Skip to main content
SpringerLink
Log in

Reconstructing the Evolution of Proteins

  • Conference paper
Book cover Redesigning the Molecules of Life

Abstract

Data from biological chemistry, including protein structurer enzymatic mechanisms, and metabolic pathways, can be unified by understanding the distinction between selected and non-selected behaviors. We outline methods for constructing functional and historical models explaining these behaviors, and show how they can be applied to organizing biochemical data, tested experimentally, and used to engineer the behavior of proteins using recombinant DNA techniques.

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

Access this chapter

Log in via an institution
Chapter
USD 29.95
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
eBook
USD 84.99
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
Softcover Book
USD 109.99
Price excludes VAT (USA)
  • Compact, lightweight edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info

Tax calculation will be finalised at checkout

Purchases are for personal use only

Institutional subscriptions

Preview

Unable to display preview. Download preview PDF.

Unable to display preview. Download preview PDF.

References

  1. Knowles JR (1987) Science 236:1252

    Article  PubMed  CAS  Google Scholar 

  2. Lewontin RC (1979) Sci Am 239:156

    Google Scholar 

  3. Kimura M (1982) Molecular Evolution Protein Polymorphism and the Neutral Theory, Berlin, Springer-Verlag

    Google Scholar 

  4. Benner SA, Nambiar KP, Chambers GK (1985) J Am Chem Soc 107:5513

    Article  CAS  Google Scholar 

  5. Dequard-Chablat M J Biol Chem 261:4117 (1986)

    PubMed  CAS  Google Scholar 

  6. Biswas TK Getz GS (1986) J Biol Chem 261:3928

    Google Scholar 

  7. Pietruszko R (1982) Meth Enzymol 89:428

    Article  PubMed  CAS  Google Scholar 

  8. Stalker DM, Hiatt WR, Cornai L (1985) J Biol Chem 260:4724

    PubMed  CAS  Google Scholar 

  9. Both GW, Shi CH, Kilbourne ED (1983) Proc Nat Acad Sci 80:6996

    Article  PubMed  CAS  Google Scholar 

  10. Benner SA; Ellington AD (in press) CRC Crit Rev Biochem

    Google Scholar 

  11. Miller JH (1979) J Mol Biol 131:249

    Article  PubMed  CAS  Google Scholar 

  12. Fersht AR, Leatherbarrow RJ, Wells TC (1987) Biochem 26:6030

    Article  CAS  Google Scholar 

  13. Shortle Dr Lin B (1985) Genetics 110:539

    PubMed  CAS  Google Scholar 

  14. Serpersu EH, Shortle D, Mildvan AS (1986) Biochem 25:68

    Article  CAS  Google Scholar 

  15. Cone JL, Cusumano CL, Taniuchi H, Anfinsen C (1971) J Biol Chem 246:3103

    PubMed  CAS  Google Scholar 

  16. Knowles JR (1988) Cold Spr Harbor Symp Quant Biol, 51

    Google Scholar 

  17. Strauss D, Raines R, Kawashima E, Knowles JR, Gilbert W (1985) Proc Nat Acad Sci 82:2272

    Article  Google Scholar 

  18. Beintema JJ, Fitch WM, Carsana A (1986) Mol Biol Evol 3 262

    PubMed  CAS  Google Scholar 

  19. Capasso S, Giordano F, Mattia CA, Mazzarella L, Zagari A (1983) Biopolymers 22:327

    Article  PubMed  CAS  Google Scholar 

  20. Piccoli R, D’Alessio G (1984) J Biol Chem 259:693

    PubMed  CAS  Google Scholar 

