scholarly journals Domain structure of human complement C4b extends with increasing NaCl concentration: implications for its regulatory mechanism

2016 ◽  
Vol 473 (23) ◽  
pp. 4473-4491 ◽  
Author(s):  
Ka Wai Fung ◽  
David W. Wright ◽  
Jayesh Gor ◽  
Marcus J. Swann ◽  
Stephen J. Perkins
Keyword(s):  
Crystal Structure ◽  
Domain Structure ◽  
Conformational Changes ◽  
Analytical Ultracentrifugation ◽  
Sedimentation Coefficient ◽  
Salt Bridge ◽  
X Ray ◽  
X Ray Scattering ◽  
Nacl Concentration ◽  
Dual Polarisation Interferometry

During the activation of complement C4 to C4b, the exposure of its thioester domain (TED) is crucial for the attachment of C4b to activator surfaces. In the C4b crystal structure, TED forms an Arg104–Glu1032 salt bridge to tether its neighbouring macroglobulin (MG1) domain. Here, we examined the C4b domain structure to test whether this salt bridge affects its conformation. Dual polarisation interferometry of C4b immobilised at a sensor surface showed that the maximum thickness of C4b increased by 0.46 nm with an increase in NaCl concentration from 50 to 175 mM NaCl. Analytical ultracentrifugation showed that the sedimentation coefficient s20,w of monomeric C4b of 8.41 S in 50 mM NaCl buffer decreased to 7.98 S in 137 mM NaCl buffer, indicating that C4b became more extended. Small angle X-ray scattering reported similar RG values of 4.89–4.90 nm for C4b in 137–250 mM NaCl. Atomistic scattering modelling of the C4b conformation showed that TED and the MG1 domain were separated by 4.7 nm in 137–250 mM NaCl and this is greater than that of 4.0 nm in the C4b crystal structure. Our data reveal that in low NaCl concentrations, both at surfaces and in solution, C4b forms compact TED–MG1 structures. In solution, physiologically relevant NaCl concentrations lead to the separation of the TED and MG1 domain, making C4b less capable of binding to its complement regulators. These conformational changes are similar to those seen previously for complement C3b, confirming the importance of this salt bridge for regulating both C4b and C3b.

Structural basis of the transactivation deficiency of the human PPARγ F360L mutant associated with familial partial lipodystrophy

2014 ◽  
Vol 70 (7) ◽  
pp. 1965-1976 ◽  
Author(s):  
Clorinda Lori ◽  
Alessandra Pasquo ◽  
Roberta Montanari ◽  
Davide Capelli ◽  
Valerio Consalvi ◽  
...  
Keyword(s):  
Crystal Structure ◽  
Conformational Changes ◽  
Partial Agonist ◽  
Salt Bridge ◽  
Van Der Waals Interactions ◽  
Structural Basis ◽  
Wild Type ◽  
Partial Lipodystrophy ◽  
X Ray ◽  
Familial Partial Lipodystrophy

The peroxisome proliferator-activated receptors (PPARs) are transcription factors that regulate glucose and lipid metabolism. The role of PPARs in several chronic diseases such as type 2 diabetes, obesity and atherosclerosis is well known and, for this reason, they are the targets of antidiabetic and hypolipidaemic drugs. In the last decade, some rare mutations in human PPARγ that might be associated with partial lipodystrophy, dyslipidaemia, insulin resistance and colon cancer have emerged. In particular, the F360L mutant of PPARγ (PPARγ2 residue 388), which is associated with familial partial lipodystrophy, significantly decreases basal transcriptional activity and impairs stimulation by synthetic ligands. To date, the structural reason for this defective behaviour is unclear. Therefore, the crystal structure of PPARγ F360L together with the partial agonist LT175 has been solved and the mutant has been characterized by circular-dichroism spectroscopy (CD) in order to compare its thermal stability with that of the wild-type receptor. The X-ray analysis showed that the mutation induces dramatic conformational changes in the C-terminal part of the receptor ligand-binding domain (LBD) owing to the loss of van der Waals interactions made by the Phe360 residue in the wild type and an important salt bridge made by Arg357, with consequent rearrangement of loop 11/12 and the activation function helix 12 (H12). The increased mobility of H12 makes the binding of co-activators in the hydrophobic cleft less efficient, thereby markedly lowering the transactivation activity. The spectroscopic analysis in solution and molecular-dynamics (MD) simulations provided results which were in agreement and consistent with the mutant conformational changes observed by X-ray analysis. Moreover, to evaluate the importance of the salt bridge made by Arg357, the crystal structure of the PPARγ R357A mutant in complex with the agonist rosiglitazone has been solved.

