ArticleProceedings of the National Academy of Sciences of the United States of America2010
Predicting the reaction coordinates of millisecond light-induced conformational changes in photoactive yellow protein.
Article in Proceedings of the National Academy of Sciences of the United States of America, 2010. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 27 papers.
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Who cites it
27 citing papers in PubMed.
- Worldwide Protein Data Bank (wwPDB): A virtual treasure for research in biotechnology.European journal of microbiology & immunology · 2022Review
- The molecular pH-response mechanism of the plant light-stress sensor PsbS.Nature communications · 2021Article
- Frontiers in Multiscale Modeling of Photoreceptor Proteins.Photochemistry and photobiology · 2021Review
- A community proposal to integrate structural bioinformatics activities in ELIXIR (3D-Bioinfo Community).F1000Research · 2020Article
- Atomistic insight into the kinetic pathways for Watson-Crick to Hoogsteen transitions in DNA.Nucleic acids research · 2019Article
- Mechanism of the electroneutral sodium/proton antiporter PaNhaP from transition-path shooting.Nature communications · 2019Article
- Allostery in Its Many Disguises: From Theory to Applications.Structure (London, England : 1993) · 2019Review
- Unbiased Atomistic Insight into the Mechanisms and Solvent Role for Globular Protein Dimer Dissociation.The journal of physical chemistry. B · 2019Article
- OpenPathSampling: A Python Framework for Path Sampling Simulations. 1. Basics.Journal of chemical theory and computation · 2019Article
- Incorporating Fast Protein Dynamics into Enzyme Design: A Proposed Mutant Aromatic Amine Dehydrogenase.The journal of physical chemistry. B · 2017Article
- Picosecond Photobiology: Watching a Signaling Protein Function in Real Time via Time-Resolved Small- and Wide-Angle X-ray Scattering.Journal of the American Chemical Society · 2016Article
- Combined probes of X-ray scattering and optical spectroscopy reveal how global conformational change is temporally and spatially linked to local structural perturbation in photoactive yellow protein.Physical chemistry chemical physics : PCCP · 2016Article
- Cooperativity and modularity in protein folding.Biophysics and physicobiology · 2016Review
- Free energy landscape of activation in a signalling protein at atomic resolution.Nature communications · 2015Article
- Mapping allostery through computational glycine scanning and correlation analysis of residue-residue contacts.Biochemistry · 2015Article
- Hierarchical Conformational Analysis of Native Lysozyme Based on Sub-Millisecond Molecular Dynamics Simulations.PloS one · 2015Article
- Multiscale approach to the determination of the photoactive yellow protein signaling state ensemble.PLoS computational biology · 2014Article
- Thermodynamics of Deca-alanine Folding in Water.Journal of chemical theory and computation · 2014Article
- Recent developments in methods for identifying reaction coordinates.Molecular simulation · 2014Article
- Allosteric activation transitions in enzymes and biomolecular motors: insights from atomistic and coarse-grained simulations.Topics in current chemistry · 2013Review
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Abstract
Understanding the dynamics of large-scale conformational changes in proteins still poses a challenge for molecular simulations. We employ transition path sampling of explicit solvent molecular dynamics trajectories to obtain atomistic insight in the reaction network of the millisecond timescale partial unfolding transition in the photocycle of the bacterial sensor photoactive yellow protein. Likelihood maximization analysis predicts the best model for the reaction coordinates of each substep as well as tentative transition states, without further simulation. We find that the unfolding of the alpha-helical region 43-51 is followed by sequential solvent exposure of both Glu46 and the chromophore. Which of these two residues is exposed first is correlated with the presence of a salt bridge that is part of the N-terminal domain. Additional molecular dynamics simulations indicate that the exposure of the chromophore does not result in a productive pathway. We discuss several possibilities for experimental validation of these predictions. Our results open the way for studying millisecond conformational changes in other medium-sized (signaling) proteins.
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