Protein-membrane systems

Here, F0id and Fnew are, respectively, the adsorption free energies of the "old" state (before the trial move) and "new" state of the protein-membrane system. If a trial move is accepted, the macromolecule is advanced to the "new" position, the CH equations for lipids are solved, and sampling of membrane deformations are performed for the newly accepted position of the adsorbate. If, on the other hand, the trial move is rejected, the protein remains at its previous position, and the same minimization step is conducted, only now with respect to the previous "old" location of the adsorbate. 

So far, we have discussed only simulations that employed simplified models of water-membrane systems. Other simulations have dealt with both interfacial and transmembrane peptides in real phospholipid bilayers. Due to limited computational resources, protein folding was not addressed in these simulations but, instead, the focus was on the short-term structural stability, orientation and dynamics of these peptides. Nevertheless, in many respects, these simulations offer a richer picture of protein-membrane systems by explicitly considering specific interactions between amino acids and lipid head groups and the effects associated with the inhomogeneous, ordered nature of the membrane environment. 

Ayton, G. S., Lyman, E., Voth, G. A. (2010). Hierarchical coarse-graining strategy for protein-membrane systems to access mesoscopic scales. Faraday Discuss, 144, 347. 

The high specificity required for the analysis of physiological fluids often necessitates the incorporation of permselective membranes between the sample and the sensor. A typical configuration is presented in Fig. 7, where the membrane system comprises three distinct layers. The outer membrane. A, which encounters the sample solution is indicated by the dashed lines. It most commonly serves to eliminate high molecular weight interferences, such as other enzymes and proteins. The substrate, S, and other small molecules are allowed to enter the enzyme layer, B, which typically consist of a gelatinous material or a porous solid support. The immobilized enzyme catalyzes the conversion of substrate, S, to product, P. The substrate, product or a cofactor may be the species detected electrochemically. In many cases the electrochemical sensor may be prone to interferences and a permselective membrane, C, is required. The response time and sensitivity of the enzyme electrode will depend on the rate of permeation through layers A, B and C the kinetics of enzymatic conversion as well as the charac-... 

Mooradian (1993) has studied the antioxidant properties of 14 steroids in a non-membranous system in which the fluorescence of the protein phycoerythrin was measured in the presence of a lipid peroxyl radical generator (ABAP). Oxidation of the protein produces a fluorescent species. Quenching of fluorescence by a test compound indicates antioxidant activity. Oestrone, testosterone, progesterone, androstenedione, dehydroepian-drosterone, cortisol, tetrahydrocortisone, deoxycorti-... 

The oscillations observed with artificial membranes, such as thick liquid membranes, lipid-doped filter, or bilayer lipid membranes indicate that the oscillation can occur even in the absence of the channel protein. The oscillations at artificial membranes are expected to provide fundamental information useful in elucidating the oscillation processes in living membrane systems. Since the oscillations may be attributed to the coupling occurring among interfacial charge transfer, interfacial adsorption, mass transfer, and chemical reactions, the processes are presumed to be simpler than the oscillation in biomembranes. Even in artificial oscillation systems, elementary reactions for the oscillation which have been verified experimentally are very few. 

Another practical limitation in complex applications lies in the fact that, if temperature is used as a control parameter, one needs to worry about the integrity of a system that is heated too much (e.g., water-membrane systems or a protein heated above its denaturation temperature). When issues such as those mentioned above are addressed, parallel tempering can be turned into a powerful and effective means of enhanced conformational sampling for free energies over a range of temperatures for various systems. 

The multilamellar bilayer structures that form spontaneously on adding water to solid- or liquid-phase phospholipids can be dispersed to form vesicular structures called liposomes. These are often employed in studies of bilayer properties and may be combined with membrane proteins to reconstitute functional membrane systems. A valuable technique for studying the properties of proteins inserted into bilayers employs a single bilayer lamella, also termed a black lipid membrane, formed across a small aperture in a thin partition between two aqueous compartments. Because pristine lipid bilayers have very low ion conductivities, the modifications of ion-conducting... 

Eukaryotic cells have evolved a complex, intracellular membrane organization. This organization is partially achieved by compartmentalization of cellular processes within specialized membrane-bounded organelles. Each organelle has a unique protein and lipid composition. This internal membrane system allows cells to perform two essential functions to sort and deliver fully processed membrane proteins, lipids and carbohydrates to specific intracellular compartments, the plasma membrane and the cell exterior, and to uptake macromolecules from the cell exterior (reviewed in [1,2]). Both processes are highly developed in cells of the nervous system, playing critical roles in the function and even survival of neurons and glia. 

The er is a three-dimensional membrane system (57-62). As visualized in a transmission electron microscope, there are two parallel membranes with an intervening electron transparent space, the lumen. The form and abundance of the er vary. The rer are flattened sacs with numerous attached ribosomes (15-20 nm). In contrast, the smooth er (ser) lacks ribosomes. The er seems to function as a communication system within cells and can be continuous with the outer nuclear envelope. Although the rer is involved in protein synthesis, the ser functions in glycosylation. 

In biological systems, one often observes membrane structures with nonzero spontaneous curvatures, e.g. in mitochondria. This type of bilayer structure is also essential in various transport related processes such as endo- and exocy-tosis (see Chapter 8 of this volume). These curved membrane systems may be stabilised by protein aggregation in the bilayer, or may be the result of the fact that biological membranes are constantly kept off-equilibrium by lipid transport and/or by (active) transport processes across the bilayer. These interesting... 

We have already described the plasma membrane systems employed in yeast for copper uptake, and here we briefly describe the chaperone proteins involved in the intracellular transport and delivery of copper to target proteins (Figure 8.10), which were first described... 

In some circumstances, it can be anticipated that continuous lifetime distributions would best account for the observed phenomena. Examples can be found in biological systems such as proteins, micellar systems and vesicles or membranes. If an a priori choice of the shape of the distribution (i.e. Gaussian, sum of two Gaussians, Lorentzian, sum of two Lorentzians, etc.) is made, a satisfactory fit of the experimental data will only indicate that the assumed distribution is compatible with the experimental data, but it will not demonstrate that this distribution is the only possible one, and that a sum of a few distinct exponentials should be rejected. 

Much of industrial chemistry takes place in organic solvents, or involves apolar compounds. Biocatalysis, in contrast, typically involves aqueous environments. Nevertheless, enzymes and microorganisms do in fact encounter apolar environments in Nature. Every cell is surrounded by at least one cell membrane, and more complex eukaryotic cells contain large amounts of intracellular membrane systems. These membranes consist of lipid bilayers into which many proteins are inserted present estimates, based on genomic information, are that about one-third of all proteins are membrane proteins, many of which are so-called intrinsic proteins that are intimately threaded through the apolar bilayer. These proteins are essentially dissolved in, and function partly within, an apolar phase. 

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