Exploring molecular biological and structural aspects of non-Pfam proteins
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A non-Pfam protein sequence, by definition, has no significant match to any sequence inthe Pfam protein family classification. Non-Pfam proteins are often species-specific and relatedto evolutional and developmental functions. They have been excluded from most structuralgenomics projects, which aim to build a complete protein fold space, due to their uniquesequences. However, these unique structures could contribute many novel protein folds. Thehigh throughput structural genomics pipelines developed at the SECSG were used to determinethe 3D structures of selected non-Pfam targets. In addition, sulfur-SAS phasing methodologywas refined and expanded to crystal having moderate low to moderate resolution. In this work,51 out of 62 selected non-Pfam proteins were expressed in large-scale media and 23 proteinswere successfully purified by chromatography methods. Crystallization hits were observed in 8proteins. Crystal structure of AF1382 was determined by sulfur-SAS phasing using mergedmedium-resolution data. AF1382 belongs to a winged-helix fold and has putative interactions toDNA. Crystal structure of TT0030 was determined by isomorphous replacement. TT0030 issimilar to a Rossmann fold. Their atomic coordinates and structure factors have been depositedinto PDB. Meanwhile, 4 non-Pfam protein crystal structures have been determined by other members of the lab. The structure of PH1580 represents a new SCOP fold and the structure ofAF2093 is very likely to represent a new fold. Proteins PF1176 and AF0160 are structurallysimilar to proteins with identified functions. This research shows that: i) the majority of non-Pfam proteins are real, foldable proteins; ii) non-Pfam proteins can make a significantcontribution to the discovery of new SCOP folds; iii) many non-Pfam proteins are biologicallyimportant; iv) sulfur-SAS is a viable phasing method with the medium-resolution data.