Skip to main content
SpringerLink
Log in
SpringerLink
Log in

Microbial and Genetic Approaches to the Study of Structure-Function Relationships of Proteins

  • Chapter
Molecular and Cellular Enzymology

Part of the book series: Progress in Molecular and Subcellular Biology ((PMSB,volume 13))

Abstract

Two opposite attitudes have been adopted by biologists in their efforts at deciphering biological processes. The reductionist approach is based on the idea that increasing the knowledge about each component of the process studied inevitably increases the understanding of the whole process. The holistic approach aims at studying the process as a whole. The first approach is favored by biochemists and biophysicists, while the second is followed by cell biologists and systematicians. A limitation of the former is that it seldom takes into account the complexity of interactions within the broader context of the cell. An intrinsic limitation of the latter lies in its global view of events which precludes targeted modification of a cellular pathway. Fortunately, this dual view is becoming less pertinent to the description of biological investigations, and the advent of techniques of molecular biology has been particularly helpful in this regard.

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

  • Beuve A, Danchin A (1992) From adenylate cyclase to guanylate cyclase: mutational analysis of a change in substrate specificity. J. Mol Biol. 225:933–938

    Article  PubMed  CAS  Google Scholar 

  • Bossi L (1985) Informational suppression. In: Scaife J, Leach D, Galizzi A (eds) Genetics of bacteria. Academic Press, pp 49–64

    Google Scholar 

  • Bortoli-German I, Brun E, Py B, Chippaux M, Barras F (1994) Periplasmic disulfide bond formation is essential for cellulase secretion by the plant pathogen Erwinia chrysanthemi. Mol. Microbiol. (in press)

    Google Scholar 

  • Branden C, Tooze J (1991) Introduction to protein structure. Garland Publishing, Inc. New York, London, pp 238–241

    Google Scholar 

  • Chabert M, Kilhoffer M-C, Watterson DM, Haiech J, Lami H (1989) Time-resolved fluorescence studies of VU-9 calmodulin, and engineered calmodulin possessing a single tryptophan residue. Biochemistry 28:6093–6098

    Article  Google Scholar 

  • Chothia C (1992) One thousand families for the molecular biologist. Nature 357:543–544

    Article  PubMed  CAS  Google Scholar 

  • Chothia C, Lesk AM (1986) The relation between the divergence of sequence and structure in proteins. EM BO J 5:823–826

    CAS  Google Scholar 

  • Derancourt J, Haiech J, Pechére J-F (1978) Binding of calcium by parvalbumin fragments. BBA 532:373–375

    PubMed  CAS  Google Scholar 

  • Epstein CJ, Goldberger RF, Anfinsen CB (1963) The genetic control of tertiary protein structure: studies with model systems. Cold Spring Harbor Symp. Quant. Biol. 28:439–449

    CAS  Google Scholar 

  • Evtunshenkov AN, Shevichika VE, Fomichev YK (1987) Expression of the pectate lyase gene of Erwinia chrysanthemi ENA49 in cells of other representatives of the genus Erwinia. Molekulyarna Genetika Mikrobiologiya i Virusologiya 5:22–25

    Google Scholar 

  • Frauenfelder H, Sligar SG, Wolynes PG (1992) The energy landscapes and motions of proteins. Science 254:1598–1603

    Article  Google Scholar 

  • Gabor Miklos GL, Campbell HD (1992) The evolution of protein domains and the organizational complexities of metazoans. Curr. Opinion Genet. Dev. 2:902–906

    Article  Google Scholar 

  • Georgopoulos C (1992) The emergence of the chaperone machines. TIBS 17:295–299 Gorini L (1970) Informational suppression. Annu. Rev. Genet. 4:107–134

    Google Scholar 

  • Haiech J, Sallantin J (1985) Computer search of calcium binding sites in gene data bank: use of learning techniques to build an expert system. Biochimie 67:555–560

    Article  PubMed  CAS  Google Scholar 

  • Haiech J, Kilhoffer M-C, Craig TA, Lukas TJ, Wilson E, Guerra-Santos L, Watterson DM (1989) Mutant analysis approaches to understanding calcium signal transduction through calmodulin and calmodulin regulated enzymes. In Calcuim binding proteins in normal and transformed cells. R Pochet, DEM Lawson, CW Heizmann eds. pp. 43–56, Plenum Publishing Corporation

    Google Scholar 

  • Haiech J, Kilhoffer M-C, Lukas TJ, Craig TA, Roberts DM, Watterson DM (1991) Restoration of the calcium binding activity of mutant calmodulins toward normal by the presence of a calmodulin binding structure. J. Biol Chem. 266:3427–3431

    PubMed  CAS  Google Scholar 

  • Hardy LW, Poteete AR (1991) Reexamination of the role of Asp20 in catalysis by bacteriophage T4 lysozyme. Biochemistry 30:9457–9463

    Article  PubMed  CAS  Google Scholar 

  • He SY, Lindeberg M, Chatterjee AK, Collmer A (1991) Erwinia chrysanthemi out genes enable Escherichia coli to selectively secrete a diverse family of heterologous proteins to its milieu. Proc. Natl Acad. Sci. USA 88:1079–1083

    Article  PubMed  CAS  Google Scholar 

  • Henrissat B, Claeyssens M, Tomme P, Lemesle L, Mornon JP (1989) Cellulase families revealed by hydrophobic cluster analysis. Gene 81:83–95

    Article  PubMed  CAS  Google Scholar 

  • Hermes JD, Blacklow SC, Knowles JR (1990) Searching sequence space by definably random mutagenesis: improving the catalytic potency of an enzyme. Proc. Natl Acad. Sci USA 87:696–700

    Article  PubMed  CAS  Google Scholar 

  • Hubbard TJP, Sander C (1991) The role of heat-shock and chaperone proteins in protein folding: possible molecular mechanisms. Prot. Eng. 4:711–717

    Article  CAS  Google Scholar 

  • Jaenicke R (1993) Role of accessory proteins folding. Curr. Op. Struct. Biol. 3:104–112

    Article  CAS  Google Scholar 

  • Karplus M, Petsko GA (1990) Molecular dynamics simulation in biology. Nature 347:631–639

    Article  PubMed  CAS  Google Scholar 

  • Kilhoflfer M-C, Haiech J, Demaille JG (1983) Ion binding to calmodulin. Mol Cell Biochem. 51:33–54

    Article  Google Scholar 

  • Kilhoflfer M-C, Roberts DM, Adibi AO, Watterson DM, Haiech J (1988) Investigation of the mechanism of calcium binding to calmodulin. Use of an isofunctional mutant with a tryptophan introduced by site-directed mutagenesis. J. Biol. Chem. 263:17023–17029

    Google Scholar 

  • Kilhoflfer M-C, Kubina M, Travers F, Haiech J (1992) Use of engineered proteins with internal tryptophan reporter groups and perturbation techniques to probe the mechanism of ligand-protein interactions: investigation of the mechanism of calcium binding to calmodulin. Biochemistry 31:8098–8106

    Article  Google Scholar 

  • Kleina LG, Miller JH (1990a) Genetic studies of the lac repressor. XIII. Extensive amino acid replacement generated by the use of natural and synthetic nonsense suppressors. J. Mol Biol. 212:295–318

    Article  PubMed  CAS  Google Scholar 

  • Kleina LG, Masson J-M, Normanly J, Abelson J, Miller JH (1990b) Construction of Escherichia coli amber suppressor tRNA genes. II. Synthesis of additional tRNA genes and improvement of suppressor efficiency. J. Mol Biol. 213:705–717

    Article  PubMed  CAS  Google Scholar 

  • Landry SJ, Gierash LM (1991) Recognition of nascent polypeptides for targeting and folding. TIBS 16:159–163

    PubMed  CAS  Google Scholar 

  • Lim WA, Sauer RT (1989) Alternative packing arrangements in the hydrophobic core of X repressor. Nature 339:31–36

    Article  PubMed  CAS  Google Scholar 

  • Lim WA, Sauer RT (1991) The role of internal packing interactions in determining the structure and stability of a protein. J. Mol Biol. 219:359–376

    Article  PubMed  CAS  Google Scholar 

  • McClain WH, Foss K (1988) Changing the acceptor identity of a transfer RNA by altering nucleotides in a “variable pocket”. Science 241:1804–1807

    Article  PubMed  CAS  Google Scholar 

  • Meiering EM, Serrano L, Fersht AR (1992) Effect of active site residues in barnase on activity and stability. J. Mol Biol. 225:585–589

    Article  PubMed  CAS  Google Scholar 

  • Michaels ML, Wan Kim C, Matthews DA, Miller JH (1990) Escherichia coli thymidylate synthase: amino acid substitutions by suppression of amber nonsense mutations. Proc. Natl Acad. Sci USA 87:3957–3961

    Article  PubMed  CAS  Google Scholar 

  • Miller JH (1991) Use of nonsense suppression to generate altered proteins. Methods Enzymol 208:543–563

    Article  PubMed  CAS  Google Scholar 

  • Miller JH, Coulondre C, Hofer M, Schmeissner U, Sommer H, Schmitz A, Lu P (1979) Genetic studies of the lac repressor. IX Generation of altered proteins by the suppression of nonsense mutations. J. Mol Biol 131:191–222

    Article  PubMed  CAS  Google Scholar 

  • Murzin AG, Chothia C (1992) Protein architecture: new superfamilies. Cur. Op. Struct. Biol. 2:895–903

    Article  CAS  Google Scholar 

  • Normanly J, Masson J-M, Kleina LG, Abelson J, Miller JH (1986) Construction of two Escherichia coli amber suppressor genes tRNAcuAPhe and tRNAcuACys. Proc. Natl Acad. Sci. USA 83:6548–6552

