Difference between revisions of "Part:BBa K2888000:Design"

 
(→‎Design Notes)
 
(2 intermediate revisions by the same user not shown)
Line 6: Line 6:
  
  
−
===Design Notes===
+
<html>
−
We directly copy the sequence from the previous experiment by Kunal Mehta, Niklaus Evitt and James Swartz. However, since it has the unexpected restriction sites, we have replaced them with corresponding code.  
+
<h4> Introduction</h4>
 +
<p>1. The aspartic and glutamic acid residues at the active site of the lysozyme would wrap around the glycosidic bond between 6 carbon conponent N-acetylmuramic acid （NAM）and N-acetylglucosamine (NAG) of the carbohydrate section of the peptidoglycan. The carboxyl group on the aspartic acid attacks the carbon on NAM, attaching the aspartic acid to the NAM. Meanwhile, an oxygen on the NAG would pick up the hydrogen proton on the glutamic acid, deprotonating the glutamic acid into a glutamate.</p>
  
 +
<p>2. The lysis of lysozyme has to take place in aqueous environment. The addition of a water molecule would complete the hydrolysis reaction by protonating the glutamate back to glutamic acid; it would also deprotonate the aspartic acid from the NAM, restoring it back to its reduced form, while leaving a hydroxyl group on the end of NAM. This way, the lysozyme would keep its own structure unchanged while degrading the carbohydrate section of the peptidoglycan into the NAM/NAG components.</p>
 +
<img src= "https://static.igem.org/mediawiki/2018/0/09/T--SBS_SH_112144--CyanoElimination3.svg" width="600" height="400/>
  
 +
<h4>Design Notes</h4>
 +
 +
 +
<p>We directly copy the sequence from the previous experiment by Kunal Mehta, Niklaus Evitt and James Swartz. However, since it has the unexpected restriction sites, we have replaced them with corresponding code.</p>
 +
 +
<p>Our cp-OS lysozyme 1 is a form of bacteriophage lysozyme that exists in virus. Once the cyanophage finish replicating in cyanobacteria, they produce the cyanophage lysozyme to lyse the cyanobacterial cell wall to get out. Through protein blasting of the cyanophage lysozyme, we found its structural similarity and homogeneity with multiple other peptidoglycan binding proteins and even a type of peptidoglycan domain protein from cyanobacterium Nostoc, and this implies the working mechanism of this lysozyme is similar to other lysozyme and is somewhat specific to cyanobacterial peptidoglycan.</p>
 +
</html>
  
 
===Source===
 
===Source===
Line 17: Line 27:
  
 
===References===
 
===References===
 +
Jensen HB, Kleppe K: Effect of ionic strength, pH, amines and divalent cations on the lytic activity of T4 lysozyme. Eur J Biochem 1972, 28:116–122.
 +
 +
Kunal Mehta, Niklaus Evitt, James Swartz: Chemical Lysis of Cyanobacteria. Journal of Biological Engineer, 9/10/2015

Latest revision as of 17:45, 17 October 2018


cyanophage lysozyme gene


Assembly Compatibility:
  • 10
    COMPATIBLE WITH RFC[10]
  • 12
    COMPATIBLE WITH RFC[12]
  • 21
    COMPATIBLE WITH RFC[21]
  • 23
    COMPATIBLE WITH RFC[23]
  • 25
    COMPATIBLE WITH RFC[25]
  • 1000
    COMPATIBLE WITH RFC[1000]


Introduction

1. The aspartic and glutamic acid residues at the active site of the lysozyme would wrap around the glycosidic bond between 6 carbon conponent N-acetylmuramic acid （NAM）and N-acetylglucosamine (NAG) of the carbohydrate section of the peptidoglycan. The carboxyl group on the aspartic acid attacks the carbon on NAM, attaching the aspartic acid to the NAM. Meanwhile, an oxygen on the NAG would pick up the hydrogen proton on the glutamic acid, deprotonating the glutamic acid into a glutamate.

2. The lysis of lysozyme has to take place in aqueous environment. The addition of a water molecule would complete the hydrolysis reaction by protonating the glutamate back to glutamic acid; it would also deprotonate the aspartic acid from the NAM, restoring it back to its reduced form, while leaving a hydroxyl group on the end of NAM. This way, the lysozyme would keep its own structure unchanged while degrading the carbohydrate section of the peptidoglycan into the NAM/NAG components.

Source

This cyanophage lysozyme is discovered by Heideburg et al in Yellowstone National Park {Heideburg:2009hb} among 29 lysozyme family.

References

Jensen HB, Kleppe K: Effect of ionic strength, pH, amines and divalent cations on the lytic activity of T4 lysozyme. Eur J Biochem 1972, 28:116–122.

Kunal Mehta, Niklaus Evitt, James Swartz: Chemical Lysis of Cyanobacteria. Journal of Biological Engineer, 9/10/2015