Secondary structure of membrane proteins

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). 

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. 

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

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. 

FT-IR spectroscopy is particularly useful for probing the structure of membrane proteins. Until recently, a lack of adequate experimental techniques has been the reason for the poor understanchng of the secondary structure of most membrane proteins. X-ray diffraction requires high quality crystals and these are not available for many membrane proteins. Circular dichroism (CD) has been widely used for studying the conformation of water-soluble proteins, but problems arise in its use for membrane proteins. The light scattering effect may distort CD spectra and lead to substantial errors in their interpretation. In addition, the reference spectra used for the analysis of CD spectra are based on globular proteins in aqueous solution and may not be applicable to membrane proteins in the hydrophobic environment of lipid bilayers. 

In the case of membrane proteins one distinguishes (1) the part that is present in the membrane and that mostly possesses the secondary structure of an a-helix and (2) the part that is outside of the membrane. This part is taken in all theoretical approaches as undefined structure although in reality it may possess the structure of an a-helix or P-strand equally to those in soluble proteins. But, because of the limited number of membrane proteins with known 3D structures, it is not possible to train the algorithm to predict the secondary structure for the soluble part of membrane proteins. Therefore, remedy algorithms for predicting the secondary structures of soluble proteins can be used. Among the available algorithms the most reliable is the PHD rnethod. ... 

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). 

Fourier-transform infrared (FTIR) spectroscopy is particularly useful for probing the structures of membrane proteins [3, 23]. This technique can be used to study the secondary structures of proteins, both in their native environment as well as after reconstitution into model membranes. Myelin basic protein (MBP) is a major protein of the nervous system and has been studied by using FTIR spectroscopy in both aqueous solution and after reconstitution in myelin lipids [24]. The amide I band of MBP in D2O solution (deconvolved and curve-fitted) is... 

CONTEXT The secondary structure of a protein is crucial to its biological activity, whether for good or ill. Snake venoms consist of saliva with a high proportion of toxic proteins. Cobra venom in particular acts on the victim by means of neurotoxins, proteins that attack the nervous system, in this case by blocking the acetylcholine receptors on the membranes of muscle cells. Normally, when acetylcholine... 

A central element in the prediction of secondary structure is the periodicity of sequence conservation, which has proven to be a good indicator in a number of membrane proteins (5). The periodicity is quantified by Fourier transform (FT) analysis. A... 

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... 

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