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.