Skip to main content
SpringerLink
Log in
Book cover

Chemical Recognition in Biology pp 43–61Cite as

Influences of Solvent Water on the Transition State Affinity of Enzymes, Protein Folding, and the Composition of the Genetic Code

  • Chapter

Part of the book series: Molecular Biology, Biochemistry and Biophysics ((MOLECULAR,volume 32))

Abstract

This symposium is a special delight for one of those who benefited from Dr. Lipmann’s kindness in accepting graduate students after his move to New York in 1957. By then he had numerous scientific progeny, and my relationship to him is complicated by the fact that I can also count myself among his scientific grandchildren through apprenticeships with Hans Bomann and Bill Jencks. A good deal of what I am going to say, about enzyme interactions with high energy intermediates in substrate transformation, had its genesis in conversations about group potential (Lipmann 1941) and in some ideas expressed a generation later by Jencks (1966) in a volume commemorating the 1941 review.

This is a preview of subscription content, 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

Learn about institutional subscriptions

Preview

Unable to display preview. Download preview PDF.

Unable to display preview. Download preview PDF.

References

  • Banner DW, Bloomer AC, Petsko GA, Phillips DC, Pogson CI, Wilson IA, Corran PH, Furth AJ, Milman JD, Offord RE, Priddle JD, Waley SG (1975) Structure of chicken muscle triose phosphate isomerase determined crystallographically at 2.5 A resolution using amino-acid sequence data. Nature 255: 609–614

    Article  PubMed  CAS  Google Scholar 

  • Bauer CA, Thompson RC, Blout ER (1976) The active center of Streptomyces griseus protease 3 and α-chymotrypsin: Enzyme-substrate interactions remote from the scissile bond. Biochemistry 15: 1291–1295

    Article  PubMed  CAS  Google Scholar 

  • Bolognesi MC, Matthews BW (1979) Binding of the biproduct analog L-benzylsuccinic acid to thermolysin determined by X-ray crystallography. J Biol Chem 254: 634–639

    PubMed  CAS  Google Scholar 

  • Brayer GD, Delbaere LTJ, James MNG, Bauer CA, Thompson RC (1979) Crystallographic and kinetic investigations of the covalent complex formed by a specific tetrapeptide aldehyde and serine protease from Streptomyces griseus. Proc Natl Acad Sci USA 76: 96–100

    Article  PubMed  CAS  Google Scholar 

  • Byers LD, Wolfenden R (1973) Binding of the bi-product analog benzylsuccinic acid by carboxy- peptidase A. Biochemistry 12: 2070–2078

    Article  PubMed  CAS  Google Scholar 

  • Campbell ID, Jones RB, Kiener PA, Richards E, Waley SG, Wolfenden R (1978) The form of 2-phosphoglycollic acid bound by triosephosphate isomerase. Biochem Biophys Res Commun 83: 347–352

    Article  PubMed  CAS  Google Scholar 

  • Cha S, Agarwal RP, Parks PE (1975) Tight-binding inhibitors 2:non-steady state nature of inhibition of milk xanthine-oxidase by allopurinol and alloxanthine and of human erythrocyte adenosine deaminase by coformycin. Biochem Pharmacol 24: 2187–2197

    Article  PubMed  CAS  Google Scholar 

  • Chothia C (1976) The nature of the accessible and buried sources of proteins. J Mol Biol 105: 1–14

    Article  PubMed  CAS  Google Scholar 

  • Clark PI, Lowe G, Nurse D (1977) Detection of enzyme-bound intermediates by cross-saturation nuclear magnetic resonance spectroscopy — investigation of papain N-benzoylaminoacetal-dehyde complex. J Chem Soc Chem Commun V 1977: 451–453

    Article  Google Scholar 

  • Cleland WW (1967) Enzyme kinetics. Annu Rev Biochem 36: 77–112

    Article  PubMed  CAS  Google Scholar 

  • Cohen RM, Wolfenden R (1971) Cytidine deaminase from Escherichia coli: Purification, properties, and inhibition by 3,4,5,6-tetrahydrouridine. J Biol Chem 246: 7561–7565