  21. Vescia S, Tramontano D (1981) Mol Cell Biochem 36:125

    Article  PubMed  CAS  Google Scholar 

  22. Levy CC, Karpetsky TP (1981) Enzymes as Drugs, Holcenberg JS, Roberts J eds

    Google Scholar 

  23. Palmer KA, Scheraga HA, Riordan JF, Vallee BL (1986) Proc Nat Acad Sci 83:1965

    Article  PubMed  CAS  Google Scholar 

  24. Shapiro R, Riordan JF, Vallee BL (1986) Biochem 25:3527

    Article  CAS  Google Scholar 

  25. Wills C; Joernvall H (1979) Eur J Biochem 99 323

    Article  PubMed  CAS  Google Scholar 

  26. Branden CL, Jornvall H, Eklund H, Furugren B (1975) The Enzymes, 3rd ed. 11:182

    Article  Google Scholar 

  27. Joernvall H, von Bahr-Lindstroem H, Jany K-D, Ulmer W, Froeschle M (1984) FEBS Lett 165:190

    Article  CAS  Google Scholar 

  28. Craik CS, Largman C, Fletcher T, Roczniak S, Barr PJ, Fletterick R, Rutter WJ (1985) Science 228:291

    Article  PubMed  CAS  Google Scholar 

  29. Kreitman M (1983) Nature 304:412

    Article  PubMed  CAS  Google Scholar 

  30. Jacq C, Miller JR, Brownlee GG (1977) Cell 12:109

    Article  PubMed  CAS  Google Scholar 

  31. Vanin EF (1984) Biochem Biophys Acta 782:231

    PubMed  CAS  Google Scholar 

  32. Miyata T, Hayashida H (1981) Proc Nat Acad Sci 78:5739

    Article  PubMed  CAS  Google Scholar 

  33. Li W-H, Wu, Chung-I L Chi-Cheng (1984) J Molec Evol 21:58

    Article  PubMed  CAS  Google Scholar 

  34. Li W-H, Gojobori T, Nei M (1981) Nature 292:237

    Article  PubMed  CAS  Google Scholar 

  35. Gitlin D, Gitlin JD (1975) The Plasma Proteins Putman FW ed, New York, Academic Press

    Google Scholar 

  36. Perler F, Efstradiatis A, Lomedico P, Gilbert W, Koler R, Dodgson J (1980) Cell 20:556

    Article  Google Scholar 

  37. Crabtree GR, Comeau CM, Fowlkes DM, Fornace Jr AJ, Malley JD, Kant JA (1985) J Mol Biol 185:1

    Article  PubMed  CAS  Google Scholar 

  38. Minghetti PP, Law SW, Dugaiczyk (1985) Mol Biol Evol 2:347

    PubMed  CAS  Google Scholar 

  39. Lewontin RC (1985) Ann Rev Genet 19:81

    Article  PubMed  CAS  Google Scholar 

  40. Weatherall DJ, Clegg JB (1976) Ann Rev Genet 10:157; Allison AC (1955) Cold Spring Harbor Symp Quant Biol 20:239

    Article  PubMed  CAS  Google Scholar 

  41. Yang Y-C, Ciarletta AB, Temple PA, Chung MP, Kovacic S, Witek-Giannotti JS, Leary AC, Kriz R, Donahue RE, Wong GG, Clark SC (1986) Cell 47:3

    Article  PubMed  CAS  Google Scholar 

  42. Hill RE, Hastie ND (1987) Nature 326:96

    Article  PubMed  CAS  Google Scholar 

  43. Stewart C-B, Schilling JW, Wilson AC (1987) Nature 330:401

    Article  PubMed  CAS  Google Scholar 

  44. Dayoff MO (1978) Atlas of Protein Sequence

    Google Scholar 

  45. Lewin R (1986) Science 232:578

    Article  Google Scholar 

  46. Diamond JM (1986) Nature 321:565

    Article  PubMed  CAS  Google Scholar 

  47. Dykhuizen DE (1978) Evolution 32:125

    Article  CAS  Google Scholar 

  48. Koch AL (1983) J Molec Evol 19:455

    Article  PubMed  CAS  Google Scholar 

  49. Li W-H (1984) Mol Biol Evol 1:213

    PubMed  CAS  Google Scholar 

  50. Benner SA (in press) Molecular Structure and Energetics, J.F. Liebman and A. Greenbergr eds., Deerfield Beachr Florida, VCH Publishers

