Additional file 11: Figure S7. of Sequence-based prediction of permissive stretches for internal protein tagging and knockdown

PSS-identified permissive stretches are enriched to be surface accessible. Each plot summarizes the predicted surface accessibility and the predicted secondary structure of each residue for all test proteins (upper panel within each plot) as well as relative surface accessibility and secondary structure calculated from available crystal structures by the DSSP algorithm (lower panel within each plot). (a) Adk, (b) Bla, (c) TpiA, (f) AtpA, (g) AtpD, and (h) GpsA. PSs are highlighted in grey. The RSA of a site is defined as the geometric mean of the RSAs of its flanking residues, while the RSA of a predicted stretch is defined as the maximum site RSA in the stretch. RSAs of stretches derived from predictions and crystal structures are summarised in Additional file 10: Table S4. For illustration, identified permissive stretches were mapped onto the surface representation of the crystal structures of TEM1 β-lactamase (PDB 1AXB) (d), TpiA (shown as dimer, PDB 1TRE) (e), and the F1 part of ATP synthase (PDB 3OAA) (i). α-subunits (AtpA) are shown in light green, β-subunits are shown in dark green, and the γ-subunit is shown in yellow. PSs are marked in grey. For permissive site numbering refer to Additional file 3: Figure S1; Additional file 4: Figure S2, and Additional file 9: Figure S6. For TpiA and Bla, two different orientations are displayed to capture all PSs. Note that PSVIII within TpiA is not surface exposed and therefore not visible. PSI and PSVII within AtpA are not resolved in the crystal structure and therefore not given. (ZIP 13 kb)

经PSS鉴定的允许区域（permissive stretches）在蛋白表面可及区域中显著富集。每个子图均汇总了所有待测蛋白各残基的预测表面可及性与预测二级结构（各子图上方面板），以及通过DSSP算法从已解析晶体结构计算得到的相对表面可及性与二级结构（各子图下方面板）。(a) Adk、(b) Bla、(c) TpiA、(f) AtpA、(g) AtpD及(h) GpsA。PSs以灰色高亮标注。相对表面可及性（Relative Surface Accessibility，以下简称RSA）的位点定义为其侧翼残基RSA的几何均值，而预测区域的RSA则定义为该区域内所有位点RSA的最大值。基于预测与晶体结构得到的区域RSA汇总于补充材料10：表S4。为便于展示，本研究鉴定得到的允许区域被映射至以下蛋白晶体结构的表面渲染图：(d) TEM1 β-内酰胺酶（PDB 1AXB）、(e) 以二聚体形式展示的TpiA（PDB 1TRE）以及(i) ATP合酶的F1结构域（PDB 3OAA）。其中α亚基（AtpA）以浅绿色展示，β亚基以深绿色展示，γ亚基以黄色展示。PSs以灰色标注。允许区域的位点编号详见补充材料3：图S1、补充材料4：图S2及补充材料9：图S6。针对TpiA与Bla，本研究展示了两种不同的视角以覆盖所有PSs。需注意，TpiA内的PSVIII未暴露于蛋白表面，因此无法在图中显示。AtpA内的PSI与PSVII未在晶体结构中解析，因此未予展示。（压缩包，13 KB）