메뉴 건너뛰기




Volumn 286, Issue 5448, 1999, Pages 2345-2348

Evolution of shape complementarity and catalytic efficiency from a primordial antibody template

Author keywords

[No Author keywords available]

Indexed keywords

ANTIBODY; PROGESTERONE;

EID: 0033579299     PISSN: 00368075     EISSN: None     Source Type: Journal    
DOI: 10.1126/science.286.5448.2345     Document Type: Article
Times cited : (117)

References (53)
  • 1
    • 84912208190 scopus 로고
    • L. Pauling, Am. Sci. 36, 51 (1948); W. P. Jencks, Catalysis in Chemistry and Enzymology (McGraw-Hill, New York, 1969).
    • (1948) Am. Sci. , vol.36 , pp. 51
    • Pauling, L.1
  • 3
    • 0028817877 scopus 로고
    • P. G. Schultz and R. A. Lerner, Science 269, 1835 (1995); Acc. Chem. Res. 26, 391 (1993); D. Hilvert, Top. Stereochem. 22, 83 (1999).
    • (1995) Science , vol.269 , pp. 1835
    • Schultz, P.G.1    Lerner, R.A.2
  • 4
    • 0000791343 scopus 로고
    • P. G. Schultz and R. A. Lerner, Science 269, 1835 (1995); Acc. Chem. Res. 26, 391 (1993); D. Hilvert, Top. Stereochem. 22, 83 (1999).
    • (1993) Acc. Chem. Res. , vol.26 , pp. 391
  • 5
    • 53149142805 scopus 로고    scopus 로고
    • P. G. Schultz and R. A. Lerner, Science 269, 1835 (1995); Acc. Chem. Res. 26, 391 (1993); D. Hilvert, Top. Stereochem. 22, 83 (1999).
    • (1999) Top. Stereochem. , vol.22 , pp. 83
    • Hilvert, D.1
  • 7
    • 0028763728 scopus 로고
    • M. R. Haynes, E. A. Stura, D. Hilvert, I. A. Wilson, Science 263, 646 (1994); P. A. Patten et al., Science 271, 1086 (1996); G. J. Wedemayer, P. A. Patten, L. H. Wang, P. G. Schultz, R. C. Stevens, Science 276, 1665 (1997); J. B. Charbonnier et al., Science 275, 1140 (1997); H. D. Ulrich et al., Nature 389, 271 (1997).
    • (1994) Science , vol.263 , pp. 646
    • Haynes, M.R.1    Stura, E.A.2    Hilvert, D.3    Wilson, I.A.4
  • 8
    • 0029991227 scopus 로고    scopus 로고
    • M. R. Haynes, E. A. Stura, D. Hilvert, I. A. Wilson, Science 263, 646 (1994); P. A. Patten et al., Science 271, 1086 (1996); G. J. Wedemayer, P. A. Patten, L. H. Wang, P. G. Schultz, R. C. Stevens, Science 276, 1665 (1997); J. B. Charbonnier et al., Science 275, 1140 (1997); H. D. Ulrich et al., Nature 389, 271 (1997).
    • (1996) Science , vol.271 , pp. 1086
    • Patten, P.A.1
  • 9
    • 0030821164 scopus 로고    scopus 로고
    • M. R. Haynes, E. A. Stura, D. Hilvert, I. A. Wilson, Science 263, 646 (1994); P. A. Patten et al., Science 271, 1086 (1996); G. J. Wedemayer, P. A. Patten, L. H. Wang, P. G. Schultz, R. C. Stevens, Science 276, 1665 (1997); J. B. Charbonnier et al., Science 275, 1140 (1997); H. D. Ulrich et al., Nature 389, 271 (1997).
    • (1997) Science , vol.276 , pp. 1665
    • Wedemayer, G.J.1    Patten, P.A.2    Wang, L.H.3    Schultz, P.G.4    Stevens, R.C.5
  • 10
    • 15444355643 scopus 로고    scopus 로고
    • M. R. Haynes, E. A. Stura, D. Hilvert, I. A. Wilson, Science 263, 646 (1994); P. A. Patten et al., Science 271, 1086 (1996); G. J. Wedemayer, P. A. Patten, L. H. Wang, P. G. Schultz, R. C. Stevens, Science 276, 1665 (1997); J. B. Charbonnier et al., Science 275, 1140 (1997); H. D. Ulrich et al., Nature 389, 271 (1997).
    • (1997) Science , vol.275 , pp. 1140
    • Charbonnier, J.B.1
  • 11
    • 0030930805 scopus 로고    scopus 로고
    • M. R. Haynes, E. A. Stura, D. Hilvert, I. A. Wilson, Science 263, 646 (1994); P. A. Patten et al., Science 271, 1086 (1996); G. J. Wedemayer, P. A. Patten, L. H. Wang, P. G. Schultz, R. C. Stevens, Science 276, 1665 (1997); J. B. Charbonnier et al., Science 275, 1140 (1997); H. D. Ulrich et al., Nature 389, 271 (1997).
