Hello Experts,
I am still a beginner in this field, and I want to understand if a certain DNA or amino acid sequence is cationic or anionic? Is there a way (not experimentally), using bioinformatics or prediction tool to determine if my gene or peptide of interest is more positively or negatively charged?
Thanks in advance!
Hi,
for peptides you can use the following link. Even though it is useful to simulate proteolytic cuttings, you can use it also to know some pysico-chemical features of your protein/peptide. In the window "select an enzyme" you have to select "no cutting" in the scrolling window
Hi,
Due to the nature of the building blocks of DNA, it is negatively charged by definition. That's slightly different with peptides as these can consist of basic (positively charged) amino acids, such as lysine (K), arginine (R) and histidine (H), as well as negatively charged amino acids, such as aspartic acid (D) and glutamic acid (E).
Please note that the charge of a peptide/protein is pH dependent! If the pH is below the so called isoelectric point (pI) of a peptide or protein, it is positively charged, if the pH is above the pI, it is negatively charged.
Hope this helps, good luck!
Thank you for your answer. But I want to make a quick assessment of the peptides I have right now? Is there a tool to predict if my putative amino acid sequence is cationic or anionic?
Thanks for your answers... I got it! So it doesn't necessary mean that if the peptide contains more positively charged amino acids, the net charge is positive. I still need to check the isoelectric point and pH of the solution. Thanks! That really helped.
I'm trying to understand the properties of my protein for surface attachment. Do you think I can use the ExPASy ProtParam tool to do this? I used the tools from ExPASy, ProtParam as well as Translate tool.
You can use these tools, it may be helpful for you.
http://www.imtech.res.in/raghava/COPid/help.html
http://crdd.osdd.net/raghava/anticp/submitfreq1.php?ran=5654
Dear Edward,
the swiss institute of bioinformatics provides a lot of different tool.
The one that you are looking for is the following: http://web.expasy.org/compute_pi/
And as Eef Dirksen said the pI depends on pH. However, in general you can simply count all basic (K, R, H) and acidic (D, E) amino acids, calculate the difference and you get an idea whether your peptide is positively or negatively charged (at pH 7).
Hope this helps, although you have already some good answers ;)
To determine whether a peptide(s) is cationic or anionic without knowing its sequence we were used to subject it (or the mixture) to high voltage electrophoresis on thin layer plates in volatile buffers (based on formiate and with pH 1.9 and pH 6.4). After the runs the plates were dried and sprayed with Ninhydrin or Dansyl or with another reagent. . If at pH 1.9 the peptide(s) move to the cathode but not at pH 6,4 it is neutral (i.e. it has equal numbers of acidic and basic groups). If at pH 1.9 the peptide(s) move to the cathode and at pH 6.4 either the peptide is cationic (i.e. has more basic groups than acidic groups). If at pH 1.9 the peptide moves to the cathode and at pH 6.4 moves to the anode, the peptide is anionic (i.e. carries more acidic groups than basic ones. If at pH 1.9 the peptide(s) does not move, its aminoterminual group is blocked or the peptide is cyclics. Conditions for a 20 cm plate are 1000 V 45 min. For further details let me know
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