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Crystal packing interaction that blocks crystallization of a site‐specific DNA binding protein–DNA complex

Crystal packing interaction that blocks crystallization of a site‐specific DNA binding... We present here three high‐resolution crystal structures of complexes between the DNA‐binding domain of the heat‐shock transcription factor (HSF) and DNA oligomers. Although the DNA oligomers contain HSF's specific binding sequence, called a heat‐shock element, the crystal structures do not contain the specific protein–DNA complex. In one crystal structure, the 10 base pair DNA oligomer is statically disordered. In the other two related structures, the 12 base pair DNA oligomers are in unique positions, but the protein–DNA contacts in these two crystals are not sequence specific. In all three structures, the DNA appears to act as a rigid, polyanion scaffold to support columns of proteins in a crystalline lattice. A robust crystal packing interface between protein monomers obscures the true DNA‐binding surface, known from previous genetic and biochemical studies. By redesigning the protein to interfere with the crystal lattice contacts, we were able to obtain physiologically relevant crystals in a specific protein–DNA complex. Thus, a crystal‐packing interface was able to prevent the weak, but physiological relevant interactions between a protein and DNA. Proteins 2001;45:219–228. © 2001 Wiley‐Liss, Inc. http://www.deepdyve.com/assets/images/DeepDyve-Logo-lg.png Proteins: Structure Function and Bioinformatics Wiley

Crystal packing interaction that blocks crystallization of a site‐specific DNA binding protein–DNA complex

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References (35)

Publisher
Wiley
Copyright
Copyright © 2001 Wiley Subscription Services
ISSN
0887-3585
eISSN
1097-0134
DOI
10.1002/prot.1142
Publisher site
See Article on Publisher Site

Abstract

We present here three high‐resolution crystal structures of complexes between the DNA‐binding domain of the heat‐shock transcription factor (HSF) and DNA oligomers. Although the DNA oligomers contain HSF's specific binding sequence, called a heat‐shock element, the crystal structures do not contain the specific protein–DNA complex. In one crystal structure, the 10 base pair DNA oligomer is statically disordered. In the other two related structures, the 12 base pair DNA oligomers are in unique positions, but the protein–DNA contacts in these two crystals are not sequence specific. In all three structures, the DNA appears to act as a rigid, polyanion scaffold to support columns of proteins in a crystalline lattice. A robust crystal packing interface between protein monomers obscures the true DNA‐binding surface, known from previous genetic and biochemical studies. By redesigning the protein to interfere with the crystal lattice contacts, we were able to obtain physiologically relevant crystals in a specific protein–DNA complex. Thus, a crystal‐packing interface was able to prevent the weak, but physiological relevant interactions between a protein and DNA. Proteins 2001;45:219–228. © 2001 Wiley‐Liss, Inc.

Journal

Proteins: Structure Function and Bioinformatics – Wiley

Published: Jan 15, 2001

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