ArticleBiophysical journal2011
Molecular simulation uncovers the conformational space of the λ Cro dimer in solution.
Article in Biophysical journal, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 7 papers.
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Who cites it
7 citing papers in PubMed.
- Replica exchange molecular dynamics simulations reveal self-association sites in M-crystallin caused by mutations provide insights of cataract.Scientific reports · 2021Article
- Extreme divergence between one-to-one orthologs: the structure of N15 Cro bound to operator DNA and its relationship to the λ Cro complex.Nucleic acids research · 2019Article
- Role of Computational Methods in Going beyond X-ray Crystallography to Explore Protein Structure and Dynamics.International journal of molecular sciences · 2018Review
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- Replica exchange molecular dynamics simulations provide insight into substrate recognition by small heat shock proteins.Biophysical journal · 2014Article
- Network visualization of conformational sampling during molecular dynamics simulation.Journal of molecular graphics & modelling · 2013Article
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2 authors.
Funding
Abstract
The significant variation among solved structures of the λ Cro dimer suggests its flexibility. However, contacts in the crystal lattice could have stabilized a conformation which is unrepresentative of its dominant solution form. Here we report on the conformational space of the Cro dimer in solution using replica exchange molecular dynamics in explicit solvent. The simulated ensemble shows remarkable correlation with available x-ray structures. Network analysis and a free energy surface reveal the predominance of closed and semi-open dimers, with a modest barrier separating these two states. The fully open conformation lies higher in free energy, indicating that it requires stabilization by DNA or crystal contacts. Most NMR models are found to be unstable conformations in solution. Intersubunit salt bridging between Arg(4) and Glu(53) during simulation stabilizes closed conformations. Because a semi-open state is among the low-energy conformations sampled in simulation, we propose that Cro-DNA binding may not entail a large conformational change relative to the dominant dimer forms in solution.
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