Shape Determination from Solution Scattering of Biopolymers

Svergun, Dmitri I.; Volkov, V. V.; Kozin, M. B.; Stuhrmann, H. B.; Barberato, Cláudio; Koch, Michel H. J.

doi:10.1107/s0021889897001714

Cited by 65 publications

(69 citation statements)

References 8 publications

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“…SAXS hRXR␣⌬AB tetramer models obtained by two independent ab initio approaches. a, upper row shows a superposition of the envelop model obtained by SASHA (34) to the average of ten DAM calculated by DAMMIN (31), and the lower row represents the superposition of the same ten DAM to the x-ray structure of the hRXR␣⌬ LBD tetramer (21) and four hRXR␣ DBDs (23). Grid space is 2 nm.…”

Section: Discussionmentioning

confidence: 99%

“…In the first procedure (33,34), the shape is represented by an angular envelope function, parameterized in terms of spherical harmonics using multipole expansion methods (35). The maximum number of the spherical harmonics L is selected to keep the number of free parameters M ϭ (L ϩ 1) Ϫ 6 close to the number of Shannon channels N s ϭ D max q max / in the experimental data (36).…”

Section: Small-angle X-ray Scattering Measurements and Data Analysis-mentioning

confidence: 99%

“…The experimental data were fitted ab initio by the scattering from an envelope function starting from a spherical initial approximation (33,34). The envelopes were represented with spherical harmonics up to L ϭ 4 (13 independent parameters) and L ϭ 10 (31 independent parameters) for dimer and tetramer, respectively.…”

Section: Ab Initio Shape Determination Using Envelope Functionsmentioning

confidence: 99%

See 2 more Smart Citations

Low Resolution Structures of the Retinoid X Receptor DNA-binding and Ligand-binding Domains Revealed by Synchrotron X-ray Solution Scattering

Fischer

Dias

Santos

et al. 2003

Journal of Biological Chemistry

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Nuclear receptors are ligand-inducible transcription factors that share structurally related DNA-binding (DBD) and ligand-binding (LBD) domains. Biochemical and structural studies have revealed the modular nature of DBD and LBD. Nevertheless, the domains function in concert in vivo. While high-resolution crystal structures of nuclear receptor DBDs and LBDs are available, there are no x-ray structural studies of nuclear receptor proteins containing multiple domains. We report the solution structures of the human retinoid X receptor DBD-LBD (hRXR␣⌬AB) region. We obtained ab initio shapes of hRXR␣⌬AB dimer and tetramer to 3.3 and 1.7 nm resolutions, respectively, and established the position and orientation of the DBD and LBD by fitting atomic coordinates of hRXR␣ DBD and LBD. The dimer is U-shaped with DBDs spaced at ϳ2 nm in a head to head orientation forming an angle of about 10°with respect to each other and with an extensive interface area provided by the LBD. The tetramer is a more elongated X-shaped molecule formed by two dimers in head to head arrangement in which the DBDs are extended from the structure and spaced at about 6 nm. The close proximity of DBDs in dimers may facilitate homodimer formation on DNA; however, for the homodimer to bind to a DNA element containing two directly repeated halfsites, one of the DBDs would need to rotate with respect to the other element. By contrast, the separation of DBDs in the tetramers may account for their decreased ability to recognize DNA.The nuclear receptor gene family in humans consists of at least 48 structurally related proteins that regulate transcription of target genes (1). These include receptors for the steroid and thyroid hormones, retinoids, vitamin D, prostaglandins, fatty acids, and unknown ligands, the orphan receptors. Nuclear receptors are comprised of single polypeptide chains that contain modular domains (2-4). The N termini of the receptors, which are the most variable in length, have transcription transactivation functions. The centrally placed and highly conserved DNA-binding domain (DBD) 1 directs receptor binding to DNA and is also involved in dimerization. The carboxyl-terminal ligand-binding domain (LBD) binds the ligand and undergoes ligand-induced conformational changes that promote dissociation of corepressors and association of coactivators that mediate receptor-induced changes in transcriptional control. The LBD also participates in receptor homodimerization, heterodimerization, and oligomerization (5, 6).Retinoids exert multiple effects on morphogenesis and differentiation in fetal and adult organs and regulate glucose and lipid homeostasis. They also act as potent inhibitors of oncogenesis in rodent models and are used as chemo-preventive and therapeutic agents in several types of cancers in humans (7-12). In mice retinoid X receptor (RXR) selective agonists function as insulin sensitizers and can decrease hyperglycemia, hypertriglyceridemia, and hyperinsulinemia (13). The three RXR isoforms (␣, ␤, and ␥) bind to 9-cis retinoic a...

