Secondary structure of membrane

Fariselli, P., Compiani, M. Casadio, R. (1993). Predicting secondary structure of membrane proteins with neural networks. Eur Biophys J 22,41-51. 

A method based on factor analysis followed by correlation of the factor loadings with structural composition has recently been proposed. This technique involves constructing a calibration set from infrared spectra of proteins whose secondary structure has been determined by X-ray. Factor analysis creates series of abstract spectra, which are combined to generate the original spectrum (Lee et al., 1990). This procedure was employed to estimate the secondary structures of membrane proteins (Lee et al., 1991). 

There is much more awareness of the possible effect of the electric fields normal to the plane of the membrane on the structure and on the function of membrane proteins. However, no such relation was experimentally documented. There is an appreciable amount of information on the potential dependence of channel conductance, which is assumed to be caused by shifts of charged groups within the channel (41). These shifts correspond to small changes in conformation that could not be detected by methods sensitive to the secondary structure of the proteins. In the present and in some previous reports (7, 8), we have shown that membrane potentials of comparable magnitude to the physiological membrane potentials are sufficient to modulate the secondary structure of membrane proteins. The effect may be direct or indirect. The indirect effect shifts part of the molecular fraction immersed... 

D. Juretic, Secondary structure of membrane proteins Prediction with conformationai preference functions of soluble proteins, Croat. Chem. Acta 65, 921-932 (1992). 

D. JuretiC and B. Lubic, Predicting the secondary structure of membrane channel proteins The performance of preference functions compared to other statistical methods, HB93 Proceedings, Zagreb (1993). 

CD spectroscopy has been used to study the conformation of a number of membrane proteins. The use of CD for determining the secondary structure of membrane proteins has been reviewed. Membrane proteins which have been solubilized by detergents generally present no special difficulties for CD analysis, but the conformation is likely to be different from that in the native environment. The study of membrane proteins in situ by CD has been the subject of considerable controversy. Two kinds of artifacts which may afflict such studies have been identified. 

It is interesting to compare the thermal-treatment effect on the secondary structure of two proteins, namely, bacteriorhodopsin (BR) and photosynthetic reaction centers from Rhodopseudomonas viridis (RC). The investigation was done for three types of samples for each object-solution, LB film, and self-assembled film. Both proteins are membrane ones and are objects of numerous studies, for they play a key role in photosynthesis, providing a light-induced charge transfer through membranes—electrons in the case of RC and protons in the case of BR. 

Information about the putative folding of the H,K-ATPase catalytic subunit through the membrane has been obtained by the combined use of hydropathy analysis according to the criteria of Kyte and Doolittle [51], identification of sites sensitive to chemical modification [46,48,50,52-55], and localization of epitopes of monoclonal antibodies [56]. The model of the H,K-ATPase catalytic subunit (Fig. 1) which has emerged from these studies shows ten transmembrane segments and contains cytosolic N- and C-termini [53]. This secondary structure of the catalytic subunit is probably a common feature of the catalytic subunits of P-type ATPases, since evidence supporting a ten a-helical model with cytosolic N- and C-termini has also been published recently for both Ca-ATPase of the sarcoplasmic reticulum and Na,K-ATPase [57-59]. 

Second, our studies of the secondary structure of the H" "-ATPase indicate that about 36% of the polypeptide chain is present in a helical configuration [27,42]. If the membrane-embedded sector of the molecule is helical as shown, only 90 or so additional residues in the molecule can be present as helices. Thus, the great majority... 

Fig. 1. Hypothetical secondary structure of a human plasma membrane Na /H exchanger. (Adapted from Sardet et al. [53].) Shaded bars, putative transmembrane segments. Hatched bars, putative amphipathic helices (numbers at tops and bottoms of bars refer to positions of amino acids). CHO, possible site of N-linked glycosylation. Solid bars, regions of the porcine renal Na /H exchanger used for immunolocalization in LLC-PK cells.

Novolac resins, as the oldest synthetic polymers, have played an important role 1n microelectronic Industry as positive photoresists. Studies of novolac dissolution have populated the literature a recent survey shows that the rate of dissolution 1s influenced by the concentration of the alkali, size of the cation, addition of salt, and the presence of dissolution Inhibitors (1-6). The voluminous experimental results, however, have not led to a clear understanding of the dissolution phenomena. Arcus (3) proposed an 1on-permeab1e membrane" model while Szmanda (1) and Hanabata (6) emphasized the Importance of secondary structures of novolac molecules, for Instance, Inter- or Intramolecular hydrogen bonding and the various isomeric configurations of the resins. These important contributions nevertheless point to a need for additional studies of the mechanism of dissolution. 

Thus, the important question of the secondary structure of the transmembrane elements can only be addressed with models and by structural comparison with other transmembrane proteins for which the structure has been resolved. Detailed information on the structure of transmembrane elements is available for the photoreaction center of Rhodopseudomonas viridis (review Deisenhofer and Michel, 1989), cytochrome c oxidase (Iwata et al., 1995) and the OmpF porin of E. coli (Cowan et al., 1992 Fig. 5.3), amongst others. In addition, high resolution electron microscopic investigations and X-ray studies of bacteriorhodopsin, a light-driven ion pump with seven transmembrane elements, have yielded valuable information on the structure and configuration of membrane-spaiming elements (Henderson et al., 1990 Kimura et al., 1997 Pebay-Peyrula et al., 1997 Fig. 5.4). With the successful crystallization of the photoreaction center of Rhodopseudomonas viridis, a membrane protein was displayed at atomic resolution for the first time (Deisenhofer et al., 1985). The membrane-... 

What can we predict about the secondary structure of the membrane-spanning portions of integral proteins An a-helical sequence of 20 to 25 residues is just long... 

Good discussion of the secondary and tertiary structures of membrane proteins and the factors that stabilize them. 

Besides Ap, other amphipathic model peptides are also studied using IRRAS. The linear sequence KLAL (KLALKLALKALKAALKLA-NH2) is a model compound to form amphipathic helices, which is able to bind to membranes and to increase the membrane permeability in a structure and target-dependent manner [71,72], Kerth et al. first studied the secondary structure of... 

Monomolecular films of the membrane protein rhodopsin have been investigated in situ at the air-water interface by PM-IRRAS and X-ray reflectivity in order to find conditions that retain the protein secondary structure [104]. The spreading of rhodopsin at 0 or 5 mN/m followed by a 30 min incubation time at 21 °C resulted in the unfolding of rhodopsin. In contrast, when spreading is performed at 5 or 10 mN/m followed by an immediate compression at, respectively, 4 or 21 °C, the secondary structure of the protein is retained. 

Rs. rubrum, with its single antenna complex, is an ideal object to probe the membrane-surface exposed regions of the antenna polypeptides. Chromatophores (inside-out vesicles, the cytoplasmic side of the membrane outside) have been chemically modified with the hydrophilic marker diazobenzenesulfonate [24], In addition, protease treatment of chromatophores [25-27] and of spheroplasts (periplasm outside) was carried out [27]. The surface location of the B880 complex was further investigated with antibodies raised to either the intact complex or to the individual polypeptides [27]. In addition, the secondary structures of the polypep-... 

---