We have modified and improved the GOR algorithm for the protein secondary structure prediction by using the evolutionary information provided by multiple sequence alignments, adding triplet statistics, and optimizing various parameters. We have expanded the database used to include the 513 non-redundant domains collected recently by Cuff and Barton (Proteins 1999;34:508-519; Proteins 2000;40:502-511). We have introduced a variable size window that allowed us to include sequences as short as 20-30 residues. A significant improvement over the previous versions of GOR algorithm was obtained by combining the PSI-BLAST multiple sequence alignments with the GOR method. The new algorithm will form the basis for the future GOR V release on an online prediction server. The average accuracy of the prediction of secondary structure with multiple sequence alignment and full jack-knife procedure was 73.5%. The accuracy of the prediction increases to 74.2% by limiting the prediction to 375 (of 513) sequences having at least 50 PSI-BLAST alignments. The average accuracy of the prediction of the new improved program without using multiple sequence alignments was 67.5%. This is approximately a 3% improvement over the preceding GOR IV algorithm (Garnier J, Gibrat JF, Robson B. Methods Enzymol 1996;266:540-553; Kloczkowski A, Ting K-L, Jernigan RL, Garnier J. Polymer 2002;43:441-449). We have discussed alternatives to the segment overlap (Sov) coefficient proposed by Zemla et al. (Proteins 1999;34:220-223).

Two-body inter-residue contact potentials for proteins have often been extracted and extensively used for threading. Here, we have developed a new scheme to derive four-body contact potentials as a way to consider protein interactions in a more cooperative model. We use several datasets of protein native structures to demonstrate that around 500 chains are sufficient to provide a good estimate of these four-body contact potentials by obtaining convergent threading results. We also have deliberately chosen two sets of protein native structures differing in resolution, one with all chains' resolution better than 1.5 A and the other with 94.2% of the structures having a resolution worse than 1.5 A to investigate whether potentials from well-refined protein datasets perform better in threading. However, potentials from well-refined proteins did not generate statistically significant better threading results. Our four-body contact potentials can discriminate well between native structures and partially unfolded or deliberately misfolded structures. Compared with another set of four-body contact potentials derived by using a Delaunay tessellation algorithm, our four-body contact potentials appear to offer a better characterization of the interactions between backbones and side chains and provide better threading results, somewhat complementary to those found using other potentials.

The protein-synthesizing ribosome undergoes large motions to effect the translocation of tRNAs and mRNA; here the domain motions of this system are explored with a coarse-grained elastic network model using normal mode analysis. Crystal structures are used to construct various model systems of the 70S complex with/without tRNA, elongation factor Tu and the ribosomal proteins. Computed motions reveal the well-known ratchet-like rotational motion of the large subunits, as well as the head rotation of the small subunit and the high flexibility of the L1 and L7/L12 stalks, even in the absence of ribosomal proteins. This result indicates that these experimentally observed motions during translocation are inherently controlled by the ribosomal shape and only partially dependent upon GTP hydrolysis. Normal mode analysis further reveals the mobility of A- and P-tRNAs to increase in the absence of the E-tRNA. In addition, the dynamics of the E-tRNA is affected by the absence of the ribosomal protein L1. The mRNA in the entrance tunnel interacts directly with helicase proteins S3 and S4, which constrain the mRNA in a clamp-like fashion, as well as with protein S5, which likely orients the mRNA to ensure correct translation. The ribosomal proteins S7, S11 and S18 may also be involved in assuring translation fidelity by constraining the mRNA at the exit site of the channel. The mRNA also interacts with the 16S 3’ end forming the Shine-Dalgarno complex at the initiation step; the 3’ end may act as a ‘hook’ to reel in the mRNA to facilitate its exit. PACS: 87.10.Pq; 87.15.bk; 87.15.kj; 87.16.dj; 87.16.dr

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We have created the GOR V web server for protein secondary structure prediction. The GOR V algorithm combines information theory, Bayesian statistics and evolutionary information. In its fifth version, the GOR method reached (with the full jack-knife procedure) an accuracy of prediction Q3 of 73.5%. Although GOR V has been among the most successful methods, its online unavailability has been a deterrent to its popularity. Here, we remedy this situation by creating the GOR V server.