1UTL

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

Summary for 1UTL

• Entry DOI: 10.2210/pdb1utl/pdb
• Related: 1BIT 1BZX 1HJ8 1UTJ 1UTK 1UTM 1UTN 1UTO 1UTP 1UTQ 2STA 2STB 2TBS
• Descriptor: TRYPSIN I, 3-PHENYLPROPYLAMINE, CALCIUM ION, ... (5 entities in total)
• Functional Keywords: hydrolase, trypsin, inhibitor specificity, electrostatic interactions, cold-adaptation, molecular dynamics, binding free energy
• Biological source: SALMO SALAR (ATLANTIC SALMON)
• Total number of polymer chains: 1
• Total formula weight: 26291.75

Authors

Leiros, H.-K.S.,Brandsdal, B.O.,Andersen, O.A.,Os, V.,Leiros, I.,Helland, R.,Otlewski, J.,Willassen, N.P.,Smalas, A.O. (deposition date: 2003-12-09, release date: 2004-01-15, Last modification date: 2024-11-20)

Primary citation

Leiros, H.-K.S.,Brandsdal, B.O.,Andersen, O.A.,Os, V.,Leiros, I.,Helland, R.,Otlewski, J.,Willassen, N.P.,Smalas, A.O.
Trypsin Specificity as Elucidated by Lie Calculations, X-Ray Structures, and Association Constant Measurements
Protein Sci., 13:1056-, 2004

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.

PubMed: 15044735
DOI: 10.1110/PS.03498604

Experimental method

X-RAY DIFFRACTION (1.7 Å)