    Article  PubMed  CAS  Google Scholar 

  • Normanly J, Kleina LG, Masson J-M, Abelson J, Miller JH (1990) Construction of Escherichia coli amber suppressor tRNA genes. III. Determination of tRNA specificity. J. Mol Biol. 213:719–726

    Article  PubMed  CAS  Google Scholar 

  • Patthy L (1991) Modular exchange principles in proteins. Curr. Op. Struct. Biol. 1:351–361

    Article  CAS  Google Scholar 

  • Poteete AR, Rennell D, Bouvier SE (1992) Functional significance of conserved amino acid residues. Proteins: Struct. Fonct. Genet. 13:38–40

    Article  CAS  Google Scholar 

  • Pugsley AP (1992) Translocation of a folded protein across the outer membrane in Escherichia coli. Proc. Natl. Acad. Sci. USA 89:12058–12062

    Article  PubMed  CAS  Google Scholar 

  • Pugsley AP (1993) The complete general secretory pathway in gram-negative bacteria. Microb. Rev. 57:50–108

    CAS  Google Scholar 

  • Py B, Bortoli-German I, Haiech J, Chippaux M, Barras F (1991a) Cellulase EGZ of Erwinia chrysanthemi: structural organisation and importance of His98 and Glu 133 residues for catalysis.Prot. Eng. 4:325–333

    Article  CAS  Google Scholar 

  • Py B, Salmond GPC, Chippaux M, Barras F (1991b) Secretion of cellulase in Erwinia chrysanthemi and E. carotovora is species-specific. FEMS Microb. Lett. 79:315–322

    Article  CAS  Google Scholar 

  • Py B, Chippaux M, Barras F (1993) Mutagenesis of cellulase EGZ for studying the general protein secretory pathway in Erwinia chrysanthemi. Mol. Microbiol. 7:785–793

    Article  CAS  Google Scholar 

  • Reidhaar-Olson JF, Sauer RT (1988) Combinatorial casette mutagenesis as a probe of the informational content of protein sequences. Science 241:53–57

    Article  PubMed  CAS  Google Scholar 

  • Rennell D, Bouvier SE, Hardy LW, Poteete AR (1991) Systematic mutation of bacteriophage T4 lysozyme.J. Mol Biol. 222:67–88

    Article  PubMed  CAS  Google Scholar 

  • Salmond GPC, Reeves PJ (1993) Membrane traffic wardens and protein secretion in Gram-negative bacteria. TIBS 18:7–12

    PubMed  CAS  Google Scholar 

  • Sauer RT, Lim WA (1992) Mutational analysis of protein stability. Curr. Opinion Struct. Biol. 2:46–51

    Article  Google Scholar 

  • Sinnott ML (1990) Catalytic mechanisms of enzyme glycosyl transfer.Chem. Rev. 90:1171–1202

    Article  CAS  Google Scholar 

  • Van Gunsteren WF, Mark AE (1992) On the interpretation of biochemical data by molecular dynamics computer simulation. Eur. J. Biochem. 204:947–961

    Article  PubMed  Google Scholar 

Download references

Author information

Authors and Affiliations

  1. Department of Molecular Microbiology, LCB-CNRS, 31 Chemin Joseph Aiguier, 13402, Marseille, Cedex 20, France

    Frédéric Barras & Isabelle Bortoli-German

  2. Department of Proteins of Signal Transduction, LCB-CNRS, 31 Chemin Joseph Aiguier, 13402, Marseille, Cedex 20, France

    Jacques Haiech

  3. Laboratoire de Biophysique, Faculté de Pharmacie, Université Louis Pasteur, BP 24, 67401, Illkirch Cedex, France

    Marie-Claude Kilhoffer

Authors
  1. Frédéric Barras
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Marie-Claude Kilhoffer
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Isabelle Bortoli-German
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Jacques Haiech
    View author publications

    You can also search for this author in PubMed Google Scholar

Editor information

Editors and Affiliations

  1. Institut de Génétique Moleculaire, C.N.R.S., 1919, Route de Mende, B.P. 5051, 34033, Montpellier Cedex 01, France

    Philippe Jeanteur

Rights and permissions

Reprints and permissions

Copyright information

© 1994 Springer-Verlag Berlin Heidelberg

About this chapter

Cite this chapter

Barras, F., Kilhoffer, MC., Bortoli-German, I., Haiech, J. (1994). Microbial and Genetic Approaches to the Study of Structure-Function Relationships of Proteins. In: Jeanteur, P. (eds) Molecular and Cellular Enzymology. Progress in Molecular and Subcellular Biology, vol 13. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-642-78581-8_2

Download citation

  • DOI: https://doi.org/10.1007/978-3-642-78581-8_2

  • Publisher Name: Springer, Berlin, Heidelberg

  • Print ISBN: 978-3-642-78583-2

  • Online ISBN: 978-3-642-78581-8

  • eBook Packages: Springer Book Archive

Publish with us

Policies and ethics

Search

Navigation