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31.
In this study we present an accurate secondary structure prediction procedure by using a query and related sequences. The most novel aspect of our approach is its reliance on local pairwise alignment of the sequence to be predicted with each related sequence rather than utilization of a multiple alignment. The residue-by-residue accuracy of the method is 75% in three structural states after jack-knife tests. The gain in prediction accuracy compared with the existing techniques, which are at best 72%, is achieved by secondary structure propensities based on both local and long-range effects, utilization of similar sequence information in the form of carefully selected pairwise alignment fragments, and reliance on a large collection of known protein primary structures. The method is especially appropriate for large-scale sequence analysis efforts such as genome characterization, where precise and significant multiple sequence alignments are not available or achievable. Proteins 27:329–335, 1997. © 1997 Wiley-Liss, Inc. 相似文献
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A domain interaction map based on phylogenetic profiling 总被引:2,自引:0,他引:2
Phylogenetic profiling is a well established method for predicting functional relations and physical interactions between proteins. We present a new method for finding such relations based on phylogenetic profiling of conserved domains rather than proteins, avoiding computationally expensive all versus all sequence comparisons among genomes. The resulting domain interaction map (DIMA) can be explored directly or mapped to a genome of interest. We demonstrate that the performance of DIMA is comparable to that of classical phylogenetic profiling and its predictions often yield information that cannot be detected by profiling of entire protein chains. We provide a list of novel domain associations predicted by our method. 相似文献
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Kerner MJ Naylor DJ Ishihama Y Maier T Chang HC Stines AP Georgopoulos C Frishman D Hayer-Hartl M Mann M Hartl FU 《Cell》2005,122(2):209-220
The E. coli chaperonin GroEL and its cofactor GroES promote protein folding by sequestering nonnative polypeptides in a cage-like structure. Here we define the contribution of this system to protein folding across the entire E. coli proteome. Approximately 250 different proteins interact with GroEL, but most of these can utilize either GroEL or the upstream chaperones trigger factor (TF) and DnaK for folding. Obligate GroEL-dependence is limited to only approximately 85 substrates, including 13 essential proteins, and occupying more than 75% of GroEL capacity. These proteins appear to populate kinetically trapped intermediates during folding; they are stabilized by TF/DnaK against aggregation but reach native state only upon transfer to GroEL/GroES. Interestingly, substantially enriched among the GroEL substrates are proteins with (betaalpha)8 TIM-barrel domains. We suggest that the chaperonin system may have facilitated the evolution of this fold into a versatile platform for the implementation of numerous enzymatic functions. 相似文献
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We describe a computational approach for finding genes that are functionally related but do not possess any noticeable sequence similarity. Our method, which we call SNAP (similarity-neighborhood approach), reveals the conservation of gene order on bacterial chromosomes based on both cross-genome comparison and context information. The novel feature of this method is that it does not rely on detection of conserved colinear gene strings. Instead, we introduce the notion of a similarity-neighborhood graph (SN-graph), which is constructed from the chains of similarity and neighborhood relationships between orthologous genes in different genomes and adjacent genes in the same genome, respectively. An SN-cycle is defined as a closed path on the SN-graph and is postulated to preferentially join functionally related gene products that participate in the same biochemical or regulatory process. We demonstrate the substantial non-randomness and functional significance of SN-cycles derived from real genome data and estimate the prediction accuracy of SNAP in assigning broad function to uncharacterized proteins. Examples of practical application of SNAP for improving the quality of genome annotation are described. 相似文献
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Meyer TE Tsapin AI Vandenberghe I de Smet L Frishman D Nealson KH Cusanovich MA van Beeumen JJ 《Omics : a journal of integrative biology》2004,8(1):57-77
Through pattern matching of the cytochrome c heme-binding site (CXXCH) against the genome sequence of Shewanella oneidensis MR-1, we identified 42 possible cytochrome c genes (27 of which should be soluble) out of a total of 4758. However, we found only six soluble cytochromes c in extracts of S. oneidensis grown under several different conditions: (1) a small tetraheme cytochrome c, (2) a tetraheme flavocytochrome c-fumarate reductase, (3) a diheme cytochrome c4, (4) a monoheme cytochrome c5, (5) a monoheme cytochrome c', and (6) a diheme bacterial cytochrome c peroxidase. These cytochromes were identified either through N-terminal or complete amino acid sequence determination combined with mass spectroscopy. All six cytochromes were about 10-fold more abundant when cells were grown at low than at high aeration, whereas the flavocytochrome c-fumarate reductase was specifically induced by anaerobic growth on fumarate. When adjusted for the different heme content, the monoheme cytochrome c5 is as abundant as are the small tetraheme cytochrome and the tetraheme fumarate reductase. Published results on regulation of cytochromes from DNA microarrays and 2D-PAGE differ somewhat from our results, emphasizing the importance of multifaceted analyses in proteomics. 相似文献
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Erik HFM van der Heijden Wouter Hoefsloot Hieronymus WH van Hees Olga CJ Schuurbiers 《Respiratory research》2015,16(1)