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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− | < | + | <br>Number of amino acids: 7 |
− | + | <br>Molecular weight: 1176.41 | |
− | + | <br>Theoretical pI: 12.30 | |
− | + | <br>Total number of negatively charged residues (Asp + Glu): 0 | |
− | + | <br>Total number of positively charged residues (Arg + Lys): 3 | |
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− | 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 | + | |
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<br>Grand average of hydropathicity (GRAVY): -2.043 | <br>Grand average of hydropathicity (GRAVY): -2.043 | ||
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+ | |||
+ | ===ExPASy Peptide Cutter Results=== | ||
+ | |||
+ | The following enzymes cleave this peptide. | ||
+ | |||
+ | <table border="1"> | ||
+ | <tr> | ||
+ | <th>Name of enzyme</th> | ||
+ | <th>No. of cleavages</th> | ||
+ | <th>Positions of cleavage sites</th> | ||
+ | </tr> | ||
+ | <tr> | ||
+ | <td>Arg-C proteinase</td> | ||
+ | <td>3</td> | ||
+ | <td>3 5 7</td> | ||
+ | </tr> | ||
+ | <tr> | ||
+ | <td>BNPS-Skatole</td> | ||
+ | <td>3</td> | ||
+ | <td>2 4 6</td> | ||
+ | </tr> | ||
+ | <tr> | ||
+ | <td>CNBr</td> | ||
+ | <td>1</td> | ||
+ | <td>1</td> | ||
+ | </tr> | ||
+ | <tr> | ||
+ | <td>Chymotrypsin-high specificity (C-term to [FYW], not before P)</td> | ||
+ | <td>3</td> | ||
+ | <td>2 4 6</td> | ||
+ | </tr> | ||
+ | <tr> | ||
+ | <td>Chymotrypsin-low specificity (C-term to [FYWML], not before P)</td> | ||
+ | <td>4</td> | ||
+ | <td>1 2 4 6</td> | ||
+ | </tr> | ||
+ | <tr> | ||
+ | <td>Clostripain</td> | ||
+ | <td>3</td> | ||
+ | <td>3 5 7</td> | ||
+ | </tr> | ||
+ | <tr> | ||
+ | <td>Iodosobenzoic acid</td> | ||
+ | <td>3</td> | ||
+ | <td>2 4 6</td> | ||
+ | </tr> | ||
+ | <tr> | ||
+ | <td>Pepsin (pH>2)</td> | ||
+ | <td>4</td> | ||
+ | <td>1 2 4 6</td> | ||
+ | </tr> | ||
+ | <tr> | ||
+ | <td>Proteinase K</td> | ||
+ | <td>3</td> | ||
+ | <td>2 4 6</td> | ||
+ | </tr> | ||
+ | <tr> | ||
+ | <td>Trypsin</td> | ||
+ | <td>3</td> | ||
+ | <td>3 5 7</td> | ||
+ | </tr> | ||
+ | </table> | ||
+ | |||
+ | |||
+ | <!-- --> | ||
+ | These enzymes do not cut the peptide | ||
+ | |||
+ | <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_K2113004 SequenceAndFeatures</partinfo> | ||
+ | |||
+ | |||
+ | <!-- Uncomment this to enable Functional Parameter display | ||
+ | ===Functional Parameters=== | ||
+ | <partinfo>BBa_K2113004 parameters</partinfo> | ||
+ | <!-- --> | ||
+ | |||
+ | |||
+ | |||
+ | |||
+ | |||
+ | ===References=== | ||
+ | <br>2. ExPASy PeptideCutter | ||
+ | <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
- 10COMPATIBLE WITH RFC[10]
- 12COMPATIBLE WITH RFC[12]
- 21COMPATIBLE WITH RFC[21]
- 23COMPATIBLE WITH RFC[23]
- 25COMPATIBLE WITH RFC[25]
- 1000COMPATIBLE WITH RFC[1000]
References
2. ExPASy PeptideCutter
3. ExPASy ProtParam