Advertisement

Introduction

Chapter
  • 559 Downloads

Abstract

This introductory chapter deals with protein structure and its synthesis The 20 α-amino-acids that compose proteins are all of the L-configuration except for glycine that is optically inactive. That a protein is a chemically pure entity was proven by Sumner in crystals of the enzyme urease. A protein molecule is defined by the size/weight of a linear polypeptide that composes it. A fundamental method of structure solution of molecules is X-ray diffraction. When applied to peptides by Pauling and Corey it supplied information about the distances between atoms and showed that the peptide bond is planar. First proteins whose structure was solved were myoglobin and haemoglobin followed by the enzymes lysozyme and chymotrypsin. The bottleneck in determining a protein structure from its diffraction intensity maxima was lack of knowledge of the phase of diffracted X-rays. This was surmounted by various techniques that go under names like MIR, MAD, SIRAS and others. Solution of a protein structure involves calculation of an enormous quantity of numerical data in the refinement and production of the electron density of the molecule. The resolution to which structure of proteins has been solved, around 2 Å, bears no comparison to 0.01 Å obtained for small molecules. All these calculations demand extensive use of computer programs. Binding-sites endow proteins with unique selectivity to small molecules and are physiologically important. The forces responsible for the binding of small molecules to binding-sites are discussed.

Keywords

Protein Molecule Protein Crystal Molecular Replacement Jack Bean Jack Bean Urease 
These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.

