Difference between revisions of "Part:BBa K2113004"
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<br>Thrombin
 
<br>Thrombin
 
<br>Tobacco etch virus protease
 
<br>Tobacco etch virus protease
 +
 +
 +
 +
 +
===References===
 +
<br>1. Ressource Parisienne en Bioinformatique Structurale.
 +
<br>2. ExPASy PeptideCutter
 +
<br>3. ExPASy ProtParam

Revision as of 07:42, 14 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.

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]



Mobyle@RPBS 3D Structure Prediction

3D Structure

MGG.gif


ProtParam Results

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

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



References


1. Ressource Parisienne en Bioinformatique Structurale.
2. ExPASy PeptideCutter
3. ExPASy ProtParam