commission of the International Union of Crystallography, Bonn/Cambridge/Chester

    Google Scholar 

  30. Allan FH, Kennard O, Taylor (1983) Acc. Chem. Res. 16: 146

    Google Scholar 

  31. Richards FM, and 173 others (1988) “Letter to the editor” J Molec. Graph. 6: 178

    Google Scholar 

  32. Hendrickson W (1985) in: Wyckoff HW, Hirs CHW, Timasheff SN (eds) pp 252–270 (Methods in Enzymology, vol 115)

    Google Scholar 

  33. Colman PM, Deisenhofer J, Huber R, Palm W (1976) J Mol Biol 100: 257

    Google Scholar 

  34. Richards FM (1991) Scientific American 264: 54

    Google Scholar 

  35. Chothia C (1988) Nature 333: 598

    Google Scholar 

  36. Rao ST, Rossmann MG (1973) J Mol Biol 76: 241

    Google Scholar 

  37. Rossmann MG, Argos P (1975) J Mol Biol Chem 250: 7525

    Google Scholar 

  38. Rossmann MG, Argos P (1976) J Mol Biol 105: 75

    Google Scholar 

  39. Rossmann MG, Argos P (1977) J Mol Biol 109: 99

    Google Scholar 

  40. Remington SJ, Matthews BW (1978) Proc Nat Acad Sci USA 75: 2180

    Google Scholar 

  41. Remington SJ, Mathews BW (1980) J Mol Biol 140: 77

    Google Scholar 

  42. Lesk AM (1979) Comm ACM 22: 219

    Google Scholar 

  43. Lesk AM (1993) J Chem Soc Farad Trans 89: 2603

    Google Scholar 

  44. Taylor WR, Orengo CA (1989) J Mol Biol 208: 1

    Google Scholar 

  45. Sali A, Blundell TL (1990) J Mol Biol 212: 403

    Google Scholar 

  46. Vriend G, Sander C (1991) Proteins: Struct Funct and Genet 11: 52

    Google Scholar 

  47. Alexandrov NN, Takahashi K, Go N (1992) J Mol Biol 225: 5

    Google Scholar 

  48. Bachar O, Fischer D, Nussinov R, Wolfson HJ (1993) Prot Eng 6: 279

    Google Scholar 

  49. Fischer D, Bachar O, Nussinov R, Wolfson H (1992) J Biomol Struct Dynam 9: 769

    Google Scholar 

  50. May ACW, Johnson MS (1994) Prot Eng 7: 475

    Google Scholar 

  51. Brint AT, Davies HM, Mitchell EM, Willett P (1989) J Mol Graph 7: 48

    Google Scholar 

  52. Mitchell EM, Artymiuk PJ, Rice DW, Willett P (1990) J Mol Biol 212: 151

    Google Scholar 

  53. Grindley HM, Artymiuk PJ, Rice DW, Willett P (1993) J Mol Biol 229: 707

    Google Scholar 

  54. Subbarao N, Haneef I (1991) Prot. Eng. 4: 877

    Google Scholar 

  55. Goodsell DS, Lauble H, Stout CD, Olson AJ (1993) Protiens: Struct Funct Genet 17: 1

    Google Scholar 

  56. Smellie AS, Crippen GM, Richards WG (1991) J Chem Inf Comput Sci 31: 386

    Google Scholar 

  57. Richards FM, Kundrot CE (1988) Proteins: Struct Funct Genet 3: 71

    Google Scholar 

  58. Willett P (1991) Three-Dimensional Chemical Structure Handling, Research Studies Press, Wiley, New York

    Google Scholar 

  59. Willett P (ed) Modern Approaches to Chemical Reaction Searching, Gower, Aldershot

    Google Scholar 

  60. Hagadone TR (1992) J Chem Inf Comp Sci 32: 515

    Google Scholar 

  61. Artymiuk PJ, Rice DW, Mitchell EM, Willett P (1990) Prot Eng 4: 39

    Google Scholar 

  62. Artymiuk PJ, Rice DW (1991) in: Ash JE, Warr WA, Willett P (eds) Chemical Structure Systems, Ellis Horwood, Chichester, pp 299–328

