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Amino Acid Table
Amino Acid
Name
Alanine
Arginine
Asparagine
Aspartic Acid
Cysteine
Glutamic Acid
Glutamine
Glycine
Histidine
Isoleucine
Leucine
Lysine
Methionine
Phenylalanine
Proline
Serine
Threonine
Tryptophan
Tyrosine
Valine
3-Letter
Code
Ala
Arg
Asn
Asp
Cys
Glu
Gln
Gly
His
Ile
Leu
Lys
Met
Phe
Pro
Ser
Thr
Trp
Tyr
Val
1-Letter
Code
A
R
N
D
C
E
Q
G
H
I
L
K
M
F
P
S
T
W
Y
V
Side Chain
Polarity
Nonpolar (hydrophobic)
Polar (soluble)
Polar
Polar
Polar
Polar
Polar
Nonpolar
Polar
Nonpolar
Nonpolar
Polar
Nonpolar
Nonpolar, aromatic
Nonpolar
Polar
Polar
Nonpolar, aromatic
Polar, aromatic
Nonpolar
Amino Acid Structures
Side Chain
Acidity/Basicity
Neutral
Basic (strongly)
Neutral
Acidic
Neutral
Acidic
Neutral
Neutral
Basic (weakly)
Neutral
Neutral
Basic
Neutral
Neutral
Neutral
Neutral
Neutral
Neutral
Neutral
Neutral
Hydropathy
Index
1.8
-4.5
3.5
-3.5
2.5
3.5
-3.5
0.4
-3.2
4.5
3.8
-3.9
1.9
2.8
-1.6
-0.8
-0.7
0.9
-1.3
4.2
Molecular
Weight
89.09
174.20
132.12
133.10
121.16
147.13
146.15
75.07
155.16
131.17
131.17
146.19
149.21
165.19
115.13
105.09
119.12
204.23
181.19
117.15
Isoelectric
Point
6.00
11.15
5.41
2.77
5.02
3.22
5.65
5.97
7.47
5.94
5.98
9.59
5.74
5.48
6.30
5.68
5.64
5.89
5.66
5.96
Peptide Design
You need to consider the following items when design your peptide.
Nonpolar, Aliphatic R Groups
－ －
－
H
H
－ －
CH3 O-
H
O
H－N+－C－C
CH OH
CH2 CH2 O-
－
－ －
H－N+－C－C
H
1. Peptide purity
For antibody generation and testing, peptide purity > 70% is enough, however, for
biological activity studies, peptide purity > 95% is required.
Proline (Pro or P)
－ －
－
H－N+－C－C
－
O-
H
－ －
H
Serine (Ser or S)
H H
O
－ －
－
－ －
－ －
－
H－N+－C－C
Alanine (Ala or A)
H H
O
OH
Glycine (Gly or G)
H H
O
Polar, Uncharged R Groups
CH2
H
－ －
H
－ －
H
H
CH2 O-
－
3. Peptide length
Peptide length governs the level of difficulty when synthesizing peptides. Peptide
antigens are recommended to contain 10-15 residues to be used in antibody
production.
CH2 O-
H
C－NH2
CH2
O－C－NH2
O
CH3
O
H－N+－C－C
H－N+－C－C
CH2 O-
－ － －
－
Glutamine (Gln or G)
O
－ －
－
－ －
－
O
S－CH2
H3C
SH
H
－
H
－ －
H
CH2 O-
H
Asparagine (Asn or N)
H
O
H－N+－C－C
CH OCH3
－ － － －
－
－ －
Methionine (Met or M)
H－N+－C－C
-
－ －
－
H
H
H
H－N －C－C
+
CH
H3C CH3
－ －
H－N+－C－C
2. Peptide amino acid composition
Amino acid composition governs every aspect of the peptide’s functionality.
Hydrophobic and hydrophilic characteristics are key factors to consider. The peptide
should incorporate antigenic amino acids sequence and avoid problematic amino
acids such as cysteine, methionine, and tryptophan.
Cysteine (Cys or C)
Threonine (Thr or T)
H H
O
CH2 O-
H
－ －
－
－ －
－
－ －
lsoleucine (Ile or I)
H H
O
CH O
CH2 CH3
O
H－N+－C－C
H CH OH3C CH3
H
H
H
－ － －
－
－ －
－
H－N+－C－C
Leucine (Leu or L)
OH
－ －
Valine (Val or V)
H H
O
Positively Charged R Groups
Aromatic R Groups
H
CH2 O
－
OH
－ －
－ － － －
－
Arginine (Arg or R)
H
O
H
CH2 O-
H
C N+H
CH
HC－N －
H
CH2
H3N+－CH2
H
O
H－N+－C－C
H－N+－C－C
CH2 OCH2
Tryptophan (Trp or W)
H H
O
H
－ －
H
－ －
－ －
Histidine (His or H)
O
CH2 OCH2
+
NH2 CH2
－
CH2 O-
H
-
H
H－N －C－C
+
－ － － －
－
H
H－N+－C－C
H
－ － － － －
－
O
－ －
H
－ －
－
－ －
H
H－N+－C－C
Tyrosine (Tyr or Y)
H H
O
－ － －
－
Phenylalanine (Phe or F)
－ － － － －
－
Lysine (Lys or K)
H2N－C－ NH
Negatively Charged R Groups
H－N+－C－C
H
O
CH2 O
H
H
O
H－N+－C－C
H－N+－C－C
H
Glutamic acid (Glu or E)
－ －
H
－ － － －
－
NH
Aspartic acid (Asp or D)
－ －
CH2 OC－ CH
－ － －
－
H
-
4. Peptide solubility
You can design peptides of varied solubility by changing the frequency of occurrence
of hydrophobic and hydrophilic amino acids. Hydrophobic amino acid content is
suggested to be kept below 50% with at least one charged residue incorporated within
every five amino acids. In addition, a single conservative replacement or addition of
polar residues to the N- or C-terminus may also improve peptide solubility.
