Conformational lipids

With respect to the carrier mechanism, the phenomenology of the carrier transport of ions is discussed in terms of the criteria and kinetic scheme for the carrier mechanism the molecular structure of the Valinomycin-potassium ion complex is considered in terms of the polar core wherein the ion resides and comparison is made to the Enniatin B complexation of ions it is seen again that anion vs cation selectivity is the result of chemical structure and conformation lipid proximity and polar component of the polar core are discussed relative to monovalent vs multivalent cation selectivity and the dramatic monovalent cation selectivity of Valinomycin is demonstrated to be the result of the conformational energetics of forming polar cores of sizes suitable for different sized monovalent cations. 

L. I. Horvath, T. Heimburg, P. Kovachev, J. B. C. Findlay, K. Hideg, D.Marsh, Integration of a K+ channel-associated peptide in a lipid bilayer Conformation, lipid-protein interactions, and rotational diffusion. Biochemistry 34 (1995) 3893. 

Figure 9 Relative accuracy of comparative models. Upper left panel, comparison of homologous structures that share 40% sequence identity. Upper right panel, conformations of ileal lipid-binding protein that satisfy the NMR restraints set equally well. Lower left panel, comparison of two independently determined X-ray structures of interleukin 1(3. Lower right panel, comparison of the X-ray and NMR structures of erabutoxin. The figure was prepared using the program MOLSCRIPT [236].

Table 2 Conformational Defects m the Hydrocarbon Chains in Fluid Phase Lipid Bilayers...

Baumgartner and coworkers [145,146] study lipid-protein interactions in lipid bilayers. The lipids are modeled as chains of hard spheres with heads tethered to two virtual surfaces, representing the two sides of the bilayer. Within this model, Baumgartner [145] has investigated the influence of membrane curvature on the conformations of a long embedded chain (a protein ). He predicts that the protein spontaneously localizes on the inner side of the membrane, due to the larger fluctuations of lipid density there. Sintes and Baumgartner [146] have calculated the lipid-mediated interactions between cylindrical inclusions ( proteins ). Apart from the... 

The amino acid compositions and sequences of the /3-strands in porin proteins are novel. Polar and nonpolar residues alternate along the /3-strands, with polar residues facing the central pore or cavity of the barrel and nonpolar residues facing out from the barrel where they can interact with the hydrophobic lipid milieu of the membrane. The smallest diameter of the porin channel is about 5 A. Thus, a maltodextrin polymer (composed of two or more glucose units) must pass through the porin in an extended conformation (like a spaghetti strand). 

The prespective to be gained thus far is that in order to pass through a lipid layer an ion must have an appropriate polar shell provided in large part by the carrier or channel structure which by virtue of its conformation and by also having lipophilic side chains provides for the polar shell to lipid shell transition. While the relative permeability of monovalent vs divalent and trivalent ions can be qualitatively appreciated from the z2 term in Eqn 2, as indicated in Figure 1B, it is essential to know structural and mechanistic detail in order even qualitatively to understand anion vs cation selectivity and to understand selectivity among monovalent cations. 

A. Side view of channel spanning the lipid layer of a planar lipid bilayer, The structure is comprised of two monomers, each in a left-handed, single stranded p -helical conformation, and joined together at the head or formyl end by means of six, intermolecular hydrogen bonds. The two formyl protons are seen at the center of the structure in this view. Replacement of these protons by methyls destabilizes the conducting dimer as shown with N-acetyl desformyl Gramicidin A (Fig. 3D). 

Ras is a G protein that cycle between two conformations, an activated Ras-GTP or inactivated form Ras-GDP. Ras, attached to the cell membrane by lipidation, is a key component in many signalling cascades, which couple growth factor receptors to downstream effectors that control such processes as cytoskeletal integrity, proliferation, cell adhesion, apoptosis and cell migration. Mutations and dysregulations of the Ras protein leading to increased invasion and metastasis, and decreased apoptosis are very common in cancers. 

Gordon, L.M., Lee, K.Y.C., Lipp, M.M., Zasadzinski, J.A., Walther, F.J., Sherman, M. A., and Waring, A.J. Conformational mapping of the N-terminal segment of surfactant protein B in lipid using C-13-enhanced Fourier transform infrared spectroscopy. J. Peptide Res. 

This pardaxin model is not unique. We have developed several similar models that are equally good energetically and equally consistent with present experimental results. It is difficult to select among these models because the helices can be packed a number of ways and the C-terminus appears very flexible. Our energy calculations are far from definitive because they do not include lipid, water, ions, membrane voltage, or entropy and because every conformational possibility has not been explored. The model presented here is intended to illustrate the general folding pattern of a family of pardaxin models in which the monomers are antiparallel and to demonstrate that these models are feasible. 

The most likely way for pardaxin molecules to insert across the membrane in an antiparallel manner is for them to form antiparallel aggregates on the membrane surface that then insert across the membrane. We developed a "raft"model (data not shown) that is similar to the channel model except that adjacent dimers are related to each other by a linear translation instead of a 60 rotation about a channel axis. All of the large hydrophobic side chains of the C-helices are on one side of the "raft" and all hydrophilic side chains are on the other side. We postulate that these "rafts" displace the lipid molecules on one side of the bilayer. When two or more "rafts" meet they can insert across the membrane to form a channel in a way that never exposes the hydrophilic side chains to the lipid alkyl chains. The conformational change from the "raft" to the channel structure primarily involves a pivoting motion about the "ridge" of side chains formed by Thr-17, Ala-21, Ala-25, and Ser-29. These small side chains present few steric barriers for the postulated conformational change. 

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