Figures from our research.

Why is binding of a divalent metal cation to a structural motif containing four carboxylate residues not accompanied by a conformational change?

The three major metal‐binding sites in the TcAChE crystal structures. The 4D site consists of Asp326, Asp389, Asp392, and Asp393; the 2nd site consists of His264 and surrounding Glu residues; the 3rd site consists of His471 and surrounding Glus. The structure shown is that of 7B38, in which all three sites are occupied (Silman et al., 2021).

Publication · Open-access archive · CC BY-NC 4.0 · Original figure

© 2024 The Author(s). Protein Science published by Wiley Periodicals LLC on behalf of The Protein Society.

GrAfSS: a webserver for substructure similarity searching and comparisons in the structures of proteins and RNA

Example of a search process that a GrAfSS user can carry out to (A) explore a thematic spatial formation by providing a conceptual amino acid arrangement and searching: (B) a database of non-redundant PDB structures or (C) a database of biological assemblies from the PDB. (D) The results of the search can then be further investigated by providing the specific arrangement as a query to determine whether there are other representative structures in the PDB that also contain a similar arrangement. All search results can then be visualized using the embedded NGL viewer as presented in (B), (C) and (D).

Publication · Open-access archive · CC BY 4.0 · Original figure

© The Author(s) 2022. Published by Oxford University Press on behalf of Nucleic Acids Research.

Graph Theoretical Methods and Workflows for Searching and Annotation of RNA Tertiary Base Motifs and Substructures

Annotation of pseudoknot motifs in RNA structures from PDB by NASSAM. (A) The 28 nucleotides (components) of a pseudoknot motif from the beet western yellow virus (PDB ID: 437D). The components selected to construct the pattern are labeled as Base 1 to Base 10. The red-colored letters indicate component types, either A, G, U, or C. The pseudo-atoms of the pattern are denoted as graph nodes (orange circles), and the distances between pseudo-atoms are denoted as graph edges (black dashed lines). Only a few of the pseudo-atoms and their distances are shown for clarity. (B) The pattern (PDB ID: 437D) base arrangements, shown as cyan-colored stick structures, are superimposed to the base arrangements of hits (PDB ID: 1L3D, 1L2X) shown as magenta-colored and purple-colored stick structures, respectively. The bases are labeled based on the sequence identifiers of the hit structures. The superimpositions of the backbones between the pattern and the hits are also shown to illustrate that the hits adopt pseudoknot structures.

Publication · Open-access archive · CC BY 4.0 · Original figure

© 2021 by the authors. Licensee MDPI, Basel, Switzerland.