PMID: 9449341Feb 4, 1998Paper

Comparison of simulated and experimentally determined dynamics for a variant of the Lacl DNA-binding domain, Nlac-P

Biophysical Journal
L Swint-KruseB Montgomery Pettitt

Abstract

Recent advances in the experimentally determined structures and dynamics of the domains within LacI provide a rare context for evaluating dynamics calculations. A 1500-ps trajectory was simulated for a variant of the LacI DNA-binding domain, which consists of the first three helices in LacI and the hinge helix of the homologous PurR. Order parameters derived from dynamics simulations are compared to those obtained for the LacI DNA-binding domain with 15N relaxation NMR spectroscopy (Slijper et al., 1997. Biochemistry. 36:249-254). The MD simulations suggest that the unstructured loop between helices II and III does not exist in a discrete state under the conditions of no salt and neutral pH, but occupies a continuum of states between the DNA-bound and free structures. Simulations also indicate that the unstructured region between helix III and the hinge helix is very mobile, rendering motions of the hinge helix essentially independent of the rest of the protein. Finally, the alpha-helical hydrogen bonds in the hinge helix are broken after 1250 ps, perhaps as a prelude to helix unfolding.

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Citations

Mar 23, 2002·Protein Science : a Publication of the Protein Society·Liskin Swint-KruseKathleen Shive Matthews
Oct 24, 2015·Archives of Biochemistry and Biophysics·Abdessamad Ababou, Mariola Zaleska
Oct 24, 2003·Protein Science : a Publication of the Protein Society·Terence C FlynnJianpeng Ma
Nov 30, 2018·PLoS Computational Biology·Brandon M ButlerS Banu Ozkan
Nov 30, 2018·Biopolymers·Danielle Seckfort, B Montgomery Pettitt
Jan 21, 2020·Biochimica Et Biophysica Acta. General Subjects·Danielle SeckfortB Montgomery Pettitt
Jul 21, 2006·The Journal of Physical Chemistry. B·Niharendu Choudhury, B Montgomery Pettitt
Mar 10, 2005·Journal of the American Chemical Society·Niharendu Choudhury, B Montgomery Pettitt

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