CH2 O-
H
CH2
C－
O
O
-
O
C－
O
5. Secondary structure
During peptide synthesis, beta sheet formation can cause incomplete dissolution of
the growing peptide thus deletion sequences in the final product. Please avoid
multiple or adjacent residues of Val, Ile, Tyr, Phe, Trp, Leu, Gln, or Thr to prevent beta
sheet formation. If the above recommendation cannot be implemented practically,
conservative replacement may help by reinserting a Gly or Pro at every third residue
or replacing Gln with Asp, or Thr with Ser.
Peptide Solubilization
Storage & Handling
1. Assign a value of -1 to acidic residues which include Asp
(D), Glu (E), and the C-terminal -COOH. Assign a value
of +1 to basic residues which include Arg (R), Lys (K),
His (H), and the N-terminal -NH2. Calculate the overall
charge of the entire peptide.
a. Storage
Lyophilized peptides should be refrigerated and stored away from bright light. For short-term
storage ranging from one week to two months, lyophilized peptides may be stored at 4°C. For
long-term storage, lyophilized peptide should be stored at -20°C in deep freezer. Even though this
condition keeps most peptides stable for several years, peptides' long term stability is at risk when
peptides expose to moisture, therefore, the vial should be tightly capped at all times. This also
requires careful experiment planning to minimize vial openings.
2. If the overall charge of the peptide is positive, try to
dissolve the peptide in water first. If water fails, try
10%-30% acetic acid solution. If the peptide still does not
dissolve, add TFA (< 50 μl) to solubilize the peptide and
then dilute the peptide solution to the desired
concentration.
3. If the overall charge of the peptide is negative, try to
dissolve the peptide in water first. If water fails, add
NH4OH (< 50 μl) and then dilute the peptide solution to
the desired concentration. If the peptide contains Cys,
then do not use basic solutions to dissolve it. Try the
alternative method listed below.
Do not store excessive peptides in solution because the shelf life of peptides in solution is very
limited, much shorter than lyophilized peptides. This is especially true for peptides whose
sequences contain cysteine, methionine, tryptophan, asparagine, glutamine, or N-terminal
glutamic acid. It is necessary to aliquot the amount of peptide you need for the day and
re-lyophilize the remaining peptide solution. Another drawback is that peptides stored in solution
are susceptible to bacterial degradation. If storage of peptide in solution is unavoidable, use sterile
buffers at pH 5-6 and store aliquots at -20°C and pass the peptide solution through a 0.2 μM filter
to rid the bacteria.
b. Handling
4. Peptide whose overall charge is zero usually dissolves in
organic solvent. First, try to add some acetonitrile,
methanol, or isopropanol. For very hydrophobic peptides,
try dissolving the peptide in a small amount of DMSO,
and then dilute the solution with water to the desired
concentration. For Cys-containing peptides, use DMF
instead of DMSO. For peptides that tend to aggregate,
add 6 M guanidine•HCl or 8 M urea, and then proceed
with the necessary dilutions.
When preparing peptides for use, please consult GenScript's following guidelines:
• Warm the peptide vial to room temperature before opening.
• Weigh out the desired quantity of peptide quickly.
• Reseal the vial tightly.
• Store the remaining peptide in a freezer, preferably below -20°C, under dry conditions.
Avoid repeated freeze and thaw cycles for both lyophilized peptides and peptide solutions. If
frequent and periodical sample takings from storage are unavoidable, GenScript recommends
making a series of aliquots in advance. Due to the fact that peptides whose sequences containing
cysteine, methionine, or tryptophan are prone to air oxidation. It is recommended that air be
purged from the peptide storage vial and replaced with inert gases such as argon or nitrogen for
storage.
Applications
Peptides with purity greater than 70% are always used for generating or testing antibodies. Peptides with purity level greater than 85% are usually used in enzymology or
biological activity studies. Peptides with purity greater than 95% are excellent for quantitative analysis.
Applications
Recommended Purity
•
•
•
•
•
•
•
•
•
•
•
•
•
•
•
Immunograde Peptide
Peptide purity >70%
Biochemistry Grade Peptide
Peptide purity >85%
High Purity Grade Peptide
Peptide purity >95%->98%
Antigen for production and affinity purification of polyclonal antibodies
ELISA tests
Peptide array
Epitope mapping
Semi-quantitative enzyme-substrate studies
Phosphorylation studies
Peptide blocking studies by Western blotting
In-vitro bioassays
Cell attachment studies
Quantitative assays
NMR studies
In-vitro bioassays
In-vivo studies
Clinical trials
SAR studies
860 Centennial Ave., Piscataway, NJ 08854, USA
Web: www.genscript.com
Toll-Free: 1-877-436-7274
Fax: 1-732-210-0262
Tel: 1-732-885-9188
Email: [email protected]