ArticleBiophysical journal2010
Analysis of the bacterial luciferase mobile loop by replica-exchange molecular dynamics.
Article in Biophysical journal, 2010. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 10 papers.
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Who cites it
10 citing papers in PubMed.
- An engineered disulfide staple restricts lid loop dynamics and alters substrate specificity of phenylalanine ammonia-lyase.bioRxiv : the preprint server for biology · 2026Article
- Structure-Function Relationships in Temperature Effects on Bacterial Luciferases: Nothing Is Perfect.International journal of molecular sciences · 2022Article
- Replica exchange molecular dynamics simulations reveal self-association sites in M-crystallin caused by mutations provide insights of cataract.Scientific reports · 2021Article
- QM/MM Investigation of the Spectroscopic Properties of the Fluorophore of Bacterial Luciferase.Journal of chemical theory and computation · 2021Article
- 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
- How do dynamic cellular signals travel long distances?Molecular bioSystems · 2012Review
- Protein-protein complexation in bioluminescence.Protein & cell · 2011Review
- Molecular simulation uncovers the conformational space of the λ Cro dimer in solution.Biophysical journal · 2011Article
- The evolution of protein structures and structural ensembles under functional constraint.Genes · 2011Article
Corrections and comments
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Authors and funding
3 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Bacterial luciferase contains an extended 29-residue mobile loop. Movements of this loop are governed by binding of either flavin mononucleotide (FMNH2) or polyvalent anions. To understand this process, loop dynamics were investigated using replica-exchange molecular dynamics that yielded conformational ensembles in either the presence or absence of FMNH2. The resulting data were analyzed using clustering and network analysis. We observed the closed conformations that are visited only in the simulations with the ligand. Yet the mobile loop is intrinsically flexible, and FMNH2 binding modifies the relative populations of conformations. This model provides unique information regarding the function of a crystallographically disordered segment of the loop near the binding site. Structures at or near the fringe of this network were compatible with flavin binding or release. Finally, we demonstrate that the crystallographically observed conformation of the mobile loop bound to oxidized flavin was influenced by crystal packing. Thus, our study has revealed what we believe are novel conformations of the mobile loop and additional context for experimentally determined structures.
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