- picture X-ray crystal structures of membrane proteins

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- picture X-ray crystal structures of membrane proteins
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bet | 10/13 | Sana | 16.05.2024 | Hajmi | 1,48 Mb. | | #237391 |
Bog'liq Structure and function of biological membranes.2.3 1- picture X-ray crystal structures of membrane proteins.
Electron microscopy can also be used to study membrane protein structure. By freezing membrane proteins in their natural lipid environments, it is possible to investigate their structure using high-resolution electron microscopy. This provides a snapshot of the naturally occurring conformation of individual proteins in the bilayer.
Interactions between lipids and proteins in biological membranes
The lipids that surround membrane proteins in biological membranes play an important role in the activity of these proteins. As was mentioned earlier, some membrane protein crystal structures include lipids bound to the outside surface of the transmembrane domains of the proteins. It is thought that these lipids bind tightly to the protein, and have a long-lived interaction with the transmembrane region. In other cases, lipids are thought to interact briefly with membrane proteins, rapidly moving away and being replaced by other membrane lipids. The activity of membrane proteins is considered to be dependent to some extent on the lipids that surround them in the membrane. Certain types of K+ channel are thought to bind to negatively charged membrane lipids, as the activity of these channels increases at higher anionic lipid concentrations. These types of interaction can be studied by placing a purified form of the protein of interest in an artificial bilayer and measuring its activity. By altering the types of lipid present in the artificial bilayer, deductions can be made about the lipids that the protein requires in order to be active. Fluorescence spectroscopy and electron spin resonance are two techniques that are used to measure how strongly membrane proteins interact with specific lipids around them.
Molecular dynamics simulations use computer algorithms to work through theoretical problems. These simulated experiments are useful for investigating interactions between membrane proteins and lipids, as in real membranes these interactions are often so fleeting that they are very difficult to measure. Molecular dynamics simulations have predicted that in the case of the nicotinic acetylcholine receptor, the negatively charged lipid, phosphatidic acid, is required for activity. These simulations have also shown that cholesterol stabilizes the receptor and that the phosphatidic acid forms a shell around the protein which is more long-lasting than the interactions with other membrane lipids. Although molecular dynamics simulations are extremely useful, they are limited by the assumptions and approximations on which they are based. As in many areas of biology, a combination of experimental and computational research is required if real progress is to be made in understanding the complexity of biological membranes.
Inside the plasma membrane that surrounds eukaryotic cells lie many other membranes which define the intracellular compartments, or organelles. Each of these organelles has distinct functions and contains specific complements of proteins adapted for these roles. With the exception of a few proteins that are coded for by the mitochondrial genome, synthesis of all of the proteins that are required in these organelles begins on ribosomes in the cytoplasm, and therefore the proteins must be directed to the correct destination. We have seen earlier how this is achieved with membrane proteins, and most organelles have some kind of signal sequence that can be recognized by various receptors and which ensures that the protein arrives at the correct organelle.
Organelles have distinct lipid compositions
Besides the specific protein complement of each organelle, the lipid make-up of the bilayers surrounding organelles varies. Lipids are synthesized in the ER, and flippases move lipid molecules between leaflets of the bilayer. For organelles in the secretory pathway and the plasma membrane, lipid transport into these compartments is mediated by vesicular membrane traffic through the pathway. The cholesterol concentration in membranes increases from the ER through the Golgi to the plasma membrane. Cholesterol makes membranes thicker and more rigid, so the low levels of cholesterol in the ER membrane render it thin and facilitate the insertion of newly synthesized membrane and secretory proteins. PC becomes relatively less abundant through this pathway, with more found in the ER than at the plasma membrane. PS and PE are found throughout the secretory pathway in the cytosolic leaflet of the membranes. This differential lipid composition through the secretory pathway is achieved by targeting specific lipids into transport vesicles. Proteins included in these vesicles act as labels and direct the lipids to the right compartment. Forward-moving (anterograde) vesicles destined for the plasma membrane are rich in cholesterol. Lipids also move backwards through the secretory pathway, from the plasma membrane towards the ER. This is known as retrograde traffic. Retrograde vesicles from the Golgi are enriched in lipids such as PC, which are concentrated in the ER.
The lipid composition of the mitochondria is very different from that of the secretory pathway compartments. Mitochondrial membranes are much richer in PE and cardiolipin than is the ER. Cardiolipin is synthesized in the mitochondria and is predominantly confined to this organelle. As membrane proteins have evolved along with their organelles and surrounding lipids, it follows that different lipid compositions are required in different organelles for the optimum activity of the proteins within their membranes. The structure of the ADP/ATP carrier in mitochondria has been solved and was found to include cardiolipin and PC molecules bound to the protein. The activity of this carrier protein is dependent on the presence of cardiolipin, which is relatively abundant in mitochondrial membranes.
Proteins must be targeted to the correct organelle for cells to function
The targeting of newly synthesized membrane and secretory proteins to the ER has already been briefly discussed. However, there are many different destinations within the cell to which a protein can be sent, and sometimes proteins are located in more than one of these. The signals and protein machinery that are required to target proteins to the correct compartment are many and various, and much of the detail of the exact mechanisms involved has yet to be clarified.
Vesicular transport
Traffic through the secretory pathway is by vesicular transport in both anterograde and retrograde directions. Proteins and lipids can be included and excluded from vesicles by various means in order to selectively determine which molecules move forward or backward through the pathway. Vesicles are coated with proteins that determine their destination. Generally these coat proteins (COPs) are directional—COPII coats anterograde vesicles, and COPI coats retrograde vesicles. Proteins that travel in vesicles (referred to as cargo) are selected either by interacting with receptors in the vesicles or by directly interacting with the coat proteins. The selection of cargo occurs at the budding stage, when the coat proteins begin to distort the donor membrane (e.g. the ER) into a vesicle. Once the cargo has been selected and the coat proteins have been assembled, the vesicle buds off and travels to the acceptor membrane (e.g. the Golgi in the case of COPII vesicles from the ER) either by diffusion or with the help of motor proteins that ‘walk’ the vesicle along the cytoskeleton. The vesicle then fuses with the acceptor membrane, depositing its cargo and constituent lipids.
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