ArticleBiophysical journal2008
Simulation-based fitting of protein-protein interaction potentials to SAXS experiments.
Article in Biophysical journal, 2008. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 12 papers.
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Who cites it
12 citing papers in PubMed.
- Chemical interactions modulate λProtein science : a publication of the Protein Society · 2023Article
- Recent Advances in the Label-Free Characterization of Exosomes for Cancer Liquid Biopsy: From Scattering and Spectroscopy to Nanoindentation and Nanodevices.Nanomaterials (Basel, Switzerland) · 2021Review
- The extracellular protein VlsE is destabilized inside cells.Journal of molecular biology · 2014Article
- Transient helical structure during PI3K and Fyn SH3 domain folding.The journal of physical chemistry. B · 2013Article
- Integrative structural modeling with small angle X-ray scattering profiles.BMC structural biology · 2012Review
- Substrate-specific reorganization of the conformational ensemble of CSK implicates novel modes of kinase function.PLoS computational biology · 2012Article
- Crowding effects on the small, fast-folding protein lambda6-85.Faraday discussions · 2012Article
- Macromolecular assembly of polycystin-2 intracytosolic C-terminal domain.Proceedings of the National Academy of Sciences of the United States of America · 2011Article
- Proteins at work: a combined small angle X-RAY scattering and theoretical determination of the multiple structures involved on the protein kinase functional landscape.The Journal of biological chemistry · 2010Article
- SoftWAXS: a computational tool for modeling wide-angle X-ray solution scattering from biomolecules.Journal of applied crystallography · 2009Article
- Slowing down downhill folding: a three-probe study.Biophysical journal · 2009Article
- X-ray scattering combined with coordinate-based analyses for applications in natural and artificial photosynthesis.Photosynthesis researchReview
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Authors and funding
3 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
We present a new method for computing interaction potentials of solvated proteins directly from small-angle x-ray scattering data. An ensemble of proteins is modeled by Monte Carlo or molecular dynamics simulation. The global x-ray scattering of the whole model ensemble is then computed at each snapshot of the simulation, and averaged to obtain the x-ray scattering intensity. Finally, the interaction potential parameters are adjusted by an optimization algorithm, and the procedure is iterated until the best agreement between simulation and experiment is obtained. This new approach obviates the need for approximations that must be made in simplified analytical models. We apply the method to lambda repressor fragment 6-85 and fyn-SH3. With the increased availability of fast computer clusters, Monte Carlo and molecular dynamics analysis using residue-level or even atomistic potentials may soon become feasible.
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