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From Proteopedia

Revision as of 02:50, 20 April 2012

Phosphatase Inhibitor complexes: pdb 1nny

Introduction

→ Function: enzyme that decreases the amount of insulin receptor in the cell, which increases the effectiveness of the insulin produced in the body

→ Why important to diabetes: type 2 diabetes is caused by the inability to use insulin effectively. Since phosphatase inhibitors increase the effectiveness of insulin in the cell, it has proved effective in treating type 2 diabetes

→ Nonselective competitive inhibitor

→ Multiple ligand binding sites – inhibitor binds with catalytic site in “open” position. Proves competitive inhibition

→ Formed by being genetically manipulated

Overall Structure

The monomer has 2 β strands and 10 β sheets - some mixed and some antiparallel and 9 α helices

Binding Interactions

PTP1B is thought to primarily be responsible for the dephosphorylation of the insulin receptor and, therefore, acts to downregulate insulin signaling. Why is this enzyme important? For a healthy individual this enzymes function does not need to be changed, but for an individual with type 2 diabetes, this enzyme significantly contributes to the body being nonresponsive to insulin signals. Inhibiting PTP1B is linked to improved insulin response and activation of the insulin pathway. PTP1B deficient mice showed a resistance to diet induced diabetes. In order to identify such an inhibiting ligand, the research group of interest first used a computer to scan a library of 10,000 organic compounds based on there NMR spectra, searching for those who have an affinity for the enzymes active site. The best match produced by the screen was diaryloxamic acid, and when the group mixed the two, NMR data showed a chemical shift in Val49, Gly220, and Gly 218, part of the active site of the enzyme. The observed kinetics indicated competitive and reversible inhibition. After their initial success, he group then reasoned that an inhibitor that took up more space would be more potent. Based off of diaryloxamic acid, the group reasoned that naphthyloxamic acid would work. Once again screening with NMR they found that in addition to binding to Val49, Gly220, and Gly 218, the new ligand bound to addition active sites, those being Gln262 and Arg221.

-This is a competitive inhibitor

-It has good selectivity over other phosphatases

-Ligand binds via 2 binding sites

-Binding is reversible

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Additional Features

The two Arg residues depicted, Arg24 and Arg254, may participate in a salt bridge or a hydrogen bonding interaction with napthoic acid, thus providing a .

Dephosphorylation of the Tyrosine-Phosphate Residue

A phosphorylated residue enters the active site of the protein, facilitated by the recognition loop residues Tyr 46 and Val 49. The base of the entrance through which it is brought is known as the PTP loop. The phosphotyrosine entering is amphipathic, thus requiring non-polar pocket for the its phenol ring while the polar end is positioned in the catalytic site. Once inside, the substrate causes a conformational change in the WPD loop, causing the substrate to be help in place for a nucleophilic attack. Also, the residue, Asp 181, is shifted, so that it can act as an acid. Binding in the PTP loop occurs, so the connection between Arg 221 and the phosphate of the substrate is maximized. The WPD loop now has a very stable conformation, as binding has increased with multiple surrounding residues. The tyrosine residue is now positioned in close proximity to the sulfur of Cys 215, allowing Cys 215 to remove the phosphate as an intermediate step in the reaction. The first step of the reaction involves Asp 181 attaching a hydrogen atom to the oxygen of tyrosine, thus neutralizing it and allowing it to diffuse from the site. Next, the phosphate binds to the Cys 215 as described above, forming the cysteinyl-phosphate intermediate.

Plan on adding green scene for recognition loop, PTP loop, WPD loop

Credits

Introduction - Jill Carlson

Overall Structure - Polina Berdnikova

Drug Binding Site - Brett Clinton

Additional Features - James Hamblin

References