Prediction of transmembrane helices

The conformation of TMS seems to be a-helical for most membrane proteins [12,13,25-27], but there are some proteins, such as porins, that have TMS in the P-sheet conformation [28]. There may also exist proteins with both helical and P-strand transmembrane segments or with transmembrane helical segments combined with still unknown topology of membrane buried P-strands [29-31]. This work is focused on the prediction of transmembrane helical segments (TMH), but our algorithms do allow the prediction of transmembrane or surface attached P-strands (TMBS) as well... 

The main goal of this work was accurate prediction of transmembrane helical structures, but we do realize that membrane proteins may exist that have both a-helices and P-strands as transmembrane structure. Preference function method is capable of predicting separately a-helical and P-strand conformation of segments that have potential to become... 

Accurate prediction of transmembrane helical segments is superimposed on the prediction of all other secondary structure elements of interest. 

P. K. Ponnuswamy and M. M. Gromiha, Prediction of transmembrane helices from hydrophobic characteristics of proteins, hit. J. Peptide Protein Res. 42, 326-341 (1993). 

Protein and DNA sequence analysis, particularly comprehensive including prediction of transmembrane helical segments, antigenic sites, and the like... 

Fig. 2 Two-dimensional model of the Arabidopsis MATE transporter TT12. (a) The prediction of transmembrane helices was performed using ConPred2. Conserved sequence motifs identified by ClutsalW are highlighted by blue boxes and single amino acids conserved in eukaryotic and prokaryotic MATE proteins (black letters) or all Arabidopsis MATE proteins (red letters) are indicated, (b) Weblogo presentation of the conserved Boxes 1-4 using all annotated Arabidopsis MATE protein sequences...

Since the outside of the barrel faces hydrophobic lipids of the membrane and the inside forms the solvent-exposed channel, one would expect the P strands to contain alternating hydrophobic and hydrophilic side chains. This requirement is not strict, however, because internal residues can be hydrophobic if they are in contact with hydrophobic residues from loop regions. The prediction of transmembrane p strands from amino acid sequences is therefore more difficult and less reliable than the prediction of transmembrane a helices. 

Starting from the protein sequence (primary structure) several algorithms can be used to analyze the primary structure and to predict secondary structural elements like beta-strands, turns, and helices. The first algorithms from Chou and Fasman occurred already in 1978. The latest algorithms find e.g., that predictions of transmembrane... 

Cserzo, M., Wallin, E., Simon, I., von Heijne, G., and Elofsson, A. (1997). Prediction of transmembrane cc-helices in prokaryotic membrane proteins the dense alignment surface method. Protein Eng. 10, 673-676. 

The membrane-bound cytochrome 655s (Bacillus subtilis) contains, according to secondary structure predictions, five transmembrane helices. It functions to anchor two other subunits of the succinate quinone oxidoreductase complex (complex II, E.C. 1.3.5.1) in the cytoplasmic membrane (68). The 1.3-2.0 hemes per covalently bound flavin have been found with the isolated enzyme. The amino acid residues that bind the heme between the a-helices are likely bis(histidine). The EPR and NIR MCD spectra are consistent with this because the EPR spectra show a g value of 3.4 with a HALS lineshape, and the MCD spectra show a low-spin CT band at 1600 nm with Ae of 380 M cm at 4.2 K and 5 T (69). This appears to be another example of a bis(histi-dine)-coordinated heme with near perpendicular alignment of the ligands. 

As previously noted, the Rp. viridis reaction center consists of four polypeptides the L-, M-, H- and C-polypeptides (C for c-type cytochrome), as shown in the model in Fig. 7. Each of the L- and M-polypep-tides contains five transmembrane helices, labeled A to E and single- and double-underlined. The single H-subunit belix is triple-underlined. As mentioned earlier, the number of transmembrane helices determined by X-ray crystallography agrees with that predicted from the hydropathy plots for all three subunits (see Eig. 4). The hehcal content in the LMH complex is 51%, in good agreement with the 50 10% value obtained from circular-dichroism measurements. ... 

Fig. 5.26 Topology ofadenylyl cyclase. The adenylyl cyclase of mammals is a transmembrane protein. It is composed of two homologous domains, which each have a transmembrane domain (Ml and M2) and a larger cytoplasmic portion (Cl and C2). Sequence analysis predicts 6 transmembrane helices for each of the domains (numbering from 1-12). The active site is formed by residues from Cl and C2.

An automated FTP service was used to obtain the predictions for all of our 168 integral membrane proteins by using the Rost et al. method [9]. A total of 11870 residues were correctly predicted in the TMH conformations, 2436 residues were overpredicted, 2512 residues were underpredicted, while 50335 residues were correctly predicted not to be in the TMH conformation. One of many different performance parameter that can be constructed by using these data is the Aj] parameter (Methods). Its value is A m = 0.656, which is inferior to our value of 0.712 (Table 9) for the same parameter. However, when tested on the subset of 63 proteins used by Rost et al. [9] the Ajj parameter, calculated from predictions returned by automated service, becomes 0.733, which is comparable to our value of Ajj = 0.740 for the same subset of proteins (Table 9). Similar test on the subset of 105 proteins, never before seen in the training process for the neural network algorithm, gave quite a low value of Ajj = 0.610 for the Rost et al. method [9]. That value is lower than our value of Ajj = 0.682 for the same subset of 105 proteins (Table 9). All of 63 proteins selected by Rost et al. [9] are also predicted as membrane proteins, but their method does not recognize 2 out of 105 membrane proteins selected by us. Underprediction of membrane proteins is due to serious underprediction of transmembrane helices 50 of observed 419 TMH are underpredicted and 11 overpredicted by Rost et al. [9]. For comparison our Table 9 results (row f) for Aj are obtained for the case of 21 underpredicted and 25 overpredicted TMH in the same test set of 105 proteins. 

False-positive predictions of transmembrane segments are not found in porins (no transmembrane helical segments predicted) and are rare in soluble proteins (11.5%),... 

Alpha helices that cross membranes are in a hydrophobic environment. Therefore, most of their side chains are hydrophobic. Long regions of hydrophobic residues in the amino acid sequence of a protein that is membrane-bound can therefore be predicted with a high degree of confidence to be transmembrane helices, as will be discussed in Chapter 12. 

In contrast, the transmembrane helices observed in the reaction center are embedded in a hydrophobic surrounding and are built up from continuous regions of predominantly hydrophobic amino acids. To span the lipid bilayer, a minimum of about 20 amino acids are required. In the photosynthetic reaction center these a helices each comprise about 25 to 30 residues, some of which extend outside the hydrophobic part of the membrane. From the amino acid sequences of the polypeptide chains, the regions that comprise the transmembrane helices can be predicted with reasonable confidence. 

The most important general lesson is that there are hydrophobic transmembrane helices, the positions of which within the amino acid sequence can be predicted with reasonable accuracy. This applies both to the single transmembrane-spanning helix within the H polypeptide chain of the reaction center and the five transmembrane helices of the L and M chains that... 

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