Net charge: Difference between revisions

(6 intermediate revisions by 2 users not shown)

Line 1:

In a solution of a given pH, a protein will have a negative or positive net charge dependent on the pKa values of the acidic and basic groups of the ~~constiuent~~ amino acids. The [[isoelectric point]], or pI, is the pH at which a protein has zero net charge. When the pH is higher than the isoelectric point, the protein has negative net charge, and when lower, positive net charge.

In a solution of a given pH, a protein will have a negative or positive net charge dependent on the pKa values of the acidic and basic groups of the constituent amino acids. The [[isoelectric point]], or pI, is the pH at which a protein has zero net charge. When the pH is higher than the isoelectric point, the protein has negative net charge, and when lower, positive net charge.

<br>You can calculate the net charge of your protein easily at a given pH or over a range:

==~~Calculating Net Charge Using~~ Protein Calculator==

==Protein Calculator==

#In Proteopedia, find the page for your structure named for PDB file code and click on [http://www.ebi.ac.uk/msd-srv/oca/oca-bin/ocamain OCA] under the structure.

#First, get the one-letter amino acid sequence of your protein of interest.

# At your PDB code in OCA, scroll down to Sequence-derived information (near the bottom).

##See the [[Isoelectric point|Isoelectric point page]] for some methods.

#Click on the link for the one-letter amino acid sequence for one chain.

##Or for a protein that has a 3D structure in Proteopedia, find the page for your structure named for PDB file code and click on [http://www.ebi.ac.uk/msd-srv/oca/oca-bin/ocamain OCA] under the structure.

#Copy the sequence and paste it into the large box at Christopher Putnam's [http://~~www~~.~~scripps~~.~~edu~~/~~~cdputnam/protcalc.html~~ Protein Calculator].

### At your PDB code in OCA, scroll down to Sequence-derived information (near the bottom).

#~~Choose your options in or near~~ the ~~second or third check boxes~~ box under Charge at the right, and click Submit Query.

###Click on the link for the one-letter amino acid sequence for one chain.

#Copy the sequence and paste it into the large box at Christopher Putnam's [http://protcalc.sourceforge.net/ Protein Calculator].

#Check the first box under Charge at the right, and click Submit Query.

==Prot-pi==

"Prot pi | Protein Tool calculates isoelectric point and net charge of proteins, as well as the exact mass and the absorption coefficient using the amino acid sequence."

*Go to [https://www.protpi.ch/Calculator/ProteinTool Prot-pi]] and follow instructions.

==See Also==

*[[Isoelectric point]]

*[[Monovalent Cation Binding in Cubic Insulin Crystals~~|9ins~~]]

*[[9ins|Monovalent Cation Binding in Cubic Insulin Crystals]]

==Content Attribution==

The calculation method was adapted from [http://www.umass.edu/molvis/workshop/osaka09m.htm a class syllabus taught by Eric Martz].

[[Category:Topic Page]]

Net charge: Difference between revisions

Navigation menu

Page actions

Page actions

Personal tools

Navigation

Search

Tools

@@ Line 1: / Line 1: @@
-In a solution of a given pH, a protein will have a negative or positive net charge dependent on the pKa values of the acidic and basic groups of the constiuent amino acids. The [[isoelectric point]], or pI, is the pH at which a protein has zero net charge. When the pH is higher than the isoelectric point, the protein has negative net charge, and when lower, positive net charge.
+In a solution of a given pH, a protein will have a negative or positive net charge dependent on the pKa values of the acidic and basic groups of the constituent amino acids. The [[isoelectric point]], or pI, is the pH at which a protein has zero net charge. When the pH is higher than the isoelectric point, the protein has negative net charge, and when lower, positive net charge.
 <br>You can calculate the net charge of your protein easily at a given pH or over a range:
-==Calculating Net Charge Using Protein Calculator==
+==Protein Calculator==
-#In Proteopedia, find the page for your structure named for PDB file code and click on [http://www.ebi.ac.uk/msd-srv/oca/oca-bin/ocamain OCA] under the structure.
+#First, get the one-letter amino acid sequence of your protein of interest.
-# At your PDB code in OCA, scroll down to Sequence-derived information (near the bottom).
+##See the [[Isoelectric point|Isoelectric point page]] for some methods.
-#Click on the link for the one-letter amino acid sequence for one chain.
+##Or for a protein that has a 3D structure in Proteopedia, find the page for your structure named for PDB file code and click on [http://www.ebi.ac.uk/msd-srv/oca/oca-bin/ocamain OCA] under the structure.
-#Copy the sequence and paste it into the large box at Christopher Putnam's [http://www.scripps.edu/~cdputnam/protcalc.html Protein Calculator].
+### At your PDB code in OCA, scroll down to Sequence-derived information (near the bottom).
-#Choose your options in or near the second or third check boxes box under Charge at the right, and click Submit Query.
+###Click on the link for the one-letter amino acid sequence for one chain.
+#Copy the sequence and paste it into the large box at Christopher Putnam's [http://protcalc.sourceforge.net/ Protein Calculator].
+#Check the first box under Charge at the right, and click Submit Query.
+==Prot-pi==
+"Prot pi | Protein Tool calculates isoelectric point and net charge of proteins, as well as the exact mass and the absorption coefficient using the amino acid sequence."
+*Go to [https://www.protpi.ch/Calculator/ProteinTool Prot-pi]] and follow instructions.
 ==See Also==
 *[[Isoelectric point]]
-*[[Monovalent Cation Binding in Cubic Insulin Crystals|9ins]]
+*[[9ins|Monovalent Cation Binding in Cubic Insulin Crystals]]
 ==Content Attribution==
 The calculation method was adapted from [http://www.umass.edu/molvis/workshop/osaka09m.htm a class syllabus taught by Eric Martz].
+[[Category:Topic Page]]