A-Helical membrane proteins

The idea of finding the best model was extended by Jones et al. (1994). A dynamic programming algorithm was used to select the most plausible model, and the same authors also presented an ambitious method to predict the three-dimensional structure of the a-helical membrane proteins (Taylor etal., 1994). Finally, HMMs were used to model the overall structure of the membrane topology by two groups of researchers (Sonn-hammer et al., 1998 Tusnady and Simon, 1998). 

From the start the /1-barrels require cooperative folding of a polypeptide chain of 100 or more residues which constitute an entropic hurdle. In contrast, an cz-helical transmembrane protein can traverse the membrane as soon as a local segment of about 20 residues becomes nonpolar. The remaining transmembrane part can then be added piece by piece, which is entropically much more favorable. Therefore the /1-barrel membrane proteins arose probably rather late during protein structure evolution, constituting an addition to the much simpler a-helical membrane proteins. 

Interpretation of the membrane proteins in an envelope virus can be assisted by the identification of transmembrane a helices. Membrane proteins represent a special class of proteins because of the predominant presence of transmembrane helices connected by extramembrane loops and domains. For example, even at 10.5-A resolution, a pair of transmembrane helices could be identified in the Semliki Forest virus El and E2 proteins (Eig. 10 see Color Insert). 

Despite these advances, Oberai et al. (3) estimate that if no acceleration of membrane protein structure determination occurs, then it will take more than three decades to determine at least one structural representative of 90% of the a-helical membrane protein sequence families (3). 

To illustrate the power of PISA wheels and dipolar waves to determine the structure of helical peptides and proteins in uniaxiaUy oriented lipid bilayers. Fig. 6a-c show SIMPSON/SIMMOL-simulated PISEMA spectra of an ideal 18-residue a-helix with a tilt angle of 10°-30° relative to Bq. In these simulations, we have tried to mimic experimental conditions by including a random distribution of the principal components of the chemical shift tensor and the dipolar coupling. The chemical shift distribution is 6 ppm for each principal element and has been established as follows we obtained — 85000 N isotropic chemical shifts reported to the BioMagResBank and selected only the — 31000 located in helical secondary stractures to have a data set independent on secondary chemical shifts. The standard deviation on the N chemical shifts for these resonances was — 6 ppm. With the lack of other statistically reliable experimental methods to establish such results for the individual principal elements of the N CSA tensor, we assumed the above variation of 6 ppm for all three principal elements. The variation of the H- N dipolar coupling was estimated by investigating the structures for a small number of a-helical membrane proteins for which the structures were established by liquid-state NMR spectroscopy. These showed standard deviations... 

Compared to the high occurrence of a-helical membrane proteins, p-barrel... 

Hong M (2006) Solid-state NMR studies of the stmcture, dynamics, and assembly of P-sheet membrane peptides and a-helical membrane proteins with antibiotic activities. Acc Chem Res 39 176-183... 

A. Gautier, Structure Determination of a-Helical Membrane Proteins by Solution-State NMR Emphasis on Retinal Proteins, Biochim. Biophys. Acta, Bioenerg., 2014, 1837, 578. 

Jones, D., Taylor, W., and Thornton, J. (1994). A model recognition approach to the prediction of all-helical membrane protein structure and topology. Biochemistry 33, 3038-3049. 

Figure 4-4. The domain organization of an integral, transmembrane protein as well as the mechanisms for interaction of proteins with membranes. The numbers illustrate the various ways by which proteins can associate with membranes I, multiple transmembrane domains formed of a-helices 2, a pore-forming structure composed of multiple transmembrane domains 3, a transmembrane protein with a single a-helical membrane-spanning domain 4, a protein bound to the membrane by insertion into the bilayer of a covalently attached fatty acid (from the inside) or 5, a glycosyl phosphatidylinositol anchor (from the outside) 6, a protein composed only of an extracellular domain and a membrane-embedded nonpolar tail 7, a peripheral membrane protein noncova-lently bound to an integral membrane protein.

We have studied the sequence determinants for helical hairpin formation during the insertion of a model membrane protein into the ER membrane. To simplify the problem, we engineered a 40-residue long poly(Leu) stretch into a membrane protein that inserts readily into ER-derived microsomes when expressed in vitro (Fig. 2A). Asn-X-Thr acceptor sites for N-linked glycosylation were used as topological markers, as they can only be modified when located in the... 

After numerous complete genomic DNA sequences had been established and after these had been interpreted to a great extent in terms of protein sequences, it became evident that about 20% of all proteins are located in membranes (Liu and Rost, 2001). This number was derived from a search for transmembrane a-helices with a computerized prediction system, the results of which are known to come with a high confidence level. Such helices can be recognized from a continuous stretch of 20 to 30 nonpolar residues with a predominance of aliphatic side chains at the center and aromatic residues at both ends (Sipos and von Heijne, 1993). The number of transmembrane a-helices per protein is broadly distributed and averages around six. 

Here we discuss structures that have been established at the atomic level revealing the exact conformation of the polypeptide chain. All were determined by X-ray diffraction analysis of a tridimensional protein crystal. Some o -helical membrane protein structures have been analyzed by electron diffraction of o-dimensional crystals, although generally with a lower accuracy. For a long time structural analyses by NMR... 

Cytochrome b is a hydrophobic membrane protein containing both heme b centers in a transmembrane arrangement. In bc complexes of mitochondria and bacteria like Para-coccus or Rhodobacter, cytochrome b has approximately 400 amino acid residues and contains eight membrane spanning helices (A - H). Cytochrome b of the b complex contains only the first four transmembrane helices (A - D) coordinating both heme centers. These helices form an all-antiparallel 4-a-helical bimdle the helices are tilted approximately 20 fi om the membrane normal. 

Senes, A., Engel, D.E., and DeGrado, W.F. (2004). Folding of helical membrane proteins the role of polar, GxxxG-like and proline motifs. Curr Opin Struct Biol 14 465 79. 

Despite its uncertain status as a membrane protein, the stmcture of Mistic from Bacillus subtilis determined in detergent micelles highlights a promising approach to solving the 3-D stmcture of multispaiming helical membrane proteins by solution-state NMR (50). Backbone and side-chain assignment was achieved by partial deuteration and full labeling of the protein. 

F. M. Marassi and S. J. Opella, A solid-state NMR index of helical membrane protein structure and topology. J. Magn. Reson.. 2000,144, 150-155. 

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