The lac repressor hinge helix in context: The effect of the DNA binding domain and symmetry

Seckfort, Danielle; Lynch, Gillian C.; Pettitt, B. Montgomery

doi:10.1016/j.bbagen.2020.129538

Cited by 4 publications

(6 citation statements)

References 52 publications

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“…In the CHARMM force field (also with the TIP3P water), isolated hinge helices in solution are disordered. 58 But they are ordered as a part of a free LacI headpiece, 58 contrary to experiment. Such an excessive stability of the hinge helices may result from using the TIP3P water model which is a poor solvent for proteins.…”

Section: Resultsmentioning

confidence: 99%

C–B–A Test of DNA Force Fields

et al. 2023

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The DNA duplex may be locally strongly bent in complexes with proteins, for example, with polymerases or in a nucleosome. At such bends, the DNA helix is locally in the noncanonical forms A (with a narrow major groove and a large amount of north sugars) or C (with a narrow minor groove and a large share of BII phosphates). To model the formation of such complexes by molecular dynamics methods, the force field is required to reproduce these conformational transitions for a naked DNA. We analyzed the available experimental data on the B–C and B–A transitions under the conditions easily implemented in modeling: in an aqueous NaCl solution. We selected six DNA duplexes which conformations at different salt concentrations are known reliably enough. At low salt concentrations, poly(GC) and poly(A) are in the B-form, classical and slightly shifted to the A-form, respectively. The duplexes ATAT and GGTATACC have a strong and salt concentration dependent bias toward the A-form. The polymers poly(AC) and poly(G) take the C- and A-forms, respectively, at high salt concentrations. The reproduction of the behavior of these oligomers can serve as a test for the balance of interactions between the base stacking and the conformational flexibility of the sugar–phosphate backbone in a DNA force field. We tested the AMBER bsc1 and CHARMM36 force fields and their hybrids, and we failed to reproduce the experiment. In all the force fields, the salt concentration dependence is very weak. The known B-philicity of the AMBER force field proved to result from the B-philicity of its excessively strong base stacking. In the CHARMM force field, the B-form is a result of a fragile balance between the A-philic base stacking (especially for G:C pairs) and the C-philic backbone. Finally, we analyzed some recent simulations of the LacI-, SOX-4-, and Sac7d-DNA complex formation in the framework of the AMBER force field.

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Section: Resultsmentioning

confidence: 99%

C–B–A Test of DNA Force Fields

et al. 2023

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“…It has been suggested in theoretical ,− as well as in structural studies ,, that the folding of the hinge region into an α helix is crucial for the specific binding of the LacI transcription factor to its operator site. Whereas the structure of the hinge region in the specific complex is known, its native structure in the dimeric full-length LacI during facilitated diffusion has not been reported besides in an NMR study of the truncated DBD. ,, To obtain the NMR structures of the nonspecific complex, the core domain of the protein was removed by truncation of the protein right after the hinge helices and a mutation, V52C, was introduced to ensure the dimerization of the LacI DBD by the formation of a disulfide bridge (Figure S1C).…”

Section: Resultsmentioning

confidence: 99%

“…First, it does not have direct interactions with DNA. , Second, its conformation is retained between apo and DNA-bound LacI . It has therefore often been excluded from simulations of both LacI’s sliding mechanisms and its conformational transitions to save computational resources. ,,, That is why, as one of the first steps in our study, we tested if the core domain has an effect of LacI’s interaction with DNA.…”

Section: Resultsmentioning

confidence: 99%

“…It has been suggested in theoretical 39 , 55 − 58 as well as in structural studies 42 , 51 , 59 that the folding of the hinge region into an α helix is crucial for the specific binding of the LacI transcription factor to its operator site. Whereas the structure of the hinge region in the specific complex is known, its native structure in the dimeric full-length LacI during facilitated diffusion has not been reported besides in an NMR study of the truncated DBD.…”

Section: Resultsmentioning

confidence: 99%

“… 43 It has therefore often been excluded from simulations of both LacI’s sliding mechanisms and its conformational transitions to save computational resources. 55 , 58 , 60 , 61 That is why, as one of the first steps in our study, we tested if the core domain has an effect of LacI’s interaction with DNA.…”

Section: Resultsmentioning

confidence: 99%

See 2 more Smart Citations

Conformational Change of Transcription Factors from Search to Specific Binding: A lac Repressor Case Study

2022

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In a process known as facilitated diffusion, DNA-binding proteins find their target sites by combining three-dimensional diffusion and one-dimensional scanning of the DNA. Following the trade-off between speed and stability, agile exploration of DNA requires loose binding, whereas, at the DNA target site, the searching protein needs to establish tight interactions with the DNA. To enable both efficient search and stable binding, DNA-binding proteins and DNA often switch conformations upon recognition. Here, we study the one-dimensional diffusion and DNA binding of the dimeric lac repressor (LacI), which was reported to adopt two different conformations when binding different conformations of DNA. Using coarse-grained molecular dynamic simulations, we studied the diffusion and the sequence-specific binding of these conformations of LacI, as well as their truncated or monomeric variants, with two DNA conformations: straight and bent. The simulations were compared to experimental observables. This study supports that linear diffusion along DNA combines tight rotation-coupled groove tracking and rotation-decoupled hopping, where the protein briefly dissociates and reassociates just a few base pairs away. Tight groove tracking is crucial for target-site recognition, while hopping speeds up the overall search process. We investigated the diffusion of different LacI conformations on DNA and show how the flexibility of LacI’s hinge regions ensures agility on DNA as well as faithful groove tracking. If the hinge regions instead form α-helices at the protein–DNA interface, tight groove tracking is not possible. On the contrary, the helical hinge region is essential for tight binding to bent, specific DNA, for the formation of the specific complex. Based on our study of different encounter complexes, we argue that the conformational change in LacI and DNA bending are somewhat coupled. Our findings underline the importance of two distinct protein conformations for facilitated diffusion and specific binding, respectively.

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What distinguishes the elephant from E. coli: Causal spreading and the biological principles of metazoan complexity

Ball¹

2023

J Biosci

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The lac repressor hinge helix in context: The effect of the DNA binding domain and symmetry

Cited by 4 publications

References 52 publications

C–B–A Test of DNA Force Fields

C–B–A Test of DNA Force Fields

Conformational Change of Transcription Factors from Search to Specific Binding: A lac Repressor Case Study

What distinguishes the elephant from E. coli: Causal spreading and the biological principles of metazoan complexity

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