Hi all,
A quick question for structural biologists, how do we determine if a region is hydrophobic or hydrophilic region? Is there a measurement that we can do once the structure is available? or do people gauge that by looking at the neighboring amino acids? I am trying to find a binding site of a ligand to this protein. I am curious what kind of electrostatic characteristics this binding site may have.
Thanks!
Cece
Display the protein 3D structure using any of the publicly available graphics software out there. Click on "surface properties" (or an equivalent button). The patches of surface that appear in red (usually) are have a net positive charge, and those that appear in blue have a net negative charge. But remember, the protein surface is in general hydrophilic overall, and the protein interior is generally hydrophobic, as this is how most proteins fold -- except for membrane proteins, in which the reverse is generally true.
Hi Cece, this should be a relatively easy assay. If the protein fragments aggregate in in water then they are hydrophobic. If they stay in solution in saline then they are hydrophilic
Dear
You have to evaluate values for the residues. Check the sequence if available and determine the site of Trp and Tyr. So Trp and tyr are considered as hydrophobic.
Please check some links:
http://www.vivo.colostate.edu/molkit/hydropathy/scales.html
http://web.expasy.org/protscale/
http://www.ibi.vu.nl/programs/scoobywww/
In Pymol, I use the following coloring scheme:
color white, all
color orange, resn Tyr+Phe+Trp
color yellow, resn Leu+Ile+Val+Met+Pro+Ala+Cys
color green, resn Asn+Gln+Ser+Thr+Gly
color cyan, resn His
color blue, resn Arg+Lys
color red, resn Asp+Glu (you might also color these blue too if you want purely hydrophobicity coloring rather than emphasizing charge interactions at the same time)
show spheres, polymer
show sticks, not polymer
Hydrophobic regions show as yellow/orange patches ("dry desert" colors, hydrophobic) on the protein surface, hydrophilic regions as green and blue ("wet, watery" colors, hydrophilic). I use the same color scheme to color sequence alignments
Hi Annemarie, I'm not sure if I understand your color map. Is it based on pbd structures?
Where do the N- and C-termini fit in?. How can His be define a color? Based on the enzyme in question it can either be a proton donor or a proton acceptor. Ser and Cys should nor be the same color because of their different properties in Ser and Cys proteinases.
I can understand your point if you are knitting sweaters, but here in the real world it is different,.
This is a pymol script. Pymol is a structure visualization program that is free for educational use. You load any pdb structure into the program. You can then either copy and paste the commands into the command line or put the commands in a text file and run it as a script. Another script colors a sequence alignment in Excl according to the same coloring scheme: http://www.bioc.uzh.ch/plueckthun/antibody/Macros/Macros/AA_Type.html
This is a quick-and-dirty way to look at the distribution of different amino acid types in the sequence alignment and on the protein surface. His is given a color (cyan) between dark blue (positively charged) and green (neutral hydrophilic) exactly because you cannot tell its charge without knowing the pH (and electrostatic environment). While you can add charge color to the apparent termini in a pdb, most structures have disordered residues at the termini, therefore coloring the fist and last visible residue in the structure as psitively and negatively charged would be wrong.
In the real word you can't stuff too much information into a single visualization, however, this coloring scheme works well for quickly seeing whether you have significant hydrophobic patches or marked charged patches in a molecule
It's one of many coloring schemes I use, depending on the feature I want to show in a specific figure. Indeed other coloring schemes highlight charges only, or structural properties, or per-residue energies in rosetta.
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