Difference between revisions of "Part:BBa K2113004"

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

@@ Line 4: / Line 4: @@
 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.
-<!-- 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>
-<!-- -->
-===ProtParam Results===
+===ProtParam Results(Physical and Chemical Properties)===
@@ Line 80: / Line 67: @@
 ===ExPASy Peptide Cutter Results===
+The following enzymes cleave this peptide.
 <table border="1">
@@ Line 170: / Line 158: @@
 <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>
+<!-- -->