ArticleEuropean biophysics journal : EBJ2010
Effect of interdomain dynamics on the structure determination of modular proteins by small-angle scattering.
Article in European biophysics journal : EBJ, 2010. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 60 papers.
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60 citing papers in PubMed.
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- An integrative structural study of the human full-length RAD52 at 2.2 Å resolution.Communications biology · 2024Article
- Crowder-directed interactions and conformational dynamics in multistimuli-responsive intrinsically disordered protein.Science advances · 2022Article
- Solution Structural Studies of Pre-amyloid Oligomer States of the Biofilm Protein Aap.Journal of molecular biology · 2022Article
- Solution structure of the type I polyketide synthase Pks13 from Mycobacterium tuberculosis.BMC biology · 2022Article
- A FRET-Based Biosensor for the Src N-Terminal Regulatory Element.Biosensors · 2022Article
- Experimental Evidence of Intrinsic Disorder and Amyloid Formation by theInternational journal of molecular sciences · 2022Article
- Molecular insights on CALX-CBD12 interdomain dynamics from MD simulations, RDCs, and SAXS.Biophysical journal · 2021Article
- Probing the oligomeric re-assembling of bacterial fimbriae in vitro: a small-angle X-ray scattering and analytical ultracentrifugation study.European biophysics journal : EBJ · 2021Article
- Ensemble description of the intrinsically disordered N-terminal domain of the Nipah virus P/V protein from combined NMR and SAXS.Scientific reports · 2020Article
- Biophysical Characterization of Cancer-Related Carbonic Anhydrase IX.International journal of molecular sciences · 2020Article
- Structural Analyses of Intrinsically Disordered Proteins by Small-Angle X-Ray Scattering.Methods in molecular biology (Clifton, N.J.) · 2020Article
- A Sustainable Biomineralization Approach for the Synthesis of Highly Fluorescent Ultra-Small Pt Nanoclusters.Biosensors · 2019Article
- Molecular recognition of ubiquitin and Lys63-linked diubiquitin by STAM2 UIM-SH3 dual domain: the effect of its linker length and flexibility.Scientific reports · 2019Article
- Dystrophin's central domain forms a complex filament that becomes disorganized by in-frame deletions.The Journal of biological chemistry · 2018Article
- Integrating NMR, SAXS, and Atomistic Simulations: Structure and Dynamics of a Two-Domain Protein.Biophysical journal · 2018Article
- Effects of the linker region on the structure and function of modular GH5 cellulases.Scientific reports · 2016Article
- The dynamic organization of fungal acetyl-CoA carboxylase.Nature communications · 2016Article
- Role of the Interdomain Linker in RNA-Activated Protein Kinase Activation.Biochemistry · 2016Article
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Abstract
Multidomain proteins in which consecutive globular regions are connected by linkers are prevalent in nature (Levitt in Proc Natl Acad Sci USA 106:11079-11084, 2009). Some members of this family have largely resisted structural characterization as a result of challenges associated with their inherent flexibility. Small-angle scattering (SAS) is often the method of choice for their structural study. An extensive set of simulated data for both flexible and rigid multidomain systems was analyzed and modeled using standard protocols. This study clearly shows that SAXS profiles obtained from highly flexible proteins can be wrongly interpreted as arising from a rigid structure. In this context, it would be important to identify features from the SAXS data or from the derived structural models that indicate interdomain motions to differentiate between these two scenarios. Features of SAXS data that identify flexible proteins are: (1) general attenuation of fine structure in the scattering profiles, which becomes more dramatic in Kratky representations, and (2) a reduced number of interdomain correlation peaks in p(r) functions that also present large D (max) values and a smooth decrease to 0. When modeling this dynamically averaged SAXS data, the structures obtained present characteristic trends: (1) ab initio models display a decrease in resolution, and (2) rigid-body models present highly extended conformations with a lack of interdomain contacts. The ensemble optimization method represents an excellent strategy to identify interdomain motions unambiguously. This study provides information that should help researchers to select the best modeling strategy for the structural interpretation of SAS experiments of multidomain proteins.
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