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Related data for publication: Novel knotted solenoid fold with order-shifted coil arrangement leads to nontrivial 31 topology

Version 1.0

Sikora, Maciej; Mozajew, Mariusz; Sikorska, Julia A.; Bruno da Silva, Fernando; Perlinska, Agata P.; Kluza, Anna; Niewieczerzal, Szymon; Lukaszewicz, Maciej; Wielgus-Kutrowska, Beata; Stachurska-Korzeniowska, Karolina; Jackson, Sophie E.; Sulkowska, Joanna I., 2026, "Related data for publication: Novel knotted solenoid fold with order-shifted coil arrangement leads to nontrivial 31 topology", https://doi.org/10.58132/3YFCPO, Dane Badawcze UW, V1

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Description

Related data for publication: Novel Knotted Solenoid fold with order-shifted coil arrangement leads to nontrivial 31 topology.

We present the first crystal structures of proteins adopting the Knotted Solenoid fold, a solenoidal architecture uniquely capable of forming a 31 knot through a ”skip-and-backtrack” shift, challenging the assumption that all β-solenoid proteins are unknotted. Knotted Solenoids occur exclusively in a specific group of bacteria and remain structurally conserved despite extreme sequence divergence. The fold forms a homodimer with a conserved interface, suggesting shared oligomerization state across all members. Biophysical analyses reveal reversible unfolding with chemical denaturants and computational studies suggest a self-tying folding pathway via a slipknot intermediate (monomer and dimer). These findings provide a model system to explore the evolutionary, structural, and functional implications of knotting and its role in shaping protein architecture.

Data include:

  • Validation report for structure 9RDS (PDF format)
  • Validation report for structure 9QIX (PDF format)
  • Validation report for structure 9SOJ (PDF format)
  • Related Dataset (csv spreadsheet)
  • 6 figures from main text (PNG format)
  • 22 figures from Supplementary Information (PNG format)

Currently the PDB crystal structures (9RDS, 9QIX, 9SOJ) are on hold prior to publication and will be publicly available in the PDB Database after the publication release. In the dataset we publish related validation reports obtained during deposition to PDB servers.

(2026)
Subject
Computer and Information Science; Medicine, Health and Life Sciences; Physics
Keyword

structural biology, non-trivial topology, Knotted Solenoid fold, protein design, evolution

CC BY - Creative Commons Attribution 4.0 CC BY - Creative Commons Attribution 4.0

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ValRep_9QIX.pdf
Adobe PDF - 609.3 KB - Apr 8, 2026 - 0 Downloads
MD5: 6a81870d86ad7144cc0f6649c60b0b9c
License: CC BY - Creative Commons Attribution 4.0
Validation Report for crystal structure 9QIX including crystal and structure parameters. Report obtained during PDB deposition process.
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ValRep_9RDS.pdf
Adobe PDF - 579.5 KB - Apr 8, 2026 - 0 Downloads
MD5: 84f08b3939cc3a24c6d25c52a26c511b
License: CC BY - Creative Commons Attribution 4.0
Validation Report for crystal structure 9RDS including crystal and structure parameters. Report obtained during PDB deposition process.
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ValRep_9SOJ.pdf
Adobe PDF - 600.8 KB - Apr 8, 2026 - 0 Downloads
MD5: 872c59d212b75e67e950ceea6fc11df1
License: CC BY - Creative Commons Attribution 4.0
Validation Report for crystal structure 9SOJ including crystal and structure parameters. Report obtained during PDB deposition process.
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solenoid_table.csv
Comma Separated Values - 12.2 KB - Apr 8, 2026 - 0 Downloads
MD5: 317ed1f95eda5df1583af1cdf3ed67a0
License: CC BY - Creative Commons Attribution 4.0
Table containing analyzed dataset with UniProt IDs in the first column and Category in the second column. Categories could be either Knotted Solenoid or CATH ID for other beta solenoids.
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FIG_1_summary-1.png
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MD5: ff8f18450acbbc719f85456fe947b5c3
License: CC BY - Creative Commons Attribution 4.0
Fig. 1. Crystal structures of Knotted Solenoid proteins with PDB ID: 9RDS, 9QIX and 9SOJ. A: Cartoon representations of structures viewed from the side and top. For each dimer shown from the side, chains on the left are colored by gradient from N to C terminal (blue to cyan, green to yellow, pink to red), while the chains on the right highlight the knot core. B: Comparison of Knotted Solenoid (9RDS, residues 13–127) with its closest unknotted homolog, a pentapeptide repeat protein (PRP) (UniProtKB: A0A4R2TS65, residues 56–173). Coils are colored and numbered to show order; in Knotted Solenoids a disrupted ”skip-and-backtrack” order is observed, absent in unknotted solenoids. C: Top view highlights other features. Knotted Solenoid coils consist of three parallel β-sheets connected by short turns, compared to four in PRPs. In both, phenylalanines form a repeating inward-pointing pattern. D: Violin plots of knot length statistics, with longer marker showing mean values.
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FIG_2_SEC_MALS-1.png
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MD5: 3fd66472af78ab9e044ff8520a386232
License: CC BY - Creative Commons Attribution 4.0
Fig. 2. Characterization of the size and compactness of Knotted Solenoid with PDB ID: 9RDS and 9QIX under native conditions. Elution and oligomerization analysis of Knotted Solenoids 9RDS (blue) and 9QIX (red) in the native state. A: FPLC purification profiles; inset shows calibration curve for MW estimation. B: Analytical SEC profiles; inset shows standard curve for MW estimation from elution volume. C: SEC-MALS analysis showing light scattering (LS), ultraviolet absorbance (UV), and differential refractive index (dRI) signals, normalized to 0–1 by dividing each spectrum by its maximum across the elution volume. Analysis for protein γ in Supplementary Information Figure S14. Protein samples in SEC buffer (50 mM Tris pH 7.4 at 25 ◦C, 200 mM NaCl, and 5% glycerol).
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FIG_3_dimer_figure-1.png
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MD5: fcc1e92e30935bf2449fab7a6e9df61c
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Fig. 3. Knotted Solenoid dimer interface and hydrophobicity. The analysis is based on the protein with PDB ID: 9QIX crystal structure (trimmed terminal six residues in both chains). Upper panel shows the sequence logo for the Knotted Solenoid group with residues colored by hydrophobicity. Below the sequence logo, the blue line represents sections of the protein forming an interface. Orange dots above represent especially conserved hydrophobic residues with side chains turned towards the channel, while pink ones represent those turned outwards. The lower panel shows side and top-down line representations of the dimer structure. Hydrophobic residues are colored according to the orientation of side chains: orange indicates side chains turned towards the channel, while pink marks those turned outwards.
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FIG_4_coordinate_profile-1.png
PNG Image - 446.4 KB - Apr 8, 2026 - 0 Downloads
MD5: 397628cfcb43f169b35f766b158e2456
License: CC BY - Creative Commons Attribution 4.0
Fig. 4 . Characterization of the Knot- ted Solenoid with comparison to pen- tapeptide repeat protein. The analy- sis is based on the protein with PDB ID: 9RDS (trimmed to residue range 13 to 127) and unknotted PRP protein (UniProtKB ID: A0A4R2TS65, trimmed to range 56 to 173) with all panels using the same color coding for each coil (Labeled C1 to C4 or C5 in the sequence order). A: Matrices visualize the RMSD similarity of individual coils. B: Two sets of coordinate profiles are shown for the y and z axis respectively. A clear difference can be observed between the two proteins, with Knotted Solenoid presenting a ”skip-and-backtrack” shift not present in the PRP. C: Fragment of the sequence logo for proteins with Knotted Solenoid fold without additional domain and PRP. Especially conserved residues repeating at the beginning of each coil are marked with red color, and a glycine-proline at the beginning of the knot core is marked with blue.
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FIG_5_stability-1.png
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MD5: a5b40aeb907655d05a13afdb39acdb6a
License: CC BY - Creative Commons Attribution 4.0
Fig. 5. Stability of Knotted Solenoid proteins against thermal and chemical denaturation. A: Apparent melting temperatures of 9RDS, 9QIX, and 9SOJ from DSF (SYPRO Orange) at increasing protein concentrations, each measured in triplicate. B: The heat capacity signal as a function of temperature. The maximum represents the midpoint of thermal unfolding whilst the area under the curve is an estimate of the ∆Happ, see Table 2. C: Time course of unfolding in 4 M guanidinium chloride for protein 9RDS, measured via far-UV CD, monitored at 220 nm; three independent replicates shown. The unfolding half-life of the protein is 26 ± 6 seconds. Fitting parameters can be found in Table S3. D: Fitting of molar ellipticity at 220 nm from far-UV CD spectra at varying urea concentrations for proteins 9RDS, 9QIX, and ϵ. Darker lines indicate unfolding and lighter ones refolding. Insets show boundary spectra: unfolded proteins in 7 M urea exhibited reduced signal, while refolded samples in 1.5 M urea closely matched native spectra in 0 M urea. Parameters of two-state model used for fitting can be found in SI, Table S2. In all experiments, the proteins were in the SEC buffer (50 mM Tris pH 7.4 at 25 ◦C, 200 mM NaCl, and 5% glycerol; CD with no glycerol).
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FIG_6_New_simulations-1.png
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MD5: 9435b19139837750279cc6da311ee305
License: CC BY - Creative Commons Attribution 4.0
Fig. 6. Folding mechanism of the Knotted Solenoid dimer (PDB ID: 9RDS) based on a structure-based coarse- grained model. A: Example of a folding trajectory shown based on the native con- tacts (Q) as a function of time. Each unit of the dimer is shown in red and blue, and the contacts at the interface are shown in magenta. Light and dark green indicate the formation of the knots. Conformations surrounding the chart are snapshots from the trajectory showing some of the most important steps, including the formation of two knots via slipknot topology. B: Diagram showing folding statistics. In 56% of the simulations, at least one chain folded and knotted successfully. In 26% trajectories, the second chain is folded after forming contacts with the already knotted chain, and in 6% of the trajectories, the second chain folds independently. In the reminding 24% of simulations, the process takes too long to observe either of the aforementioned scenarios. C: Free energy landscape as a function of Q and RMSD for the folding and unfolding of a single chain (independent equilibrium simulation of the monomer) and the struc- turally closest unknotted solenoid (PRP, shown in Figure 1B) and one-dimensional plot showing F(Q) for both proteins.
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