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Conformational effects in biological catalysis: an antibody-catalyzed oxy-cope rearrangement.

Mundorff EC, Hanson MA, Varvak A, Ulrich H, Schultz PG, Stevens RC
Biochemistry 39 627-32 (2000)
Related entries: 1d5b, 1d5i

Cited: 26 times
EuropePMC logo PMID: 10651626

Abstract

Antibody AZ-28 was generated against the chairlike transition-state analogue (TSA) 1 and catalyzes the oxy-Cope rearrangement of substrate 2 to product 3. The germline precursor to AZ-28 catalyzes the reaction with a 35-fold higher rate (k(cat)/k(uncat) = 163 000), despite a 40-fold lower binding affinity for TSA.1 (K(D) = 670 nM). To determine the structural basis for the differences in the binding and catalytic properties of the germline and affinity-matured antibodies, the X-ray crystal structures of the unliganded and TSA.1 complex of antibody AZ-28 have been determined at 2.8 and 2.6 A resolution, respectively; the structures of the unliganded and TSA.1 complex of the germline precursor to AZ-28 were both determined at 2. 0 A resolution. In the affinity-matured antibody.hapten complex the TSA is fixed in a catalytically unfavorable conformation by a combination of van der Waals and hydrogen-bonding interactions. The 2- and 5-phenyl substituents of TSA.1 are almost perpendicular to the cyclohexyl ring, leading to decreased orbital overlap and decreased stabilization of the putative transition state. The active site of the germline antibody appears to have an increased degree of flexibility-CDRH3 moves 4.9 A outward from the active site upon binding of TSA.1. We suggest that this conformational flexibility in the germline antibody, which results in a lower binding affinity for TSA.1, allows dynamic changes in the dihedral angle of the 2-phenyl substituent along the reaction coordinate. These conformational changes in turn lead to enhanced orbital overlap and increased catalytic rate. These studies suggest that protein and substrate dynamics play a key role in this antibody-catalyzed reaction.

Articles - 1d6v mentioned but not cited (4)

  1. Structural insights into the antigenicity of myelin oligodendrocyte glycoprotein. Breithaupt C, Schubart A, Zander H, Skerra A, Huber R, Linington C, Jacob U. Proc. Natl. Acad. Sci. U.S.A. 100 9446-9451 (2003)
  2. Preference of small molecules for local minimum conformations when binding to proteins. Wang Q, Pang YP. PLoS One 2 e820 (2007)
  3. A complete, multi-level conformational clustering of antibody complementarity-determining regions. Nikoloudis D, Pitts JE, Saldanha JW. PeerJ 2 e456 (2014)
  4. Structural Analysis of Anti-Hapten Antibodies to Identify Long-Range Structural Movements Induced by Hapten Binding. Al Qaraghuli MM, Kubiak-Ossowska K, Ferro VA, Mulheran PA. Front Mol Biosci 8 633526 (2021)


Reviews citing this publication (4)

  1. Catalytic antibodies: hapten design strategies and screening methods. Xu Y, Yamamoto N, Janda KD. Bioorg. Med. Chem. 12 5247-5268 (2004)
  2. Novel reactions catalysed by antibodies. Golinelli-Pimpaneau B. Curr. Opin. Struct. Biol. 10 697-708 (2000)
  3. Structural diversity of antibody catalysts. Golinelli-Pimpaneau B. J. Immunol. Methods 269 157-171 (2002)
  4. The elicitation of carboxylesterase activity in antibodies by reactive immunization with labile organophosphorus antigens: a role for flexibility. Schowen RL. J. Immunol. Methods 269 59-65 (2002)

Articles citing this publication (18)

