High resolution pair-distance distribution function P(r) of protein solutions

2009 ◽  
Vol 94 (8) ◽  
pp. 083903 ◽  
Author(s):  
Xinguo Hong ◽  
Quan Hao
Keyword(s):  
Distribution Function ◽  
High Resolution ◽  
Distance Distribution ◽  
Protein Solutions ◽  
Distance Distribution Function ◽  
Pair Distance Distribution Function

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

2021 ◽  
Vol 54 (1) ◽  
Author(s):  
Karen Manalastas-Cantos ◽  
Petr V. Konarev ◽  
Nelly R. Hajizadeh ◽  
Alexey G. Kikhney ◽  
Maxim V. Petoukhov ◽  
...  
Keyword(s):  
Distribution Function ◽  
Small Angle ◽  
Small Angle Scattering ◽  
Distance Distribution ◽  
Scattering Data ◽  
Mode Analysis ◽  
Distance Distribution Function ◽  
Search Volume ◽  
Angle Scattering ◽  
Pair Distance Distribution Function

The ATSAS software suite encompasses a number of programs for the processing, visualization, analysis and modelling of small-angle scattering data, with a focus on the data measured from biological macromolecules. Here, new developments in the ATSAS 3.0 package are described. They include IMSIM, for simulating isotropic 2D scattering patterns; IMOP, to perform operations on 2D images and masks; DATRESAMPLE, a method for variance estimation of structural invariants through parametric resampling; DATFT, which computes the pair distance distribution function by a direct Fourier transform of the scattering data; PDDFFIT, to compute the scattering data from a pair distance distribution function, allowing comparison with the experimental data; a new module in DATMW for Bayesian consensus-based concentration-independent molecular weight estimation; DATMIF, an ab initio shape analysis method that optimizes the search model directly against the scattering data; DAMEMB, an application to set up the initial search volume for multiphase modelling of membrane proteins; ELLLIP, to perform quasi-atomistic modelling of liposomes with elliptical shapes; NMATOR, which models conformational changes in nucleic acid structures through normal mode analysis in torsion angle space; DAMMIX, which reconstructs the shape of an unknown intermediate in an evolving system; and LIPMIX and BILMIX, for modelling multilamellar and asymmetric lipid vesicles, respectively. In addition, technical updates were deployed to facilitate maintainability of the package, which include porting the PRIMUS graphical interface to Qt5, updating SASpy – a PyMOL plugin to run a subset of ATSAS tools – to be both Python 2 and 3 compatible, and adding utilities to facilitate mmCIF compatibility in future ATSAS releases. All these features are implemented in ATSAS 3.0, freely available for academic users at https://www.embl-hamburg.de/biosaxs/software.html.

Analytical solution of the PELDOR inverse problem using the integral Mellin transform

2017 ◽  
Vol 19 (48) ◽  
pp. 32381-32388 ◽  
Author(s):  
Anna G. Matveeva ◽  
Vyacheslav M. Nekrasov ◽  
Alexander G. Maryasov
Keyword(s):  
Inverse Problem ◽  
Distribution Function ◽  
Analytical Solution ◽  
Short Distance ◽  
Mellin Transform ◽  
Distance Distribution ◽  
Distance Distribution Function ◽  
Distance Range ◽  
Model Free ◽  
Model Free Approach

The model-free approach used does not introduce systematic distortions in the computed distance distribution function between two spins and appears to result in noise grouping in the short distance range.

Small-Angle X-Ray Scattering Studies of ADAMTS13 Demonstrate a Conformational Response to Substrate Binding in Solution

Blood ◽  
2011 ◽  
Vol 118 (21) ◽  
pp. 1191-1191
Author(s):  
Jian Zhu ◽  
Joshua Muia ◽  
Joseph D. Batchelor ◽  
Bruce C. Linders ◽  
Niraj H. Tolia ◽  
...  
Keyword(s):  
Ab Initio ◽  
Conformational Changes ◽  
Distance Distribution ◽  
Distance Distribution Function ◽  
Saxs Data ◽  
X Ray ◽  
X Ray Scattering ◽  
293 Cells ◽  
Pair Distance Distribution Function ◽  
A2 Domain