    Google Scholar 

  51. Domingo E, Sabo D, Taniguchi T, Weissmann C (1978) Cell 13:735

    Article  PubMed  CAS  Google Scholar 

  52. Sharp PM, Rogers MS, McConnell DJ (1985) J Molec Evol 21:150

    Article  CAS  Google Scholar 

  53. Grantham R, Gautier C, Gouy M, Jacobzone M, Mercier R (1981) Nucl Acids Res 9:r43

    Article  PubMed  CAS  Google Scholar 

  54. Gouy M, Gautier C (1982) Nucl Acids Res 10:7056

    Article  Google Scholar 

  55. Konigsberg W, Godson GN (1983) Proc Nat Acad Sci 80:687

    Article  PubMed  CAS  Google Scholar 

  56. Bennetzen J, Hall B (1982) J Biol Chem 257:3026

    PubMed  CAS  Google Scholar 

  57. Grosjean E, Fiers W (1982) Gene 18:199

    Article  PubMed  CAS  Google Scholar 

  58. Blaisdell BE (1983) J Molec Evol 19:226

    Article  PubMed  CAS  Google Scholar 

  59. Rubin CM, Houck CM, Deininger PL, Friedmann T, Schmid CW (1980) Nature 284:372

    Article  PubMed  CAS  Google Scholar 

  60. Modiano G, Battistuzzi G, Motulsky AG (1981) Proc Nat Acad Sci 78:1110

    Article  PubMed  CAS  Google Scholar 

  61. Lipman DJ, Wilbur WJ (1983) J Mol Biol 163:363

    Article  PubMed  CAS  Google Scholar 

  62. Lanave C, Preparata G, Saccone C (1985) J Mol Evol 21:346

    Article  CAS  Google Scholar 

  63. Benner, SA (submitted) Chem Rev

    Google Scholar 

  64. Ellington AD, Benner, SA (1987) J Theor Biol 127:491

    Article  PubMed  CAS  Google Scholar 

  65. Ellington AD (1988) Thesisr Harvard University

    Google Scholar 

  66. Liang N, Pielak GJ, Mauk AG, Smith M, Hoffman BM (1987) Proc Nat Acad Sci 84:1249

    Article  PubMed  CAS  Google Scholar 

  67. Place AR, Powers DA (1979) Proc Nat Acad Sci 76:2354

    Article  PubMed  CAS  Google Scholar 

  68. Borgman V, Moon TW (1975) Can J Biochem 53:998

    Article  Google Scholar 

  69. Hennessey Jr JP, Siebenaller JF (1987) Biochem Biophys Acta 913:285

    Article  PubMed  CAS  Google Scholar 

  70. Koehn RK (1969) Science 163:943

    Article  PubMed  CAS  Google Scholar 

  71. Merritt RB (1972) Am Nat 106:173

    Article  CAS  Google Scholar 

  72. Day TH, Hiller PC, Clarke B (1974) Biochem Genet 11:141

    Article  PubMed  CAS  Google Scholar 

  73. Day TH, Needham L (1974) Biochem Genet 11:167

    Article  PubMed  CAS  Google Scholar 

  74. Glasfeld A (1988) Thesis, Harvard University

    Google Scholar 

  75. Zimmermann T, Kulla HG, Leisinger T (1983) Experientia 39:1429

    Google Scholar 

  76. Campbell HH, Lengyel JA, Langridge J (1973) Proc Nat Acad Sci 70:1841

    Article  PubMed  CAS  Google Scholar 

  77. Boronat A, Aguilar J (1981) Biochim Biophys Acta 672:98

    Article  PubMed  CAS  Google Scholar 

  78. Burleigh BD Jr, Rigby PWJ, Hartley BS (1974) Biochem J 143:341

