Structure of the complex of lac repressor headpiece and an 11 base-pair half-operator determined by nuclear magnetic resonance spectroscopy and restrained molecular dynamics.Chuprina, V.P., Rullmann, J.A., Lamerichs, R.M., van Boom, J.H., Boelens, R., Kaptein, R.
(1993) J.Mol.Biol. 234: 446-462
- PubMed: 8230225
- DOI: 10.1006/jmbi.1993.1598
- Primary Citation of Related Structures:
- PubMed Abstract:
- Combined Procedure of Distance Geometry and Restrained Molecular Dynamics Techniques for Protein Structure Determination from Nuclear Magnetic Resonance Data: Application to the DNA Binding Domain of Lac Repressor from Escherichia Coli
De Vlieg, J.,Scheek, R.M.,Van Gunsteren, W.F.,Berendsen, H.J.C.,Kaptein, R.,Thomason, J.
(1988) Proteins 3: 209
- Complex of Lac Repressor Headpiece with a 14 Base Pair Lac Operator Fragment Studied by Two-Dimensional Nuclear Magnetic Resonance
Boelens, R.,Scheek, R.M.,Van Boom, J.H.,Kaptein, R.
(1987) J.Mol.Biol. 193: 213
- Restrained Molecular Dynamics Procedure for Protein Tertiary Structure Determination from NMR Data: A Lac Repressor Headpiece Structure Based on Information on J-Coupling and from Presence and Absence of Noes
De Vlieg, J.,Boelens, R.,Scheek, R.M.,Kaptein, R.,Van Gunsteren, W.F.
(1986) Isr.J.Chem. 27: 181
- Two-Dimensional NMR Study of a Protein-DNA Complex. Lac Repressor Headpiece-Operator Interaction
Kaptein, R.,Lamerichs, R.M.J.N.,Boelens, R.,Rullmann, J.A.C.
(1990) Biochem.Pharm. 40: 89
- 1H NMR Study of a Complex between the Lac Repressor Headpiece and a 22 Base Pair Symmetric Lac Operator
Lamerichs, R.M.J.N.,Boelens, R.,Van Der Marel, G.A.,Van Boom, J.H.,Kaptein, R.,Buck, F.,Fera, B.,Rueterjans, H.
(1989) Biochemistry 28: 2985
- NMR Based Docking Studies of Lac Repressor Headpiece on a Lac Operator Fragment
Rullmann, J.A.C.,Boelens, R.,Kaptein, R.
(1989) Ucla Symp.Mol.Cell.Biol., New Ser. 95: 11
- The Interaction of Lac Repressor Headpiece with its Operator: An NMR View
Boelens, R.,Lamerichs, R.M.J.N.,Rullmann, J.A.C.,Van Boom, J.H.,Kaptein, R.
(1988) Protein Seq.Data Anal. 1: 487
- A Two-Dimensional NMR Study of the Complex of Lac Repressor Headpiece with a 14 Base Pair Lac Operator Fragment
Boelens, R.,Scheek, R.M.,Lamerichs, R.M.J.N.,De Vlieg, J.,Van Boom, J.H.,Kaptein, R.
(1987) Nato Asi Ser.,Ser.A 137: 191
- Assignment of the 1H-NMR Spectrum of a Lac Repressor Headpiece-Operator Complex in H2O and Identification of Noes. Consequences for Protein-DNA Interaction
Lamerichs, R.M.J.N.,Boelens, R.,Van Der Marel, G.A.,Van Boom, J.H.,Kaptein, R.
(1990) Eur.J.Biochem. 194: 629
The structure of the complex of lac repressor headpiece and an 11 base-pair lac half-operator has been determined by NMR spectroscopy and restrained Molecular Dynamics calculations. In total 508 distances were derived from two-dimensional nuclear Ove ...
The structure of the complex of lac repressor headpiece and an 11 base-pair lac half-operator has been determined by NMR spectroscopy and restrained Molecular Dynamics calculations. In total 508 distances were derived from two-dimensional nuclear Overhauser enhancement measurements, 260 of which are within the headpiece, 212 within the operator and 36 between operator and headpiece. An equilibrium restrained Molecular Dynamics calculation of the complex in aqueous solution, spanning 85 picoseconds, has been used to analyze the structure. Configuration sampling by an annealing procedure has been undertaken as well in order to estimate the precision of the structure determination. Our data confirm the results of previous two-dimensional NMR studies that the orientation of the recognition helix of lac repressor in the major groove of DNA with respect to the operator dyad axis is opposite to the orientation found in complexes of other DNA binding proteins of the helix-turn-helix class. We find a number of tight contacts between the protein and the operator that are in agreement with the available genetic and biochemical data. The anchoring of lac headpiece on the operator is similar to that of other repressors. Other features are unique for lac headpiece: relative few direct hydrogen bonds between side-chains and bases; extensive apolar contacts; many direct and water-bridged contacts to phosphates from residues in or close to the recognition helix. Overall, an interconnected set of interactions is observed, involving base-specific contacts, phosphate contacts, intra-protein and water-bridged hydrogen bonds. Several of these interactions appear to be dynamic, i.e. fluctuating in time, rather than static.
Bijvoet Center for Biomolecular Research, University of Utrecht, The Netherlands.