Difference between revisions of "Part:BBa K2113004"

 
 
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It consists of cationic anti-microbial peptides (AMP) with consecutive sequences of arginine and tryptophan (WRWRWR).This can be used as an antimicrobial agent against a wide range of gram positive and gram negative bacteria.
 
It consists of cationic anti-microbial peptides (AMP) with consecutive sequences of arginine and tryptophan (WRWRWR).This can be used as an antimicrobial agent against a wide range of gram positive and gram negative bacteria.
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===ProtParam Results(Physical and Chemical Properties)===
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<!-- -->
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<br>Number of amino acids: 7
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<br>Molecular weight: 1176.41
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<br>Theoretical pI: 12.30
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<br>Total number of negatively charged residues (Asp + Glu): 0
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<br>Total number of positively charged residues (Arg + Lys): 3
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<strong>Atomic composition:</strong>
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<br>Carbon      (C)         56
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<br>Hydrogen    (H)         77
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<br>Nitrogen    (N)         19
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<br>Oxygen      (O)         8
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<br>Sulfur      (S)         1
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<br>Formula: C<sub>56</sub>H<sub>77</sub>N<sub>19</sub>O<sub>8</sub>S<sub>1</sub>
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<br>Total number of atoms: 161
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<br><strong>Extinction coefficients:</strong>
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<br>Extinction coefficients are in units of  M<sup>-1</sup> cm<sup>-1</sup>, at 280 nm measured in water.
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<br>Ext. coefficient:    16500
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<br>Abs 0.1% (=1 g/l):  14.026
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<br><strong>Estimated half-life:</strong>
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<br>The N-terminal of the sequence considered is M (Met).
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<br>The estimated half-life is: 30 hours (mammalian reticulocytes, in vitro).
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<br>                            >20 hours (yeast, in vivo).
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<br>                            >10 hours (Escherichia coli, in vivo).
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<strong>Instability index:</strong>
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<br>The instability index (II) is computed to be 172.23
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<br>This classifies the protein as unstable.
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<br>Aliphatic index: 0.00
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<br>Grand average of hydropathicity (GRAVY): -2.043
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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>
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<th>Name of enzyme</th>
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<th>No. of cleavages</th>
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<th>Positions of cleavage sites</th>
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</tr>
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<tr>
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<td>Arg-C proteinase</td>
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<td>3</td>
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<td>3 5 7</td>
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</tr>
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<tr>
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<td>BNPS-Skatole</td>
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<td>3</td>
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<td>2 4 6</td>
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</tr>
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<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>2 4 6</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 2 4 6</td>
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</tr>
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<tr>
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<td>Clostripain</td>
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<td>3</td>
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<td>3 5 7</td>
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</tr>
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<tr>
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<td>Iodosobenzoic acid</td>
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<td>3</td>
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<td>2 4 6</td>
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</tr>
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<tr>
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<td>Pepsin (pH>2)</td>
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<td>4</td>
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<td>1 2 4 6</td>
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</tr>
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<tr>
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<td>Proteinase K</td>
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<td>3</td>
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<td>2 4 6</td>
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</tr>
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<tr>
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<td>Trypsin</td>
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<td>3</td>
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<td>3 5 7</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
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<br>Asp-N endopeptidase + N-terminal Glu
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<br>Caspase1
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<br>Caspase10
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<br>Caspase2
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<br>Caspase3
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<br>Caspase4
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<br>Caspase5
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<br>Caspase6
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<br>Caspase7
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<br>Caspase8
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<br>Caspase9
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<br>Enterokinase
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<br>Factor Xa
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<br>Formic acid
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<br>Glutamyl endopeptidase
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<br>GranzymeB
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<br>Hydroxylamine
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<br>LysC
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<br>LysN
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<br>NTCB (2-nitro-5-thiocyanobenzoic acid)
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<br>Pepsin (pH1.3)
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<br>Proline-endopeptidase
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<br>Staphylococcal peptidase I
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<br>Thermolysin
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<br>Thrombin
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<br>Tobacco etch virus protease
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<!-- Add more about the biology of this part here
 
<!-- Add more about the biology of this part here
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<partinfo>BBa_K2113004 parameters</partinfo>
 
<partinfo>BBa_K2113004 parameters</partinfo>
 
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===References===
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<br>2. ExPASy PeptideCutter
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<br>3. ExPASy ProtParam

Latest revision as of 05:07, 17 October 2016


AMP without glycine

It consists of cationic anti-microbial peptides (AMP) with consecutive sequences of arginine and tryptophan (WRWRWR).This can be used as an antimicrobial agent against a wide range of gram positive and gram negative bacteria.


ProtParam Results(Physical and Chemical Properties)


Number of amino acids: 7
Molecular weight: 1176.41
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) 56
Hydrogen (H) 77
Nitrogen (N) 19
Oxygen (O) 8
Sulfur (S) 1



Formula: C56H77N19O8S1
Total number of atoms: 161



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): 14.026



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 172.23
This classifies the protein as unstable.



Aliphatic index: 0.00


Grand average of hydropathicity (GRAVY): -2.043


ExPASy Peptide Cutter Results

The following enzymes cleave this peptide.

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


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


2. ExPASy PeptideCutter
3. ExPASy ProtParam