    PubMed  CAS  Google Scholar 

  • Cohen SG, Vaidya VM, Schultz RM (1970) Active site of α-chymotrypsin. Activation by association-desolvation. Proc Natl Acad Sci USA 66: 249–256

    Article  PubMed  CAS  Google Scholar 

  • Crick FHC (1968) The origin of the genetic code. J Mol Biol 38: 367–379

    Article  PubMed  CAS  Google Scholar 

  • Crosby J, Lienhard GE (1970) Mechanisms of thiamine-catalyzed reactions. A kinetic analysis of the decarboxylation of pyruvate by 3,4-dimethylthiazolium ion in water and in ethanol. J Am Chem Soc 92: 5707–5713

    Article  PubMed  CAS  Google Scholar 

  • Duax WL, Hauptman H, Weeks CM, Norton DA (1972) Valinomycin crystal structure by direct methods. Science 176: 911–914

    Article  PubMed  CAS  Google Scholar 

  • Evans B, Wolfenden R (1970) A potential transition state analog for adenosine deaminase. J Am Chem Soc 92: 4751–4752

    Article  PubMed  CAS  Google Scholar 

  • Evans B, Wolfenden R (1972) Hydratase activity of a hydrolase. Adenosine deaminase. J Am Chem Soc 94: 5902–5903

    Article  PubMed  CAS  Google Scholar 

  • Evans BE, Mitchell G, Wolfenden R (1975) The action of bacterial cytidine deaminase on 5,6-dihydrocytidine. Biochemistry 14: 621–624

    Article  PubMed  CAS  Google Scholar 

  • George P, Witonsky RJ, Trachtman M, Wu C, Dorwart W, Richman L, Richman W, Shurayh F, Lentz B (1970) “Squiggle-H2O”: An enquiry into the importance of solvation effects in phosphate ester and anhydride reactions. Biochim Biophys Acta 223: 1–15

    Article  PubMed  CAS  Google Scholar 

  • Ghisla S, Massey V (1977) Studies on mechanism of action of flavoenzyme lactate oxidase — proton uptake and release during binding of transition state analogs. J Biol Chem 252: 6729–6735

    PubMed  CAS  Google Scholar 

  • Gutowski JA, Lienhard GE (1976) Transition state analogs for thiamin pyrophosphate-dependent enzymes. J Biol Chem 251: 2863–2866

    PubMed  CAS  Google Scholar 

  • Hartman FC, Lamuraglia GC, Tomozawa Y, Wolfenden R (1975) The influence of pH on the interaction of inhibitors with triosephosphate isomerase and determination of the pKa of the active site carboxyl group. Biochemistry 14: 5274–5279

    Article  PubMed  CAS  Google Scholar 

  • Hayes DM, Kenyon GL, Kollman PA (1978) Theoretical calculations of the hydrolysis energy of some “high-energy” molecules. 2. A survey of some biologically important hydrolytic reactions. J Am Chem Soc 100: 4331–4340

    Article  CAS  Google Scholar 

  • Hine J, Mookerjee PK (1975) The intrinsic hydrophilic character of organic compounds. Correlations in terms of structural contributions. J Org Chem 40: 292–298

    Article  CAS  Google Scholar 

  • Jencks WP (1966) Strain and conformation change in enzyme catalysis. In: Kaplan NO, Kennedy EP (eds) Current aspects of biochemical energetics, pp 273–298. Academic Press, New York

    Google Scholar 

  • Jencks WP (1975) Binding energy specificity and enzyme catalysis — the circe effect. Adv Enzymol 43: 219–410

    PubMed  CAS  Google Scholar 

  • Johnson LN, Wolfenden R (1970) Changes in absorption spectrum and crystal structure of triose phosphate isomerase brought about by 2-phosphoglycollate, a potential transition state analog. J Mol Biol 47: 93–100

    Article  PubMed  CAS  Google Scholar 

  • Kalckar HM (1941) The nature of energetic coupling in biological synthesis. Chem Rev 28: 71–178

