macpymol software  (DeLano Scientific LLC PyMOL)

Journal: The Journal of Biological Chemistry

Article Title: Characterization of Microfibrillar-associated Protein 4 (MFAP4) as a Tropoelastin- and Fibrillin-binding Protein Involved in Elastic Fiber Formation *

doi: 10.1074/jbc.M115.681775

Figure Lengend Snippet: Structure of the S1 binding site of MFAP4. A, sequence alignment of the S1 site in MFAP4, FIBCD1, l-ficolin, and TL5A. The numbers on top and bottom refer to MFAP4 and TL5A sequences, respectively. Conserved residues are highlighted in gray. Residues in the S1 site are marked in red. The mutations performed in this study are indicated. The accession numbers were as follows: MFAP4, AAH62415.1; l-ficolin, NP_001994.2; FIBCD1, NP_116232.3; and TL5A, 1JC9_A. B, gel filtration elution profile of MFAP4 mutant variants. Elution positions of WT rMFAP4 are indicated with dashed lines. C, modeling of S1 binding site in WT MFAP4, with the indicated amino acids mutated in this study. The structure of l-ficolin (Protein Data Bank code 2J3O) was used as a template for modeling by SWISS-MODEL 8.05, and the figures were prepared using MacPyMOL software.

Article Snippet: A homology model of FReD was built by the server, and the figures were prepared using the MacPyMol software (DeLano Scientific).

Techniques: Binding Assay, Sequencing, Filtration, Mutagenesis, Software

Journal:

Article Title: Thermal Domain Motions of CheA Kinase in Solution: Disulfide Trapping Reveals the Motional Constraints Leading to Trans-autophosphorylation †

doi: 10.1021/bi900033r

Figure Lengend Snippet: The CheA homodimer and the disulfide trapping approach: (A) The present study focuses on the homodimeric histidine kinase CheA of Salmonella typhimurium. Shown is a structural model, with one identical subunit in ribbon format (blue) and the other in space filling (gold), pieced together from the high-resolution structures of (i) the P1 substrate domain of S. typhimurium CheA (17), (ii) the P2 CheY/B binding domain of E. coli CheA, which is highly homologous to S. typhimurium CheA (20), and (iii) the dimeric core region of the homologous Thermatoga maritima CheA, containing the P3 dimerization domain, the P4 catalytic domain, and the P5 regulatory domain (15). Also shown are simplified models of the long, presumably unstructured P1–P2 and P2–P3 linkers that are 25 and 30 residues in length in S. typhimurium CheA, respectively (17, 20, 22, 23, 25). Structural evidence indicates that an antiparallel interaction between symmetric β-strands at the N-terminus of the P3 dimerization domain directs the end of the P2–P3 linker toward the sister subunit in the same homodimer, as illustrated (15). MacPyMol graphics software (Delano Scientific) was used to build random coil, polyalanine segments of the same length as P1–P2 and P2–P3 and to display all structural elements. (B) Collisions between two cysteine residues can be trapped by oxidative disulfide bond formation. The rate of disulfide formation is defined largely by the collision rate and the efficiency of the oxidation reaction. Local environmental factors, including accessibility to oxidation agent, constraints on collision geometry, and altered sulfhydryl pKa can also modulate the overall reaction rate (27–32).

Article Snippet: MacPyMol graphics software (Delano Scientific) was used to build random coil, polyalanine segments of the same length as P1–P2 and P2–P3 and to display all structural elements. (B) Collisions between two cysteine residues can be trapped by oxidative disulfide bond formation.

Techniques: Binding Assay, Software