SUMO1 known 3D structure conformations covered by PFVM
The SUMO1_HUMAN protein has more than 50 of 3D structures available in PDB, and it is not surprised that these structures have both similarity and difference in folding conformations. Here, seven of 3D structures of SUMO1_HUMAN (Table 2) as examples are taken to compare the folding conformations. First, these 3D structures were obtained by different measurement methods, under different environments and interaction with different molecules. Second, many conformations can be generated from these protein 3D structures. 1A5R has 10 of conformations which is NMR experimental data in water solution.11Bayer, P., Arndt, A., Metzger, S., Mahajan, R., Melchior, F., Jaenicke, R., Becker, J. Structure determination of the small ubiquitin-related modifier SUMO-1 [J]. Journal of Molecular Biology, 280(2):275, (1998). The rest of protein complex structures were measured by X-ray crystal diffraction, 1Y8R has two chains and 3KYD, 1WYW, , 2PE6, 3KYC and 2BF8 has one chain respectively22Olsen SK1, Capili AD, Lu X, Tan DS, Lima CD.,Active site remodelling accompanies thioester bond formation in the SUMO E1, Nature. 463(7283):906-12, (2010).,33Baba D, Maita N, Jee J G, et al. Crystal structure of thymine DNA glycosylase conjugated to SUMO-1[J]. Nature, 435(7044):979-82, (2005).,44Lois L M, Lima C D. Structures of the SUMO E1 provide mechanistic insights into SUMO activation and E2 recruitment to E1[J]. Embo Journal, 24(3):439-51, (2005).,55Capili A D, Lima C D. Structure and Analysis of a Complex between SUMO and Ubc9 Illustrates Features of a Conserved E2-Ubl Interaction[J]. Journal of Molecular Biology, 369(3):608-618, (2007).,66Pichler A, Knipscheer P, Oberhofer E, et al. SUMO modification of the ubiquitin-conjugating enzyme E2-25K[J]. Nature Structural & Molecular Biology, 12(3):264-9, (2005).. Thus, these seven SUMO1 protein structures contain total of 17 folding conformations, and they are respectively converted into 17 of PFSC strings according their coordinates of alpha C-atoms. The PFSC strings for fragment (21-84) for 17 folding conformations of SUMO1_HUMAN are aligned and listed in the top section of Table 5.
It is easy to compare the similarity or dissimilarity of structure conformations with alignment of PFSC alphabetical strings. We try to find out how many of different types of local folding shapes in each column exist for 17 of folding conformations for seven 3D structures. In order to do so, all PFSC letters for conformation of 1A5R-01 (model 1) are firstly counted and marked by yellow background color. Then, for the rest of 16 PFSC strings, any PFSC letter in same column not same as 1A5R-01 or other will be highlighted by yellow. Thus, the PFSC letters with yellow color on each column will reveal what different types of folding shapes exist for each of 5 successive amino acid residues. For the 17 known conformations, the fragment (21-84) in SUMO1 has 64 columns, i.e. 64 sets of 5 successive amino acid residues in structure. There are 9 columns which have the identical local folding shapes as 1A5R-01, and the remainder 55 columns have at least one different local folding shape from 1A5R-01. Therefore, it is not too hard to detect the similarity or dissimilarity for 17 conformations with alignment of PFSC strings. First, all 17 conformations have similar secondary structures distributed along sequence which is observed by the PFSC letter colors. Second, none of 16 conformations are matching 1A5R-01. Third, it is apparent that each structure has unique folding conformations and can be distinguished from each other. Specifically all six structures from X-ray crystallography have larger alterations of local folds than 1A5R-01 conformations from NMR measurement. In summary, despite overall similarity of secondary structure, the known 3D structures of SUMO1 protein have different folding conformations which are well revealed by alignment of PFSC strings.
The PFVM of SUMO1_HUMAN protein contains the comprehensive folding information which embraces all 17 folding conformations of known structures. The PFVM for SUMO1_HUMAN protein is displayed on the bottom section of Table 5. The PFSC letters on each column represent the possible folds for each 5 successive amino acids. In order to show the PFVM covering the folds in the known structures, any PFSC letters in PFVM, which already have appeared on same column for known structures, are marked by yellow. It is apparently that all folding letters with yellow in the known structures are enclosed by the PFVM. For example, the PFVM in column 38 has 3 types of folds (W, B and L) covering the folds of “W” and “L” in given structures; the PFVM in column 39 has 4 types of folds (C, S, W and R) covering the folds of “C”, “S” and “R” in given structures; the PFVM in column 40 has 6 types of folds (Y, S, V, Z, B and C) covering the folds of “V”, “B” and “Y” in the given structures and etc. Thus, the PFVM has complete local folding variations, which is able to cover the folding changes in given 3D structures of SUMO1 protein. Furthermore, the most possible conformations are able to be predicted by PFVM. The PFSC string on first row of PFVM in Table 5, which is comprised of the local folding shapes with the most tendencies, directly present one of the most possible conformations for SUMO1 protein. With yellow colors of PFSC letters, it is apparent that the predicted conformation is overall aligned well with all of 17 conformations from known 3D structural. Also, the most possible conformation has 60 among 64 PFSC letters with the marked yellow color, which indicated the most possible conformations is matched with the known structures. In conclusion, the PFSC string on first row in PFVM provides one of well predicted conformations. Also, comprehensive local folding variations in PFVM are able to cover the various conformations of SUMO1 protein from known 3D structures.