    PubMed  CAS  Google Scholar 

  79. Betz JL, Brown PR, Smyth MJ, Clarke PH (1974) Nature 247:261

    Article  PubMed  CAS  Google Scholar 

  80. Hall A, Knowles JR (1976) Nature 264:803

    Article  PubMed  CAS  Google Scholar 

  81. Wills C (1976) Nature 261:26

    Article  PubMed  CAS  Google Scholar 

  82. Brooker RJ, Wilson TH (1985) Proc Nat Acad Sci 82:3959

    Article  PubMed  CAS  Google Scholar 

  83. Murray M, Osborne S, Sinnott ML (1983) J Chem Soc Perkin Trans II 1595

    Google Scholar 

  84. Hall BG, Yokoyama S, Calhoun DH (1984) Molec Biol Evol 1:109

    Google Scholar 

  85. Llewellyn DJ, Daday A, Smith GD (1983) J Biol Chem 255:2077

    Google Scholar 

  86. Grimshaw CE, Sogo SG, Copley SD, Knowles JR (1984) J Am Chem Soc 106:2699

    Article  CAS  Google Scholar 

  87. Haniu M, Izanagi T, Miller P, Lee TD, Shively JE (1986) Biochem 25:7906

    Article  CAS  Google Scholar 

  88. Stephens PE, Lewis HM, Darlison MG, Guest JR (1983) Eur J Biochem 135:519

    Article  PubMed  CAS  Google Scholar 

  89. Nyunoya H, Broglie KE, Lusty CJ (1985) Proc Nat Acad Sci 82:2244

    Article  PubMed  CAS  Google Scholar 

  90. Belfaiza J, Parsot Cl, Martel A, Bouthier de la Tour C, Margarita D, Cohen GN, Saint-Girons I (1986) Proc Nat Acad Sci 83:867

    Article  PubMed  CAS  Google Scholar 

  91. Yeh W-K, Fletcher P, Ornston LN (1980) J Biol Chem 255:6342

    PubMed  CAS  Google Scholar 

  92. You K-S (1985) CRC Crit Rev Biochem 17:313

    Article  PubMed  CAS  Google Scholar 

  93. Benner SA (1982) Experientia 38:633

    Article  PubMed  CAS  Google Scholar 

  94. Jornvall E, Persson M, Jeffrey J (1981) Proc Nat Acad Sci 78:4226

    Article  PubMed  CAS  Google Scholar 

  95. Rossmann MJ, Liljas A, Braenden C-I (1975) The Enzymes 11:61

    Article  Google Scholar 

  96. Garavito RM, Rossmann MG, Argos P, Eventoff W (1977) Biochem 16:5065

    Article  CAS  Google Scholar 

  97. Goerisch H, Hartl T, Grussebueter W, Stezowski J (1982) Biochem J 226:885

    Google Scholar 

  98. Allemann R, Hung R, Benner SA (in press) J Am Chem Soc 110

    Google Scholar 

  99. Matthews DA, Smith SL, Baccanari DP, Burchall JJ, Oatley SM, Kraut J (1986) Biochem 25:4194

    Article  CAS  Google Scholar 

  100. Dugan RE, Porter JW (1971) J Biol Chem 246:5361

    PubMed  CAS  Google Scholar 

  101. Beedle AS, Munday KA, Wilton DC (1972) Eur J Biochem 28:151

    Article  PubMed  CAS  Google Scholar 

  102. Cronin CN, Malcolm BA, Kirsch, JF (1987) J Am Chem Soc 109:2222

    Article  CAS  Google Scholar 

  103. Oppenheimer NJ (1986) “Proceedings of the Steenbock Symposium” Madison Wisconsin July (1985) New York Elsevier (1986) 29–43

