Multiple sequence alignment

As shown in Table 1, the trend in CYP homology model building is clearly toward a multi-integrated approach using multiple sequence alignments (multiple), structural alignments in combination with mutational, spectroscopic and enzyme kinetic experimental data and new or available pharmacophore models,... 

Pairvnse seQuence Alignment Multiple sequence AJignment WoiiecuiBr Slmllsr y araf Momiling... 

Fig. 10.20 Schematic illustration of the creation of a multiple sequence alignment for five sequences A-E. In the fi step sequences C and E are aligned. In the second step sequences A and D are aligned. In the third step the pair Cl aligned with the pair AD. Finally, the quartet CEAD is aligned with B.

Ortiz A R, A Kolinski and J Skolnick 1998. Fold Assembly of Small Proteins Using Monte C Simulations Driven by Restraints Derived from Multiple Sequence Alignments. Jourru Molecular Biology 277 419-446. 

WR Taylor. Multiple protein sequence alignment Algorithms and gap insertion. Methods Enzymol 266 343-367, 1996. 

P Briffeuil, G Baudoux, C Lambert, X De Bolle, C Vmals, E Feytmans, E Depiereux. Comparative analysis of seven multiple protein sequence alignment servers Clues to enhance reliability of predictions. Biomformatics 14 357-366, 1998. 

AD Baxevams. Pi actical aspects of multiple sequence alignment. Methods Biochem Anal 39 172-188, 1998. 

E Jeanmougm, JD Thompson, M Gouy, DG Eliggms, TJ Gibson. Multiple sequence alignment with clustal X. Trends Biochem Sci 23 403-405, 1998. 

WR Taylor, K Hatrick. Compensating changes m protein multiple sequence alignments. Protein Eng 7 341-348, 1994. 

AR Ortiz, A Kolinski, J Skolnick. Fold assembly of small proteins using Monte Carlo simulations driven by restraints derived from multiple sequence alignments. J Mol Biol 277 419-448, 1998. 

CX.0 = Z(=iCx.r represents the total number of counts that the prior distribution represents, and the a, the counts for each type of amino acid (not necessarily integers). Because different distributions will occur in multiple sequence alignments, the prior distribution for any position should be represented as a mixture of N Dirichlet distributions ... 

Sjdlander et al. [16] describe the process assumed in their model of sequence alignments, which is how the counts for a particular position in a multiple sequence alignment would arise from the mixture Dirichlet prior ... 

Thompson and Goldstein [89] improve on the calculations of Stolorz et al. by including the secondary structure of the entire window rather than just a central position and then sum over all secondary strucmre segment types with a particular secondary structure at the central position to achieve a prediction for this position. They also use information from multiple sequence alignments of proteins to improve secondary structure prediction. They use Bayes rule to fonnulate expressions for the probability of secondary structures, given a multiple alignment. Their work describes what is essentially a sophisticated prior distribution for 6 i(X), where X is a matrix of residue counts in a multiple alignment in a window about a central position. The PDB data are used to form this prior, which is used as the predictive distribution. No posterior is calculated with posterior = prior X likelihood. 

Families of similar sequences contain information on sequence evolution in the form of specific conservation patterns at all sequence positions. Multiple sequence alignments are useful for... 

This branch of bioinformatics is concerned with computational approaches to predict and analyse the spatial structure of proteins and nucleic acids. Whereas in many cases the primary sequence uniquely specifies the 3D structure, the specific rules are not well understood, and the protein folding problem remains largely unsolved. Some aspects of protein structure can already be predicted from amino acid content. Secondary structure can be deduced from the primary sequence with statistics or neural networks. When using a multiple sequence alignment, secondary structure can be predicted with an accuracy above 70%. 

The other subfamily, SLC1, includes the Na+-dependent glutamate transporters. It encompasses some amino- and carboxylic-acid transporters including glutamate transporters that are expressed in bacteria. X-ray diffraction data have been obtained from crystals of one of these [43] (Fig. 5-13). Analysis of multiple sequence alignments indicates that this molecule has a high degree of structural... 

Thompson, J. D., Gibson, T. J., Plewniak, F., Jeanmougin, F. and Higgins, D. G. The CLUSTAL X windows interface flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Res. 25 4876-4882, 1997. 

Due to the ready accessibility of SH2 domains by molecular biology techniques, numerous experimentally determined 3D structures of SH2 domains derived by X-ray crystallography as well as heteronuclear multidimensional NMR spectroscopy are known today. The current version of the protein structure database, accessible to the scientific community by, e.g., the Internet (http //www.rcsb.org/pdb/) contains around 80 entries of SH2 domain structures and complexes thereof. Today, the SH2 domain structures of Hck [62], Src [63-66], Abl [67], Grb2 [68-71], Syp [72], PLCy [73], Fyn [74], SAP [75], Lck [76,77], the C- and N-terminal SH2 domain ofp85a [78-80], and of the tandem SH2 domains Syk [81,82], ZAP70 [83,84], and SHP-2 [85] are determined. All SH2 domains display a conserved 3D structure as can be expected from multiple sequence alignments (Fig. 4). The common structural fold consists of a central three-stranded antiparallel ft sheet that is occasionally extended by one to three additional short strands (Fig. 5). This central ft sheet forms the spine of the domain which is flanked on both sides by regular a helices [49, 50,60]. 

Fig. 4. Multiple sequence alignment of six distinct SH2 domain sequences. The SH2 domain notifiers are given on the left, the bottom line represents the consensus sequence as analyzed from the alignment. Highly conserved sequence positions are marked with capital letters. The sequential position of the major secondary structure elements (helices and sheets) are indicated by boxes...

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