    Article  CAS  Google Scholar 

  • Koshland DE Jr (1959) Mechanisms of transfer enzymes. In: Boyer PD, Lardy H, Myrback K (eds) The enzymes, vol I, pp 305–346. Academic Press, New York

    Google Scholar 

  • Lee B, Richards FM (1971) The interpretation of protein structures: Estimation of static accessibility. J Mol Biol 55: 379–400

    Article  PubMed  CAS  Google Scholar 

  • Lewis CA Jr, Wolfenden R (1977) Thiohemiacetal formation by inhibitory aldehydes at the active site of papain. Biochemistry 16: 4890–4895

    Article  PubMed  CAS  Google Scholar 

  • Lienhard GE (1973) Enzymatic catalysis and transition state theory. Science 180: 149–154

    Article  PubMed  CAS  Google Scholar 

  • Lipmann F (1941) Metabolic generation and utilization of phosphate bond energy. Adv Enzymol 1: 99–162

    CAS  Google Scholar 

  • Milner-White EJ, Watts DC (1971) Inhibition of adenosine 5′-triphosphatecreatine phosphotransferase by substrate-anion complexes. Biochem J 122: 727–741

    PubMed  CAS  Google Scholar 

  • Nirenberg MW, Jones OW, Leder P, Clark BFC, Sly WS, Pestka S (1963) On the coding of genetic information. Cold Spring Harbor Symp Quant Biol 28: 549–558

    CAS  Google Scholar 

  • Nozaki Y, Tanford C (1971) The solubility of amino acids and two glycine peptides in aqueous ethanol and dioxane solutions. Establishment of a hydrophobicity scale. J Biol Chem 246: 2211–2217

    PubMed  CAS  Google Scholar 

  • Ohno S, Yagisawa N, Shibahara S, Kondo S, Maeda K, Umezawa H (1974) Synthesis of coformycin. J Am Chem Soc 96: 4326–4327

    Article  CAS  Google Scholar 

  • Olmstead WN, Brauman JI (1977) Gas-phase nucleophilic displacement reactions. J Am Chem Soc 99: 4219–4228

    Article  CAS  Google Scholar 

  • Perutz MF (1965) Structure and function of haemoglobin I. A tentative model of horse oxyhaemo-globin. J Mol Bil 13: 646–668

    Article  CAS  Google Scholar 

  • Reed GH, Barlow CH, Burns RA Jr (1978) Investigations of anion binding sites in transition state analogue complexes of creatine kinase by infrared spectroscopy. J Biol Chem 253: 4153–4158

    PubMed  CAS  Google Scholar 

  • Rowe WB, Ronzio RA, Meister A (1969) Inhibition of glutamine synthetase by methionine sulfo-ximine. Studies on methionine sulfoximine phosphate. Biochemistry 8: 2674–2680

    Article  PubMed  CAS  Google Scholar 

  • Sinnott ML (1978) Ions, ion-pairs and catalysis by LacZ beta-galactosidase of E. coli. FEBS Lett 94: 1–9

    Article  PubMed  CAS  Google Scholar 

  • Sonneborn TM (1965) Degeneracy of the genetic code: Extent, nature and genetic implications. In: Bryson V, Vogel HJ (eds) Evolving genes and proteins, pp 377–397. Academic Press, New York

    Google Scholar 

  • Palmer AR, Ellis PD, Wolfenden R (1980) The ionization state of benzylsuccinate bound by carbo-xypeptidase A. Fed Proc 39: in press

    Google Scholar 

  • Thompson RC (1973) Use of peptide aldehydes to generate transition state analogs of elastase. Biochemistry 12: 47–51

    Article  PubMed  CAS  Google Scholar 

  • Thompson RC (1974) Binding of peptides to elastase: Implications for the mechanism of substrate hydrolysis. Biochemistry 13: 5495–5501

    Article  PubMed  CAS  Google Scholar 

  • Villafranca JJ, Ash DE, Wedler FC (1975) Evidence for methionine sulfoximine as a transition state analog for glutamine synthetase from NMR and EPR data. Biochem Biophys Res Commun 66: 1003–1010