    Google Scholar 

  104. Garavito RM, Rossmann MG, Argos P, Eventoff W (1977) Biochem 16:5065

    Article  CAS  Google Scholar 

  105. Piccirilli JA, Benner SA (1987) J Am Chem Soc 109:8084

    Article  CAS  Google Scholar 

  106. Nambiar KP, Stackhouse J, Stauffer DM, Kennedy WP, Eldredge JK, Benner SA (1984) Science 222:1299

    Article  Google Scholar 

  107. Presnell SR (2988) Thesis, Harvard University

    Google Scholar 

  108. Walsh C (1979) Enzymatic Reaction Mechanisms, San Francisco Freeman

    Google Scholar 

  109. Hogenkamp HPC, Follmann H, Thauer RK (1987) FEBS Lett 219:197

    Article  CAS  Google Scholar 

  110. Nes WR, Nes WD (1980) Lipids in Evolution, NY Plenum Press

    Google Scholar 

  111. Vogel HJ (1965) Evolving Genes and Proteins, Bryson V and Vogel HJ eds, NY, Academic Press

    Google Scholar 

  112. Kannangara CG, Gough SP, Oliver RP, Rasmussen SK (1984) Carlsberg Res Comm 49:417

    Article  CAS  Google Scholar 

  113. Schoen A, Krupp G, Gough S, Berry-Lowe S, Kannangara CG, Soell D (1986) Nature 322:281

    Article  CAS  Google Scholar 

  114. Weinstein JD, Beale SI (1985) Arch Biochem Biophys 239:87

    Article  PubMed  CAS  Google Scholar 

  115. Huang D-D, Wang W-Y, Gough SP, Kannangara CG (1984) Science 225:1482

    Article  PubMed  CAS  Google Scholar 

  116. Nandi DL (1978) Arch Biochem Biophys 188:266

    Article  PubMed  CAS  Google Scholar 

  117. Gerdes HJ, Leistner E (1979) Phytochem 18:771

    Article  CAS  Google Scholar 

  118. Benner SA, Piccirilli JA (submitted) Top Stereochem

    Google Scholar 

  119. Scott TA, Bellion E, Mattey, M (1969) Eur J Biochem 10:318

    Article  PubMed  CAS  Google Scholar 

  120. Neunlist S, Rohmer M (1985) Biochem J 228:769

    PubMed  CAS  Google Scholar 

  121. Jencks WP (1975) Adv Enzymol 43:219

    PubMed  CAS  Google Scholar 

  122. Benner SA, Ellington AD (in press) Nature 329:295; Benner SA et al., Cold Spring Harbor Sym. Quant. Biol. 51

    Google Scholar 

  123. Gilbert W (1986) Nature 319:818

    Article  Google Scholar 

  124. Woese CR (1987) Microbiol Rev 51:221

    PubMed  CAS  Google Scholar 

  125. Woese CR (1967) The Origins of the Genetic Code, Harper & Row

    Google Scholar 

  126. Crick F (1968) J Mol Biol 38:367

    Article  PubMed  CAS  Google Scholar 

  127. Orgel LE (1968) J Mol Biol 38:381

    Article  PubMed  CAS  Google Scholar 

  128. Lehninger A (1972) Biochemistry, New York, Worth Publishers

    Google Scholar 

  129. Usher DA, McHale AH (1976) Proc Nat Acad Sci 73:1149

    Article  PubMed  CAS  Google Scholar 

  130. White III HB (1976) J Molec Evol 7:101

    Article  PubMed  CAS  Google Scholar 

  131. Visser CM, Kellogg RM (1978) J Mol Evol 11:171

    Article  PubMed  CAS  Google Scholar 

  132. Bass BL, Cech TR (1984) Nature 308:820

    Article  PubMed  CAS  Google Scholar 

  133. Guerrier-Takada C, Altman S (1983) Science 223:285

    Article  Google Scholar 

  134. Darnell JE, Doolittle WF (1986) Proc Natl Acad Sci 83:1271

    Article  PubMed  CAS  Google Scholar 

  135. Weiner AM, Maizels N (1987) Proc Nat Acad Sci 84:7383

    Article  PubMed  CAS  Google Scholar 

  136. Alberts BM (1986) Amer Zool 26:781–796

    CAS  Google Scholar 

  137. Cantoni GL (1962) Methods Enzymol 5:743

    Article  CAS  Google Scholar 

  138. Siu PML, HG Wood (1962) J Biol Chem 237:3044

    PubMed  CAS  Google Scholar 

  139. Maizels N, Weiner AM (1987) Nature 330:616

    Article  PubMed  CAS  Google Scholar 

  140. Hanson KN, Rose IA (1975) Acc Chem Res 14:1

    Article  Google Scholar 

  141. Carlson TA, Chelm BK (1986) Nature 322:568

    Article  CAS  Google Scholar 

  142. Leunissen JAM, de Jong WW (1986) J Mol Evol 23:250

    Article  CAS  Google Scholar 