Masking of the Fc region in human IgG4 by constrained X-ray scattering modelling: implications for antibody function and therapy

2010 ◽  
Vol 432 (1) ◽  
pp. 101-114 ◽  
Author(s):  
Yuki Abe ◽  
Jayesh Gor ◽  
Daniel G. Bracewell ◽  
Stephen J. Perkins ◽  
Paul A. Dalby
Keyword(s):  
Concentration Dependence ◽  
Solution Structure ◽  
Analytical Ultracentrifugation ◽  
Sedimentation Coefficient ◽  
Radius Of Gyration ◽  
X Ray ◽  
X Ray Scattering ◽  
Starting Point ◽  
Self Association ◽  
Ray Scattering

Of the four human IgG antibody subclasses IgG1–IgG4, IgG4 is of interest in that it does not activate complement and exhibits atypical self-association, including the formation of bispecific antibodies. The solution structures of antibodies are critical to understand function and therapeutic applications. Thus IgG4 was studied by synchrotron X-ray scattering. The Guinier X-ray radius of gyration RG increased from 5.0 nm to 5.1 nm with an increase of concentration. The distance distribution function P(r) revealed a single peak at 0.3 mg/ml, which resolved into two peaks that shifted to smaller r values at 1.3 mg/ml, even though the maximum dimension of IgG4 was unchanged at 17 nm. This indicated a small concentration dependence of the IgG4 solution structure. By analytical ultracentrifugation, no concentration dependence in the sedimentation coefficient of 6.4 S was observed. Constrained scattering modelling resulted in solution structural determinations that showed that IgG4 has an asymmetric solution structure in which one Fab–Fc pair is closer together than the other pair, and the accessibility of one side of the Fc region is masked by the Fab regions. The averaged distances between the two Fab–Fc pairs change by 1–2 nm with the change in IgG4 concentration. The averaged conformation of the Fab regions appear able to hinder complement C1q binding to the Fc region and the self-association of IgG4 through the Fc region. The present results clarify IgG4 function and provide a starting point to investigate antibody stability.

Structural refinement by restrained molecular-dynamics algorithm with small-angle X-ray scattering constraints for a biomolecule

2004 ◽  
Vol 37 (1) ◽  
pp. 103-109 ◽  
Author(s):  
Masaki Kojima ◽  
Alexander A. Timchenko ◽  
Junichi Higo ◽  
Kazuki Ito ◽  
Hiroshi Kihara ◽  
...  
Keyword(s):  
Crystal Structure ◽  
Molecular Dynamics ◽  
Small Angle ◽  
Protein Structures ◽  
Saxs Data ◽  
X Ray ◽  
X Ray Scattering ◽  
Saxs Curve ◽  
Restrained Molecular Dynamics ◽  
Ray Scattering

A new algorithm to refine protein structures in solution from small-angle X-ray scattering (SAXS) data was developed based on restrained molecular dynamics (MD). In the method, the sum of squared differences between calculated and observed SAXS intensities was used as a constraint energy function, and the calculation was started from given atomic coordinates, such as those of the crystal. In order to reduce the contribution of the hydration effect to the deviation from the experimental (objective) curve during the dynamics, and purely as an estimate of the efficiency of the algorithm, the calculation was first performed assuming the SAXS curve corresponding to the crystal structure as the objective curve. Next, the calculation was carried out with `real' experimental data, which yielded a structure that satisfied the experimental SAXS curve well. The SAXS data for ribonuclease T1, a single-chain globular protein, were used for the calculation, along with its crystal structure. The results showed that the present algorithm was very effective in the refinement and adjustment of the initial structure so that it could satisfy the objective SAXS data.

scholarly journals Vibrational anisotropy of <i>δ</i>-(Al,Fe)OOH single crystals as probed by nuclear resonant inelastic X-ray scattering

