Question: Lipid-Protein Interaction
5
gravatar for Pratheep
5.5 years ago by
Pratheep120
Pratheep120 wrote:

Hi to all, How to identify the lipid binding region (amino acid residues) in the protein? Any specialized online/commercial tools is there.

protein structure docking • 5.1k views
ADD COMMENTlink modified 2.6 years ago by Biostar ♦♦ 20 • written 5.5 years ago by Pratheep120
9
gravatar for Larry_Parnell
5.5 years ago by
Larry_Parnell15k
Boston, MA USA
Larry_Parnell15k wrote:

You can try CGDB - a database of membrane protein/lipid interactions. You can also try the predictive algorithm for lipid-binding sites using three-dimensional structural data, described by Scott, et al.

It would be of interest to you to read "The Human Plasma Lipidome" by Quehenberger and Dennis in N Engl J Med 365:1812-23. This paper gives a hint as to the complexity of the issue of protein-lipid binding. Figure 5 shows "For example, in the eicosanoid biosynthetic pathways, 28 known genes and their corresponding enzymatic gene products are responsible for the production of more than 150 bioactive lipids derived from dihomo-gamma-linolenic acid (20:3), arachidonic acid (20:4), eicosapentaenoic acid (20:5), and docosahexaenoic acid (22:6), of which 76 have been detected in normal human plasma." This implies that enzymatic pathways will be very helpful to you, but so will lipid transporters as many lipids are breakdown products of gut bacteria.

ADD COMMENTlink modified 5.5 years ago • written 5.5 years ago by Larry_Parnell15k
5
gravatar for Neilfws
5.5 years ago by
Neilfws47k
Sydney, Australia
Neilfws47k wrote:

You could start at PFAM, do a keyword search for "lipid-binding", then download appropriate domain models and use them to search your sequence(s) using HMMER.

ADD COMMENTlink written 5.5 years ago by Neilfws47k
4
gravatar for Paul
5.4 years ago by
Paul40
Paul40 wrote:

The web-server heliquest (http://heliquest.ipmc.cnrs.fr/) might be of use.

I found the following papers making use of this web-server with the focus on the search for (helical) lipid binding regions:

Keller RCA (2011) The prediction of novel multiple lipid-binding regions in protein translocation motor proteins: a possible general feature. Cell Mol Biol Lett. 16(1):40-54. Keller RCA (2011) New user-friendly approach to obtain an eisenberg plot and its use as a practical tool in protein sequence analysis. Int J Mol Sci. 12(9):5577-91.

Good luck!

ADD COMMENTlink written 5.4 years ago by Paul40
1
gravatar for Paul
4.6 years ago by
Paul10
Paul10 wrote:

See also the following blog:

paul2reach.blog.com

Good luck!

ADD COMMENTlink modified 4.6 years ago • written 4.6 years ago by Paul10
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