Team:Washington/Gram Positive/Design

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=Making CapD a Better Anthrax Treatment=
=Making CapD a Better Anthrax Treatment=
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There are two main obstacles limiting natural CapD as an Anthrax therapeutic.  First, natural CapD is a difficult to express dimer, requiring an auto-cleavage to activate.  Second, CapD is a better transpeptidase than poly-γ-D-glutamate hydrolase, limiting its Anthrax decapsulating potential.  To solve the first problem, we created a circular permuted, monomeric version of CapD that is easy to express and quantify.  To improve hydrolysis, we used FoldIt, a computational toolbox, to design active site mutations aimed to increase hydrolysis over transpeptidation.  
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There are two main obstacles limiting natural CapD as an Anthrax therapeutic.  First, natural CapD is a difficult to express dimer, requiring an auto-cleavage to activate [[#References | [1]]].  Second, CapD is a better poly-γ-D-glutamate transpeptidase than poly-γ-D-glutamate hydrolase, limiting its Anthrax decapsulating potential.[[#References | [1]]] To solve the first problem, we created a circular permutated, monomeric version of CapD that is easy to express and quantify.  To improve hydrolysis, we used [https://2010.igem.org/Team:Washington/Project/Tools/FoldIt FoldIt], a computational toolbox, to design active site mutations aimed to increase hydrolysis over transpeptidation.  
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==Circular Permutation of CapD==
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When natural CapD is first translated, the key catalytic threonine residue is buried in the active site, inaccessible to poly-γ-D-glutamate. After auto-cleavage, this critical threonine becomes the new N terminus, which can take its place in the active site. By reordering the protein so the threonine is the first residue, and putting a FoldIt designed linker between the natural N and C terminus, we make a circular permutation of CapD that we named CapD_CP.  CapD_CP is a monomer, historically easier to purify and more stable than dimers. 
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<span id = capdcp>
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[[Image:CapDSimplifiedDiagram.jpg|thumb|360px|left|Schematic of natural CapD]]
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==Is CapD_CP a better version of CapD?==
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[[Image:CapDCPSimplifiedDiagram.jpg|thumb|360px|right|Schematic of Circular Permutated CapD (CapD_CP)]]
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[[Image:Washington_DtoCP_Graphic2.jpg|520px|right|Schematic of how we made a circularly permutated capD]]
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Since the first residue of any nascent protein must be methionine, we rely on E. Coli’s naturally occurring methionine aminopeptidase to remove the first methionine, making CapD_CP catalytically active.  The removal of the first methionine has been verified via mass spectrometry.
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When natural CapD is first translated, the key catalytic threonine residue is buried in the active site, rendering it inaccessible to poly-γ-D-glutamate. After auto-cleavage, this critical threonine becomes the new N terminus, which can take its place in the active site [[#References | [1]]]. By reordering the protein so the threonine is the first residue, and putting a FoldIt designed linker between the natural N and C terminus, we make a circular permutation of CapD that we named CapD_CP.  CapD_CP is a monomer, historically easier to purify and more stable than dimers. 
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Since the first residue of any nascent protein must be methionine, we rely on    E. Coli’s naturally occurring methionine aminopeptidase to remove the first methionine, making CapD_CP catalytically active.  The removal of the first methionine has been verified via mass spectrometry.
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[[Image:CapDandCapDCPGell.jpg|thumb|400px|left|Left: CapD_CP as expected.  Right: CapD has ambiguous bands, making quantifying difficult and assaying protein activity less accurate]]
 
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==Advantages of CapD_CP==
 
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In addition to the fact that CapD_CP is easy to express, it has one more crucial advantage over CapD.  When purifying CapD_CP, given our mass spec data, we can assume a massive majority of the purified CapD_CP is functional.  CapD, however, is a much more ambiguous case, as illustrated by our protein gel results.  The lower two bands of CapD correspond to the two subunits of cleaved CapD, which are active.  The upper band may be uncleaved, therefore unfunctional, CapD, or dimeric, active CapD that simply did not denature, or a combination of both.  Because of this, its difficult to quantify how much active protein is in a solution of purified CapD, making assaying activity a nightmare.  For this reason, we made our active site mutations to CapD_CP.
 
