NUCPLOT: a program to generate schematic diagrams of protein-nucleic acid interactions.

AUTOR(ES)

Luscombe, N M

RESUMO

Proteins that bind to DNA are found in all areas of genetic activity within the cell. To help understand how these proteins perform their various functions, it is useful to analyse which residues are involved in binding to the DNA and how they interact with the bases and sugar-phosphate backbone of nucleic acids. Here we describe a program called NUCPLOT which can automatically identify these interactions from the 3D atomic coordinates of the complex from a PDB file and generate a plot that shows all the interactions in a schematic manner. The program produces a PostScript output file representing hydrogen, van der Waals and covalent bonds between the protein and the DNA. The resulting diagram is both clear and simple and allows immediate identification of important interactions within the structure. It also facilitates comparison of binding found in different structures. NUCPLOT is a completely automatic program, which can be used for any protein-DNA complex and will also work for certain protein-RNA structures.

Documentos Relacionados

• Methylphosphonates as probes of protein-nucleic acid interactions.
• Use of gel retardation to analyze protein-nucleic acid interactions.
• A double-filter method for nitrocellulose-filter binding: application to protein-nucleic acid interactions.
• Ribosomal protein-nucleic acid interactions. I. Isolation of a polypeptide fragment from 30S protein S8 which binds to 16S rRNA.
• A simple procedure for visualising protein-nucleic acid complexes by photochemical crosslinking.