Abstract Abstract 1191 The metalloprotease ADAMTS13 inhibits the growth of platelet thrombi by cleaving the Tyr1605-Met1606 peptide bond in the A2 domain of von Willerbrand factor (VWF). Previous studies have shown that when subjected to tensile stress in solution, bound to platelets, or on endothelial cell surfaces, VWF changes conformation and interacts with multiple exosites on ADAMTS13 through a combination of structural features. These close contacts enhance the highly specific interaction between ADAMTS13 and VWF in vivo. Like VWF, ADAMTS13 is a large multidomain protein that could be regulated by large-scale conformational changes induced by substrate binding. Here we report the use of small-angle X-ray scattering (SAXS) to study the structure of ADAMTS13 and its interactions with VWF peptides in solution. ADAMTS13 truncated after the spacer domain, consisting of metalloprotease (M), disintegrin-like (D), thrombospondin type 1 (TSP1, T), Cys-rich (C) and spacer (S) domains (MDTCS), was produced in either T-Rex 293 cells (MDTCS-t) or HEK293S GNTI cells (MDTCS-g). GNTI cells do not have N-acetylglucosaminyltransferase I activity and expressed proteins lack complex N-glycans. In addition, a variant with the mutation E225Q in the M domain was produced in T-Rex 293 cells (MqDTCS-t). Construct MqDTCS-t lacks enzymatic activity but binds normally to VWF. Two VWF peptides were prepared: cVWF63 is a C-terminal A2 domain cleavage product consisting of VWF residues Met1606-Arg1668, and VWF71 consists of VWF residues Gln1599-Arg1668 with an additional Gly at the N-terminus. SAXS data were collected at the SIBYLS beamline (Lawrence Berkeley National Laboratory) for MDTCS variants without and with bound cVWF63 or VWF71. The quality of the SAXS data was evaluated by comparison to an atomic model of ADAMTS13. The M domain was modeled on ADAMTS4, DTCS domains were from the corresponding crystal structure (PDB: 3ghm). The addition of N-glycans to the atomic structure with GLYPROT improved the agreement with experimental scattering profiles determined with CRYSOL, achieving excellent values of X (Chi) < 2.0 (Table 1). Low resolution ab initio solution structures for MDTCS-g were generated from scattering profiles using DAMMIN, averaged (n = 15) using DAMAVER and superimposed on the atomic structure of MDTCS, which also demonstrated excellent agreement (Figure 1. M at top, S at bottom. Views differ by 90° rotation). Pair distance distribution functions were obtained from scattering profiles using DATGNOM. As shown in Figure 2 for MDTCS-g and MqDTCS-t, the entire pair distance distribution shifts upon binding of cVWF63 with a decrease in the maximum particle dimension (Dmax) from 143 angstroms to 132 angstroms, and 148 angstroms to 141 angstroms, respectively, indicating that bound product constrains the conformation of the enzyme. Binding of VWF71 to MqDTCS-t gave similar results.Figure 1.Ab initio model of MDTCS-g.Figure 1. Ab initio model of MDTCS-g.Figure 2.Pair distance distribution function of MDTCS with or without cVWF63.Figure 2. Pair distance distribution function of MDTCS with or without cVWF63. These results show that SAXS clearly distinguishes the structure of ADAMTS13 with or without bound product or substrate analog. ADAMTS13 domains distal to the spacer domain also contribute to VWF binding, and stepwise addition of these TSP-1 and CUB domains to MDTCS will allow the visualization of conformational changes induced by interaction with larger substrate analogs, and construction of a model for a physiologically relevant enzyme-substrate complex. Disclosures: No relevant conflicts of interest to declare.

scholarly journals Ca2+-bound calmodulin forms a compact globular structure on binding four trifluoperazine molecules in solution

2000 ◽  
Vol 347 (1) ◽  
pp. 211-215 ◽  
Author(s):  
Norio MATSUSHIMA ◽  
Nobuhiro HAYASHI ◽  
Yuji JINBO ◽  
Yoshinobu IZUMI
Keyword(s):  
Distribution Function ◽  
Conformational Changes ◽  
Small Angle ◽  
Structural Changes ◽  
Radius Of Gyration ◽  
Distance Distribution Function ◽  
Globular Structure ◽  
X Ray ◽  
X Ray Scattering ◽  
Pair Distance Distribution Function

Small-angle X-ray scattering (SAXS), which determines the radius of gyration, Rg, and the pair distance distribution function, was used to investigate the conformational changes of calmodulin (CaM) on binding to an antagonist, trifluoperazine (TFP), with or without Ca2+ in solution. We previously applied this SAXS method to CaM complexed with N-(6-aminohexyl)-5-chloro-1-naphthalenesulphonamide (W-7) [Osawa, Kuwamoto, Izumi, Yap, Ikura, Shibanuma, Yokokura, Hidaka and Matsushima (1999) FEBS Lett. 442, 173-177] and found that the binding of two W-7 TFP molecules to one Ca2+-saturated CaM molecule induces structural changes from a ‘dumb-bell’ shape to a compact globular shape. We report here that the most compact globular shape whose size is consistent with that of the 1:2 Ca2+-saturated CaM-W-7 complex is formed by the binding of four TFP molecules to one Ca2+-saturated CaM molecule. Even in the absence of Ca2+, the conformational changes of CaM occur on TFP binding, giving a slightly smaller Rg than Ca2+-free CaM alone.

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