Research Article

Structure prediction of a complex between the chromosomal protein HMG-D and DNA

  1. Alexander Balaeff1,2,
  2. Mair E.A. Churchill2,3,
  3. Klaus Schulten1,2,4,*

Article first published online: 7 DEC 1998

DOI: 10.1002/(SICI)1097-0134(19980201)30:2<113::AID-PROT2>3.0.CO;2-O

Issue

Proteins: Structure, Function, and Bioinformatics

Proteins: Structure, Function, and Bioinformatics

Volume 30, Issue 2, pages 113–135, 1 February 1998

Additional Information

How to Cite

Balaeff, A., Churchill, M. E. and Schulten, K. (1998), Structure prediction of a complex between the chromosomal protein HMG-D and DNA. Proteins: Structure, Function, and Bioinformatics, 30: 113–135. doi: 10.1002/(SICI)1097-0134(19980201)30:2<113::AID-PROT2>3.0.CO;2-O

Author Information

  1. 1

    Beckman Institute, University of Illinois at Urbana-Champaign, Urbana, Illinois

  2. 2

    Center for Biophysics and Computational Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois

  3. 3

    Department of Cell and Structural Biology, University of Illinois at Urbana-Champaign, Chemistry and Life Sciences Laboratory, Urbana, Illinois

  4. 4

    Department of Physics, University of Illinois at Urbana-Champaign, Urbana, Illinois

*Beckman Institute, 405 N. Mathews Avenue, Urbana, IL 61801

Publication History

  1. Issue published online: 7 DEC 1998
  2. Article first published online: 7 DEC 1998
  3. Manuscript Accepted: 9 SEP 1997
  4. Manuscript Received: 2 JUL 1997

Funded by

  • Roy J. Carver Charitable Trust
  • National Institute of Health. Grant Number: PHS 5 P41 RR05969-04
  • National Science Foundation (K.S., A.B.). Grant Number: BIR-9318159
  • National Institute of Health, Shannon Award (M.E.A.C). Grant Number: GM52100

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Keywords:

  • HMG proteins;
  • protein-DNA complex;
  • HMG-box;
  • nonsequence-specificity;
  • molecular dynamics

Abstract

Non-histone chromosomal proteins are an important part of nuclear structure and function due to their ability to interact with DNA to form and modulate chromatin structure and regulate gene expression. However, the understanding of the function of chromosomal proteins at the molecular level has been hampered by the lack of structures of chromosomal protein–DNA complexes. We have carried out a molecular dynamics modeling study to provide insight into the mode of DNA binding to the chromosomal HMG-domain protein, HMG-D. Three models of a complex of HMG-D bound to DNA were derived through docking the protein to two different DNA fragments of known structure. Molecular dynamics simulations of the complexes provided data indicating the most favorable model. This model was further refined by molecular dynamics simulation and extensively analyzed. The structure of the corresponding HMG-D-DNA complex exhibits many features seen in the NMR structures of the sequence-specific HMG-domain-DNA complexes, lymphoid enhancer factor 1 (LEF-1) and testis determining factor (SRY). The model reveals differences from these known structures that suggest how chromosomal proteins bind to many different DNA sequences with comparable affinity. Proteins 30:113–135, 1998. © 1998 Wiley-Liss, Inc.

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