Journal: PLoS ONE

Article Title: Nanobody Mediated Crystallization of an Archeal Mechanosensitive Channel

doi: 10.1371/journal.pone.0077984

Figure Lengend Snippet: (A) Examples of initial crystallization hits for different T2/nanobody complexes obtained in various conditions of the JCSG+ and ProComplex screens. The scale bar for size estimations of the crystal is shown. (B) Table with initial crystallization hits obtained for the different T2/nanobody complexes in the two commercially available crystallization screens JCSG+ and ProComplex. (D) Diffraction image from one of the crystals obtained from the initial crystal screening (T2/nanobody 21 complex) diffracting to 8 Å resolution.

Article Snippet: The two sparse matrix screens, ProComplex and JCSG+ (Qiagen) were used for initial crystallization trials at 20 °C.

Techniques: Crystallization Assay

Journal: Cell chemical biology

Article Title: Ras Binder Induces a Modified Switch-II Pocket in GTP- and GDP-States

doi: 10.1016/j.chembiol.2017.08.025

Figure Lengend Snippet: Key Resources Table

Article Snippet: NeXtal DWBlock ProComplex , Qiagen , 130915.

Techniques: Virus, Recombinant, Phospho-proteomics, Plasmid Preparation, Mass Spectrometry, Protease Inhibitor

Journal: Scientific Reports

Article Title: Bacterial protease uses distinct thermodynamic signatures for substrate recognition

doi: 10.1038/s41598-017-03220-y

Figure Lengend Snippet: Data collection and refinement statistics.

Article Snippet: PeDPP11 22-717 S652A in the alternate conformation (PeDPP11 altconf ) was crystallized initially in the condition B2 of ProComplex screen (Qiagen®): 0.1 M calcium acetate, 10% w/v PEG 4000, 0.1 M sodium acetate pH 4.5.

Techniques:

Journal: Scientific Reports

Article Title: Bacterial protease uses distinct thermodynamic signatures for substrate recognition

doi: 10.1038/s41598-017-03220-y

Figure Lengend Snippet: Structure of Porphyromonas endodontalis DPP11. (a) Domain architecture of PeDPP11. SP is signal peptide. The locations of catalytic triad amino acids are indicated by “red stars”. (b) Ribbon representation of PeDPP11 structure. Domains are coloured as in item (a) and helix α14 is shown in dark blue. Upper panel shows two perpendicular views of unbound PeDPP11. Lower panel shows two perpendicular views of PeDPP11 as in complex with peptides (binding pocket shown as yellow surface). (c) Active site of PeDPP11:RD (peptide RD shown in green). Catalytic triad is underlined. Note that S652 is mutated to alanine. (d) Active site of PeDPP11:LDVW (peptide LDVW shown in magenta), peptide omit map contoured at 3σ, shown in blue.

Article Snippet: PeDPP11 22-717 S652A in the alternate conformation (PeDPP11 altconf ) was crystallized initially in the condition B2 of ProComplex screen (Qiagen®): 0.1 M calcium acetate, 10% w/v PEG 4000, 0.1 M sodium acetate pH 4.5.

Techniques: Binding Assay

Journal: Scientific Reports

Article Title: Bacterial protease uses distinct thermodynamic signatures for substrate recognition

doi: 10.1038/s41598-017-03220-y

Figure Lengend Snippet: Microcalorimetric analysis. Isothermal titration calorimetry experiments performed by titrating LD (left panel) and LDVW (right panel) into PeDPP11. Upper panel shows time-dependent deflection of heat for each injection (top). Integrated calorimetric data for the respective interactions (bottom). The continuous curve represents the best fit using a one-site binding model. Lower panel shows the graphical representation of thermodynamics parameters.

Article Snippet: PeDPP11 22-717 S652A in the alternate conformation (PeDPP11 altconf ) was crystallized initially in the condition B2 of ProComplex screen (Qiagen®): 0.1 M calcium acetate, 10% w/v PEG 4000, 0.1 M sodium acetate pH 4.5.

Techniques: Isothermal Titration Calorimetry, Injection, Binding Assay

Journal: Scientific Reports

Article Title: Bacterial protease uses distinct thermodynamic signatures for substrate recognition

doi: 10.1038/s41598-017-03220-y

Figure Lengend Snippet: Thermodynamic analysis. (a) PeDPP11 binding to LD. (b) PeDPP11 binding to LDVW. Upper panels: Temperature dependence of ∆ G , ∆ H and − T ∆S. Middle panel: Table with thermodynamic data derived from the ITC measurements at different temperatures. Lower panel: Entropy parameters estimations. Conformational entropy was calculated using the following equation: ∆ S conf = ∆ S tot − ∆ S sol − ∆ S rt . Where ∆ S sol = ∆ Cp ln (298 K/385 K) and ∆ S rt is estimated using the “cratic entropy” value of −33.3 J.mol. −1 K −1 .

Article Snippet: PeDPP11 22-717 S652A in the alternate conformation (PeDPP11 altconf ) was crystallized initially in the condition B2 of ProComplex screen (Qiagen®): 0.1 M calcium acetate, 10% w/v PEG 4000, 0.1 M sodium acetate pH 4.5.

Techniques: Binding Assay, Derivative Assay

Journal: Scientific Reports

Article Title: Bacterial protease uses distinct thermodynamic signatures for substrate recognition

doi: 10.1038/s41598-017-03220-y

Figure Lengend Snippet: PeDPP11 conformational changes. (a) Close-up view of the main PeDPP11 regions that unfold upon binding to LDVW, as observed in the crystal structures. (b) Loop F441-K451 region superposition of unbound PeDPP11 (blue), PeDPP11:LDVW (magenta, dashed line) and PeDPP11:RD (green). Unbound PeDPP11 is represented as ribbons and peptide binding pocket as yellow surface. (c) Cartoon representation depicting a DPP11 helix unfolding. Upon substrate binding, energy is absorbed from the solution to break polar contacts, which causes helix destabilization. In the disordered stage, the helix accesses different structural states, increasing system entropy. (d) Close-up view of the helix α14 missing region in PeDPP11 altconf . Intra-main chain polar contacts are indicated with orange dashed lines.

Article Snippet: PeDPP11 22-717 S652A in the alternate conformation (PeDPP11 altconf ) was crystallized initially in the condition B2 of ProComplex screen (Qiagen®): 0.1 M calcium acetate, 10% w/v PEG 4000, 0.1 M sodium acetate pH 4.5.

Techniques: Binding Assay