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From Proteopedia

Revision as of 15:29, 24 April 2012

1-JVQ: Devourer of Memories

Introduction

Dementia sucks. Slowly losing one's mind is no fun, and it is especially hard on the people who have to watch it happen to one of their loved ones. We can all agree that dementia is a disease worth curing: to do that we must first determine its cause. The most likely culprit for the cause of dementias are a group of protease inhibitors called serpins. Serpins are an unusual group as inhibitors go because while most inhibitors simply block the binding site, serpins undergo conformational changes when they bind. Mutations can alter those conformational changes. When this happens, the serpins can no longer function as inhibitors. This can lead to a massive buildup of mutated proteins in the cell, eventually killing it. In addition, the mutated serpins can polymerize, creating long chains that can do a great deal of damage to anything they come in contact with. After the cell is destroyed, the mutant inhibitor polymers continue to grow, spreading throughout the surrounding tissue, eventually resulting in organ failure. Mutations in the conformational structure of neuroserpin, a protease inhibitor found in neurons, has been blamed for the deterioration of brain function seen in dementia.

Overall Structure

The serpin molecule consists of two β-sheets and numerous α-helices. Of particular interest are the β-sheets: the main (A) sheet and the secondary (B) sheet. Each sheet consists of 6 anti-parallel strands, and the two sheets are arranged almost perpendicularly. The main sheet is where the reactive loop is inserted and therefore the location of the binding site for polymerization. It is also where the tetrapeptide WMDF binds in order to prevent polymerization. When serpin molecules polymerize, they form fibrils, and this aggregation of the protein is what leads to disease.

Binding Interactions

Quite a few forms of dementia arise due to serpins forming long chains with one another. Mutant serine protease inhibitors link their reactive site loop into the middle strand (s4A) position of the A beta-sheet of another (insert green scene here). They will continue hooking on to one another and create very long polymers.

Professors at the University of Cambridge have found a couple of ways in order to negate these linkages, but only one way has been shown to be practical. The reason why the serpins are allowed to form chains with one another is due to their A sheet "opening" and allowing a domain exchange with the insertion of the P8-3 portion of the loop on another molecule into the lower half of the s4A position (insert green scene here). The originally discovered that serpin polymerization could be blocked with synthetic P14-3 or P7-2 peptides. However, in terms of practicality, they were ineffective. The peptides were far too large for mimetic drug design, and many tests proved that the binding of these peptides were far too unpredictable. They would conduct crystallographic studies and find their synthetic peptides attached to other parts of the serpin.

The molecule that was effective was a tetrapeptide called WMDF (Trp-Met-Asp-Phe). Derived from cholecystokinin, this tetrapeptide blocked the polymerisation of antitrypsin and antithrombin. The structure of this peptide was observed at greater detail and the professors at Cambridge started to test out the effectiveness of other tetra and tripeptides. What they found out is that WMDF binds to the P14-8 peptide-antithrombin binary complex (). Specifically, it occupies the P7-P4 vacancy and forms 8 hydrogen bonds with the adjacent residues. The tetrapeptide's bulky side chains are what contributes to its effectiveness as a blocker of serpin polymerisation. The P4 & P6 locations are very critical; WMDF has methionine at the P6 location and phenylalanine at the P4 location. The hydrophobicity of these regions results in a shift of the connecting loop when compared to latent antithrombin, which results in successful anithrombin polymerisation inhibition. Peptides that were homologous in the P4 & P6 regions to WMDF were also effective (FMRF & FLRF)

Additional Features

Since Alzheimer's is such a common threat there have been many attempts at finding ways to prevent and cure it. The main goal is to prevent intermolecular linkages from being formed from beta strands. With this goal in mind they are trying develop therapies to aid in the prevention of these linkages. 10 million Europeans carry what we call the Z allele of antitrypsin. This doesn't directly mean you are at health risk though. The Z allele gives your body the ability to polymerize and store up to half of their antitrypsin in their liver cells. The problem arises when the formation exceeds the limits of the liver cells.

Therapeutic techniques have been developed to help stop this over-formation of antitrypsin. Instead of trying to just stop the formation of antitrypsin, researchers have found a way on how they can actually change the direction of equilibrium so that it will favor dissociation. This can be achieved by the use of an agent to bind to the unstable protein forms to slowdown and stop the formation.

At first the only way they would be able to accomplish this binding was with a minimum of 6 amino acids. The problem with this is that the peptides were not going to be small enough. What they found out was that they could block this now by the use of only 3-4 amino acids. Now these smaller peptides are of more use because now they can be used for oral drug therapy which is the best way to target all the intercellular problems. This was found out by how glycerol was able to bind to the site that was responsible for the polymerisation. This showed that with enough glycerol to bind to these sites that we could effectively prevent the formation of antirypsin.

Credits

Introduction - Kevin Dillon

Overall Structure - Max Nowak

Drug Binding Site - Kyle Reed

Additional Features - Chris Carr

References