Trypsin specificity as elucidated by LIE calculations, X-ray structures and association constant measurements

Experimental Data Snapshot

  • Resolution: 1.30 Å
  • R-Value Free: 0.183 
  • R-Value Observed: 0.141 

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Trypsin Specificity as Elucidated by Lie Calculations, X-Ray Structures, and Association Constant Measurements

Leiros, H.-K.S.Brandsdal, B.O.Andersen, O.A.Os, V.Leiros, I.Helland, R.Otlewski, J.Willassen, N.P.Smalas, A.O.

(2004) Protein Sci 13: 1056

  • DOI: https://doi.org/10.1110/ps.03498604
  • Primary Citation of Related Structures:  
    1UTJ, 1UTK, 1UTL, 1UTM, 1UTN, 1UTO, 1UTP, 1UTQ

  • PubMed Abstract: 

    The variation in inhibitor specificity for five different amine inhibitors bound to CST, BT, and the cold-adapted AST has been studied by use of association constant measurements, structural analysis of high-resolution crystal structures, and the LIE method. Experimental data show that AST binds the 1BZA and 2BEA inhibitors 0.8 and 0.5 kcal/mole more strongly than BT. However, structural interactions and orientations of the inhibitors within the S1 site have been found to be virtually identical in the three enzymes studied. For example, the four water molecules in the inhibitor-free structures of AST and BT are channeled into similar positions in the S1 site, and the nitrogen atom(s) of the inhibitors are found in two cationic binding sites denoted Position1 and Position2. The hydrophobic binding contributions for all five inhibitors, estimated by the LIE calculations, are also in the same order (-2.1 +/- 0.2 kcal/mole) for all three enzymes. Our hypothesis is therefore that the observed variation in inhibitor binding arises from different electrostatic interactions originating from residues outside the S1 site. This is well illustrated by AST, in which Asp 150 and Glu 221B, despite some distance from the S1 binding site, lower the electrostatic potential of the S1 site and thus enhance substrate binding. Because the trends in the experimentally determined binding energies were reproduced by the LIE calculations after adding the contribution from long-range interactions, we find this method very suitable for rational studies of protein-substrate interactions.

  • Organizational Affiliation

    University of Tromsø, N-9037 Tromsø, Norway.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
TRYPSINOGEN243Bos taurusMutation(s): 0 
Find proteins for P00760 (Bos taurus)
Explore P00760 
Go to UniProtKB:  P00760
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP00760
Sequence Annotations
  • Reference Sequence
Small Molecules
Binding Affinity Annotations 
IDSourceBinding Affinity
PBN PDBBind:  1UTP Kd: 3.60e+7 (nM) from 1 assay(s)
Binding MOAD:  1UTP Kd: 3.60e+7 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Resolution: 1.30 Å
  • R-Value Free: 0.183 
  • R-Value Observed: 0.141 
  • Space Group: P 31 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 54.6α = 90
b = 54.6β = 90
c = 107.1γ = 120
Software Package:
Software NamePurpose
DENZOdata reduction
SCALAdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2004-01-15
    Type: Initial release
  • Version 1.1: 2011-06-02
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance