Protein , folding patterns motifs

FIGURE 4-20 Stable folding patterns in proteins, (a) Two simple and common motifs that provide two layers of secondary structure. Amino acid side chains at the interface between elements of secondary structure are shielded from water. Note that the f) strands in the loop... 

Greek key motif A geometric motif found in Greek pottery that can be used to describe a certain type of folding pattern of a protein structure. 

In addition to conventional sequence motifs (Prosite, BLOCKS, PRINTS, etc.), the compilation of structural motifs indicative of specific functions from known structures has been proposed [268]. This should improve even the results obtained with multiple (one-dimensional sequence) patterns exploited in the BLOCKS and PRINTS databases. Recently, the use of models to define approximate structural motifs (sometimes called fuzzy functional forms, FFFs [269]) has been put forward to construct a library of such motifs enhancing the range of applicability of motif searches at the price of reduced sensitivity and specificity. Such approaches are supported by the fact that, often, active sites of proteins necessary for specific functions are much more conserved than the overall protein structure (e.g. bacterial and eukaryotic serine proteases), such that an inexact model could have a partly accurately conserved part responsible for function. As the structural genomics projects produce a more and more comprehensive picture of the structure space with representatives for all major protein folds and with the improved homology search methods linking the related sequences and structures to such representatives, comprehensive libraries of highly discriminative structural motifs are envisionable. 

X-ray crystal structure analyses have shown that each protein does not have an entirely different folding pattern, but that most protein structures are made up from one or more of a number of possible structural motifs, most of which have, by now, been identified. The questions that could be asked include why does the protein have the amino acid sequence that it does what is the significance of each amino acid why does the molecule fold in the way that it does and what are the functional results of such a folding The controls imposed on protein folding include the interactions between main-chain and side-chain atoms in the folded polypeptide chain the manner in which subunits, if any, interact with each other and the way in which the active site, if the protein is an enzyme, is formed. These controls lead to the ultimate size and... 

Each protein is built up of such units that are assembled to give the entire folding pattern. We can, therefore, from an examination of crystal structure determinations build up a large stockpile of motifs normally found in the folding patterns of proteins. Of course, these individual motifs interact with... 

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