2021 ◽  
Vol 33 (4) ◽  
pp. 485-502
Author(s):  
Johannes Buchen ◽  
Wolfgang Sturhahn ◽  
Takayuki Ishii ◽  
Jennifer M. Jackson
Keyword(s):  
Crystal Structure ◽  
High Pressure ◽  
Single Crystals ◽  
Vibrational Properties ◽  
Phonon Density ◽  
Phonon Density Of States ◽  
X Ray ◽  
X Ray Scattering ◽  
The Mean ◽  
Vibrational Anisotropy

Abstract. The formation of high-pressure oxyhydroxide phases spanned by the components AlOOH–FeOOH–MgSiO2(OH)2 in experiments suggests their capability to retain hydrogen in Earth's lower mantle. Understanding the vibrational properties of high-pressure phases provides the basis for assessing their thermal properties, which are required to compute phase diagrams and physical properties. Vibrational properties can be highly anisotropic, in particular for materials with crystal structures of low symmetry that contain directed structural groups or components. We used nuclear resonant inelastic X-ray scattering (NRIXS) to probe lattice vibrations that involve motions of 57Fe atoms in δ-(Al0.87Fe0.13)OOH single crystals. From the recorded single-crystal NRIXS spectra, we calculated projections of the partial phonon density of states along different crystallographic directions. To describe the anisotropy of central vibrational properties, we define and derive tensors for the partial phonon density of states, the Lamb–Mössbauer factor, the mean kinetic energy per vibrational mode, and the mean force constant of 57Fe atoms. We further show how the anisotropy of the Lamb–Mössbauer factor can be translated into anisotropic displacement parameters for 57Fe atoms and relate our findings on vibrational anisotropy to the crystal structure of δ-(Al,Fe)OOH. As a potential application of single-crystal NRIXS at high pressures, we discuss the evaluation of anisotropic thermal stresses in the context of elastic geobarometry for mineral inclusions. Our results on single crystals of δ-(Al,Fe)OOH demonstrate the sensitivity of NRIXS to vibrational anisotropy and provide an in-depth description of the vibrational behavior of Fe3+ cations in a crystal structure that may motivate future applications of NRIXS to study anisotropic vibrational properties of minerals.

scholarly journals Solution-Based Structural Analysis of the Decaheme Cytochrome, MtrA, by Small-Angle X-ray Scattering and Analytical Ultracentrifugation

2011 ◽  
Vol 115 (38) ◽  
pp. 11208-11214 ◽  
Author(s):  
Mackenzie A. Firer-Sherwood ◽  
Nozomi Ando ◽  
Catherine L. Drennan ◽  
Sean J. Elliott
Keyword(s):  
Structural Analysis ◽  
Small Angle ◽  
Analytical Ultracentrifugation ◽  
X Ray ◽  
X Ray Scattering ◽  
Ray Scattering

Analysis of structural MtrC models based on homology with the crystal structure of MtrF

2012 ◽  
Vol 40 (6) ◽  
pp. 1181-1185 ◽  
Author(s):  
Marcus J. Edwards ◽  
James K. Fredrickson ◽  
John M. Zachara ◽  
David J. Richardson ◽  
Thomas A. Clarke
Keyword(s):  
Crystal Structure ◽  
Outer Membrane ◽  
Domain Structure ◽  
Spectroscopic Data ◽  
Sequence Similarity ◽  
Shewanella Oneidensis ◽  
Significant Sequence Similarity ◽  
X Ray ◽  
X Ray Crystallography ◽  
Homology Models

The outer-membrane decahaem cytochrome MtrC is part of the transmembrane MtrCAB complex required for mineral respiration by Shewanella oneidensis. MtrC has significant sequence similarity to the paralogous decahaem cytochrome MtrF, which has been structurally solved through X-ray crystallography. This now allows for homology-based models of MtrC to be generated. The structure of these MtrC homology models contain ten bis-histidine-co-ordinated c-type haems arranged in a staggered cross through a four-domain structure. This model is consistent with current spectroscopic data and shows that the areas around haem 5 and haem 10, at the termini of an octahaem chain, are likely to have functions similar to those of the corresponding haems in MtrF. The electrostatic surfaces around haem 7, close to the β-barrels, are different in MtrF and MtrC, indicating that these haems may have different potentials and interact with substrates differently.

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