Fold space

L Holm, C Sander. Touring protein fold space with Dali/FSSP. Nucleic Acids Res 26 316-319, 1998. 

Minary, P. and M. Levitt (2008). Probing protein fold space with a simplified model. J Mol Biol 375(4) 920-933. 

DNA shuffling improves the search of local fold space via a random yet correlated combination of homologous coding fragments that contain limited numbers of beneficial amino acid substitutions. As in experimental evolutions (Stemmer, 1994 Crameri et al., 1998 Zhang et al, 1997 Moore et al, 1997), the simulated shuffling improved protein function significantly better than did point mutation alone (see Table III and Fig. 6b). However, local... 

The protein structural similarity is generally described in terms of folds. However, evolutionarily related proteins may contain different folds, and proteins sharing the same fold do not necessarily descend from a common ancestor. Structural similarity may occur due to the limited number of favorable arrangements for secondary structure elements in fold space. Four of the most common mechanisms for protein-fold change (Grishin, 2001 Lupas et al, 2001) include ... 

Detecting evolutionary relationships across existing fold space, using... 

L. Holm and C. Sander, Nucl. Acids Res., 26, 316 (1998). Touring Protein Fold Space with... 

A Consensus View of Fold Space Combining SCOP, CATH, and the DALI Domain... 

The take-home message from this assessment is that proteins with varying numbers and patterns of amino acids adopt similar 3-D shapes the emptiness of protein fold space is most likely attributable to the finding that many protein shapes are architecturally unstable. Even with this knowledge, it is still... 

Figure 1 The 3-D representation illustrates the clustering of structures along separate axes and highlights obvious voids in protein fold space. (Reproduced with permission from FNAS, 2003 100(5) 2386.)...

A. Cuff, O. C. Redfern, L. Greene, I. Sillitoe, T. Lewis, M. Dibley, A. Reid, F. Pearl, T. Dall-man, A. Todd, R. Garratt, J. Thornton, and C. Otengo, Structure, 17(8), 1051-1062 (2009). The CATH Hierarchy Revisited - Structural Divergence in Domain Superfamilies and the Continuity of Fold Space. 

A. L. Jonsson, R. D. Schaeffer, M. W. van der Kamp, and V. Daggett, BioMol. Concepts, 335 (2011). Dynameomics Protein Dynamics and Unfolding Across Fold Space. 

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