    Article  PubMed  CAS  Google Scholar 

  • Warshel A (1978) Energetics of enzyme catalysis. Proc Natl Acad Sci USA 75: 5250–5254

    Article  PubMed  CAS  Google Scholar 

  • Wentworth DF, Wolfenden R (1974) Slow binding of D-galactal, a “reversible” inhibitor of bacterial β-galactosidase. Biochemistry 13: 4715–4720

    Article  PubMed  CAS  Google Scholar 

  • Westerik JO, Wolfenden R (1972) Aldehydes as inhibitors of papain. J Biol Chem 247: 8195–8197

    PubMed  CAS  Google Scholar 

  • White JU (1942) Long optical paths of large aperture. J Opt Soc Am 32: 285–288

    Article  Google Scholar 

  • Woese C (1969) Models for the evolution of coding assignments. J Mol Biol 43: 235–240

    Article  PubMed  CAS  Google Scholar 

  • Wolfenden R (1969a) On the rate-determining step in the action of adenosine deaminase. Biochemistry 8: 2409–2412

    Article  PubMed  CAS  Google Scholar 

  • Wolfenden R (1969b) Transition state analogs for enzyme catalysis. Nature 223: 704–705

    Article  PubMed  CAS  Google Scholar 

  • Wolfenden R (1972) Analog approaches to the structure of the transition state in enzyme reactions. Accounts of Chemical Research 5: 10–18

    Article  CAS  Google Scholar 

  • Wolfenden R (1974) Enzyme catalysis: Conflicting requirements of substrate access and transition state affinity. Mol Cell Biochem 3: 207–211

    Article  PubMed  CAS  Google Scholar 

  • Wolfenden R (1976) Transition state analog inhibitors and enzyme catalysis. Annu Rev Biophys Bioeng 5: 271–306

    Article  PubMed  CAS  Google Scholar 

  • Wolfenden R (1978) Interaction of the peptide bond with solvent water: A vapor phase analysis. Biochemistry 17: 201–204

    Article  PubMed  CAS  Google Scholar 

  • Wolfenden R, Kaufman J, Macon JB (1969) Ring-modified substrates of adenosine deaminase. Biochemistry 8: 2312–2415

    Article  Google Scholar 

  • Wolfenden R, Wentworth DF, Mitchell GN (1977) The influence of substituent ribose on transition state affinity in reactions catalyzed by adenosine deaminase. Biochemistry 16: 5071–5077

    Article  PubMed  CAS  Google Scholar 

  • Wolfenden R, Cullis P, Southgate C (1979) Water, protein folding and the genetic code. Science 206: 575–577

    Article  PubMed  CAS  Google Scholar 

Download references

Author information

Authors and Affiliations

  1. Department of Biochemistry, University of North Carolina, Chapel Hill, North Carolina, 27514, USA

    R. Wolfenden

Authors
  1. R. Wolfenden
    View author publications

    You can also search for this author in PubMed Google Scholar

Editor information

Editors and Affiliations

  1. CNRS, Inst. de recherche en biologie moléculaire, Université Paris VII, Tour 43, 2 Place Jussieu, F-75221, Paris Cedex 05, France

    F. Chapeville  & A.-L. Haenni  & 

Rights and permissions

Reprints and permissions

Copyright information

© 1980 Springer-Verlag Berlin · Heidelberg

About this chapter

Cite this chapter

Wolfenden, R. (1980). Influences of Solvent Water on the Transition State Affinity of Enzymes, Protein Folding, and the Composition of the Genetic Code. In: Chapeville, F., Haenni, AL. (eds) Chemical Recognition in Biology. Molecular Biology, Biochemistry and Biophysics, vol 32. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-642-81503-4_4

Download citation

  • DOI: https://doi.org/10.1007/978-3-642-81503-4_4

  • Publisher Name: Springer, Berlin, Heidelberg

  • Print ISBN: 978-3-642-81505-8

  • Online ISBN: 978-3-642-81503-4

  • eBook Packages: Springer Book Archive

Publish with us

Policies and ethics

Search

Navigation