    • (1997) Nature , vol.389 , pp. 271
    • Ulrich, H.D.1
  • 13
    • 0003562572 scopus 로고    scopus 로고
    • Gaussian Inc., Pittsburgh, PA
    • Quantum mechanical calculations at the RHF/6-31G(d) level were performed to optimize the geometries of reactants, intermediates, and transition states; energies were evaluated at the B3LYP/6-31G(d) level. Stationary points were characterized by RHF/3-21G frequency calculations (M. J. Frisch et al., Gaussian, Gaussian Inc., Pittsburgh, PA). The calculations show transition state 5 to be rate determining. The computed activation energy is 19.9 kcal/mol and increases to 22.1 kcal/mol in water (SCI-PCM) [M. Cossi et al., Chem. Phys. Lett. 255, 327 (1996)]. A single hydrogen bond from a water molecule to NEM 2 lowers the activation energy by 0.6 kcal/mol. Calculations predict no effect on hydrogen bonding of water to the thiophene dioxide.
    • Gaussian
    • Frisch, M.J.1
  • 14
    • 84962359221 scopus 로고    scopus 로고
    • A single hydrogen bond from a water molecule to NEM 2 lowers the activation energy by 0.6 kcal/mol. Calculations predict no effect on hydrogen bonding of water to the thiophene dioxide
    • Quantum mechanical calculations at the RHF/6- 31G(d) level were performed to optimize the geometries of reactants, intermediates, and transition states; energies were evaluated at the B3LYP/6- 31G(d) level. Stationary points were characterized by RHF/3-21G frequency calculations (M. J. Frisch et al., Gaussian, Gaussian Inc., Pittsburgh, PA). The calculations show transition state 5 to be rate determining. The computed activation energy is 19.9 kcal/mol and increases to 22.1 kcal/mol in water (SCI-PCM) [M. Cossi et al., Chem. Phys. Lett. 255, 327 (1996)]. A single hydrogen bond from a water molecule to NEM 2 lowers the activation energy by 0.6 kcal/mol. Calculations predict no effect on hydrogen bonding of water to the thiophene dioxide.
    • (1996) Chem. Phys. Lett. , vol.255 , pp. 327
    • Cossi, M.1
  • 16
    • 0343354810 scopus 로고    scopus 로고
    • V. E. Gouverneur et al., Science 275, 1140 (1997); A. A. P. Meekel, M. Resmini, U. K. Pandit, J. Chem. Soc. Chem. Commun. 571 (1995).
    • (1997) Science , vol.275 , pp. 1140
    • Gouverneur, V.E.1
  • 20
    • 0033102314 scopus 로고    scopus 로고
    • B. Seelig and A. Jäschke, Chem. Biol. 6, 167 (1999); T. M. Tarasow, S. L. Tarasow, B. E. Eaton, Nature 389, 54 (1997).
    • (1999) Chem. Biol. , vol.6 , pp. 167
    • Seelig, B.1    Jäschke, A.2
  • 22
    • 0002709543 scopus 로고
    • The full length IgG1 was expressed from mouse myeloma cells and purified as described in (5). The 1E9 Fab fragment was generated by enzymatic digestion with 2% papain in the presence of cysteine
    • E. A. Stura, G. G. Fieser, I. A. Wilson, Immunomethods 3, 164 (1993). The full length IgG1 was expressed from mouse myeloma cells and purified as described in (5). The 1E9 Fab fragment was generated by enzymatic digestion with 2% papain in the presence of cysteine.
    • (1993) Immunomethods , vol.3 , pp. 164
    • Stura, E.A.1    Fieser, G.G.2    Wilson, I.A.3
  • 24
    • 0027686741 scopus 로고
    • J. H. Arevalo, M. J. Taussig, I. A. Wilson, Nature 365, 859 (1993); J. H. Arevalo et al., J. Mol. Biol. 231, 103 (1993); J. H. Arevalo et al., J. Mol. Biol. 241, 663 (1994).
    • (1993) Nature , vol.365 , pp. 859
    • Arevalo, J.H.1    Taussig, M.J.2    Wilson, I.A.3
  • 25
