PubMed Health⌕ Search
Home/Archive/PubMed

PubMed · 14769062

Using cross-links to study ribosomal dynamics.

Valery I Ivanov·Jason A Mears
View original source ↗Export metadata ↓

Abstract

After publications of 3-D models of a static ribosome and its large and small subunits, one of the next tasks is to recognize movable ribosomal elements responsible for mechanical shifts during protein synthesis. Statistic analysis of available cross-linking data allowed us to reveal three well separated groups of motions in the ribosome: I, mean magnitude of 10 A; II, most abundant, centered at 20 A and of wide dispersion, and III, sparsely populated, with large distances up to 95 A. The last group, III, comprises elements, like the L7/12-stalk and the L1- protuberance, that adopt different positions in crystallographic or electron micrographic structures, and neighboring hairpins 88 and 89, indicating mobility. We demonstrate that the cross-linking method can be applied to study ribosomal dynamics, including large-scale functional movements and, in particular, to estimate which structures participate in molecular switches.

Explore related subjects

Cross-Linking ReagentsEscherichia coliModels, MolecularNucleic Acid ConformationProtein BiosynthesisProtein Structure, TertiaryRibosomesJournal ArticleResearch Support, Non-U.S. Gov'tResearch Support, U.S. Gov't, P.H.S.

Keep this discovery

Explore connections, maps & timelines

BibTeXRIS

Valery I Ivanov, Jason A Mears. 2004. Using cross-links to study ribosomal dynamics.. https://pubmed.ncbi.nlm.nih.gov/14769062/

Cite the original work for its findings. Save a collection to share your selection of sources.

KEEP EXPLORING

Related citations

PubMed2026

To cleave or not to cleave: a systemic evaluation of DSS versus DSSO for cross-linking mass spectrometry analysis.

Cross-linking mass spectrometry is a powerful method for structural analysis, but choosing between cleavable and non-cleavable cross-linkers remains challenging. We rigorously compared non-cleavable DSS with cleavable DSSO and found that DSS consistently yields more cross-link identifications from isolated protein complexes to bacterial lysates. The advantage of DSS diminishes as sample complexity increases. At the highest complexity tested-human cell lysate-the trend reverses, with DSSO outperforming DSS. The superior performance of DSS in less complex samples is likely explained by its longer and more flexible spacer arm, which interrogates a spatial volume >40% larger than that of DSSO. For both cross-linkers, the number of identified cross-links decreases as the search space expands, but more steeply for DSS. This sharper decline arises from DSS cross-links producing slightly lower fragment ion coverage, not from the absence of signature ions that could reduce search space. Fragment ion coverage is key to interactome mapping: when coverage reaches 85% or above, identification sensitivity hardly decreases as the search space expands, regardless of the cross-linker used. In summary, we recommend DSS for samples no more complex than bacterial lysates. For interactome mapping of mammalian cells, although DSSO outperforms DSS, neither achieves deep interactome coverage.

Cross-Linking Reagents↗
PubMed2004

pH-sensitive PEG lipids containing orthoester linkers: new potential tools for nonviral gene delivery.

The synthesis and properties of pH-sensitive polyethylene glycol (PEG) lipids are described. The sensitivity of these conjugates to slightly acidic pH was clearly related to the structure of the orthoester linkage involved. It was found that pH-sensitive PEG lipids stabilized cationic lipid/DNA isoelectric complexes as efficiently as their non-pH-sensitive PEG analogs at neutral pH. Lowering the pH resulted in the precipitation of the complexes bearing pH-sensitive PEG lipids as a consequence of their degradation. In contrast, insertion of non-pH-sensitive PEG lipids maintained the complex colloidal stability even at lower pH. In vitro results showed a significant increase in transfection with formulations containing pH-sensitive PEG lipids versus non-pH-sensitive analogs. These conjugates show promising properties as lipoplex-stabilizing agents at neutral pH, which could be triggered by a mild acidic environment such as that occurring in solid tumors, inflammatory tissues, and intracellular endosomal compartments.

Cross-Linking Reagents↗
PubMed2004

Observations of instability, hysteresis, and oscillation in low-Reynolds-number flow past polymer gels.

We perform a set of experiments to study the nonlinear nature of an instability that arises in low-Reynolds-number flow past polymer gels. A layer of a viscous liquid is placed on a polydimethylsiloxane (PDMS) gel in a parallel-plate rheometer which is operated in stress-controlled mode. As the shear stress on the top plate increases, the apparent viscosity stays relatively constant until a transition stress where it sharply increases. If the stress is held at a level slightly above the transition stress, the apparent viscosity oscillates with time. If the stress is increased to a value above the transition stress and then decreased back to zero, the apparent viscosity shows hysteretic behavior. If the stress is instead decreased to a constant value and held there, the apparent viscosity is different from its pretransition value and exhibits sustained oscillations. This can happen even if the stress is held at values below the transition stress. Our observations suggest that the instability studied here is subcritical and leads to a flow that is oscillatory and far from viscometric. The phenomena reported here may be useful in applications such as microfluidics, membrane separations, and polymer processing. They may also provide insight into the rheological behavior of complex fluids that undergo flow-induced gelation.

Cross-Linking Reagents↗