Proteins homologous

CD38 is a multifunctional protein expressed primarily on lymphoid cells but also in other tissues (Malavasi et al, 1994). It has been shown to be a bifunctional enzyme expressing both ADP-ribosyl cyclase and cADPR hydrolase activities (Howard et al., 1993 Sum-merhill et al., 1993), and has sequence homology with the Aplysia ADP-ribosyl cyclase enzyme (States et al., 

ADP-ribosyl cyclase and cADPR hydrolase activities have been shown to be widespread in mammalian and other tissues (see Sections III.B and III.C). However, the demonstration that these enzymes are bifunctional in that they are resident on the same protein has led to the suggestion that many common ecto-NAD glycohydrolases, which covert NAD+ to ADP-ribose, may do so via cADPR as an intermediate (Kim et al., 1993b). This might suggest that many of these 

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At present, the data base used for the fit was not specially selected to avoid homologous proteins. Thus, a further improvement can be expected from using data for one of the specially prepared lists of PDB files (cf. Hobohm et al. [9]). We also expect further improvements from replacing the polynomial fits in the potential estimation procedure by piecewise cubic fits though at the moment it is not clear how to select the number of nodes needed to get a good but not overfitting approximation to the density. Finally, we are considering... 

Bah A1995. Modelling Mutations and Homologous Proteins. Current Opinion in Biotedinobgy6 437-I5 l... 

Tiers N L, W D Carlson and M Karplus 1987 Analysis of Side-Chain Orientations in Homologous Proteins. Journal of Molecular Biology 196 175-198. 

A Sail. Modelling mutations and homologous proteins. Cuit Opin Biotech 6 437-451, 1995. 

MJ Sutcliffe, I Haneef, D Carney, TL Blundell. Knowledge based modelling of homologous proteins. Part I Three dimensional frameworks derived from the simultaneous superposition of multiple structures. Protein Eng 1 377-384, 1987. 

MJ Sutcliffe, ERE Hayes, TL Blundell. Knowledge based modeling of homologous proteins. Part II Rules for the conformation of substituted side-chains. Protein Eng 1 385-392, 1987. 

CA Schiffer, JW Caldwell, PA Kollman, RM Stroud. Prediction of homologous protein structures based on conformational searches and energetics. Pi otems 8 30-43, 1990. 

C Wilson, LM Gregoret, DA Agard. Modeling side-chain conformation for homologous proteins using an energy-based rotamer search. J Mol Biol 229 996-1006, 1993. 

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 structure and function... 

Homologous proteins have conserved structural cores and variable loop regions... 

Prediction methods for secondary structure benefit from multiple alignment of homologous proteins... 

Several programs are now available that use multiple alignment of homologous proteins for prediction of secondary structure. One such program, called PHD, which was developed by Chris Sander and coworkers, EMBL, Heidelberg, has reached a mean accuracy of prediction of 72% for new structures. 

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. 

Methods for the prediction of the secondary structure of a set of homologous proteins can reach an accuracy of about 75%, most of the errors occur at the ends of a helices or p strands. The central regions of these secondary structure elements are often correctly predicted but the methods do not always correctly distinguish between a helices and p strands. 

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/). 

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