Membrane topology
Encyclopedia
In biochemistry
, the membrane topology of an transmembrane protein
describes which portions of the amino-acid
sequence of the protein lie within the plane of the surrounding lipid bilayer
and which portions protrude into the watery environment on either side. More succinctly, the membrane topology describes which regions of the polypeptide chain span the membrane.
of a gene
). Such predictions are most reliably based on the assumption that the lipid bilayer-spanning portions of a transmembrane protein will assume an alpha-helical
secondary structure
.
Since membrane topology is frequently the first available structural information about a protein after sequencing, integral membrane proteins are often classified or grouped according to this feature. In classifying proteins in this way, biologists look at the number of times the peptide chain is predicted to cross the membrane and may in fact name a class on this basis (e.g. "7TM receptors"
).
Membrane topology predictions also can be invaluable for developing antibodies, drugs or other reagents that will bind and/or affect the function of the protein.
Biochemistry
Biochemistry, sometimes called biological chemistry, is the study of chemical processes in living organisms, including, but not limited to, living matter. Biochemistry governs all living organisms and living processes...
, the membrane topology of an transmembrane protein
Transmembrane protein
A transmembrane protein is a protein that goes from one side of a membrane through to the other side of the membrane. Many TPs function as gateways or "loading docks" to deny or permit the transport of specific substances across the biological membrane, to get into the cell, or out of the cell as...
describes which portions of the amino-acid
Amino acid
Amino acids are molecules containing an amine group, a carboxylic acid group and a side-chain that varies between different amino acids. The key elements of an amino acid are carbon, hydrogen, oxygen, and nitrogen...
sequence of the protein lie within the plane of the surrounding lipid bilayer
Lipid bilayer
The lipid bilayer is a thin membrane made of two layers of lipid molecules. These membranes are flat sheets that form a continuous barrier around cells. The cell membrane of almost all living organisms and many viruses are made of a lipid bilayer, as are the membranes surrounding the cell nucleus...
and which portions protrude into the watery environment on either side. More succinctly, the membrane topology describes which regions of the polypeptide chain span the membrane.
Description
Because biochemists know the hydrophobicity of amino acids individually, the membrane topology of a protein (and indeed whether or not it is an integral membrane protein in the first place) often may be predicted accurately on the basis of a protein's sequence alone (which of course in turn may be predicted solely from the nucleotide sequenceDNA sequence
The sequence or primary structure of a nucleic acid is the composition of atoms that make up the nucleic acid and the chemical bonds that bond those atoms. Because nucleic acids, such as DNA and RNA, are unbranched polymers, this specification is equivalent to specifying the sequence of...
of a gene
Gene
A gene is a molecular unit of heredity of a living organism. It is a name given to some stretches of DNA and RNA that code for a type of protein or for an RNA chain that has a function in the organism. Living beings depend on genes, as they specify all proteins and functional RNA chains...
). Such predictions are most reliably based on the assumption that the lipid bilayer-spanning portions of a transmembrane protein will assume an alpha-helical
Transmembrane helix
Transmembrane domain usually denotes a single transmembrane alpha helix of a transmembrane protein. It is called a "domain" because an alpha-helix in a membrane can fold independently from the rest of the protein, similar to domains of water-soluble proteins...
secondary structure
Secondary structure
In biochemistry and structural biology, secondary structure is the general three-dimensional form of local segments of biopolymers such as proteins and nucleic acids...
.
Since membrane topology is frequently the first available structural information about a protein after sequencing, integral membrane proteins are often classified or grouped according to this feature. In classifying proteins in this way, biologists look at the number of times the peptide chain is predicted to cross the membrane and may in fact name a class on this basis (e.g. "7TM receptors"
G protein-coupled receptor
G protein-coupled receptors , also known as seven-transmembrane domain receptors, 7TM receptors, heptahelical receptors, serpentine receptor, and G protein-linked receptors , comprise a large protein family of transmembrane receptors that sense molecules outside the cell and activate inside signal...
).
Membrane topology predictions also can be invaluable for developing antibodies, drugs or other reagents that will bind and/or affect the function of the protein.