Structure, function, and evolution mapping of the protein structure universe

There are more than trillion different proteins on earth, but they are made of combinatorial linkage and variation of much smaller number of protein structural motifs. Furthermore, these proteins function as individual unit or as components of much larger functional complexes. Each motif can be considered as a center of a protein structure “galaxy” consisting of many proteins of similar or related structures, and the protein structure universe is composed of a large number of such galaxies. We have developed a computational method to “map” the protein structure universe represented by the protein structural motifs, in which four major fold classes are found to be segregated into four elongated clusters, and similar protein folds and functions in each class are located near each other in three‐dimensional fold space. This “mapping” reveals features that may be interpretable in terms of evolution of protein structures and functions, and provides a global view of the distribution of protein folds with respect to various molecular functions such as biochemical functions, metal binding, and others. Funded by NIH (P50 GM62412) Website to try out to locate your structures in the protein structure universe: CGbio.lbl.gov