Membrane-like environments

The structures calculated in a membrane-like environment agree with the experimental ones. 

A detailed understanding of the transport of the linear gramicidins requires not only the structure of the channel but also a knowledge of channel properties. The dependence of channel properties on the amino acid residues, position in the sequence and side-chain orientation, have been used to assist in elucidating the molecular mechanism of ion transport through the channel. The side-chains are important contributors to the formation and stability of the channel in the membrane-like environments. They are regulators of the... 

The NMR structures of target proteins generally are determined in a solution or membrane-like environment, which is similar to the physiological state of most systems. Often, however, the NMR-determined protein structures are studied at low pH. whereas the resulting structures sometimes can show significant pH-dependent variation and the protein backbone may display considerable motion and unfolding at different pH values (110). 

It is obvious why the spectroscopist wants to investigate the structure of integral membrane proteins or enzymes, whose biological action is linked to the presence of phospholipids such as phospholipase, in a membrane-mimicking environment Why such an environment should also be used for other peptides like hormones becomes more clear when we take into account the membrane compartment theory [10-12] as postulated by R. Schwyzer. This theory states that peptides that target membrane-embedded receptors... 

As host defense peptides are membrane-active molecules, safety mechanisms must be employed to avoid deleterious contacts with host cells. These mechanisms may involve the limitation of peptide activation to specific environments or niche-specific amplification. That most ct-helical peptides remain unstructured in aqueous solution and undergo conformational transitions to an activated state within hydrophobic environments supports this postulate. It has also been postulated that the order of anionic phospholipids in microbial plasma membranes likely induces optimal periodicity of polar residues within host defense peptides at the membrane surface. ... 

In the mid-seventies. Law et al. studying ACTH-(1-39) and fragments, found a transition from random coil to a helix structure when the solvent water was gradually replaced by trifluoroethanol (TFE) (43). This latter solvent had been shown to favour the establishment of ordered structures ( 3-sheet or a-helix) like a membrane-receptor environment ("membrane-receptor mimetic" properties) (47). Subsequent work of the groups of Low and Fermandjian on ACTH-(1-39) and several large fragments and... 

A key contribution of solid-state NMR is the ability to make detailed structural measurements of membrane proteins in their native environment, the lipid bilayer. This can make it possible to do correlated struc-ture/function studies on membrane proteins under the same sample conditions, for example, to examine the structural differences between functional states of a protein. A number of bilayer-like environments have been introduced that confer different advantages appropriate for particular membrane proteins or experiments. Three such media are discussed below as potential alternatives to reconstituting membrane proteins in proteoliposomes bicelles, nanodiscs and templating vesicles. 

The resonance Raman spectra for the interfacial aggregates were measured by means of CLM Raman microspectroscopy, and the Raman intensity ratio of the imine and azo forms (/azo/fimine) was determined as shown in Table 10.5. The ratio was smaller in more polar solutions such as at the interface. This observation indicated that the nanoenvironment of the azo-group in the membrane-like aggregate of cationic PdL-l,4-Dz was more polar than that of the crystal-like PdL-l,2-Dz cation, although both were in more polar environment than the toluene solutions. 

One can dso obtain NMR spectra for proteins in micelles, which may allow the study of membrane protein structure in an environment approximating their native one. A combination of labels (l N,13c) was used for NMR studies of detergent-solubilized M13 coat protein. Although most of die resonances in the spectrum have not been assigned, there was clear indication that many of the protein residues had two distinct resonances of equal intensity. This was interpreted to mean (in combination with the results of sedimentation equilibrium, Raman and CD studies) that the protein was present in two conformers that represent the non-equivalent monomers of an asymmetric dimer. NMR has also been used to determine the spatial structures of gramicidin A and -labeled bacteriorhodopsin fragments in a membrane-like milieu b... 

Because viruses cannot grow or reproduce on their own, they are not considered to be alive. To survive, a virus must infect a host cell and take over its internal machinery to synthesize viral proteins and in some cases to replicate the viral genetic material. When newly made viruses are released, the cycle starts anew. Viruses are much smaller than cells, on the order of 100 nanometer (nm) in diameter in comparison, bacterial cells are usually > 1000 nm (1 nm= 10 meters). A virus is typically composed of a protein coat that encloses a core containing the genetic material, which carries the information for producing more viruses (Chapter 4). The coat protects a virus from the environment and allows it to stick to, or enter, specific host cells. In some viruses, the protein coat is surrounded by an outer membrane-like envelope. 

Because of the greater flexibility imparted them by the lack of head-to-tail covalent linkage, the carboxylic ionophores respond much more strongly to environmental forces such as local polarity than do the neutral macrocyclic ionophores. Upon leaving a membrane interface during the course of a catalytic transport cycle, an ionophore does not experience an abrupt change from a polar aqueous environment to an apolar hydrocarbon-like environment. The polarity boundary is rather diffuse. In order to properly evaluate the factors affecting carboxylic ionophore mediated transport, it is necessary to determine the effects of each of the microenvironments encountered within the membrane on the conformation of the ionophore and the stability of the ionophore-ion inclusion complex. 

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