  143. Lewin R (1985) Science 227:1020

    Article  PubMed  CAS  Google Scholar 

  144. Syvanen M (1985) J Theor Biol 112:333

    Article  PubMed  CAS  Google Scholar 

  145. Ciechanover A, Wolin SL, Steitz JA, Lodish HF (1985) Proc Natl Acad Sci 82:1341

    Article  PubMed  CAS  Google Scholar 

  146. Eschenmoser A (in press) Angew Chem

    Google Scholar 

  147. Miller SL (1955) J Am Chem Soc 77:2351

    Article  CAS  Google Scholar 

  148. Benner SA, Ellington AD (in preparation)

    Google Scholar 

  149. Gropp F, Reiter WD, Sentenac A, Zillig W, Schnabel R, Thomm M, Stetter KO (1986) System Appl Microbiol 7:95

    Article  CAS  Google Scholar 

  150. Lin A-NI, Ashley GW, Stubbe J (1987) 26:6905

    Google Scholar 

  151. Krautler B, Moll J, Thauer RK (1987) Eur J Biochem 162:275

    Article  PubMed  CAS  Google Scholar 

  152. Strother PK Barghoorn (1980) Origins of Life and Evolution, Halvorsen HO, van Holde KE eds, New York, Liss

    Google Scholar 

  153. Bradford AP, Aitken A, Beg F, Cook KG, Yeaman SJ (1987) FEBS Letters 222: 211

    Article  PubMed  CAS  Google Scholar 

  154. Frantz B, Chakrabarty AM, (1987) Proc Natl Acad Sci 84:4460

    Article  PubMed  CAS  Google Scholar 

  155. Grenett HE, Ledley FD, Reed LL, Woo SLC, (1987) Proc Natl Acad Sci 84:5530

    Article  PubMed  CAS  Google Scholar 

  156. Sikorav J-L, Krejci E, Massoulie J (1987) EMBO J 6:1865

    PubMed  CAS  Google Scholar 

  157. Schinina ME, Maffey L, Barra D, Bossa F, Puget K, Michelson AM (1987) FEBS Letters 221:87

    Article  PubMed  CAS  Google Scholar 

  158. Shanske S, Sakoda S, Hermodson MA, DiMauro S, Schon EA (1987) J Biol Chem 262:14612

    PubMed  CAS  Google Scholar 

  159. Parson CA (1987) Proc Natl Acad Sci 84:5207

    Article  Google Scholar 

  160. Anton IA, Duncan K, Coggins JR (1987) J Mol Biol 197:367

    Article  PubMed  CAS  Google Scholar 

  161. Jornvall H, Hoog J-O, Bahr-Lindstrom von H, Vallee BL (1987) Proc Natl Acad Sci 84:2580

    Article  PubMed  CAS  Google Scholar 

  162. Volokita M, Somerville CR (1987) J Biol Chem 262:15825

    PubMed  CAS  Google Scholar 

  163. Pilkis SJ, Lively MO, El-Maghrabi MR (1987) J Biol Chem 262

    Google Scholar 

  164. Hammond GL, Smith CL, Goping IS, Underhill DA, Harley MJ, Reventos J, Musto NA, Gunsalus GL, Bardin, CW (1987) Proc Natl Acad Sci 84:5153

    Article  PubMed  CAS  Google Scholar 

  165. Wu YD, Houk KN (1987) J Am Chem Soc 109:2226

    Article  CAS  Google Scholar 

  166. Ohno A, Ohara M, Oka S (1986) J Am Chem Soc 108:6438

    Article  CAS  Google Scholar 

  167. Kaplan NO (1967) Methods Enzymol 10:317

    Article  CAS  Google Scholar 

Download references

Author information

Authors and Affiliations

  1. Laboratory for Organic Chemistry, E.T.H., Zurich, CH-8092, Switzerland

    Steven A. Benner

Authors
  1. Steven A. Benner
    View author publications

    You can also search for this author in PubMed Google Scholar

Editor information

Editors and Affiliations

  1. Laboratory for Organic Chemistry, Federal Institute of Technology (ETH), ETH Zürich, CH-8092, Zürich, Switzerland

    Steven A. Benner

Rights and permissions

Reprints and permissions

Copyright information

© 1988 Springer-Verlag Berlin Heidelberg

About this paper

Cite this paper

Benner, S.A. (1988). Reconstructing the Evolution of Proteins. In: Benner, S.A. (eds) Redesigning the Molecules of Life. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-642-73594-3_5

Download citation

  • DOI: https://doi.org/10.1007/978-3-642-73594-3_5

  • Publisher Name: Springer, Berlin, Heidelberg

  • Print ISBN: 978-3-540-19166-7

  • Online ISBN: 978-3-642-73594-3

  • eBook Packages: Springer Book Archive

Publish with us

Policies and ethics

Search

Navigation