Difference between revisions of "Part:BBa K2113005"
 
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This part contains the anti-microbial peptides (AMP) with consecutive sequences of arginine and tryptophan.These peptides have antimicrobial activity against wide range of microbes. In order to increase the shelf life and stability of the peptide glycine residues are added at the N terminal(GGWRWRWR).
 
This part contains the anti-microbial peptides (AMP) with consecutive sequences of arginine and tryptophan.These peptides have antimicrobial activity against wide range of microbes. In order to increase the shelf life and stability of the peptide glycine residues are added at the N terminal(GGWRWRWR).
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<!-- Add more about the biology of this part here
 
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===Usage and Biology===
 
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<span class='h3bb'>Sequence and Features</span>
 
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<partinfo>BBa_K2113005 SequenceAndFeatures</partinfo>
 
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===Functional Parameters===
 
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<partinfo>BBa_K2113005 parameters</partinfo>
 
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===ProtParam Results===
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===ProtParam Results(Physical and Chemical Properties)===
  
  
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<strong>Atomic composition:</strong>
 
<strong>Atomic composition:</strong>
  
−
<br>Carbon      (C)         60
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<br>Carbon      (C):         60
−
<br>Hydrogen    (H)         83
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<br>Hydrogen    (H):         83
−
<br>Nitrogen    (N)         21
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<br>Nitrogen    (N):         21
−
<br>Oxygen      (O)         10
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<br>Oxygen      (O):         10
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<br>Sulfur      (S)         1
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<br>Sulfur      (S):         1
  
  
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<br>Grand average of hydropathicity (GRAVY): -1.678
 
<br>Grand average of hydropathicity (GRAVY): -1.678
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 +
 +
===ExPASy Peptide Cutter Results===
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 +
The following enzymes cleave this peptide.
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 +
<table border="1">
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<tr>
 +
<th>Name of enzyme</th>
 +
<th>No. of cleavages</th>
 +
<th>Positions of cleavage sites</th>
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</tr>
 +
<tr>
 +
<td>Arg-C proteinase</td>
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<td>3</td>
 +
<td>5 7 9</td>
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</tr>
 +
<tr>
 +
<td>BNPS-Skatole</td>
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<td>3</td>
 +
<td>4 6 8</td>
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</tr>
 +
<tr>
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<td>CNBr</td>
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<td>1</td>
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<td>1</td>
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</tr>
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<tr>
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<td>Chymotrypsin-high specificity (C-term to [FYW], not before P)</td>
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<td>3</td>
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<td>4 6 8</td>
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</tr>
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<tr>
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<td>Chymotrypsin-low specificity (C-term to [FYWML], not before P)</td>
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<td>4</td>
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<td>1 4 6 8</td>
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</tr>
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<tr>
 +
<td>Clostripain</td>
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<td>3</td>
 +
<td>5 7 9</td>
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</tr>
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<tr>
 +
<td>Iodosobenzoic acid</td>
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<td>3</td>
 +
<td>4 6 8</td>
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</tr>
 +
<tr>
 +
<td>Pepsin (pH>2)</td>
 +
<td>4</td>
 +
<td>3 4 6 8</td>
 +
</tr>
 +
<tr>
 +
<td>Proteinase K</td>
 +
<td>3</td>
 +
<td>4 6 8</td>
 +
</tr>
 +
<tr>
 +
<td>Trypsin</td>
 +
<td>3</td>
 +
<td>5 7 9</td>
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</tr>
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</table>
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 +
 +
<!-- -->
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These enzymes do not cut the peptide:
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 +
<br>Asp-N endopeptidase
 +
<br>Asp-N endopeptidase + N-terminal Glu
 +
<br>Caspase1
 +
<br>Caspase10
 +
<br>Caspase2
 +
<br>Caspase3
 +
<br>Caspase4
 +
<br>Caspase5
 +
<br>Caspase6
 +
<br>Caspase7
 +
<br>Caspase8
 +
<br>Caspase9
 +
<br>Enterokinase
 +
<br>Factor Xa
 +
<br>Formic acid
 +
<br>Glutamyl endopeptidase
 +
<br>GranzymeB
 +
<br>Hydroxylamine
 +
<br>LysC
 +
<br>LysN
 +
<br>NTCB (2-nitro-5-thiocyanobenzoic acid)
 +
<br>Pepsin (pH1.3)
 +
<br>Proline-endopeptidase
 +
<br>Staphylococcal peptidase I
 +
<br>Thermolysin
 +
<br>Thrombin
 +
<br>Tobacco etch virus protease
 +
 +
 +
 +
<!-- Add more about the biology of this part here
 +
===Usage and Biology===
 +
 +
<!-- -->
 +
<span class='h3bb'>Sequence and Features</span>
 +
<partinfo>BBa_K2113005 SequenceAndFeatures</partinfo>
 +
 +
 +
<!-- Uncomment this to enable Functional Parameter display
 +
===Functional Parameters===
 +
<partinfo>BBa_K2113005 parameters</partinfo>
 +
<!-- -->
 +
  
