Membrane proteins description

An important approach to the study of biological membranes has been the preparation and study of model membranes. According to current usage, model membranes include lipid bilayers and lipid bilayers into which have been incorporated additional components such as one or more membrane proteins. It is through the study of such model membranes that one has the best opportunity to isolate and study fundamental physical chemical and biophysical processes, and it is for this reason that the present report emphasizes these systems. A discussion of model membranes necessarily starts with a description of the chemical compositions and physical properties of lipid molecules. 

Standard molecular mechanics (MM) force fields have been developed that provide a good description of protein structure and dynamics,21 but they cannot be used to model chemical reactions. Molecular dynamics simulations are very important in simulations of protein folding and unfolding,22 an area in which they complement experiments and aid in interpretation of experimental data.23 Molecular dynamics simulations are also important in drug design applications,24 and particularly in studies of protein conformational changes,25,26 simulations of the structure and function of ion channels and other membrane proteins,27-29 and in studies of biological macromolecular assemblies such as F-l-ATPase.30... 

Thermodynamic measurements will, in the end, provide the quantitative descriptions of the atomic interactions needed for computational predictions of membrane proteins. With membrane proteins, of course, these interactions must include all the interactions among the water,... 

A hydrophobic mismatch between a membrane protein and the surrounding lipids may create a lateral force that would pull membrane proteins together. A general theoretical description of this force, referred to as a lateral capillary force, has been presented by Kralchevsky and co-workers (Kralchevsky, 1997 Kralchevsky and Nagayama, 2000). Although experimental verification of this force for membrane proteins in a bilayer has not been demonstrated, the force can be observed in larger systems, such as 1.7 fim latex beads at an air/water interface, and would be expected to operate on membrane proteins (Kralchevsky, 1997). 

In the popular fluid mosaic model for biomembranes, membrane proteins and other membrane-embedded molecules are in a two-dimensional fluid formed by the phospholipids. Such a fluid state allows free motion of constituents within the membrane bilayer and is extremely important for membrane function. The term "membrane fluidity" is a general concept, which refers to the ease of motion for molecules in the highly anisotropic membrane environment. We give a brief description of physical parameters associated with membrane fluidity, such as rotational and translational diffusion rates, order parameters etc., and review physical methods used for their determination. We also show limitations of the fluid mosaic model and discuss recent developments in membrane science that pertain to fluidity, such as evidence for compartmentalization of the biomembrane by the cell cytoskeleton. 

The retinal proteins of halobacteria constitute a unique set of light energy transduction devices, based on similar chemistry but designed to perform different functions. The contributions of bacteriorhodopsin to our understanding of the structure and function of membrane proteins have been, and will no doubt continue to be, spectacular. As descriptions of the properties of the other two halobacterial retinal pigments are now becoming available, they promise to provide further insights into how membrane proteins function. 

Two data bases of soluble proteins of known structure used to find false positive prediction results (Table I and Table II). Gaussian parameters needed for evaluation of preference functions based on the Kyte-Doolittle hydropathy scale [17] (Table III). Table with detailed prediction results for transmembrane helices in 168 integral membrane proteins (Table IV). Table with a detailed comparison of prediction results for 10 best known membrane proteins for our and three other algorithms (Table V). All these tables together with the FORTRAN 77 source code are available from the anonymous ftp server mia.os.camet.hr in the /pub/pssp directory. The anonymous login is ftp and the e-mail address is accepted as password. The list of files with short descriptions is contained in the 00index.txt file. 

Fig. 15.14. Fate of proteins synthesized on the RER. Proteins synthesized on ribosomes attached to the ER travel in vesicles to the cis face of the Golgi complex. After the membranes fuse, the proteins enter the Golgi complex. Structural features of the proteins determine their fate. Some remain in the Golgi complex, and some return to the RER. Others bud from the trans face of the Golgi complex in vesicles. These vesicles can become lyso-somes or secretory vesicles, depending on their contents. Secretory proteins are released from the cell when secretory vesicles fuse with the cell membrane (exocytosis). Proteins with hydrophobic regions embedded in the membrane of secretory vesicles become cell membrane proteins. See Chapter 10 for descriptions of the endoplasmic reticulum, Golgi complex, lysosomes, and the cell membrane, and also for an explanation of the process of exocytosis.

A very simple and informative description of helices is provided by drawing a wheel. One looks from the NH2 end and displaces neighboring amino acids by exactly 100°, (e.g., Gly 1 and He 2 in melittin) (Fig, 9.2.7) (Juvvadi et al., 1996). One thus obtains an alignment of the amino acids along the circumference of the total helix. In membrane proteins, such as melittin, one often obtains circumferences where one side is hydrophobic or membrane oriented and the other side is hydrophilic or prone to domain and water-filled pore formation in membranes. 

Thus, utilizing Figure 8.26, the initial description of structure becomes enumeration of the constituent protein subunits and their number of repetitions given as a subscript for each of the four structural components (1) The membranous protein subunits are the 10 repeats of protein subunit c, that is, Cio. (2) The motor housing for the membranous rotor utilizes the a protein subunit in combination with the lipid bilayer. (3) The extramembranous rotor is comprised of the Y and e protein subunits. (4) The motor housing for the extramembranous rotor utilizes three a and three P protein subunits. (5) The stator component for interlocking the two motor housings utilizes two b protein subunits in combination with the 5 protein subunit. 

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