Integral membrane proteins, those that are embedded in the membrane bilayer, med

Question

Integral membrane proteins, those that are embedded in the membrane bilayer, mediate cellular communication, and solute transport across the plasma membrane.

a. How is the amino acid distribution of integral membrane proteins different to that of soluble proteins? Compare and Contrast.

b. One method of predicting the presence of transmembrane (TM) segments in integral membrane proteins involves the identification of 20 residue segments that have high hydrophobicity. Bioinformatics analysis has shown that such an analysis is capable of identifying possible TM segments with high accuracy when it is known that the protein is an integral membrane protein. However, the presence of a 20 residue hydrophobic segment is not a predictor of a protein being an integral membrane protein versus a soluble protein. Explain these seemingly contradictory observations.

c. Almost all of the known structures of membrane proteins contain either -helical transmembrane segments, or -strand TM segments that form -barrels. Membrane protein do not tend to contain transmembrane segments that lack secondary structure. Why don’t the transmembrane segments of membrane proteins contain unstructured regions (i.e. why are -helices and -barrels the predominant structures of membrane proteins)?

Explanation / Answer

An integral membrane protein (IMP) is a type of membrane protein that is permanently attached to the biological membrane. All transmembrane proteins are IMPs, but not all IMPs are transmembrane proteins. They are composed of the same 20 amino acids found in soluble proteins. Membrane proteins are either buried into the membrane or anchored on the outer part of the membrane. The buried proteins have their hydrophobic amino acids interact with the membrane while the anchored proteins have some linker lipid molecule attached to the protein.

Soluble proteins are present in the cytoplasm and other organelles like mitochondria and the nucleus. Their outer part contains hydrophilic amino acids which interact with the solvent and help solubilize the protein. The hydrophobic amino acids are buried deep inside the protein.

It was discovered very early on that the presence of stretches of hydrophobic residues in a protein sequence is a good indicator that this sequence encodes a membrane protein [6]. Because most transmembrane helices are hydrophobic, they appear as periodic stretches of non-polar amino acids of length 17–25 in the primary sequence. These stretches of hydrophobic residues cross the lipid membrane multiple times, and are connected by loops containing more polar residues. Such periodicity of hydrophobicity can be easily detected, and early methods for membrane protein prediction were based on calculation of a hydrophobicity index of residues within a window sliding along the protein sequence.

Predicting -barrel membrane proteins is more challenging. Although residues facing the lipid membrane are predominantly hydrophobic, those facing the interior of the barrel can be quite polar. Unlike helical membrane proteins, there are no clear stretches of hydrophobic residues in their primary sequences.

The topology of a membrane protein refers to the number of transmembrane segments and the sidedness of the terminal ends of the protein, namely, whether the N- and C-end are on the non-translocated side or on the translocated side.

For -barrel membrane proteins, there are several characteristic observations that can help to determine their topology. First, the periplasmic loops are always short compared to extracellular loops, although this may not be true for mitochondrial and chloroplast outer membrane proteins. Second, there is a significant, albeit less dramatic bias in the topological sidedness of the distribution of charged residues. Different from the “positive-inside” rule for helical membrane proteins, there exists an overall “positive-outside” distribution. The extracellular cap region of the -barrel membrane proteins is disproportionately enriched with positively charged Arg and Lys, which are disfavored in the periplasmic cap region. This is likely due to the asymmetric distribution of the two leaflets of the lipid bilayer, in which negatively charged lipopolysaccharides (LPS) are enriched in the outer-leaflet of the outer membrane.

The two kinds of transmembrane proteins are alpha-helical and beta-barrels. Most of the amino acid sidechains of transmembrane segments must be non-polar (e.g. Ala, Val, Leu, Ile, Phe). Second, the very polar CONH groups (peptide bonds) of the polypeptide backbone of transmembrane segments must participate in hydrogen bonds (H-bonds) in order to lower the cost of transferring them into the hydrocarbon interior. This H-bonding is most easily accomplished with alpha-helices for which all peptide bonds are H-bonded internally. It can also be accomplished with beta-sheets provided that the beta-strands form closed structures such as the beta-barrel. All membrane proteins of known three-dimensional structure adhere to these principles.

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