Article
Molecular recognition: Conformational analysis of limited proteolytic sites and serine proteinase protein inhibitors

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Abstract

The conformations of known tryptic limited proteolytic sites have been analysed and compared to the structures of the binding regions of serine proteinase inhibitors, as they are found when complexed to a serine proteinase. Conformational parameters studied include main-chain torsion angles, root-mean-square fits, accessibility, mobility and protrusion indices. As observed before, the inhibitors share a common main-chain conformation at the binding loop from P3–P′3 (Schechter, Berger notation), which is maintained throughout all the serine proteinase inhibitor families for which X-ray data is available, despite lack of similarity in the rest of the protein. This canonical structure is not found amongst the limited proteolytic sites (or nicksites), which differ markedly from the inhibitor binding loop conformation, and also amongst themselves. The experimentally determined nicksites are in general both accessible and protruding; as are the inhibitor binding loops, as well as being typically flexible regions of structure, as denoted by elevated temperature factors from crystallographic determinations. For cleavage by serine proteinases these loops must radically alter their local conformations and a large motion of the loop relative to the structure, in some cases, would be required to orientate these sites for cleavage.

References (61)

  • E. Papamokos et al.

    Crystallographic refinement of Japanese quail ovomucoid, a Kazal-type inhibitor, and model building studies of complexes with serine proteases

    J. Mol. Biol.

    (1982)
  • A. Ruhlmann et al.

    Structure of the complex formed by bovine trypsin and bovine pancreatic trypsin inhibitor

    J. Mol. Biol.

    (1973)
  • I. Schechter et al.

    On the size of the active site in proteases. I. Papain

    Biochem. Biophys. Res. Commun.

    (1967)
  • H. Taniuchi et al.

    Steps in the formation of active derivatives of staphylococcal nuclease during trypsin digestion

    J. Biol. Chem.

    (1968)
  • E. Weber et al.

    Crystallization, crystal structure analysis and molecular model of the third domain of Japanese quail ovomucoid a Kazal type inhibitor

    J. Mol. Biol.

    (1981)
  • A. Wlodawer et al.

    The refined crystal structure of ribonuclease Å at 2.0 A resolution

    J. Biol. Chem.

    (1982)
  • A. Wlodawer et al.

    Structure of bovine pancreatic trypsin inhibitor

    J. Mol. Biol.

    (1984)
  • A.G. Amit et al.

    Three-dimensional structure of an antigen-antibody complex

    Science

    (1986)
  • S.Y. Babu et al.

    Three dimensional structure of calmodulin

    Nature (London)

    (1985)
  • A. Baici et al.

    Kinetics of the inhibition of human leucocyte elastase by eglin from the leech Hirudo medicinalis

    Biochem. J.

    (1984)
  • F.C. Bernstein et al.

    The protein data bank: a computer-based archival file for macromolecular structures

    J. Mol. Biol.

    (1977)
  • W. Bode et al.

    The crystal and molecular structure of the third domain of silver pheasant ovomucoid (OMSVP3)

    Eur. J. Biochem.

    (1985)
  • W. Bode et al.

    Refined 1·2 Å crystal structure of the complex formed between subtilisin Carlsberg and the inhibitor eglin c. Molecular structure of eglin and its detailed interaction with subtilisin

    EMBO J.

    (1986)
  • W. Bode et al.

    The high-resolution X-ray structure of the complex formed between subtilisin Carlsberg, and an elastase inhibitor from leech Hirudo medicinalis

    Eur. J. Biochem.

    (1987)
  • M. Bolognesi et al.

    X-ray crystal structure of the bovine α-chymotrypsin/eglin c complex at 2.6 Å resolution

    J. Mol. Recog.

    (1990)
  • C. Chothia

    The nature of the accessible and buried surface in proteins

    J. Mol. Biol.

    (1976)
  • P.M. Colman et al.

    Three-dimensional structure of a complex of antibody with influenza virus neuramidase

    Nature (London)

    (1987)
  • F.A. Cotton et al.

    Staphylococcal nuclease. Proposed mechanism of action based on structure of enzyme-thymidine 3′, 5′-bisphosphate calcium ion complex at 1.5 Å resolution

  • W. Draibikowski et al.

    Tryptic fragments of calmodulin

    J. Biol. Chem.

    (1982)
  • A.V. Efimov

    Standard conformations of a poly-peptide chain in irregular regions of proteins

    Mol. Biol. (Moscow)

    (1986)
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    S.J.H. is supported by a CASE/SERC studentship, ref. no. 88504710.

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