<i>ATSAS 3.0</i>: expanded functionality and new tools for small-angle scattering data analysis

Manalastas-Cantos, Karen; Konarev, Petr V.; Hajizadeh, Nelly R.; Kikhney, Alexey; Petoukhov, Maxim V.; Molodenskiy, Dmitry; Panjkovich, Alejandro; Mertens, Haydyn D. T.; Gruzinov, Andrey; Borges, Clemente; Jeffries, Cy M.; Svergun, Dmitri I.; Franke, Daniel

doi:10.1107/s1600576720013412

Cited by 655 publications

(579 citation statements)

References 107 publications

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“…We also compared our results with what could be the typical procedure using easily accessible and widespread tools, that is generating an envelope using the programs provided in ATSAS [50] and performing a fit into the envelope with normal modes, using for example the program iMODFIT [51] that is easily integrated in the visualization software Chimera [52] (work presented in SI section E). The first observation is that the straightforward application of the fit from a partially unfolded structure does not give satisfying results.…”

Section: Discussionmentioning

confidence: 99%

Biasing RNA coarse-grained folding simulations with Small–Angle X–ray Scattering (SAXS) data

Mazzanti

Alferkh

Frezza

et al. 2021

Preprint

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RNA molecules can easily adopt alternative structures in response to different environmental conditions. As a result, a molecule's energy landscape is rough and can exhibits a multitude of deep basins. In the absence of a high-resolution structure, Small Angle X-ray Scattering data (SAXS) can narrow down the conformational space available to the molecule and be used in conjunction with physical modeling to obtain high-resolution putative structures to be further tested by experiments. Because of the low-resolution of this data, it is natural to implement the integration of SAXS data into simulations using a coarse-grained representation of the molecule, allowing for much wider searches and faster evaluation of SAXS theoretical intensity curves than with atomistic models. We present here the theoretical framework and the implementation of a simulation approach based on our coarse-grained model HiRE-RNA combined with SAXS evaluations "on-the-fly" leading the simulation toward conformations agreeing with the scattering data, starting from partially folded structures as the ones that can easily be obtained from secondary structures predictions based tools. We show on three benchmark systems how our approach can successfully achieve high-resolution structures with remarkable similarity with the native structure recovering not only the overall shape, as imposed by SAXS data, but also the details of initially missing base pairs.

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Section: Discussionmentioning

confidence: 99%

Biasing RNA coarse-grained folding simulations with Small–Angle X–ray Scattering (SAXS) data

Mazzanti

Alferkh

Frezza

et al. 2021

Preprint

View full text Add to dashboard Cite

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“…BioXTAS RAW version 2.0.2 was used for SAXS data collection and data reduction (Hopkins et al, 2017). The RAW interface was also used for Guinier analysis of the scattering data and the indirect Fourier transform methods implemented in GNOM (Svergun, 1992), part of the ATSAS package (Manalastas-Cantos et al, 2021), for pair-distance distribution analysis. Domains 2 to 5 for mKirrel3 were modeled using the I-TASSER server (Roy et al, 2010; Yang and Zhang, 2015).…”

Section: Methodsmentioning

confidence: 99%

Molecular and Structural Basis of Olfactory Sensory Neuron Coalescence by Kirrel Receptors

Wang

Vaddadi

Pak

et al. 2021

Preprint

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Projections from sensory neurons of olfactory systems coalesce into glomeruli in the brain. The Kirrel receptors are believed to homodimerize via their ectodomains and help separate sensory neuron axons into Kirrel2- or Kirrel3-expressing glomeruli. Here we present the crystal structures of homodimeric Kirrel receptors and show that the closely related Kirrel2 and Kirrel3 have evolved specific sets of polar and hydrophobic interactions, respectively, disallowing heterodimerization while preserving homodimerization, likely resulting in proper segregation and coalescence of Kirrel-expressing axons into glomeruli. We show that the dimerization interface at the N-terminal IG domains is necessary and sufficient to create homodimers, and fail to find evidence for a secondary interaction site in Kirrel ectodomains. Furthermore, we show that abolishing dimerization of Kirrel3 in vivo leads to improper formation of glomeruli in the mouse accessory olfactory bulb as observed in Kirrel3-/- animals. Our results provide strong evidence for Kirrel3 homodimerization controlling axonal coalescence.

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“…These nucleosome samples contain, respectively, isotope-labeled H2A, H3 or H2A with co-sedimented LANA peptide and are listed as samples 1-3 in Table 1 below. Isotope-labeled histones were fractionally deuterated to reduce line width and increase sensitivity in 1 H-detected ss-NMR experiments (Mance et al, 2015). For this study we prepared two new H3-labeled nucleosome samples, one with nucleosomes in their free state (sample 4 in Table 1) and with a co-sedimented PHD2 domain of CHD4 (PHD2).…”

Section: Sample Preparationmentioning

confidence: 99%

Characterization of nucleosome sediments for protein interaction studies by solid-state NMR spectroscopy

et al. 2021

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Abstract. Regulation of DNA-templated processes such as gene transcription and DNA repair depend on the interaction of a wide range of proteins with the nucleosome, the fundamental building block of chromatin. Both solution and solid-state NMR spectroscopy have become an attractive approach to study the dynamics and interactions of nucleosomes, despite their high molecular weight of ∼200 kDa. For solid-state NMR (ssNMR) studies, dilute solutions of nucleosomes are converted to a dense phase by sedimentation or precipitation. Since nucleosomes are known to self-associate, these dense phases may induce extensive interactions between nucleosomes, which could interfere with protein-binding studies. Here, we characterized the packing of nucleosomes in the dense phase created by sedimentation using NMR and small-angle X-ray scattering (SAXS) experiments. We found that nucleosome sediments are gels with variable degrees of solidity, have nucleosome concentration close to that found in crystals, and are stable for weeks under high-speed magic angle spinning (MAS). Furthermore, SAXS data recorded on recovered sediments indicate that there is no pronounced long-range ordering of nucleosomes in the sediment. Finally, we show that the sedimentation approach can also be used to study low-affinity protein interactions with the nucleosome. Together, our results give new insights into the sample characteristics of nucleosome sediments for ssNMR studies and illustrate the broad applicability of sedimentation-based NMR studies.

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ATSAS 3.0: expanded functionality and new tools for small-angle scattering data analysis

Cited by 655 publications

References 107 publications

Biasing RNA coarse-grained folding simulations with Small–Angle X–ray Scattering (SAXS) data

Biasing RNA coarse-grained folding simulations with Small–Angle X–ray Scattering (SAXS) data

Molecular and Structural Basis of Olfactory Sensory Neuron Coalescence by Kirrel Receptors

Characterization of nucleosome sediments for protein interaction studies by solid-state NMR spectroscopy

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