Difference between revisions of "Part:BBa K2319010:Design"

 
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===Design Notes===
 
===Design Notes===
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This will be explained soon.
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<html>
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<p><i>H. salinarum</i> is a halophile that tolerates hypersaline environments with ease — using a "salt-in" strategy, its cellular environment has evolved to be hypersaline itself! The vast majority of proteins synthesized by H. salinarum have negatively-charged acidic side chains and require 4-5 M salt concentrations to function. GvpC is one such protein. GvpC contains seven internal repeats of the domain that interlocks between GvpA "ribs" and strengthens the gas vesicle, followed by an acidic tail at the C-terminus which stabilizes the protein through effective solvation.</p>
  
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<pre>
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<b>GvpC protein sequence from <i>Halobacterium salinarum</i> NRC-1, showing seven internal repeats and acidic tail</b>
  
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                        MSVTDKRDEMSTARDKFAESQQEFESYADEFAADITAKQDDVSDLVDAITDFQAEMTNTT
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                                                |  | |||||      |    | |  |     
 +
                                              DAFHTYGDEFAAEVDHLRADIDAQRDVIREMQ     
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                                              |||  | | ||        ||      |         
 +
                                              DAFEAYADIFATDIADKQ-DIGNLLAAIEALRTEMNSTH
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                                              ||||||| || | |    ||  | |||    |   
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                                              GAFEAYADDFAADVAALR-DISDLVAAIDDFQEEFIAVQ
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                                              ||  || || |        |  | ||| |    | | 
 +
                                              DAFDNYAGDFDAE-------IDQLHAAIADQHDSFDATA
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                                              |||  |  |                             
 +
                                              DAFAEYRDEFYRIEVEALLEAINDFQQDIGDFRAEFETTE
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                                              |||      ||  |  |  |                  |
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                                              DAFVAFARDFYGHEITAEEGAAEAEAEPVEADADVEAEAE*
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                                            #VSPDEAGGESAGTEEEETEPAEVETAAPEVEGSPADTADE
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                                              AEDTEAEEETEEEAPEDMVQCRVCGEYYQAITEPHLQTHD
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                                              MTIQEYRDEYGEDVPLRPDDKT
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* denotes the truncation site (denoted C3 truncation site)
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# denotes the start of the acidic tail (note the abundance of aspartate and glutamate residues)
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Adapted from DasSarma et al (2013)
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</pre>
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<p>For our proposed fusions, this is a problem: haloarchaeal gas vesicles "shrug off" their surface GvpC if high salt concentrations are not maintained. As a result, we removed this acidic tail that destabilizes the GvpC-gas vesicle binding at low salt concentrations, and used this truncated GvpC for our fusions.</p>
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</html>
  
 
===Source===
 
===Source===

Revision as of 10:23, 1 November 2017


gvpC from Halobacterium salinarum NRC-1 (truncated)


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]


Design Notes

H. salinarum is a halophile that tolerates hypersaline environments with ease — using a "salt-in" strategy, its cellular environment has evolved to be hypersaline itself! The vast majority of proteins synthesized by H. salinarum have negatively-charged acidic side chains and require 4-5 M salt concentrations to function. GvpC is one such protein. GvpC contains seven internal repeats of the domain that interlocks between GvpA "ribs" and strengthens the gas vesicle, followed by an acidic tail at the C-terminus which stabilizes the protein through effective solvation.

GvpC protein sequence from Halobacterium salinarum NRC-1, showing seven internal repeats and acidic tail

                         MSVTDKRDEMSTARDKFAESQQEFESYADEFAADITAKQDDVSDLVDAITDFQAEMTNTT
                                                |  | |||||       |     | |   |       
                                              DAFHTYGDEFAAEVDHLRADIDAQRDVIREMQ       
                                              |||  | | ||        ||      |           
                                              DAFEAYADIFATDIADKQ-DIGNLLAAIEALRTEMNSTH
                                               ||||||| || | |    ||  | |||     |     
                                              GAFEAYADDFAADVAALR-DISDLVAAIDDFQEEFIAVQ
                                               ||  || || |        |  | ||| |    | |  
                                              DAFDNYAGDFDAE-------IDQLHAAIADQHDSFDATA
                                              |||  |   |                              
                                              DAFAEYRDEFYRIEVEALLEAINDFQQDIGDFRAEFETTE
                                              |||      ||  |  |   |                  |
                                              DAFVAFARDFYGHEITAEEGAAEAEAEPVEADADVEAEAE*
                                             #VSPDEAGGESAGTEEEETEPAEVETAAPEVEGSPADTADE
                                              AEDTEAEEETEEEAPEDMVQCRVCGEYYQAITEPHLQTHD
                                              MTIQEYRDEYGEDVPLRPDDKT

* denotes the truncation site (denoted C3 truncation site)
# denotes the start of the acidic tail (note the abundance of aspartate and glutamate residues)
Adapted from DasSarma et al (2013)

For our proposed fusions, this is a problem: haloarchaeal gas vesicles "shrug off" their surface GvpC if high salt concentrations are not maintained. As a result, we removed this acidic tail that destabilizes the GvpC-gas vesicle binding at low salt concentrations, and used this truncated GvpC for our fusions.

Source

This comes from the gvp gene cluster of Halobacterium salinarum, found on a megaplasmid.

References