Nejvíce citovaný článek - PubMed ID 28319376
Anomalous Protein-Protein Interactions in Multivalent Salt Solution
The contributions from anions and cations from salt are inseparable in their perturbation of molecular systems by experimental and computational methods, rendering it difficult to dissect the effects exerted by the anions and cations individually. Here we investigate the solvation of a small molecule, caffeine, and its perturbation by monovalent salts from various parts of the Hofmeister series. Using molecular dynamics and the energy-representation theory of solvation, we estimate the solvation free energy of caffeine and decompose it into the contributions from anions, cations, and water. We also decompose the contributions arising from the solute-solvent and solute-ions interactions and that from excluded volume, enabling us to pin-point the mechanism of salt. Anions and cations revealed high contrast in their perturbation of caffeine solvation, with the cations salting-in caffeine via binding to the polar ketone groups, while the anions were found to be salting-out via perturbations of water. In agreement with previous findings, the perturbation by salt is mostly anion dependent, with the magnitude of the excluded-volume effect found to be the governing mechanism. The free-energy decomposition as conducted in the present work can be useful to understand ion-specific effects and the associated Hofmeister series.
- Publikační typ
- časopisecké články MeSH
Transcription elongation factor Spt6 associates with RNA polymerase II (RNAP II) via a tandem SH2 (tSH2) domain. The mechanism and significance of the RNAP II-Spt6 interaction is still unclear. Recently, it was proposed that Spt6-tSH2 is recruited via a newly described phosphorylated linker between the Rpb1 core and its C-terminal domain (CTD). Here, we report binding studies with isolated tSH2 of Spt6 (Spt6-tSH2) and Spt6 lacking the first unstructured 297 residues (Spt6ΔN) with a minimal CTD substrate of two repetitive heptads phosphorylated at different sites. The data demonstrate that Spt6 also binds the phosphorylated CTD, a site that was originally proposed as a recognition epitope. We also show that an extended CTD substrate harboring 13 repetitive heptads of the tyrosine-phosphorylated CTD binds Spt6-tSH2 and Spt6ΔN with tighter affinity than the minimal CTD substrate. The enhanced binding is achieved by avidity originating from multiple phosphorylation marks present in the CTD. Interestingly, we found that the steric effects of additional domains in the Spt6ΔN construct partially obscure the binding of the tSH2 domain to the multivalent ligand. We show that Spt6-tSH2 binds various phosphorylation patterns in the CTD and found that the studied combinations of phospho-CTD marks (1,2; 1,5; 2,4; and 2,7) all facilitate the interaction of CTD with Spt6. Our structural studies reveal a plasticity of the tSH2 binding pockets that enables the accommodation of CTDs with phosphorylation marks in different registers.
- Klíčová slova
- CTD, RNA polymerase II, Spt6, NMR structure, phosphorylation,
- MeSH
- epitopy genetika MeSH
- fosforylace genetika MeSH
- genetická transkripce * MeSH
- histonové chaperony genetika MeSH
- RNA-polymerasa II genetika MeSH
- Saccharomyces cerevisiae - proteiny genetika MeSH
- Saccharomyces cerevisiae genetika MeSH
- sekvence aminokyselin genetika MeSH
- src homologní domény genetika MeSH
- transkripční elongační faktory genetika MeSH
- vazba proteinů genetika MeSH
- Publikační typ
- časopisecké články MeSH
- práce podpořená grantem MeSH
- Názvy látek
- epitopy MeSH
- histonové chaperony MeSH
- RNA-polymerasa II MeSH
- Saccharomyces cerevisiae - proteiny MeSH
- SPT6 protein, S cerevisiae MeSH Prohlížeč
- transkripční elongační faktory MeSH
Amyloid aggregates are associated with a range of human neurodegenerative disorders, and it has been shown that neurotoxicity is dependent on aggregate size. Combining molecular simulation with analytical theory, a predictive model is proposed for the adsorption of amyloid aggregates onto oppositely charged surfaces, where the interaction is governed by an interplay between electrostatic attraction and entropic repulsion. Predictions are experimentally validated against quartz crystal microbalance-dissipation experiments of amyloid beta peptides and fragmented fibrils in the presence of a supported lipid bilayer. Assuming amyloids as rigid, elongated particles, we observe nonmonotonic trends for the extent of adsorption with respect to aggregate size and preferential adsorption of smaller aggregates over larger ones. Our findings describe a general phenomenon with implications for stiff polyions and rodlike particles that are electrostatically attracted to a surface.