    • 0027299695 scopus 로고
    • J. H. Arevalo, M. J. Taussig, I. A. Wilson, Nature 365, 859 (1993); J. H. Arevalo et al., J. Mol. Biol. 231, 103 (1993); J. H. Arevalo et al., J. Mol. Biol. 241, 663 (1994).
    • (1993) J. Mol. Biol. , vol.231 , pp. 103
    • Arevalo, J.H.1
  • 26
    • 0028074882 scopus 로고
    • J. H. Arevalo, M. J. Taussig, I. A. Wilson, Nature 365, 859 (1993); J. H. Arevalo et al., J. Mol. Biol. 231, 103 (1993); J. H. Arevalo et al., J. Mol. Biol. 241, 663 (1994).
    • (1994) J. Mol. Biol. , vol.241 , pp. 663
    • Arevalo, J.H.1
  • 29
    • 11644261806 scopus 로고    scopus 로고
    • G. M. Morris et al., J. Comp. Chem. 19, 1639 (1998); G. M. Morris et al., J. Comput. Aided Mol. Des. 10, 293 (1996); D. S. Goodsell and A. J. Olson, Proteins Struct. Funct. Genet. 8, 195 (1990).
    • (1998) J. Comp. Chem. , vol.19 , pp. 1639
    • Morris, G.M.1
  • 30
    • 0030203710 scopus 로고    scopus 로고
    • G. M. Morris et al., J. Comp. Chem. 19, 1639 (1998); G. M. Morris et al., J. Comput. Aided Mol. Des. 10, 293 (1996); D. S. Goodsell and A. J. Olson, Proteins Struct. Funct. Genet. 8, 195 (1990).
    • (1996) J. Comput. Aided Mol. Des. , vol.10 , pp. 293
    • Morris, G.M.1
  • 31
    • 0025135112 scopus 로고
    • G. M. Morris et al., J. Comp. Chem. 19, 1639 (1998); G. M. Morris et al., J. Comput. Aided Mol. Des. 10, 293 (1996); D. S. Goodsell and A. J. Olson, Proteins Struct. Funct. Genet. 8, 195 (1990).
    • (1990) Proteins Struct. Funct. Genet. , vol.8 , pp. 195
    • Goodsell, D.S.1    Olson, A.J.2
  • 32
    • 0004032583 scopus 로고
    • U.S. Public Health Service, National Institutes of Health, Bethesda, MD, ed. 5, See also the antibody database Web page
    • E. A. Kabat, T. T. Wu, H. M. Perry, K. S. Gottesman, C. Foeller, Sequences of Proteins of Immunological Interest (U.S. Public Health Service, National Institutes of Health, Bethesda, MD, ed. 5, 1991). See also the antibody database Web page http://www.biochem. ucl.ac.uk/̃martin/abs/
    • (1991) Sequences of Proteins of Immunological Interest
    • Kabat, E.A.1    Wu, T.T.2    Perry, H.M.3    Gottesman, K.S.4    Foeller, C.5
  • 33
    • 0342919547 scopus 로고    scopus 로고
    • note
    • H3, respectively, resulting in a Phe at this position. Residue H100, which provides one of the walls of the cavity, arises from the DJ junction; it is an Arg in 1E9 and 39-A11 and a Trp in DB3. The H97 residue (Thr in 1E9, Tyr in DB3, and Arg in 39-A11) interacts primarily with the linker moiety in the 1E9 and 39-A11 structures, whereas in DB3 it provides a lid over one end of the hydrophobic cavity.
  • 35
    • 0343354807 scopus 로고    scopus 로고
    • note
    • 3CN to give 7 (73%). All new compounds gave satisfactory spectroscopic data.
  • 36
    • 0342919548 scopus 로고    scopus 로고
    • note
    • 2 bleaching at 606 nm. Initial velocities were determined at several concentrations of one substrate while the concentration of the other was kept constant. The uncatalyzed reaction was carried out under identical conditions and also in acetonitrile.
  • 39
    • 0025862151 scopus 로고
    • C. Lewis, T. Krämer, S. Robinson, D. Hilvert, Science 253, 1019 (1991); S. N. Thorn, R. G. Daniels, M.-T. M. Auditor, D. Hilvert, Nature 373, 228 (1995); F. Hollenfelder, A. J. Kirby, D. Tawfik, Nature 383, 60 (1996); K. Kikuchi and D. Hilvert, J. Am. Chem. Soc. 118, 8184 (1996).
    • (1991) Science , vol.253 , pp. 1019
    • Lewis, C.1    Krämer, T.2    Robinson, S.3    Hilvert, D.4
  • 40
    • 0028869408 scopus 로고
