New developments in the<i>ATSAS</i>program package for small-angle scattering data analysis

Petoukhov, Maxim V.; Franke, Daniel; Shkumatov, Alexander V.; Tria, Giancarlo; Kikhney, Alexey; Gajda, Michał J.; Gorba, Christian; Mertens, Haydyn D. T.; Konarev, Petr V.; Svergun, Dmitri I.

doi:10.1107/s0021889812007662

Cited by 1,646 publications

(1,951 citation statements)

References 48 publications

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“…The scattering curves were analysed using the programs Scatter and the package ATSAS to obtain the radius of gyration ( R g ), the maximum particle dimension ( D max ), the excluded particle volume ( V p ), the cross‐sectional radius and the pair distribution function (P(r)) (Petoukhov et al , 2012). The molecular mass of the scattering particles was estimated using a method described by Rambo (Rambo & Tainer, 2013).…”

Section: Methodsmentioning

confidence: 99%

Functional role of TRIM E3 ligase oligomerization and regulation of catalytic activity

et al. 2016

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TRIM E3 ubiquitin ligases regulate a wide variety of cellular processes and are particularly important during innate immune signalling events. They are characterized by a conserved tripartite motif in their N‐terminal portion which comprises a canonical RING domain, one or two B‐box domains and a coiled‐coil region that mediates ligase dimerization. Self‐association via the coiled‐coil has been suggested to be crucial for catalytic activity of TRIMs; however, the precise molecular mechanism underlying this observation remains elusive. Here, we provide a detailed characterization of the TRIM ligases TRIM25 and TRIM32 and show how their oligomeric state is linked to catalytic activity. The crystal structure of a complex between the TRIM25 RING domain and an ubiquitin‐loaded E2 identifies the structural and mechanistic features that promote a closed E2~Ub conformation to activate the thioester for ubiquitin transfer allowing us to propose a model for the regulation of activity in the full‐length protein. Our data reveal an unexpected diversity in the self‐association mechanism of TRIMs that might be crucial for their biological function.

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Section: Methodsmentioning

confidence: 99%

Functional role of TRIM E3 ligase oligomerization and regulation of catalytic activity

et al. 2016

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“…The data treatment of the scattering data includes normalization of the intensity, background subtraction, and normalization to absolute scale among several steps, which depends on the specific characteristics of the experimental setup. The overall data treatment process and necessary procedure for proper reduction of the scattering data are described in many articles and books in the literature and will not be presented here [7,12,14,15,[23][24][25][26][27][28][29]. In this chapter we will focus on methods for calculation of the SAS intensity, either for oriented or randomly oriented particles.…”

Section: Modeling Methods For Sas Datamentioning

confidence: 99%

“…Several good reviews can be found in the literature for this subject [14,17,36,50,60,65,[67][68][69].…”

Section: Small Angle Scattering and Diffractionmentioning

confidence: 99%

“…Further implementations performed for the use of ab initio methods applied to the study of macromolecules in solution took advantage of the known atomic resolution information for proteins, available in the protein data bank (https://www.wwpdb.org/) [47], and composes the ATSAS program suite [17,41,[57][58][59][60][61][62][63][64][65][66][67][68][69]. Several good reviews can be found in the literature for this subject [14,17,36,50,60,65,[67][68][69].…”

Section: Small Angle Scattering and Diffractionmentioning

confidence: 99%

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Calculation of Small-Angle Scattering Patterns

Alves¹,

Oliveira²

2018

Small Angle Scattering and Diffraction

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Small-angle scattering (SAS) experiments applied to nano-scaled systems allow the investigation of the constituents' overall shape, size, internal structure and arrangement. A standard scattering experiment requires a relatively simple setup and is often applied to investigate a system of particles. In these cases, the measured scattering intensity represents an average over a large number of particles illuminated by the incoming beam. The calculation and modeling of the scattering intensity can be performed by the use of analytical/semi-analytical expressions or by the use of numerical methods. In this book chapter, an overview of current available simulation/modeling methods for SAS will be shown either for systems composed of oriented or for randomly oriented particles. Examples demonstrating the use of the finite element method are presented as well as a newly developed method for calculating scattering intensity for oriented particles.

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“…Molecular weights were also determined without a standard protein from the SAXS data alone, using the SAXS MoW procedure 65 . The raw data were processed with BioXTAS RAW 66 , and the ATSAS package 67 was used for further analyses and structure modelling. Specifically, distance distribution functions were generated by GNOM 68 , and the programs DAMMIF, GASBOR, BUNCH, and CORAL were used for ab initio and rigid-body modelling 67,69,70 .…”

Section: Small-angle X-ray Scatteringmentioning

confidence: 99%

Self-Assembly Characteristics of a Crystalline–Amorphous Diblock Copolymer in Nanoscale Thin Films

Kim

Ahn

et al. 2013

Macromolecules

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Abstract2H phosphoesterases catalyze reactions on nucleotide substrates and contain two conserved histidine residues in the active site. Very limited information is currently available on the details of the active site and substrate/product binding during the catalytic cycle of these enzymes. We performed a comprehensive X-ray crystallographic study of mouse 2',3'-cyclic nucleotide 3'-phosphodiesterase (CNPase), a membrane-associated enzyme present at high levels in the tetrapod myelin sheath. We determined crystal structures of the CNPase phosphodiesterase domain complexed with substrate, product, and phosphorothioate analogues. The data provide detailed information on the CNPase reaction mechanism, including substrate binding mode and coordination of the nucleophilic water molecule. Linked to the reaction, an open/close motion of the β5-α7 loop is observed. The role of the N terminus of helix α7 -unique for CNPase in the 2H family -during the reaction indicates that 2H phosphoesterases differ in their respective reaction mechanisms, despite the conserved catalytic residues. Furthermore, based on small-angle X-ray scattering, we present a model for the full-length enzyme, indicating the two domains of CNPase form an elongated molecule. Finally, based on our structural data and a comprehensive bioinformatics study, we discuss the conservation of CNPase in various organisms.

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New developments in theATSASprogram package for small-angle scattering data analysis

Abstract: The paper presents new developments and amendments to the ATSAS package (version 2.4) for processing and analysis of isotropic small-angle scattering data.

Cited by 1,646 publications

References 48 publications

Functional role of TRIM E3 ligase oligomerization and regulation of catalytic activity

Functional role of TRIM E3 ligase oligomerization and regulation of catalytic activity

Calculation of Small-Angle Scattering Patterns

Self-Assembly Characteristics of a Crystalline–Amorphous Diblock Copolymer in Nanoscale Thin Films

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