ArticlePloS one2013
Two distinct states of the HAMP domain from sensory rhodopsin transducer observed in unbiased molecular dynamics simulations.
Article in PloS one, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 13 papers.
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Who cites it
13 citing papers in PubMed.
- Conformational diversity in poly-HAMP arrays and its implications for signal transduction.Protein science : a publication of the Protein Society · 2026Article
- Cryo-EM structure of the SRI-HtrI complex reveals the cytoplasmic coupling in an archaeal phototaxis system.Nature communications · 2026Article
- Surface Density-Dependent Interactions between Photoactivated Sensory Rhodopsin 2 and Its Transducer.ACS omega · 2026Article
- AlphaFold2 captures the conformational landscape of the HAMP signaling domain.Protein science : a publication of the Protein Society · 2024Article
- Nitrate- and Nitrite-Sensing Histidine Kinases: Function, Structure, and Natural Diversity.International journal of molecular sciences · 2021Review
- Quantum Mechanical and Molecular Mechanics Modeling of Membrane-Embedded Rhodopsins.The Journal of membrane biology · 2019Review
- Conformational sampling of CpxA: Connecting HAMP motions to the histidine kinase function.PloS one · 2018Article
- Stability and Conformation of a Chemoreceptor HAMP Domain Chimera Correlates with Signaling Properties.Biophysical journal · 2017Article
- Signaling and Adaptation Modulate the Dynamics of the Photosensoric Complex of Natronomonas pharaonis.PLoS computational biology · 2015Article
- Article
- Bacterial chemoreceptor dynamics correlate with activity state and are coupled over long distances.Proceedings of the National Academy of Sciences of the United States of America · 2015Article
- A 2-component system is involved in the early stages of the Pisolithus tinctorius-Pinus greggii symbiosis.Plant signaling & behavior · 2014Article
- A phenylalanine rotameric switch for signal-state control in bacterial chemoreceptors.Nature communications · 2013Article
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3 authors.
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Abstract
HAMP domain is a ubiquitous module of bacterial and archaeal two-component signaling systems. Considerable progress has been made recently in studies of its structure and conformational changes. However, the mechanism of signal transduction through the HAMP domain is not clear. It remains a question whether all the HAMPs have the same mechanism of action and what are the differences between the domains from different protein families. Here, we present the results of unbiased molecular dynamics simulations of the HAMP domain from the archaeal phototaxis signal transducer NpHtrII. Two distinct conformational states of the HAMP domain are observed, that differ in relative position of the helices AS1 and AS2. The longitudinal shift is roughly equal to a half of an α-helix turn, although sometimes it reaches one full turn. The states are closely related to the position of bulky hydrophobic aminoacids at the HAMP domain core. The observed features are in good agreement with recent experimental results and allow us to propose that the states detected in the simulations are the resting state and the signaling state of the NpHtrII HAMP domain. To the best of our knowledge, this is the first observation of the same HAMP domain in different conformations. The simulations also underline the difference between AMBER ff99-SB-ILDN and CHARMM22-CMAP forcefields, as the former favors the resting state and the latter favors the signaling state.
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