Journal: PLoS ONE

Article Title: Structural Insights into the Globular Tails of the Human Type V Myosins Myo5a, Myo5b, and Myo5c

doi: 10.1371/journal.pone.0082065

Figure Lengend Snippet: ( A–C ) Surface envelopes calculated from SAXS data revealed that Myo5a GD (A), Myo5b GD (B), and Myo5c GD (C) have very similar shapes in solution. See Figure S1 in for details of SAXS measurements. ( D ) Ribbon representation of the Myo5a GD crystal structure at 2.2 Å, with the small C-terminal beta-sheet shown in orange. The missing loop I (1640 to 1658) is depicted as a blue dashed line, loop II is highlighted in green. ( E ) Same structure as in (D), but rotated 180° around the vertical axis. Rainbow color-coding follows the peptide chain from its N-terminus in blue to its C-terminus in red. ( F ) Ribbon representation of the Myo5b GD crystal structure at 3.1 Å resolution. First and last residue of the missing loops I and II are depicted in blue or green, respectively. ( G ) Ribbon representation of the modeled structure of the GD from Myo5c, calculated with the program Modeller and the structures of Myo5a (D–E) and Myo5b (F) as templates. For a Ramachandran plot of the computed model, see Figure S4 in . ( H ) Close-up of (D), slightly rotated to better show the position of the small beta-sheet (orange) that connects the very N-terminus with the C-terminus. Figures were generated with the program Pymol.

Article Snippet: Protein Databank ID for Myo5a GD and for Myo5b GD are 4LLI and 4LNZ, respectively.

Techniques: Residue, Generated

Journal: PLoS ONE

Article Title: Structural Insights into the Globular Tails of the Human Type V Myosins Myo5a, Myo5b, and Myo5c

doi: 10.1371/journal.pone.0082065

Figure Lengend Snippet: Data collection, phasing and refinement statistics for Myo5a globular domain (MAD).

Article Snippet: Protein Databank ID for Myo5a GD and for Myo5b GD are 4LLI and 4LNZ, respectively.

Techniques:

Journal: PLoS ONE

Article Title: Structural Insights into the Globular Tails of the Human Type V Myosins Myo5a, Myo5b, and Myo5c

doi: 10.1371/journal.pone.0082065

Figure Lengend Snippet: Orientation is as shown in (left) and rotated by 180° around the vertical axis (right). ( A ) Amino acid conservation between human Myo5a, Myo5b, and Myo5c GDs based on alignment shown in Figure S3 in and plotted on the structure of Myo5a GD. Green indicates high sequence conservation, yellow partial conservation, and white a lack of conservation. ( B–D ) Unique surface residues in Myo5a (B), Myo5b (C), or Myo5c (D), when compared to their respective paralogs, are shown in red. ( E–G ) Representation of surface potentials of Myo5a (E), Myo5b (F), and Myo5c (G). Red and blue indicate surface areas with negative and positive surface charges, respectively. White regions indicate hydrophobic regions. The surface region encircled by a red dotted line is an area with high similarity of overall surface charges amongst the three type V myosins (see also Figure S6 in ). This similarity might hint at a common function in all three paralogs. ( H ) Amino acids required for Rab11a binding are highlighted in magenta, residues in red are essential for motor autoinhibition.

Article Snippet: Protein Databank ID for Myo5a GD and for Myo5b GD are 4LLI and 4LNZ, respectively.

Techniques: Sequencing, Binding Assay

Journal: PLoS ONE

Article Title: Structural Insights into the Globular Tails of the Human Type V Myosins Myo5a, Myo5b, and Myo5c

doi: 10.1371/journal.pone.0082065

Figure Lengend Snippet: ( A ) Surface representation of Myo5a GD with residues K1708 and K1781 highlighted in red. Their mutation resulted in a loss of autoinhibition . ( B ) Comparison of electrostatic surface potentials of K1708 and K1781 (red circles) with identical positions in Myo5b and Myo5c and the conservation of these residues in all three paralogs (Figure S3 in ) suggests that autoinhibition might be a general feature of human type V myosins. Figures were generated with the program Pymol.

Article Snippet: Protein Databank ID for Myo5a GD and for Myo5b GD are 4LLI and 4LNZ, respectively.

Techniques: Mutagenesis, Comparison, Generated

Journal: PLoS ONE

Article Title: Structural Insights into the Globular Tails of the Human Type V Myosins Myo5a, Myo5b, and Myo5c