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Section: Discussionmentioning

confidence: 99%

Section: Small-angle X-ray Scattering Measurements and Data Analysis-mentioning

confidence: 99%

Section: Ab Initio Shape Determination Using Envelope Functionsmentioning

confidence: 99%

See 1 more Smart Citation

Low Resolution Structures of the Retinoid X Receptor DNA-binding and Ligand-binding Domains Revealed by Synchrotron X-ray Solution Scattering

Fischer

Dias

Santos

et al. 2003

Journal of Biological Chemistry

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“…The multipole expansion method proposed by Stuhrmann (28) and developed by Svergun et al (29) was used to obtain the molecular shape of human ETF. The smoothed scattering profile of reduced human ETF was fitted ab initio by the scattering from an envelope function starting from an ellipsoidal initial approximation (consistent with the experimental R g and D max values).…”

Section: Methodsmentioning

confidence: 99%

Protein Dynamics Enhance Electronic Coupling in Electron Transfer Complexes

Chohan¹,

Jones²,

Grossmann³

et al. 2001

Journal of Biological Chemistry

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“…Rotation of the monomer by the Euler angles ␣, ␤, and ␥, followed by its displacement by the vector r ϭ (r,,) and generation of all symmetry mates, permits one to construct a symmetric oligomer. The partial scattering amplitudes of the rotated and shifted monomer (B lm (s) ϭ B lm (s,␣,␤,␥,r)) can be analytically expressed via the amplitudes (A lm (s)) and the elements of the finite rotation matrix (25) as described (26). Assuming without loss of generality that the n-fold axis coincides with the z axis and that the 2-fold axis in the case of Pn2 symmetry coincides with the y axis, symmetry mate generation leads to selection rules for the spherical harmonics so that the scattering from the entire oligomer is as in Equation 4,…”

Section: Methodsmentioning

confidence: 99%

Quaternary Structure of Azospirillum brasilense NADPH-dependent Glutamate Synthase in Solution as Revealed by Synchrotron Radiation X-ray Scattering

Petoukhov

Svergun

Konarev

et al. 2003

Journal of Biological Chemistry

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Azospirillum brasilense glutamate synthase (GltS) is the prototype of bacterial NADPH-dependent enzymes, a class of complex iron-sulfur flavoproteins essential in ammonia assimilation processes. The catalytically active GltS ␣␤ holoenzyme and its isolated ␣ and ␤ subunits (162 and 52 kDa, respectively) were analyzed using synchrotron radiation x-ray solution scattering. The GltS ␣ subunit and ␣␤ holoenzyme were found to be tetrameric in solution, whereas the ␤ subunit was a mixture of monomers and dimers. Ab initio low resolution shapes restored from the scattering data suggested that the arrangement of ␣ subunits in the (␣␤) 4 holoenzyme is similar to that in the tetrameric ␣ 4 complex and that ␤ subunits occupy the periphery of the holoenzyme. The structure of ␣ 4 was further modeled using the available crystallographic coordinates of the monomeric ␣ subunit assuming P222 symmetry. To model the entire ␣␤ holoenzyme, a putative ␣␤ protomer was constructed from the coordinates of the ␣ subunit and those of the N-terminal region of porcine dihydropyrimidine dehydrogenase, which is similar to the ␤ subunit. Rigid body refinement yielded a model of GltS with an arrangement of ␣ subunits similar to that in ␣ 4 , but displaying contacts also between ␤ subunits belonging to adjacent protomers. The holoenzyme model allows for independent catalytic activity of the ␣␤ protomers, which is consistent with the available biochemical evidence.Glutamate synthase (GltS) 1 is a complex iron-sulfur flavoprotein that catalyzes the reductive transfer of the L-glutamine amide group to C-2 of 2-oxoglutarate (2-OG) using either reduced pyridine nucleotides (NADH or NADPH) or reduced ferredoxin as the physiological electron donor, depending on the enzyme species (1). The enzyme forms, with glutamine synthetase, the main pathway for ammonia assimilation in microorganisms and plants and has an unknown role in animals. Bacteria contain an NADPH-dependent GltS (NADPHGltS) whose catalytically active ␣␤ protomer (␣ subunit, 162 kDa; and ␤ subunit, 52.3 kDa) contains one FAD, one FMN, and three different iron-sulfur clusters. Eukaryotic GltS is reported to be NADH-dependent and is formed by a single polypeptide chain derived from the fusion of bacterial ␣ and ␤ subunits. On the basis of sequence similarities, NADH-dependent GltS should have a cofactor content and overall architecture similar to those of the well characterized Azospirillum brasilense NADPH-GltS. Finally, cyanobacteria and plants contain an Fd-dependent GltS (Fd-GltS) similar in size, primary and tertiary structure, cofactor content, and function to the ␣ subunit of NADPH-GltS. In these organisms, Fd-GltS is reported to be mainly involved in re-assimilation of ammonia released during photorespiration or from storage compounds, whereas NADH-dependent GltS appears to be mainly responsible for primary ammonia assimilation in roots (2).A. brasilense NADPH-GltS is, indeed, the best studied GltS form. By combining a number of kinetic and spectroscopic studies on the ␣␤ holoenzyme a...

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Shape Determination from Solution Scattering of Biopolymers

Cited by 65 publications

References 8 publications

Low Resolution Structures of the Retinoid X Receptor DNA-binding and Ligand-binding Domains Revealed by Synchrotron X-ray Solution Scattering

Low Resolution Structures of the Retinoid X Receptor DNA-binding and Ligand-binding Domains Revealed by Synchrotron X-ray Solution Scattering

Protein Dynamics Enhance Electronic Coupling in Electron Transfer Complexes

Quaternary Structure of Azospirillum brasilense NADPH-dependent Glutamate Synthase in Solution as Revealed by Synchrotron Radiation X-ray Scattering

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