Abstract
An essential step in the regulation of gene expression is the binding of a regulatory protein to a specific DNA sequence in the promotor region of the gene. The understanding of protein-DNA recognition is, therefore, a major theme in structural biology. Much progress has been made since the early ’80s when the first structures of bacterial DNA-binding proteins and protein-DNA complexes were solved by X-ray crystallography (for reviews see Steitz (1990), Pabo and Sauer (1992) and Travers (1993)). NMR started to contribute around 1985 with the structure elucidation of the lac repressor headpiece (Kaptein et al., 1985) and a low resolution structure of the headpiece-operator complex (Boelens et al., 1987). These first prokaryotic DNA-binding proteins all contained the helix-turn-helix motif as the DNA-binding subdomain. However, subsequently a large number of other structural motifs has been characterized including zinc-fingers, leucine zippers, helix-loop-helix proteins and β-sheet DNA binding proteins.
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Discussion
Carol Post - Rob, when you put in those additional terms for the Monte Carlo potential field, how do you give an effective force constant.
Robert Kaptein - This has to be calibrated somehow. There’s always noise in these calculations. So you have to put a number there that is significant in terms of the noise that you generate in the structures. That is just by trial and error. There’s no a priori way one could do that.
Mike Mossing - The other class of mutagenesis data would be the sequence of the DNA. Have you cross checked these things by changing the sequence of the operator to something that it wouldn’t recognize?
Kaptein - We haven’t done that yet. Well, in a way we have by shifting it, out of register. That’s a complete different sequence.
Mossing - Is it something it didn’t recognize? Let’s say a single base pair change in the operator.
Kaptein - No, we haven’t done that.
Marc Adler - In your structures of protein and DNA, there seems to be a fair amount of wobble between the packing of the protein against the DNA. I was wondering if some of the changes are concerted. This could be shown by cluster analysis where you might be giving concerted change in sidechain packing.
Kaptein - We haven’t analyzed it really that way. Of course, what one expects is that there is a change in conformation disrupting a hydrogen bond that it will be forming another hydrogen bond, but whether there are concerted changes other than that, I don’t know. Mengli Cai - When you do the dimer protein you collected a set of NMR data. What’s a good indication or evidence to say this protein is a dimer?
Kaptein - This was known before we started work on this system. It was just by some type of molecular weight analysis that it was known that this is a dimer. So we did not do that. Sometimes of course, you will have to establish that first.
Cai - Second question, how much time is needed to run restrained molecular dynamics for 80 ps. How long does it take to complete that?
Kaptein - That was a long run. That took, in fact, several months for one structure done three years ago. That was a big calculation.
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Kaptein, R., Slijper, M., Chuprina, V.P., Rullmann, J.A.C., Knegtel, R.M.A., Boelens, R. (1996). Protein-DNA Interaction from NMR and Monte Carlo Docking. In: Rao, B.D.N., Kemple, M.D. (eds) NMR as a Structural Tool for Macromolecules. Springer, Boston, MA. https://doi.org/10.1007/978-1-4613-0387-9_14
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