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==Using [[Team:Washington/Tools_Used/Software|FoldIt]] to Make CapD_CP a Better Hydrolase==
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==Using FoldIt to Make CapD_CP a Better Hydrolase==
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[[Image:WashingtonPointMutation.png|270px|frameless|right]][[Image:WashingtonShake.png|270px|frameless|right]]
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[[Image:WashingtonPointMutation.png|220px|frameless|right]][[Image:WashingtonShake.png|220px|frameless|right]]
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To increase the hydrolytic ability of CapD_CP, we made point mutations to the active site. We focused our attention on two types of mutations. [[Image:WashingtonWiggle.png|270px|frameless|right]] First type of mutations is to increase hydrolysis by lowering the activation energy. To accomplish this, we created point mutations that can establish hydrogen bondings to a modeled transition state of our substrate. Second type of mutations concerns with the openness and polarity of the active site. To accomplish this, we mutated the active site into a more open and polar area so water molecules can enter and participate in hydrolysis easily.  
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To increase the hydrolytic ability of CapD_CP, we made point mutations to the active site. We focused our attention on two types of mutations. [[Image:WashingtonWiggle.png|220px|frameless|right]]First, we created point mutations that can establish hydrogen bondings to a modeled transition state of our substrate in an attempt to lower the activation energy, making hydrolysis more favorable. Second, we mutated the active site into a more open and polar area in an attempt to increase the ease with which water can enter and participate in a hydrolysis reaction.  
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To make these point mutations, we used a computer program named FoldIt to predict how changes in protein structure and composition will affect protein stability.  FoldIt provides a 3D representation of a protein's crystal structure that can be manipulated. Manipulation functions include point mutations, insertions, deletions, repacking of side chains (rotamer optimization), and backbone movement, which FoldIt then assesses for stability. This allows the user to quickly interact with a protein and easily predict how mutations will affect a protein.
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To make these point mutation designs, we used a computer program named FoldIt to predict how changes in protein structure and composition will affect protein stability.  FoldIt provides a 3D representation of a protein's crystal structure that can be manipulated. Manipulation functions include point mutations, insertions, deletions, repacking of side chains (rotamer optimization), and backbone movement, which FoldIt then assesses for stability. This allows the user to quickly interact with a protein and easily predict how mutations will affect a protein.
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[[Team:Washington/Tools_Used/Software|A more in depth explanation of FoldIt here.]]
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[https://2010.igem.org/Team:Washington/Project/Tools/FoldIt A more in depth explanation of FoldIt here.]
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==References==
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1. Wu R, Richter S, Zhang RG, Anderson VJ, Missiakas D, Joachimiak A. Crystal structure of Bacillus anthracis transpeptidase enzyme CapD.  J Biol Chem. 2009 Sep 4;284(36):24406-14. Epub 2009 Jun 16. PMID: 19535342
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Latest revision as of 06:05, 27 October 2010

Making CapD a Better Anthrax Treatment

There are two main obstacles limiting natural CapD as an Anthrax therapeutic. First, natural CapD is a difficult to express dimer, requiring an auto-cleavage to activate [1]. Second, CapD is a better poly-γ-D-glutamate transpeptidase than poly-γ-D-glutamate hydrolase, limiting its Anthrax decapsulating potential. [1] To solve the first problem, we created a circular permutated, monomeric version of CapD that is easy to express and quantify. To improve hydrolysis, we used FoldIt, a computational toolbox, to design active site mutations aimed to increase hydrolysis over transpeptidation.

Is CapD_CP a better version of CapD?

Schematic of how we made a circularly permutated capD

When natural CapD is first translated, the key catalytic threonine residue is buried in the active site, rendering it inaccessible to poly-γ-D-glutamate. After auto-cleavage, this critical threonine becomes the new N terminus, which can take its place in the active site [1]. By reordering the protein so the threonine is the first residue, and putting a FoldIt designed linker between the natural N and C terminus, we make a circular permutation of CapD that we named CapD_CP. CapD_CP is a monomer, historically easier to purify and more stable than dimers.

Since the first residue of any nascent protein must be methionine, we rely on E. Coli’s naturally occurring methionine aminopeptidase to remove the first methionine, making CapD_CP catalytically active. The removal of the first methionine has been verified via mass spectrometry.



Using FoldIt to Make CapD_CP a Better Hydrolase

WashingtonPointMutation.png
WashingtonShake.png
To increase the hydrolytic ability of CapD_CP, we made point mutations to the active site. We focused our attention on two types of mutations.
WashingtonWiggle.png
First type of mutations is to increase hydrolysis by lowering the activation energy. To accomplish this, we created point mutations that can establish hydrogen bondings to a modeled transition state of our substrate. Second type of mutations concerns with the openness and polarity of the active site. To accomplish this, we mutated the active site into a more open and polar area so water molecules can enter and participate in hydrolysis easily.


To make these point mutation designs, we used a computer program named FoldIt to predict how changes in protein structure and composition will affect protein stability. FoldIt provides a 3D representation of a protein's crystal structure that can be manipulated. Manipulation functions include point mutations, insertions, deletions, repacking of side chains (rotamer optimization), and backbone movement, which FoldIt then assesses for stability. This allows the user to quickly interact with a protein and easily predict how mutations will affect a protein.

A more in depth explanation of FoldIt here.


References

1. Wu R, Richter S, Zhang RG, Anderson VJ, Missiakas D, Joachimiak A. Crystal structure of Bacillus anthracis transpeptidase enzyme CapD. J Biol Chem. 2009 Sep 4;284(36):24406-14. Epub 2009 Jun 16. PMID: 19535342






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