Secondary structure 216 INDEX

Thus, /(Ni,C i), J(Ni,C i), and possibly other J-couplings could definitely be used as a secondary structure index, that is, to discriminate between most different conformations such as helical and beta-sheet, but one should abstain to use the corresponding Karplus fits to establish quantitative relations with dihedral angles. The use of these Karplus fits to estimate the J-coupling values from the averaging over an MD simulation trajectory that does sample the entire dihedral angle space is questionable [110]. 

D. S. Wishart, B. D. Sykes and F. M. Richards, The chemical shift index A fast and simple method for the assignment of protein secondary structure through NMR spectroscopy, Biochemistry, 1992, 31, 1647-1651. 

Analysis (PSA) server of BMERC predicts secondary structures and folding classes from a query sequence. On the PSA home page at http //bmerc-www.bu.edu/psa/ index.html, select Submit a sequence analysis request to submit the query sequence and your e-mail address. The returned results include (a) probability distribution plots (conventional X/Y and contour plots) for strand, turn, and helix and (b) a list of structure probabilities for loop, helix, turn, and strand for every amino acid residues. 

The prediction of the secondary structures can be made by the structure similarity search of PDB collection at the site. Several servers provide such prediction method. The Jpred, which aligns the query sequence against PDB library, can be accessed at http //jura.ebi.ac.uk 8888/index.html. To predict the secondary structures, however, check Bypass the current Brookhaven Protein Database box and then click Run Secondary Structure Prediction on the home page of Jped to open the query page (Figure 12.10). Upload the sequence file via browser or paste the query sequence into the sequence box. Enter your e-mail address (optional) and click the Run Secondary Structure Prediction button. The results with the consensus structures are returned either online (linked file) or via e-mail (if e-mail address is entered). 

Submit the following sequence to a structure prediction by displaying the secondary structure and core index in the multiple alignment of the query sequence, and with the representative sequences of proteins whose 3D structures are known. 

Two of the hydrophihcity scales in Table 2 were derived from experimental measures of the behavior of amino acids in various solvents, namely partitioning coefficients [K-D index of Kyte and Doolittle (30)] or mobility in paper chromatography [Rf index of Zimmerman et al. (31)]. By contrast, the Hp index was obtained from quantum mechanics (QM) calculations of electron densities of side chain atoms in comparison with water (32). The Hp index is correlated highly with these two established hydrophobicity scales (Table 4). Therefore, like the polarizability index, it is possible to represent fundamental chemical properties of amino acids (hydrophUicity, Hp) with parameters derived from ab initio calculations of electronic properties. However, in contrast to polarizabihty (steric effects), hydrophihcity shows significant correlation with preference for secondary structure. Thus, hydrophobic amino acids prefer fi-strands (and fi-sheet conformations) and typically are buried in protein structures, whereas hydrophilic residues are found commonly in turns (coil structure) at the protein surface. 

The first step in the analysis was to obtain the secondary structure prediction for the 148 proteins in the test database with the selected methods. The accuracy results in terms of the Q3 index can be examined in table III. 

D Correlation Spectroscopy. A simple, quahtative approach has been described for the determination of membrane protein secondary structure and topology in lipid bilayer membranes." The new approach is based on the observation of wheel-like resonance patterns in the NMR H- N/ N polarization inversion with spin exchange at the magic angle (PISEMA) and H/ N HETCOR spectra of membrane proteins in oriented lipid bilayers. These patterns, named Pisa wheels, have been previously shown to reflect helical wheel projections of residues that are characteristic of a-helices associated with membranes. This study extends the analysis of these patterns to P-strands associated with membranes and demonstrates that, as for the case of a-helices, Pisa wheels are extremely sensitive to the tilt, rotation, and twist of P-strands in the membrane and provide a sensitive, visually accessible, qualitative index of membrane protein secondary structure and topology. 

Table 17.2. a Compilation of database-retrieved hexapeptides related to the peptide YLQTYH (residues 13 -18) of barnase. For each peptide a folding score is calculated as the product of fold pattern weight and similarity index. The cumulative scores for the four fold types are given at the bottom. The hexapeptide YLQTYH is the C-terminal end of an early formed helix [37] in barnase and adopts the secondary structure hhhhhn in the crystal [67]... 

Peptide Similar peptides From protein Peptide distance Similarity index Secondary structure Folding pattern Pattern weight Fold score... 

---