ArticleJournal of molecular biology2006
PAS domain allostery and light-induced conformational changes in photoactive yellow protein upon I2 intermediate formation, probed with enhanced hydrogen/deuterium exchange mass spectrometry.
Article in Journal of molecular biology, 2006. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 22 papers.
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Who cites it
22 citing papers in PubMed.
- Human Cellular Retinol Binding Protein II Forms a Domain-Swapped Trimer Representing a Novel Fold and a New Template for Protein Engineering.Chembiochem : a European journal of chemical biology · 2020Article
- Hydrogen-Deuterium Exchange and Hydroxyl Radical Footprinting for Mapping Hydrophobic Interactions of Human Bromodomain with a Small Molecule Inhibitor.Journal of the American Society for Mass Spectrometry · 2019Article
- Applications of hydrogen deuterium exchange (HDX) for the characterization of conformational dynamics in light-activated photoreceptors.Frontiers in molecular biosciences · 2015Review
- Structural basis of SUFU-GLI interaction in human Hedgehog signalling regulation.Acta crystallographica. Section D, Biological crystallography · 2013Article
- Identification of regions of rabbit muscle pyruvate kinase important for allosteric regulation by phenylalanine, detected by H/D exchange mass spectrometry.Biochemistry · 2013Article
- Validation of macromolecular flexibility in solution by small-angle X-ray scattering (SAXS).European biophysics journal : EBJ · 2012Review
- Structural tuning of the fluorescent protein iLOV for improved photostability.The Journal of biological chemistry · 2012Article
- The ebola virus interferon antagonist VP24 directly binds STAT1 and has a novel, pyramidal fold.PLoS pathogens · 2012Article
- Structural basis of photosensitivity in a bacterial light-oxygen-voltage/helix-turn-helix (LOV-HTH) DNA-binding protein.Proceedings of the National Academy of Sciences of the United States of America · 2011Article
- Mechanism of substrate specificity in 5'-methylthioadenosine/S-adenosylhomocysteine nucleosidases.Journal of structural biology · 2011Article
- Structural dynamics in DNA damage signaling and repair.Current opinion in structural biology · 2010Review
- Structural dynamics of soluble chloride intracellular channel protein CLIC1 examined by amide hydrogen-deuterium exchange mass spectrometry.Biochemistry · 2009Article
- Location of inhibitors bound to group IVA phospholipase A2 determined by molecular dynamics and deuterium exchange mass spectrometry.Journal of the American Chemical Society · 2009Article
- Hydrogen bond dynamics in the active site of photoactive yellow protein.Proceedings of the National Academy of Sciences of the United States of America · 2009Article
- A phospholipid substrate molecule residing in the membrane surface mediates opening of the lid region in group IVA cytosolic phospholipase A2.The Journal of biological chemistry · 2008Article
- Surface sites for engineering allosteric control in proteins.Science (New York, N.Y.) · 2008Article
- Interaction of group IA phospholipase A2 with metal ions and phospholipid vesicles probed with deuterium exchange mass spectrometry.Biochemistry · 2008Article
- Dynamic structural changes during complement C3 activation analyzed by hydrogen/deuterium exchange mass spectrometry.Molecular immunology · 2008Article
- Calcium binding rigidifies the C2 domain and the intradomain interaction of GIVA phospholipase A2 as revealed by hydrogen/deuterium exchange mass spectrometry.The Journal of biological chemistry · 2008Article
- Conformational studies of the manganese transport regulator (MntR) from Bacillus subtilis using deuterium exchange mass spectrometry.Journal of biological inorganic chemistry : JBIC : a publication of the Society of Biological Inorganic Chemistry · 2007Article
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6 authors.
Funding
Abstract
Photoactive yellow protein (PYP) is a small bacterial photoreceptor that undergoes a light-activated reaction cycle. PYP is also the prototypical Per-Arnt-Sim (PAS) domain. PAS domains, found in diverse multi-domain proteins from bacteria to humans, mediate protein-protein interactions and function as sensors and signal transducers. Here, we investigate conformational and dynamic changes in solution in wild-type PYP upon formation of the long-lived putative signaling intermediate I2 with enhanced hydrogen/deuterium exchange mass spectrometry (DXMS). The DXMS results showed that the central beta-sheet remains stable but specific external protein segments become strongly deprotected. Light-induced disruption of the dark-state hydrogen bonding network in I2 produces increased flexibility and opening of PAS core helices alpha3 and alpha4, releases the beta4-beta5 hairpin, and propagates conformational changes to the central beta-sheet. Surprisingly, the first approximately 10 N-terminal residues, which are essential for fast dark-state recovery from I2, become more protected. By combining the DXMS results with our crystallographic structures, which reveal detailed changes near the chromophore but limited protein conformational change, we propose a mechanism for I2 state formation. This mechanism integrates the results from diverse biophysical studies of PYP, and links an allosteric T to R-state conformational transition to three pathways for signal propagation within the PYP fold. On the basis of the observed changes in PYP plus commonalities shared among PAS domain proteins, we further propose that PAS domains share this conformational mechanism, which explains the versatile signal transduction properties of the structurally conserved PYP/PAS module by framework-encoded allostery.
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