Homologous proteins sequences

Structurally important role, by allowing unusual main chain conformations. This may explain why a high proportion of Gly residues in homologous protein sequences are conserved. 

While the information contained in one primary sequence alone seems to be insufficient to predict a protein s secondary structure, multiply aligned sequences (see below) offer a means to push the limits of the prediction. Originally due to Zvelebil et al. [26] this line of attack on the problem is the basis of the PHD method by Rost and Sander [27]. The PHD method takes as input a multiple alignment of a set of homologous protein sequences and... 

SY Chung, S Subbiah. A structural explanation for the twilight zone of protein sequence homology. Structure 4 1123-1127, 1996. 

K Sjdlander, K Karplus, M Brown, R Hughey, A Krogh, IS Mian, D Haussler. Dirichlet mixtures A method for improved detection of weak but significant protein sequence homology. Comput Appl Biosci 12 327-345, 1996. 

WC Barker, MO Dayhoff. Evolution of homologous physiological mechanisms based on protein sequence data. Comp Biochem Physiol [B] 62 1-5, 1979. 

An effective method for localizing causes of redox potentials is to plot the total backbone and side chain contributions to ( ) per residue for homologous proteins as functions of the residue number using a consensus sequence, with insertions treated by summing the contribution of the entire insertion as one residue. The results for homologous proteins should be examined for differences in the contributions to ( ) per residue that correlate with observed redox potential differences. These differences can then be correlated with any other sequence-redox potential data for proteins that lack crystal or NMR structures. In addition, any sequences of homologous proteins that lack both redox potentials and structures should be examined, because residues important in defining the redox potential are likely to have semi-sequence conservation of a few key amino acid types. 

Homologous proteins have similar three-dimensional structures. They contain a core region, a scaffold of secondary structure elements, where the folds of the polypeptide chains are very similar. Loop regions that connect the building blocks of the scaffolds can vary considerably both in length and in structure. From a database of known immunoglobulin structures it has, nevertheless, been possible to predict successfully the conformation of hyper-variable loop regions of antibodies of known amino acid sequence. 

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/). 

Homologous Proteins from Different Organisms Have Homologous Amino Acid Sequences... 

Compare the DNA sequence to known protein sequences to verify exons, etc. with homologous sequences... 

Three-dimensional models can be obtained most easily if the 3D structure of a homologous protein is known (homology modelling, comparative modelling). A homology model can only be as good as the sequence... 

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