References

  1. Abrahams SC, Robertson JM, White JG (1949) The crystal and molecular structure of naphthalene. II. Structure investigation by the triple Fourier series method. Acta Crystallogr 2:238–244CrossRefGoogle Scholar
  2. Ball P (2003) Molecules of life come in waves. Nature (Science Update, Sept 6)Google Scholar
  3. Bernal JD (1958) Structure arrangements of macromolecules. Discuss Faraday Soc 25:7–18CrossRefGoogle Scholar
  4. Blake CC, Koenig DF, Mair GA, North AC, Phillips DC, Sarma VR (1965) Structure of hen egg-white lysozyme. A three-dimensional Fourier synthesis at 2 Å resolution. Nature 206:757–761CrossRefPubMedGoogle Scholar
  5. Blow D (2005) Outline of crystallography for biologists. Oxford University Press, New York, p 214Google Scholar
  6. Blow DM, Birktoft JJ, Hartley BS (1969) Role of a buried acid group in the mechanism of action of chymotrypsin. Nature 221:337–340CrossRefPubMedGoogle Scholar
  7. Bracewell RN (1989) The Fourier Transform. Sci Am:62–69Google Scholar
  8. Corey RB (1938) The crystal structure of diketopiperazine. Proc Natl Acad Sci U S A 60:1598–1604Google Scholar
  9. Dickerson RE, Geis I (1969) The structure and action of proteins. Harper & Row, Publishers, New YorkGoogle Scholar
  10. Doerr A (2014) A method ahead of its time. Nature, Milestone 13/Nature Milestones/Crystallography, August 2014Google Scholar
  11. Frolow F, Kalb AJ, Yariv J (1993) Location of haem in bacterioferritin of E. coli. Acta Crystallogr D 49:597–600CrossRefPubMedGoogle Scholar
  12. Goffeau A, Nakai K, Slonimski P, Risler J-P (1993) The membrane proteins encoded by yeast chromosome III genes. FEBS Lett 325:112–117CrossRefPubMedGoogle Scholar
  13. Hackermüller L, Uttenthaler S, Hornberger K, Reiger E, Brezger B, Zeilinger A, Arndt M (2003) Wave nature of biomolecules and florofullerenes. Phys Rev Lett 91:090408 (1–4)Google Scholar
  14. Henderson R (2013) Ion channel seen by electron microscopy. Nature 504:93–94CrossRefPubMedGoogle Scholar
  15. Hendrickson WA, Horton JR, LeMaster DM (1990) Selenomethionyl proteins produced for analysis by multiwavelength anomalous diffraction (MAD): a vehicle for direct determination of three-dimensional structure. EMBO J 9:1665–1672PubMedPubMedCentralGoogle Scholar
  16. James RW (1953) X-Ray crystallography, 5th edn. Methuen & Co. Ltd, London, p 93Google Scholar
  17. Karle J (1989) Macromolecular structure from anomalous dispersion. Phys Today 42:22–29Google Scholar
  18. Kemp M (1998) Kendrew constructs; Geis gazes. Nature 396:525CrossRefPubMedGoogle Scholar
  19. Kendrew JC (1961) The three-dimensional structure of a protein molecule. Sci Am 205:96–110CrossRefPubMedGoogle Scholar
  20. Kendrew JC (1966) The thread of life: an introduction to molecular biology, figure 9. G. Bell and Sons Ltd, LondonGoogle Scholar
  21. Liao M, Cao E, Julius D, Cheng Y (2013) Structure of the TRPV1 ion channel determined by electron cryo-microscopy. Nature 504:107–118CrossRefPubMedPubMedCentralGoogle Scholar
  22. London F (1943) Intermolecular attraction between macromolecules. Surf Chem 21:141–149Google Scholar
  23. Löwe D (2010) Molecular modellings $10 million come back? Nature 7 May, pp 1–3 (online)Google Scholar
  24. Magagno E, Honig B, Chasin L (2014) Cyrus Levinthal 1922–1990. Biographical Memoirs, National Academy of SciencesGoogle Scholar
  25. Matthews BW, Sigler PB, Henderson R, Blow DM (1967) Three-dimensional structure of tosyl-a-chymotrypsin. Nature 214:652–656CrossRefPubMedGoogle Scholar
  26. Paterlini M (2008) A protein ghost etched in glass. Nature 452:155CrossRefGoogle Scholar
  27. Pauling L (1993) How my interest in proteins developed. Protein Sci 2:1060–1063CrossRefPubMedPubMedCentralGoogle Scholar
  28. Pauling L, Corey RB, Branson HR (1951) The structure of proteins: two hydrogen-bonded helical configurations of the polypeptide chain. Proc Natl Acad Sci U S A 37:205–211CrossRefPubMedPubMedCentralGoogle Scholar
  29. Penrose R (1994) Shadows of the mind. Oxford University Press, OxfordGoogle Scholar
  30. Perutz MF (1987) I wish I’d made you angry earlier. Scientist 1:9Google Scholar
  31. Richards FM (1958) On the enzymic activity of subtilisin-modified ribonuclease. Proc Natl Acad Sci U S A 44:162–166CrossRefPubMedPubMedCentralGoogle Scholar
  32. Richards FM (1997) Whatever happened to the Fun? An autobiographical investigation. Annu Rev Biophys Biomol Struct 26:1–25CrossRefPubMedGoogle Scholar
  33. Robertson JM (1938) X-Ray analysis and application of Fourier series methods to molecular structures. Rep Prog Phys 4:332–367CrossRefGoogle Scholar
  34. Rossmann MG, Blow DM (1962) The detection of sub-units within the crystallographic asymmetric unit. Acta Crystallogr 15:24–31CrossRefGoogle Scholar
  35. Schiltz M, Fourme R, Prangé T (2003) Use of noble gases xenon and krypton as heavy atoms in protein structure determination. Methods Enzymol 374:83–119CrossRefPubMedGoogle Scholar
  36. Schoeneborn BP, Watson HC, Kendrew JC (1965) Binding of xenon to sperm whale myoglobin. Nature 207:28–30CrossRefGoogle Scholar
  37. Smith JMA, Ford GC, Harrison PM, Yariv J, Kalb (Gilboa) AJ (1989) Molecular size and symmetry of bacterioferritin of Escherichia coli: X-ray crystallographic characterization of four crystal forms. J Mol Biol 205:465–467CrossRefPubMedGoogle Scholar
  38. Sumner JB (1946) The chemical nature of enzymes. Nobel Lecture, 12 December 1946, pp 114–123Google Scholar
  39. Swindells MB, Orengo CA, Jones DT, Hutchinson EG, Thornton JM (1998) Contemporary approaches to protein structure classification. BioEssays 20:884–891CrossRefPubMedGoogle Scholar
  40. Vijayan M (2001) Obituary: G. N. Ramachandran (1922–2001). Nature 411:544CrossRefPubMedGoogle Scholar
  41. Yariv J, Kalb AJ, Sperling R, Bauminger ER, Cohen SG, Ofer S (1981) The composition and the structure of bacterioferritin of Escherichia coli. Biochem J 197:171–175CrossRefPubMedPubMedCentralGoogle Scholar

Copyright information

© Springer International Publishing Switzerland 2016

Authors and Affiliations

  1. 1.CaesareaIsrael

Personalised recommendations