  

Latest revision as of 05:08, 17 October 2016


AMP with glycine

This part contains the anti-microbial peptides (AMP) with consecutive sequences of arginine and tryptophan.These peptides have antimicrobial activity against wide range of microbes. In order to increase the shelf life and stability of the peptide glycine residues are added at the N terminal(GGWRWRWR).


Mobyl@RPBS

3D structural view

MGG.gif


ProtParam Results(Physical and Chemical Properties)


Number of amino acids: 9
Molecular weight: 1290.51
Theoretical pI: 12.30
Total number of negatively charged residues (Asp + Glu): 0
Total number of positively charged residues (Arg + Lys): 3


Atomic composition:


Carbon (C): 60
Hydrogen (H): 83
Nitrogen (N): 21
Oxygen (O): 10
Sulfur (S): 1


Formula: C60H83N21O10S1
Total number of atoms: 175


Extinction coefficients:


Extinction coefficients are in units of M-1 cm-1, at 280 nm measured in water.


Ext. coefficient: 16500
Abs 0.1% (=1 g/l): 12.786


Estimated half-life:


The N-terminal of the sequence considered is M (Met).


The estimated half-life is: 30 hours (mammalian reticulocytes, in vitro).
>20 hours (yeast, in vivo).
>10 hours (Escherichia coli, in vivo).


Instability index:


The instability index (II) is computed to be 163.60
This classifies the protein as unstable.




Aliphatic index: 0.00


Grand average of hydropathicity (GRAVY): -1.678


ExPASy Peptide Cutter Results

The following enzymes cleave this peptide.

Name of enzyme No. of cleavages Positions of cleavage sites
Arg-C proteinase 3 5 7 9
BNPS-Skatole 3 4 6 8
CNBr 1 1
Chymotrypsin-high specificity (C-term to [FYW], not before P) 3 4 6 8
Chymotrypsin-low specificity (C-term to [FYWML], not before P) 4 1 4 6 8
Clostripain 3 5 7 9
Iodosobenzoic acid 3 4 6 8
Pepsin (pH>2) 4 3 4 6 8
Proteinase K 3 4 6 8
Trypsin 3 5 7 9


These enzymes do not cut the peptide:


Asp-N endopeptidase
Asp-N endopeptidase + N-terminal Glu
Caspase1
Caspase10
Caspase2
Caspase3
Caspase4
Caspase5
Caspase6
Caspase7
Caspase8
Caspase9
Enterokinase
Factor Xa
Formic acid
Glutamyl endopeptidase
GranzymeB
Hydroxylamine
LysC
LysN
NTCB (2-nitro-5-thiocyanobenzoic acid)
Pepsin (pH1.3)
Proline-endopeptidase
Staphylococcal peptidase I
Thermolysin
Thrombin
Tobacco etch virus protease


Sequence and Features


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]




References


1. Ressource Parisienne en Bioinformatique Structurale.(Mobyl@RPBS)
2. ExPASy PeptideCutter
3. ExPASy ProtParam