1utm: Difference between revisions
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'''TRYPSIN SPECIFICITY AS ELUCIDATED BY LIE CALCULATIONS, X-RAY STRUCTURES AND ASSOCIATION CONSTANT MEASUREMENTS''' | {{Structure | ||
|PDB= 1utm |SIZE=350|CAPTION= <scene name='initialview01'>1utm</scene>, resolution 1.5Å | |||
|SITE= <scene name='pdbsite=AC1:Ca+Binding+Site+For+Chain+A'>AC1</scene> | |||
|LIGAND= <scene name='pdbligand=CA:CALCIUM+ION'>CA</scene> and <scene name='pdbligand=PEA:2-PHENYLETHYLAMINE'>PEA</scene> | |||
|ACTIVITY= [http://en.wikipedia.org/wiki/Trypsin Trypsin], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.4.21.4 3.4.21.4] | |||
|GENE= | |||
}} | |||
'''TRYPSIN SPECIFICITY AS ELUCIDATED BY LIE CALCULATIONS, X-RAY STRUCTURES AND ASSOCIATION CONSTANT MEASUREMENTS''' | |||
==Overview== | ==Overview== | ||
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==About this Structure== | ==About this Structure== | ||
1UTM is a [ | 1UTM is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Salmo_salar Salmo salar]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1UTM OCA]. | ||
==Reference== | ==Reference== | ||
Trypsin specificity as elucidated by LIE calculations, X-ray structures, and association constant measurements., Leiros HK, Brandsdal BO, Andersen OA, Os V, Leiros I, Helland R, Otlewski J, Willassen NP, Smalas AO, Protein Sci. 2004 Apr;13(4):1056-70. PMID:[http:// | Trypsin specificity as elucidated by LIE calculations, X-ray structures, and association constant measurements., Leiros HK, Brandsdal BO, Andersen OA, Os V, Leiros I, Helland R, Otlewski J, Willassen NP, Smalas AO, Protein Sci. 2004 Apr;13(4):1056-70. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/15044735 15044735] | ||
[[Category: Salmo salar]] | [[Category: Salmo salar]] | ||
[[Category: Single protein]] | [[Category: Single protein]] | ||
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[[Category: binding free energy]] | [[Category: binding free energy]] | ||
[[Category: cold-adaptation]] | [[Category: cold-adaptation]] | ||
[[Category: electrostatic | [[Category: electrostatic interaction]] | ||
[[Category: inhibitor specificity]] | [[Category: inhibitor specificity]] | ||
[[Category: molecular | [[Category: molecular dynamic]] | ||
[[Category: trypsin]] | [[Category: trypsin]] | ||
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Mar 20 14:36:40 2008'' | ||
Revision as of 15:36, 20 March 2008
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| , resolution 1.5Å | |||||||
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| Sites: | |||||||
| Ligands: | and | ||||||
| Activity: | Trypsin, with EC number 3.4.21.4 | ||||||
| Coordinates: | save as pdb, mmCIF, xml | ||||||
TRYPSIN SPECIFICITY AS ELUCIDATED BY LIE CALCULATIONS, X-RAY STRUCTURES AND ASSOCIATION CONSTANT MEASUREMENTS
OverviewOverview
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.
About this StructureAbout this Structure
1UTM is a Single protein structure of sequence from Salmo salar. Full crystallographic information is available from OCA.
ReferenceReference
Trypsin specificity as elucidated by LIE calculations, X-ray structures, and association constant measurements., Leiros HK, Brandsdal BO, Andersen OA, Os V, Leiros I, Helland R, Otlewski J, Willassen NP, Smalas AO, Protein Sci. 2004 Apr;13(4):1056-70. PMID:15044735
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