[Me_123]

Hello everyone 

The question is:

"Explain where the positive and negative amino acids are located (inside or outside) in a transmembrane helix. Your answer has to be based on the characteristics of the structure of membranes and the structure of an α-helix. "

I know that membranes have hydrofilic heads and hydrophobic tails. I also know that a transmembrane helix has it's hydrophobic amino acids on the outside of the helix. But I don't understand what positive or negative amino acids are and how you're supposed to know where they're located.

I'm sorry for any grammatical mistakes or language errors, but English isn't my native language.

[Yggdrasil]

Positively-charged amino acids are the basic amino acids that get protonated at physiological pH and acquire a positive charge (such as lysine, arginine, and sometimes histidine).  Negatively-charged amino acids are the acidic amino acids that get deprotonated at physiological pH and acquire a negative charge (such as aspartate and glutamate).

You are also correct that the side-chains of an alpha helix point outwards from the alpha helix.

[Me_123]

Okay, I get what positive and negative amino acids are.. But how are they located in a transmembrane helix? Which ones are on the outside and which ones are on the inside of the transmembrane helix?

The hydrofilic amino acids will be on the inside and the hydrophobic amino acids will be on the outside. But I don't know which amino acids (positive or negative) are hydrophobic?

My guess is that a positive amino acid is hydrofilic, because it "gains" a proton and it will be able to interact with water. A negative amino acid will lose a proton, so it isn't able to interact with water anymore?

So the positive amino acids will be on the inside and the negative amino acids will be on the outside, am I right?

[Me_123]

I think I'm wrong, no? Because amino acids with a charge are always hydrofilic? But I don't know what else it could be...

[Arkcon]

Try also to consider what amino acids side chans will be needed to insure the transmembrane protein is in a stable conformation in its environment.  You already defined the membrane as a bilayer of hydrophillic heads and hydrophobic tails.  Try to consider what residues will need to be where in the protein than spans the membrane.

[Me_123]

I really have no idea.. Something with hydrogen bonds?

[Me_123]

Or maybe this is the answer:

phospholipids with a negative charge are located in the intracellular side of the membrane. The phospholipids with a positive charge are on the extracellular side of the membrane.
So, positive amino acids will be needed on the outside of the transmembrane protein to insure a stable conformation?

[Babcock_Hall]

me_123, I may be interpreting this problem a little bit differently from other commenters.  This question might be referring to a transmembrane helix within a protein with multiple transmembrane helices.  If so, then "inside or outside" would correspond to the interior and exterior of the protein, respectively, and the exterior of the protein would be the portion facing the membrane.  Is there any way that you could ask for clarification about whether this problem refers to a protein with a single transmembrane helix or multiple transmembrane helices?

[Me_123]

Hello Babcock_Hall,

I think it refers to a protein with a single transmembrane helix..  But I still have no idea what the answer should be   

[Arkcon]

You should definitely start with the amino acid sequence needed to form an alpha helix.  You should also identify what the environment of the transmembrane protein actually is.  These are definitions, and you can look them up in your text book.  Once you start writing it out (right here where we can see it) more things may come to you, or we might offer you some hints or corrections.

[Babcock_Hall]

I would agree with the statement that charged amino acid side chains are hydrophilic, and amino acids with H-bond donors and acceptors are also hydrophilic.  There are several reasonable hints in the thread.  What don't you understand at this point?

[Me_123]

The only thing mentioned in my text book about transmembrane helices is that the hydrophobic amino acids are located on the outside.

The question was :
"Explain where the positive and negative amino acids are located (inside or outside) in a transmembrane helix. Your answer has to be based on the characteristics of the structure of membranes and the structure of an α-helix. "

Positive and negative amino acids are charged, so they are hydrophilic? So, both of these kind amino acids should be on the inside of the transmembrane helix, but apparently one has to be on the inside and the other should be on the outside, so that's something I don't understand, because something that's hydrophilic can't react with something that's hydrophobic, no?


The membrane is defined as a bilayer of hydrophillic heads and hydrophobic tails. So the environment of the transmembrane protein is hydrophobic?

And to answer the question about what amino acid sequence is needed to form an alpha helix, I'm not sure what you mean. The  carbonyl group of the peptide bound forms a hydrogen bond with the amino group of a amino acid that is located 4 places further. This is how an alpha helix is formed?

The only thing I can think of is this (what I already said) :
phospholipids with a negative charge are located in the intracellular side of the membrane. The phospholipids with a positive charge are on the extracellular side of the membrane.
So, positive amino acids will be needed on the outside of the transmembrane protein to insure a stable conformation?

I hope it's clear for you. It's very hard to express myself in a language that isn't my native language.
 

[Babcock_Hall]

The only thing mentioned in my text book about transmembrane helices is that the hydrophobic amino acids are located on the outside.

I don't think that the statement above sounds correct.  I will assume that "inside" means on or near the cytoplasmic face of the bilayer and outside means on or near the extracellular face (in other words, that my previous interpretation of the question was wrong).  If that interpretation is correct, then what you wrote earlier ("phospholipids with a negative charge are located in the intracellular side of the membrane. The phospholipids with a positive charge are on the extracellular side of the membrane.") is on the right track.  There is more phosphatidylserine on the inside leaflet of the membrand than the outside, for instance.  Do you know of any specific examples of proteins that have a single TM helix, and if so, have you looked at their sequence.



   

[Me_123]

I've looked up some proteins with a single TM helix, and I think I've come up with a new explanation:


The part of the transmembrane helix which is located in the membrane itself is hydrophobic. Two parts of the transmembrane helix stick out of the membrane, one part to the intracellular side and the other part to the extracellular side. These two parts are hydrophilic, so they are able to "carry" amino acids with a charge. In an alpha helix, there are hydrogen bonds which all point in the same direction, so we have a dipole moment: a positive N-terminus and a negative C-terminus. To compensate this, the amino acids with a negative charge will be on the N-terminus side and the amino acids with a positive charge will be on the C-terminus side.

[Babcock_Hall]

Glycophorin is one protein you may already have looked up.  I think that there is at least one explanation besides the dipole of the alpha helix itself that may be important.  Phospholipids with a head group bearing a net negative charge (PS and phosphatidylinositol) are in the inner leaflet of the plasma membrane.  Phospholipids bearing one negative and one positive charge (PC and sphingomyelin) are found in the outer leaflet.  The proteins have residues, at least some of which extend beyond the alpha-helix, which tend to be complementary: positively charged residues facing the cytoplasm, and negatively charged residues facing the exterior of the cell.  Your explanation might be falsified by examining both Type I (N terminal outside) and Type II (N terminal inside) integral membrane proteins.  Glycophorin is a Type I protein, but I don't have a Type II handy.  Our models make opposite predictions for what to expect in a Type II protein.