Journal: PLOS ONE

Article Title: B-cell epitope discovery: The first protein flexibility-based algorithm–Zika virus conserved epitope demonstration

doi: 10.1371/journal.pone.0262321

Figure Lengend Snippet: From left to right: Weighted isolated protein flexibility, weighted VLP protein flexibility, and the linearly combined, flexibility model are depicted over the mature ZIKV cryo-EM reconstruction (PDB ID: 5IRE) (scales shown). VLP structures are oriented with the five-fold rotational icosahedral symmetry axis coming out of the figure plane.

Article Snippet: ZIKV chains A, B, C, and E were extracted from a 3.80 Å resolution, cryogenic electron microscopy (cryo-EM) structure (Protein Databank (PDB) ID: 5IRE) [ ].

Techniques: Isolation, Cryo-EM Sample Prep

Journal: PLOS ONE

Article Title: B-cell epitope discovery: The first protein flexibility-based algorithm–Zika virus conserved epitope demonstration

doi: 10.1371/journal.pone.0262321

Figure Lengend Snippet: Predicted conserved epitopes are represented in yellow on the ZIKV cryo-EM reconstruction backbone (red) (PDB ID: 5IRE) . The cryo-EM reconstruction is shown with the five-fold rotational icosahedral symmetry axis coming out of the figure plane.

Article Snippet: ZIKV chains A, B, C, and E were extracted from a 3.80 Å resolution, cryogenic electron microscopy (cryo-EM) structure (Protein Databank (PDB) ID: 5IRE) [ ].

Techniques: Cryo-EM Sample Prep

Journal: Scientific Reports

Article Title: A molecular analysis of substituted phenylethylamines as potential microtubule targeting agents through in silico methods and in vitro microtubule-polymerization activity

doi: 10.1038/s41598-023-41600-9

Figure Lengend Snippet: A stick and ball representation using Pymol of docked colchicine, 25B-NBF, and 25C-NBF, DMBMPP and the crystal structure of colchicine. The docked structure of colchicine, 25B-NBF, 25C-NBF and DMBMPP follows this atomic coloring scheme: C: yellow, O: red, N: blue, Cl: green, Br: maroon, FL: light blue. ( A ) Colchicine (yellow) in a docked pose (left), and the overlay of the crystal pose of colchicine (grey) from PDB 4O2B and the docked colchicine (yellow)(right), RMSD = 0.2593 Å. ( B ) The docked pose of 25B-NBF (yellow) (left), and the overlay of the crystal pose of colchicine (grey) and the docked 25B-NBF (yellow)(right). ( C ) The docked pose of 25C-NBF (yellow) (left), and the overlay of the crystal pose of colchicine (grey) and the docked 25C-NBF (yellow) (right). ( D ) The docked pose of DMBMPP (yellow) (left), and the overlay of the crystal pose of colchicine (grey) and the docked DMBMPP (yellow) (right).

Article Snippet: The Protein Databank structure PDB 4O2B was used to model the tubulin-colchicine complex.

Techniques:

Journal: PLoS Pathogens

Article Title: Immunosuppressive Yersinia Effector YopM Binds DEAD Box Helicase DDX3 to Control Ribosomal S6 Kinase in the Nucleus of Host Cells

doi: 10.1371/journal.ppat.1005660

Figure Lengend Snippet: A) YopM_34–481 was crystallized and its structure was solved ( ; ). Stereo view shows ribbon representation of one asymmetric unit of the YopM_34–481 crystal (PDB code 4OW2). The asymmetric unit contains four molecules equivalent to two biological assemblies each represented by a dimer. YopM molecules of one dimer are colored in yellow and green and of the other dimer in light grey and grey. (B-D) The YopM_34–481 dimer, the DDX3_51–418 construct and the YopM_34-481/DDX3_51–418 complex were analyzed by small angle X-ray scattering (SAXS). B) The SASREF-model of YopM_34–481 shown as transparent grey surface representation and the crystal structure of the YopM_34–481 dimer in ribbon representation are superimposed. C) The SASREF-model of DDX3_51–418 shown as transparent grey surface representation and the crystal structure of the ATPase domain of DDX3 (residues 167–418, PDB code 2I4I) are superimposed. D) The SASREF-model of the YopM_34-481/DDX3_51–418 complex shown as transparent grey surface representation is superimposed with the crystal structures of DDX3 (residues 167–418; and the YopM_34–481 dimer (as presented in A). For experimental SAXS data see and .

Article Snippet: Relevant data of the YopM_34-481 crystal structure from Y. enterocolitica WA314 are deposited at the Protein Databank (PDB) ( http://www.rcsb.org/pdb/home/home.do ) with entry code 4OW2.

Techniques: Construct