    Google Scholar 

  63. Artymiuk PJ, Grindley HM, Park JE, Rice DW, Willett P (1992) FEBS Lett 303: 48

    Google Scholar 

  64. Artymiuk PJ, Grindley HM, Kumar K, Rice DW, Willett P (1993) FEBS Lett 324: 15

    Google Scholar 

  65. Artymiuk PJ, Grindley HM, MacKenzie AB, Rice DW, Ujah EC, Willett P (1994) in: Carbo R (ed) Molecular Similarity and Reactivity: from quantum chemical to phenomenological approach, Klure Academic Press (in the press)

    Google Scholar 

  66. Artymiuk PJ, Poirrette AR, Grindley HM, Rice DW and Willett P (1994) J Mol Biol 243: 327–344

    Google Scholar 

  67. Kabsch W, Sander C (1983) Biopolymers 22: 2577

    Google Scholar 

  68. Brint AT, Willett P (1987) J Mol Graph 5: 49

    Google Scholar 

  69. Brint AT, Willett P (1987) J Chem Inf Comput Sci 27: 152

    Google Scholar 

  70. Ullmann JR (1976) J.ACM 16: 31

    Google Scholar 

  71. Bron C, Kerbosch J (1973) Comm ACM 16: 575

    Google Scholar 

  72. Barrow HG, Burstall RM (1976) Inf. Proc. Lett. 4: 83

    Google Scholar 

  73. Richardson JS (1977) Nature 268: 495

    Google Scholar 

  74. Artymiuk PJ, Grindley HM, Poirrette AR, Rice DW, Ujah EC, Willett P (1994) J Chem Inf Comput Sci 34: 54

    Google Scholar 

  75. Ujah EC (1992) Study of beta-sheet motifs at different levels of structural abstraction using graph-theoretic and dynamic programming techniques. PhD Thesis, University of Sheffield, Sheffiled

    Google Scholar 

  76. Goff SP (1990) J AIDS 3: 817

    Google Scholar 

  77. Mitsuya H, Yarchoan R, Broder S (1990) Science 249: 1533

    Google Scholar 

  78. Wlodawer A (1992) Science 256: 1766

    Google Scholar 

  79. Kohlsatedt LA, Wang J, Friedman JM, Rice PA and Steitz TA (1992) Science 256: 1783

    Google Scholar 

  80. Kraulis PJ (1991) J Appl Cryst 24: 946

    Google Scholar 

  81. Peliska JA, Bencovic SJ (1992) Science 258: 1112

    Google Scholar 

  82. Blow DM (1990) Nature, 343: 694

    Google Scholar 

  83. Islam SA, Sternberg MJE (1989) Prot Eng 2: 431

    Google Scholar 

  84. Delhaise P, Bardiaux M, Wodak S (1985) J Mol. Graph. 3: 116

    Google Scholar 

  85. Singh J, Thornton JM (1985) FEBS Lett. 191: 1

    Google Scholar 

  86. Sing J, Thornton JM, Snarey M, Campbell SF (1987) FEBS Lett 224: 161

    Google Scholar 

  87. Gardner SJ, Thornton JM (1990) in: Abstracts of International Conference on Computing in Molecular Biology, Chester UK

    Google Scholar 

  88. Burley SK, Petsko GA (1985) Science 229: 23

    Google Scholar 

  89. Burley SK, Petsko GA (1988) Adv Prot Chem 39: 1215

    Google Scholar 

  90. Singh J, Thornton JM, Snarey M, Campbell SF (1987) FEBS Lett. 224: 161

    Google Scholar 

  91. Singh J, Thornton JM (1990) J Mol Biol 211: 595

    Google Scholar 

  92. Vedani A, Zbinden P, Snyder JP (1993) J Receptor Res. 13: 163

    Google Scholar 

  93. Bartlett PA, Shea GT, Telfer SJ, Waterman S (1990) in: Roberts SM (ed) Molecular Recognition: Chemical and Biochemical Problems, Royal Society of Chemistry, Cambridge, pp. 182–196

