ArticleProceedings of the National Academy of Sciences of the United States of America2010
Water's role in the force-induced unfolding of ubiquitin.
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 13 papers.
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Who cites it
13 citing papers in PubMed.
- Correlation between chemical denaturation and the unfolding energetics of Acanthamoeba actophorin.Biophysical journal · 2023Article
- Implementation of Telescoping Boxes in Adaptive Steered Molecular Dynamics.Journal of chemical theory and computation · 2022Article
- Article
- Molecular mechanisms underlying the extreme mechanical anisotropy of the flaviviral exoribonuclease-resistant RNAs (xrRNAs).Nature communications · 2020Article
- Effects of ligand binding on the mechanical stability of protein GB1 studied by steered molecular dynamics simulation.Journal of molecular modeling · 2016Article
- The role of binding site on the mechanical unfolding mechanism of ubiquitin.Scientific reports · 2015Article
- Atomic-level description of ubiquitin folding.Proceedings of the National Academy of Sciences of the United States of America · 2013Article
- Mechanism of enhanced mechanical stability of a minimal RNA kissing complex elucidated by nonequilibrium molecular dynamics simulations.Proceedings of the National Academy of Sciences of the United States of America · 2012Article
- Worm-like Ising model for protein mechanical unfolding under the effect of osmolytes.Biophysical journal · 2012Article
- Dynamic prestress in a globular protein.PLoS computational biology · 2012Article
- Direct quantification of the attempt frequency determining the mechanical unfolding of ubiquitin protein.The Journal of biological chemistry · 2011Article
- Probing osmolyte participation in the unfolding transition state of a protein.Proceedings of the National Academy of Sciences of the United States of America · 2011Article
- First passage time distribution in stochastic processes with moving and static absorbing boundaries with application to biological rupture experiments.The Journal of chemical physics · 2010Article
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3 authors.
Funding
Abstract
In atomic force spectroscopic studies of the elastomeric protein ubiquitin, the β-strands 1-5 serve as the force clamp. Simulations show how the rupture force in the force-induced unfolding depends on the kinetics of water molecule insertion into positions where they can eventually form hydrogen bonding bridges with the backbone hydrogen bonds in the force-clamp region. The intrusion of water into this region is slowed down by the hydrophobic shielding effect of carbonaceous groups on the surface residues of β-strands 1-5, which thereby regulates water insertion prior to hydrogen bond breakage. The experiments show that the unfolding of the mechanically stressed protein is nonexponential due to static disorder. Our simulations show that different numbers and/or locations of bridging water molecules give rise to a long-lived distribution of transition states and static disorder. We find that slowing down the translational (not rotational) motions of the water molecules by increasing the mass of their oxygen atoms, which leaves the force field and thereby the equilibrium structure of the solvent unchanged, increases the average rupture force; however, the early stages of the force versus time behavior are very similar for our "normal" and fictitious "heavy" water models. Finally, we construct six mutant systems to regulate the hydrophobic shielding effect of the surface residues in the force-clamp region. The mutations in the two termini of β-sheets 1-5 are found to determine a preference for different unfolding pathways and change mutant's average rupture force.
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