Sequencing comparison

Ithough knowledge-based potentials are most popular, it is also possible to use other types potential function. Some of these are more firmly rooted in the fundamental physics of iteratomic interactions whereas others do not necessarily have any physical interpretation all but are able to discriminate the correct fold from decoy structures. These decoy ructures are generated so as to satisfy the basic principles of protein structure such as a ose-packed, hydrophobic core [Park and Levitt 1996]. The fold library is also clearly nportant in threading. For practical purposes the library should obviously not be too irge, but it should be as representative of the different protein folds as possible. To erive a fold database one would typically first use a relatively fast sequence comparison lethod in conjunction with cluster analysis to identify families of homologues, which are ssumed to have the same fold. A sequence identity threshold of about 30% is commonly... 

Altschul S F 1996. Sequence Comparison and Alignment. In Sternberg M E (Editor) Protein Strucii. 

Pearson W R 1990, Rapid and Sensitive Sequence Comparison with FASTP and FASTA. Methoc Enzymology 183 63-98. 

Pearson W R and D J Lipman 1988. Improved Tools for Biological Sequence Comparison. Proceeding the National Academy of Sciences USA 85 2444-2448. 

SE Brenner, C Chothia, TJ Hubbard. Assessing sequence comparison methods with reliable... 

MS Johnson, JP Ovenngton. A structural basis for sequence comparisons An evaluation of scoring methodologies. J Mol Biol 233 716-738, 1993. 

M Levitt, M Gerstein. A unified statistical framework for sequence comparison and structure comparison. Proc Natl Acad Sci USA 95 5913-5920, 1998. 

The World Wide Web has transformed the way in which we obtain and analyze published information on proteins. What only a few years ago would take days or weeks and require the use of expensive computer workstations can now be achieved in a few minutes or hours using personal computers, both PCs and Macintosh, connected to the internet. The Web contains hundreds of sites of Interest to molecular biologists, many of which are listed in Pedro s BioMolecular Research Tools (http // www.fmi.ch/biology/research tools.html). Many sites provide free access to databases that make it very easy to obtain information on structurally related proteins, the amino acid sequences of homologous proteins, relevant literature references, medical information and metabolic pathways. This development has opened up new opportunities for even non-specialists to view and manipulate a structure of interest or to carry out amino-acid sequence comparisons, and one can now rapidly obtain an overview of a particular area of molecular biology. We shall here describe some Web sites that are of interest from a structural point of view. Updated links to these sites can be found in the Introduction to Protein Structure Web site (http // WWW.ProteinStructure.com/). 

Prasher, D. C., McCann, R. O., Longiaru, M., and Cormier, M. J. (1987). Sequence comparisons of complememtary DNAs encoding aequorin isotypes. Biochemistry 26 1326-1332. 

Histone Deacetylases (HDACs) catalyze the removal of the acetyl groups from lysines (see Fig. 1). Together with the HATs they are responsible for maintaining the level of histone acetylation throughout the genome. The family of HDAC proteins has been divided into four classes based on phylogenetic analysis and sequence comparison. HDACs of the classes I and II share the same Zn2+-based reaction and are evolutionary related. Class IV HDACs also possess a Zn2+-based reaction... 

Figure 1. An unrooted phylogenetic tree of the myosins based on the amino acid sequence comparison of their head domains demonstrating the division of the myosin superfamily into nine classes. The lengths of the branches are proportional to the percent of amino acid sequence divergence and a calibration bar for 5% sequence divergence is shovk n. The different classes of myosins have been numbered using Roman numerals in rough order of their discovery and hypothetical models of the different myosin structures are shown. Question marks indicate either hypothetical or unknown structural features, and only a fraction of the known myosins are shown. (Taken, in modified form, from Cheney et al., 1993).

Figure 2. Universal phylogenetic tree determined from rRNA sequence comparisons. A matrix of evolutionary distances (99) was calculated from an alignment (260) of representative 16S RRNA sequences from each of the three urkingdoms. The length of the lines is proportional to the phylogenetic difference. (Reproduced with permission from ret 16. Copyright 19. American Society for Microbiology.)...

Only a few residues show more than 75% sequence identity, including four glycine residues, a proline residue at the beginning of the Pro loop, and a phenylalanine residue in a position corresponding to the conserved residue Tyr 165 of the bovine heart Rieske protein. However, structure prediction and sequence comparison with Rieske proteins from bci complexes suggests that the fold will be very similar in all Rieske-type ferredoxins, as in the other Rieske or Rieske-type proteins (see Section III,B,1). 

Sequence Comparison Between the N-Terminal Part of the Fepr Genes from Desulfovibrio desulfuricans (Dd) and Desulfovibrio vulgaris (Dv), Carbon Monoxide Dehydrogenase from Methanothrix soehngenii (Ms), Methanosarcina frisia Gdl (Mf), Clostridium thermoaceticum (Ct), Rhodospirillum rubrum (Rr), and Anaerobic Ribonucleotide Reductase from Escherichia coli (Ec) ... 

Fig. 1. (a) Schematic representation of the three types of anoxygenic ([1] and [2]) and oxygenic ([3]) photosynthesis found in plants and bacteria, (b) Phylogenetic tree based on 16S-rRNA sequence comparisons featuring only photo synthetic phyla. 

Fig. 3. Sequence comparison of the FA/FB-binding subunits of PSl from tobacco and the RC of green sulfur bacteria with that of the 2[4Fe-4S] ferredoxin from Peptococcus aerogenes. Cysteine ligands to the right-hand cluster in the three structures of Fig. 2 (i.e., cluster Fb for the case of the FA/FB-protein) are marked by open boxes Emd residues ligating the left-hand cluster by hatched boxes.

Sequence comparisons of Rieske proteins from various species prior to the cystal structures 120, 121) noted a high degree of conservation in the C-terminal part of the protein, that is, the segment including... 

Fig. 6. Sequence comparisons of Rieske proteins from spinach chloroplasts, beef heart mitochondria, green sulfur bacteria, and firmicutes. The extended insertion of proteobacterial Rieske proteins as compared to the mitochondrial one is indicated by a dotted arrow. The redox-potential-influencing Ser residue is marked by a vertical arrow. The top and the bottom sequence numberings refer to the spinach and bovine proteins, respectively. Fully conserved residues are marked by dark shading, whereas the residues conserved in the b6f-group are denoted by lighter shading.

Bakker, E. T., Yassibades, D. D., Morton, C. and Savolainen, V. 1998. Phylogenetic relationships of Biebersteinia Stephan (Geraniaceae) inferred from rbcL and utpB sequence comparisons. Bot. J. Linn. Soc. 127 149-158. 

Figure 8. Sequence comparison of PGIPs (adapted from Stotz etal., [10]). Black = Glycosylation site. Gray = greater than 70% sequence homology.

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