ArticleBiophysical journal2006
Atomistic simulation approach to a continuum description of self-assembled beta-sheet filaments.
Article in Biophysical journal, 2006. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 19 papers.
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Who cites it
19 citing papers in PubMed, 48 citations in OpenAlex.
- Principles and Biomedical Applications of Self-Assembled Peptides: Potential Treatment of Type 2 Diabetes Mellitus.Pharmaceutics · 2024Review
- A theoretical study of polymorphism in VQIVYK fibrils.Biophysical journal · 2021Article
- Mechanical properties of tubulin intra- and inter-dimer interfaces and their implications for microtubule dynamic instability.PLoS computational biology · 2019Article
- Nanomechanics and intermolecular forces of amyloid revealed by four-dimensional electron microscopy.Proceedings of the National Academy of Sciences of the United States of America · 2015Article
- Bone marrow enriched graft, modified by self-assembly peptide, repairs critically-sized femur defects in goats.International orthopaedics · 2014Article
- Formation of ordered biomolecular structures by the self-assembly of short peptides.Journal of visualized experiments : JoVE · 2013Article
- Ensemble-based characterization of unbound and bound states on protein energy landscape.Protein science : a publication of the Protein Society · 2013Article
- Nanomechanics of functional and pathological amyloid materials.Nature nanotechnology · 2011Review
- Physical properties of polymorphic yeast prion amyloid fibers.Biophysical journal · 2011Article
- Interaction of β-sheet folds with a gold surface.PloS one · 2011Article
- Anisotropic elastic network modeling of entire microtubules.Biophysical journal · 2010Article
- Synergistic effects of tethered growth factors and adhesion ligands on DNA synthesis and function of primary hepatocytes cultured on soft synthetic hydrogels.Biomaterials · 2010Article
- Thermodynamic selection of steric zipper patterns in the amyloid cross-beta spine.PLoS computational biology · 2009Article
- Critical buckling length versus persistence length: what governs biofilament conformation?Physical review letters · 2009Article
- Modulation of elasticity in functionally distinct domains of the tropomyosin coiled-coil.Cellular and molecular bioengineering · 2009Article
- NUMERICAL SIMULATION OF NANOINDENTATION AND PATCH CLAMP EXPERIMENTS ON MECHANOSENSITIVE CHANNELS OF LARGE CONDUCTANCE IN ESCHERICHIA COLI.Shi yan li xue = Journal of experimental mechanics · 2009Article
- Mechanical design of translocating motor proteins.Cell biochemistry and biophysics · 2009Review
- Elastic deformation and failure in protein filament bundles: Atomistic simulations and coarse-grained modeling.Biomaterials · 2008Article
- The elastic properties of the structurally characterized myosin II S2 subdomain: a molecular dynamics and normal mode analysis.Biophysical journal · 2008Article
Corrections and comments
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Authors and funding
4 authors at 2 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
We investigated the supramolecular structure and continuum mechanical properties of a beta-sheet nanofiber comprised of a self-assembling peptide ac-[RARADADA]2-am using computer simulations. The supramolecular structure was determined by constructing candidate filaments with dimensions compatible with those observed in atomic force microscopy and selecting the most stable ones after running molecular dynamics simulations on each of them. Four structures with different backbone hydrogen-bonding patterns were identified to be similarly stable. We then quantified the continuum mechanical properties of these identified structures by running three independent simulations: thermal motion analysis, normal mode analysis, and steered molecular dynamics. Within the range of deformations investigated, the filament showed linear elasticity in transverse directions with an estimated persistence length of 1.2-4.8 microm. Although side-chain interactions govern the propensity and energetics of filament self-assembly, we found that backbone hydrogen-bonding interactions are the primary determinant of filament elasticity, as demonstrated by its effective thickness, which is smaller than that estimated by atomic force microscopy or from the molecular geometry, as well as by the similar bending stiffness of a model filament without charged side chains. The generality of our approach suggests that it should be applicable to developing continuum elastic ribbon models of other beta-sheet filaments and amyloid fibrils.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.