ArticleBiophysical journal2004
Probing protein mechanics: residue-level properties and their use in defining domains.
Article in Biophysical journal, 2004. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 18 papers.
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Who cites it
18 citing papers in PubMed.
- Localized Rigidification and Allosteric Modulation Mechanisms of SARS-CoV-2 Spike Neutralization by Class 3 and Class 4 Antibodies at Atomic Resolution: An Integrated Computational Study of Binding, Dynamics, and Allostery.bioRxiv : the preprint server for biology · 2026Article
- Toward the design and development of peptidomimetic inhibitors of the Ataxin-1 aggregation pathway.Biophysical journal · 2022Article
- Structural communication between the GTPase Sec4p and its activator Sec2p: Determinants of GEF activity and early deformations to nucleotide release.Computational and structural biotechnology journal · 2022Article
- Structural Water Stabilizes Protein Motifs in Liquid Protein Phase: The Folding Mechanism of Short β-Sheets Coupled to Phase Transition.International journal of molecular sciences · 2021Article
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- Computational modeling of allosteric regulation in the hsp90 chaperones: a statistical ensemble analysis of protein structure networks and allosteric communications.PLoS computational biology · 2014Article
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- Thermal fluctuations of haemoglobin from different species: adaptation to temperature via conformational dynamics.Journal of the Royal Society, Interface · 2012Article
- Nucleotide binding switches the information flow in ras GTPases.PLoS computational biology · 2011Article
- Accounting for large amplitude protein deformation during in silico macromolecular docking.International journal of molecular sciences · 2011Article
- Modeling the early stage of DNA sequence recognition within RecA nucleoprotein filaments.Nucleic acids research · 2010Article
- Structure-based predictive models for allosteric hot spots.PLoS computational biology · 2009Article
- Tensile mechanics of alanine-based helical polypeptide: force spectroscopy versus computer simulations.Biophysical journal · 2009Article
- Protein mechanics: a route from structure to function.Journal of biosciences · 2007Review
- Anisotropic deformation response of single protein molecules.Proceedings of the National Academy of Sciences of the United States of America · 2006Article
- Investigating the local flexibility of functional residues in hemoproteins.Biophysical journal · 2006Article
- Cadherin mechanics and complexation: the importance of calcium binding.Biophysical journal · 2005Article
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3 authors.
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Abstract
It is becoming clear that, in addition to structural properties, the mechanical properties of proteins can play an important role in their biological activity. It nevertheless remains difficult to probe these properties experimentally. Whereas single-molecule experiments give access to overall mechanical behavior, notably the impact of end-to-end stretching, it is currently impossible to directly obtain data on more local properties. We propose a theoretical method for probing the mechanical properties of protein structures at the single-amino acid level. This approach can be applied to both all-atom and simplified protein representations. The probing leads to force constants for local deformations and to deformation vectors indicating the paths of least mechanical resistance. It also reveals the mechanical coupling that exists between residues. Results obtained for a variety of proteins show that the calculated force constants vary over a wide range. An analysis of the induced deformations provides information that is distinct from that obtained with measures of atomic fluctuations and is more easily linked to residue-level properties than normal mode analyses or dynamic trajectories. It is also shown that the mechanical information obtained by residue-level probing opens a new route for defining so-called dynamical domains within protein structures.
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