    • C. Lewis, T. Krämer, S. Robinson, D. Hilvert, Science 253, 1019 (1991); S. N. Thorn, R. G. Daniels, M.-T. M. Auditor, D. Hilvert, Nature 373, 228 (1995); F. Hollenfelder, A. J. Kirby, D. Tawfik, Nature 383, 60 (1996); K. Kikuchi and D. Hilvert, J. Am. Chem. Soc. 118, 8184 (1996).
    • (1995) Nature , vol.373 , pp. 228
    • Thorn, S.N.1    Daniels, R.G.2    Auditor, M.-T.M.3    Hilvert, D.4
  • 41
    • 0029793086 scopus 로고    scopus 로고
    • C. Lewis, T. Krämer, S. Robinson, D. Hilvert, Science 253, 1019 (1991); S. N. Thorn, R. G. Daniels, M.-T. M. Auditor, D. Hilvert, Nature 373, 228 (1995); F. Hollenfelder, A. J. Kirby, D. Tawfik, Nature 383, 60 (1996); K. Kikuchi and D. Hilvert, J. Am. Chem. Soc. 118, 8184 (1996).
    • (1996) Nature , vol.383 , pp. 60
    • Hollenfelder, F.1    Kirby, A.J.2    Tawfik, D.3
  • 42
    • 0029810652 scopus 로고    scopus 로고
    • C. Lewis, T. Krämer, S. Robinson, D. Hilvert, Science 253, 1019 (1991); S. N. Thorn, R. G. Daniels, M.-T. M. Auditor, D. Hilvert, Nature 373, 228 (1995); F. Hollenfelder, A. J. Kirby, D. Tawfik, Nature 383, 60 (1996); K. Kikuchi and D. Hilvert, J. Am. Chem. Soc. 118, 8184 (1996).
    • (1996) J. Am. Chem. Soc. , vol.118 , pp. 8184
    • Kikuchi, K.1    Hilvert, D.2
  • 44
    • 0028155689 scopus 로고
    • note
    • m values. The free energy of binding of transition state 5 is -8.9 kcal/mol. Thus, the predicted activation energy of the cycloaddition is lowered 5.7 kcal/mol relative to that in water (6).
    • (1994) Protein Eng. , vol.7 , pp. 385
    • Åqvist, J.1    Medina, C.2    Samuelsson, J.E.3
  • 46
    • 0032549734 scopus 로고    scopus 로고
    • A. Heine et al., Science 279, 1934 (1998).
    • (1998) Science , vol.279 , pp. 1934
    • Heine, A.1
  • 50
    • 0033120221 scopus 로고    scopus 로고
    • A. T. Brünger, X-PLOR, Version 3.1: A System for X-Ray and NMK (Yale Univ. Press, New Haven, CT, 1992); J. Badger et al., Proteins Struct. Funct. Genet. 35, 25 (1999).
    • (1999) Proteins Struct. Funct. Genet. , vol.35 , pp. 25
    • Badger, J.1
  • 52
    • 0026319199 scopus 로고
    • with a probe radius of 1.4 Å, and the volume enclosed in each surface was then computed. The gap volume is taken as the difference between the volume of the complex and the sum of the volumes of the antibody and the antigen. Gap index is the gap volume divided by the buried surface area
    • The molecular surfaces of the antibody, antigen, and antibody-antigen complex were constructed separately with the program GRASP [A. Nicholls, K. A. Sharp, B. Honig, Proteins Struct. Funct. Genet. 11, 281 (1991)] with a probe radius of 1.4 Å, and the volume enclosed in each surface was then computed. The gap volume is taken as the difference between the volume of the complex and the sum of the volumes of the antibody and the antigen. Gap index is the gap volume divided by the buried surface area.
    • (1991) Proteins Struct. Funct. Genet. , vol.11 , pp. 281
    • Nicholls, A.1    Sharp, K.A.2    Honig, B.3
  • 53
    • 0343354805 scopus 로고    scopus 로고
    • note
    • Supported by NIH grants CA27489 (I.A.W.) and GM38273 (D.H.) and NSF grant CHE-9616772 (K.N.H.). We thank T. Horton, N. Jiang, and M. Auditor for technical assistance; the staff of SSRL beamline 9-1; R. A. Lerner, A. Heine, and D. J. Edwards for helpful discussions; the referees for helpful comments; N. R. Klinman for advice on germ line gene analysis; and K. Renner for computational assistance.


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.