I am trying to compare the hydropathicity of 2 proteins belonging to the same family (about 75% identity). So far I have been using the ProtScale tool in Expasy with the Kyte & Doolittle scale, but one can only analyse one protein at a time. Is there any other tool that allows to align the 2 proteins and to show a graph of their aminoacids hydropathicity in the same plot? I want to do this because I am comparing the structures of the two proteins and I want to focus on the differing bits of the two structure and to highlight possible differences in these regions as hydropathicity.
Thanks!
Hi! you can also try ClustalW. you can copy several sequences and run all of them.
http://www.ebi.ac.uk/Tools/msa/clustalw2/
hope this will help you!
cheers,
Cris
It may worth having then a look by domain since minute changes at particular locations may drive significant secondary structure alterations. If available, examine local hydropathy changes with observed or calculated secondary structures.
If you can get an alignment, then you can use Jalview to color according to hydrophobicity. Jalview can export to many graphics formats. Jalview can be used as a standalone program and also on the web on many of the web-servers, such as ClustalW as mentioned by Cristina. You can use DALI, MultiProt or Matt to get a sequence alignment based on the two structures you have.
Try this tool: http://best.bio.jhu.edu/HePCaT/
It will optimally align the hydropathy data of multiple sequences by inserting gaps as appropriate. It is like doing a sequence alignment with the hydropathy values rather than amino acids as input. This tool was designed by Jamie Wrabl and Omar Hadzipasic in the lab of Vince Hilser at Johns Hopkins University.
AEP
Thank you all for your suggestion, they are all extremely helpful!
@ Stéphane: I did do what you suggested by exporting the verbose version of the hydrophaticity of my residues and than I aligned them in excel to build the graph. It does the job indeed, but it is a bit time consuming and so I was looking for some tools that would do it automatically
@ Ammon: thanks! this is the type of tool I was looking for! It would be even better if I could plot the secondary structure on the bottom of the graph to see where the changes are, as suggested by Olivier.
@ Petrus: DNASTAR looks promising too, I will install it and give that a go
Hey Matteo,
We have optimized a program for the alignment of membrane protein sequences incl. hydrophobicity by eiter using scales or membrane predictions. The program is called AlignMe and it is available as a web server: http://www.bioinfo.mpg.de/AlignMe/AlignMe.html
You can generate alignments using only hydrophobicity scales with the "fast" mode. An alignment is then generated using the scale from Hessa, White & vanHeinje which we found to be more accurate than the one of K&D. However, if you click on "Show detailed alignment parameters!" you can change the scale to any scale that you want to use. If you have any questions or issues with using the program then feel free to write us!
Best,
Marcus
@ Marcus: thanks a lot for your suggestion, the tool you have developed works really well! Cheers
Hello ! Kyte & Doolittle function for Excel (paste into a Visual Basic module) is below (of course, you can type in coefficients from some other hydrophobicity scale):
Function hphob(Segment As String)
'Mike and Steve 1-9-10 from VB
Static aa As String, ch$
Static Residue As String
Static MultiVal, KDVal
Static i%
NumKDH = 0: aa = ""
For i% = 1 To Len(Segment)
ch$ = Mid(Segment, i%, 1)
If InStr("ACDEFGHIKLMNQPRSTVWY", ch$) > 0 Then aa = aa & ch$
Next i%
MultiVal = 0
For i% = 1 To Len(aa)
Residue = Mid(aa, i%, 1)
GoSub GET_KD
MultiVal = MultiVal + KDVal
Next i%
hphob = Round(MultiVal / Len(aa), 3)
Exit Function
GET_KD:
Select Case Residue
Case "Ile", "I"
KDVal = 4.5
Case "Val", "V"
KDVal = 4.2
Case "Leu", "L"
KDVal = 3.8
Case "Phe", "F"
KDVal = 2.8
Case "Cys", "C"
KDVal = 2.5
Case "Met", "M"
KDVal = 1.9
Case "Ala", "A"
KDVal = 1.8
Case "Gly", "G"
KDVal = -0.4
Case "Thr", "T"
KDVal = -0.7
Case "Trp", "W"
KDVal = -0.9
Case "Ser", "S"
KDVal = -0.8
Case "Tyr", "Y"
KDVal = -1.3
Case "Pro", "P"
KDVal = -1.6
Case "His", "H"
KDVal = -3.2
Case "Glu", "E"
KDVal = -3.5
Case "Gln", "Q"
KDVal = -3.5
Case "Asp", "D"
KDVal = -3.5
Case "Asn", "N"
KDVal = -3.5
Case "Lys", "K"
KDVal = -3.9
Case "Arg", "R"
KDVal = -4.5
Case Else
End Select
Return
End Function
= = = = = =
If your one-letter sequence is in cell A1, typing "=hphob(A1)" into cell B1 displays the hydropathy there.
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