doi: 10.1371/journal.pone.0082065

Figure Lengend Snippet: ( A ) Docking of our high resolution Myo5a GD structure into a previously published 24 Å electron density map of the inhibited Myo5a motor (PDB-ID of published model lacking the globular domain: 2DFS). Shown are three modeled myosin dimers in the EM density (meshed surface rendering) that are arranged in a flower-like fashion. The color scheme is as follows: blue, Myo5a GD; green, motor domain, lever arm, light chains, coiled coil domain; turquoise, neighboring dimers. ( B ) Close-up of (A), depicting the Myo5a head complex (green) and the fitted GD (blue). Residues previously reported to be required for autoinhibition are shown as colored spheres. ( C ) Close-up of the upper rectangle in (B). ( D ) Close-up of the lower rectangle in (B). Loop I is disordered in the structural data. Depicted are three computed models for the flexible loop I, highlighted in yellow, orange, and magenta. ( E ) Atomic model of Myo5a. Missing amino acids of the flexible loop I GD are depicted as a blue dashed line (disordered loop I: 1640–1658), loop II in green (1787–1797), and amino acids important for interaction with the motor domain are highlighted in red (K1708, K1781). Residues important for Rab11a binding (Y1721 and Q1755) are shown in magenta and the beta-sheet is depicted in orange. Computed models for the flexible loop I were depicted in yellow, orange, and magenta (see also D). Figures were generated with the program Pymol.

Article Snippet: Protein Databank ID for Myo5a GD and for Myo5b GD are 4LLI and 4LNZ, respectively.

Techniques: Binding Assay, Generated

Journal: PLoS ONE

Article Title: Structural Insights into the Globular Tails of the Human Type V Myosins Myo5a, Myo5b, and Myo5c

doi: 10.1371/journal.pone.0082065

Figure Lengend Snippet: ( A ) Diagram shows a representative steady-state binding experiment with surface-coupled Myo5a GD and its motor complex (Myo5a HMM) using a multi-injection protocol. The K d = 30±20 nM was derived from two independent measurements, as recommended by the manufacturer. ( B, C ) Kinetic binding experiments of Myo5a GD interaction with its motor complex (Myo5a HMM). (B) shows sensograms with representative kinetic measurements (thick lines) at 77 nM, 38.6 nM, and 9.7 nM Myo5a (HMM) and the corresponding curve fittings (thin lines). Off-rates were determined from this concentration range using bivalent curve fitting. Curve fittings with chi 2 <0.2 (n = 5) were used to determine average K off values (C).

Article Snippet: Protein Databank ID for Myo5a GD and for Myo5b GD are 4LLI and 4LNZ, respectively.

Techniques: Binding Assay, Injection, Derivative Assay, Concentration Assay

Journal: Bioinformation

Article Title: Functional interpretation and structural insights of Arabidopsis lyrata cytochrome P450 CYP71A13 involved in auxin synthesis

doi: 10.6026/97320630011330

Figure Lengend Snippet: Sequence alignment of human cytochrome P450 (P10635) and Arabidopsis lyrata cytochrome P450. The alignment was generated using the program MAFFT program (15). Red tubes denote α-helices and cyan β-sheets. Residues shown on a green background are involved in heme anchoring and residues on a magenta background are within five angstroms of the docked substrate.

Article Snippet: A BLAST search of the Protein Databank demonstrated strongest similarity with human cytochrome P450 PDB code 3QM4 [ ].

Techniques: Sequencing, Generated

Journal: Bioinformation

Article Title: Functional interpretation and structural insights of Arabidopsis lyrata cytochrome P450 CYP71A13 involved in auxin synthesis

doi: 10.6026/97320630011330

Figure Lengend Snippet: Ramachandran plot of Φ-ψ distribution of modeled cytochrome P450 CYP71A13 produced by PROCHECK after homology modeling and energy minimization. (A, B, L) most favoured regions; (a, b, l, p) additional allowed region; (-a, -b, -l, -p) generously allowed region; white areas are disallowed regions.

Article Snippet: A BLAST search of the Protein Databank demonstrated strongest similarity with human cytochrome P450 PDB code 3QM4 [ ].

Techniques: Produced

Journal: Bioinformation

Article Title: Functional interpretation and structural insights of Arabidopsis lyrata cytochrome P450 CYP71A13 involved in auxin synthesis

doi: 10.6026/97320630011330

Figure Lengend Snippet: Overview of the modeled cytochrome P450 CYP71A13 structure. The overall structure of cytochrome P450 CYP71A13 was coloured blue to red from N-terminus to Cterminus. The letters indicate the name of the helices.

Article Snippet: A BLAST search of the Protein Databank demonstrated strongest similarity with human cytochrome P450 PDB code 3QM4 [ ].

Techniques:

Journal: Bioinformation

Article Title: Functional interpretation and structural insights of Arabidopsis lyrata cytochrome P450 CYP71A13 involved in auxin synthesis

doi: 10.6026/97320630011330

Figure Lengend Snippet: Active site of cytochrome P450 CYP71A13 from Arabidopsis lyrata A) Surface representation of amino acid hydrophobicity in cytochrome P450 CYP71A13 with a color scale that varies from blue to white, representing dodger blue for the most hydrophilic, to white for the most hydrophobic residues; B and C show features of the substrate indole-3-acetaldoxime binding pocket of cytochrome P450 CYP71A13 and D represents amino acids involved in stabilization of heme in cytochrome P450 CYP71A

Article Snippet: A BLAST search of the Protein Databank demonstrated strongest similarity with human cytochrome P450 PDB code 3QM4 [ ].

Techniques: Binding Assay