    Google Scholar 

  94. Gregory DS, Martin ACR, Cheetham JC, Rees AR (1993) Prot Eng 6: 29

    Google Scholar 

  95. Cotton FA, Hazen EE, Legg MJ (1979) Proc Natl Acad Sci USA 76: 2551

    Google Scholar 

  96. Montfort WR, Perry KM, Fauman EB, Finer-Moore JS, Maley GF, Hardy L, Maley F, Stroud RM (1990) Biochemistry 29: 6964

    Google Scholar 

  97. Kester WR, Matthews BW (1977) J Biol Chem 252: 7704

    Google Scholar 

  98. Rees DC, Lewis M, Lipscomb WN (1983) J Mol Biol 168: 367

    Google Scholar 

  99. Kam C-M, Nishino N, Powers JC (1979) Biochemistry 18: 3032

    Google Scholar 

  100. von Itzstein M, Wu W-Y, Kok GB, Pegg MS, Dyason JC, Jin B, Phan TV, Smythe ML, White HF, Oliver SW, Colman PM, Varghese JN, Ryan DM, Woods JM, Bethell RC, Hotham VJ, Cameron JM, Penn CR (1993) Nature 363: 418

    Google Scholar 

  101. Chong AKG, Pegg MS, Taylor NR, von Itzstein M (1992) Eur J Biochem 207: 225

    Google Scholar 

  102. Varghese JN, McKimm-Braschkin J, Caldwell JB, Korrt AA, Coman PM (1992) Proteins 14: 327

    Google Scholar 

  103. Goodford PJ (1985) J Med Chem 28: 849

    Google Scholar 

  104. Taylor GL (1993) Nature 363: 401

    Google Scholar 

  105. Varghese JN, Colman PM (1991) J Mol Biol 221: 473

    Google Scholar 

  106. Poirrette AR, Artymiuk PJ, Grindley HM, Rice DW and Willett P (1994) Protein Science 3: 1128–1130

    Google Scholar 

  107. Hurley JH, Dean AM, Sohl JL, Koshland DE Jr, Stroud RM (1990) Science 249: 1012

    Google Scholar 

  108. Bersohn M, Fujiwara S, Fujiwara Y (1986) J Comput Chem 7: 129

    Google Scholar 

  109. Heringa J, Argos P (1993) Proteins Struct Funct Genet 17: 391

    Google Scholar 

  110. Kasinos N, Lilley GA, Subbarao N, Hanneef I (1992) Prot Eng 5: 69

    Google Scholar 

  111. Koch I, Kaden F, Selbig J (1992) Prot: Stuct Funct Genet 12: 314

    Google Scholar 

  112. Rufino SD, Blundell TL (1994) J of Computer-Aided Molecular Design 8: 5

    Google Scholar 

  113. Rooman MJ, Wodak SJ (1988) Nature 445: 45

    Google Scholar 

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Authors and Affiliations

  1. Krebs Institute for Biomolecular Research, Department of Molecular Biology and Biotechnology, University of Sheffield, S10 2TN, Sheffield, United Kingdom

    Peter J. Artymiuk & David W. Rice

  2. Krebs Institute for Biomolecular Research, Department of Information Studies, University of Sheffield, S10 2TN, Sheffield, United Kingdom

    Andrew R. Poirrette & Peter Willett

Authors
  1. Peter J. Artymiuk
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  2. Andrew R. Poirrette
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  3. David W. Rice
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  4. Peter Willett
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Kali Das Sen

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Artymiuk, P.J., Poirrette, A.R., Rice, D.W., Willett, P. (1995). The use of graph theoretical methods for the comparison of the structures of biological macromolecules. In: Sen, K.D. (eds) Molecular Similarity II. Topics in Current Chemistry, vol 174. Springer, Berlin, Heidelberg. https://doi.org/10.1007/3-540-58672-5_24

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  • DOI: https://doi.org/10.1007/3-540-58672-5_24

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