  1. Structural plasticity and the evolution of antibody affinity and specificity. Yin J, Beuscher AE, Andryski SE, Stevens RC, Schultz PG. J. Mol. Biol. 330 651-656 (2003)
  2. The primary antibody repertoire represents a linked network of degenerate antigen specificities. Manivel V, Bayiroglu F, Siddiqui Z, Salunke DM, Rao KV. J Immunol 169 888-897 (2002)
  3. Thermodynamic and kinetic aspects of antibody evolution during the immune response to hapten. Sagawa T, Oda M, Ishimura M, Furukawa K, Azuma T. Mol. Immunol. 39 801-808 (2003)
  4. Rapid formation of the stable tyrosyl radical in photosystem II. Faller P, Debus RJ, Brettel K, Sugiura M, Rutherford AW, Boussac A. Proc. Natl. Acad. Sci. U.S.A. 98 14368-14373 (2001)
  5. Multi-constraint computational design suggests that native sequences of germline antibody H3 loops are nearly optimal for conformational flexibility. Babor M, Kortemme T. Proteins 75 846-858 (2009)
  6. Structural evidence for substrate strain in antibody catalysis. Yin J, Andryski SE, Beuscher AE, Stevens RC, Schultz PG. Proc. Natl. Acad. Sci. U.S.A. 100 856-861 (2003)
  7. Effects of somatic mutations on CDR loop flexibility during affinity maturation. Wong SE, Sellers BD, Jacobson MP. Proteins 79 821-829 (2011)
  8. Predicting antibody complementarity determining region structures without classification. Choi Y, Deane CM. Mol Biosyst 7 3327-3334 (2011)
  9. Diversity in hapten recognition: structural study of an anti-cocaine antibody M82G2. Pozharski E, Moulin A, Hewagama A, Shanafelt AB, Petsko GA, Ringe D. J. Mol. Biol. 349 570-582 (2005)
  10. Antibodies as a model system for comparative model refinement. Sellers BD, Nilmeier JP, Jacobson MP. Proteins 78 2490-2505 (2010)
  11. Molecular mechanism of enantioselective proton transfer to carbon in catalytic antibody 14D9. Zheng L, Baumann U, Reymond JL. Proc. Natl. Acad. Sci. U.S.A. 101 3387-3392 (2004)
  12. Genetic and fluorescence studies of affinity maturation in related antibodies. Pauyo T, Hilinski GJ, Chiu PT, Hansen DE, Choi YJ, Ratner DI, Shah-Mahoney N, Southern CA, O'Hara PB. Mol. Immunol. 43 812-821 (2006)
  13. Repertoire Analysis of Antibody CDR-H3 Loops Suggests Affinity Maturation Does Not Typically Result in Rigidification. Jeliazkov JR, Sljoka A, Kuroda D, Tsuchimura N, Katoh N, Tsumoto K, Gray JJ. Front Immunol 9 413 (2018)
  14. Crystal structure of tissue factor in complex with antibody 10H10 reveals the signaling epitope. Teplyakov A, Obmolova G, Malia TJ, Wu B, Zhao Y, Taudte S, Anderson GM, Gilliland GL. Cell. Signal. 36 139-144 (2017)
  15. Structural basis of the transition-state stabilization in antibody-catalyzed hydrolysis. Sakakura M, Takahashi H, Shimba N, Fujii I, Shimada I. J. Mol. Biol. 367 133-147 (2007)
  16. Anti-ROR1 scFv-EndoG as a Novel Anti-Cancer Therapeutic Drug Bemani P, Mohammadi M, Hakakian A. Asian Pac. J. Cancer Prev. 19 97-102 (2018)
  17. Molecular mechanisms of improvement of hydrolytic antibody 6D9 by site-directed mutagenesis. Takahashi-Ando N, Shimazaki K, Kakinuma H, Fujii I, Nishi Y. J. Biochem. 140 509-515 (2006)
  18. Towards a rational design of antibody catalysts through computational chemistry. Martí S, Andrés J, Moliner V, Silla E, Tuñón I, Bertrán J. Angew. Chem. Int. Ed. Engl. 44 904-909 (2005)


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