Publications by authors named "Nelly R Hajizadeh"

8 Publications

  • Page 1 of 1

Anomalous SAXS at P12 beamline EMBL Hamburg: instrumentation and applications.

J Synchrotron Radiat 2021 May 14;28(Pt 3):812-823. Epub 2021 Apr 14.

European Molecular Biology Laboratory (EMBL), Hamburg Outstation c/o DESY, Notkestrasse 85, 22607 Hamburg, Germany.

Small-angle X-ray scattering (SAXS) is an established method for studying nanostructured systems and in particular biological macromolecules in solution. To obtain element-specific information about the sample, anomalous SAXS (ASAXS) exploits changes of the scattering properties of selected atoms when the energy of the incident X-rays is close to the binding energy of their electrons. While ASAXS is widely applied to condensed matter and inorganic systems, its use for biological macromolecules is challenging because of the weak anomalous effect. Biological objects are often only available in small quantities and are prone to radiation damage, which makes biological ASAXS measurements very challenging. The BioSAXS beamline P12 operated by the European Molecular Biology Laboratory (EMBL) at the PETRA III storage ring (DESY, Hamburg) is dedicated to studies of weakly scattering objects. Here, recent developments at P12 allowing for ASAXS measurements are presented. The beamline control, data acquisition and data reduction pipeline of the beamline were adapted to conduct ASAXS experiments. Modelling tools were developed to compute ASAXS patterns from atomic models, which can be used to analyze the data and to help designing appropriate data collection strategies. These developments are illustrated with ASAXS experiments on different model systems performed at the P12 beamline.
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http://dx.doi.org/10.1107/S1600577521003404DOI Listing
May 2021

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

J Appl Crystallogr 2021 Feb 1;54(Pt 1):343-355. Epub 2021 Feb 1.

European Molecular Biology Laboratory, Hamburg Site, Notkestrasse 85, Building 25 A, Hamburg, 22607, Germany.

The 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 package are described. They include , for simulating isotropic 2D scattering patterns; , to perform operations on 2D images and masks; , a method for variance estimation of structural invariants through parametric resampling; , which computes the pair distance distribution function by a direct Fourier transform of the scattering data; , to compute the scattering data from a pair distance distribution function, allowing comparison with the experimental data; a new module in for Bayesian consensus-based concentration-independent molecular weight estimation; , an shape analysis method that optimizes the search model directly against the scattering data; , an application to set up the initial search volume for multiphase modelling of membrane proteins; , to perform quasi-atomistic modelling of liposomes with elliptical shapes; , which models conformational changes in nucleic acid structures through normal mode analysis in torsion angle space; , which reconstructs the shape of an unknown intermediate in an evolving system; and and , for modelling multilamellar and asymmetric lipid vesicles, respectively. In addition, technical updates were deployed to facilitate maintainability of the package, which include porting the graphical interface to Qt5, updating - a plugin to run a subset of tools - to be both Python 2 and 3 compatible, and adding utilities to facilitate mmCIF compatibility in future releases. All these features are implemented in , freely available for academic users at https://www.embl-hamburg.de/biosaxs/software.html.
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http://dx.doi.org/10.1107/S1600576720013412DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7941305PMC
February 2021

Simulation of small-angle X-ray scattering data of biological macromolecules in solution.

J Appl Crystallogr 2020 Apr 18;53(Pt 2):536-539. Epub 2020 Feb 18.

European Molecular Biology Laboratory, Notkestrasse 85 c/o DESY, Hamburg, 22607, Germany.

This article presents , an application to simulate two-dimensional small-angle X-ray scattering patterns and, further, one-dimensional profiles from biological macromolecules in solution. implements a statistical approach yielding two-dimensional images in TIFF, CBF or EDF format, which may be readily processed by existing data-analysis pipelines. Intensities and error estimates of one-dimensional patterns obtained from the radial average of the two-dimensional images exhibit the same statistical properties as observed with actual experimental data. With initial input on an absolute scale, [cm]/c[mg ml], the simulated data frames may also be scaled to absolute scale such that the forward scattering after subtraction of the background is proportional to the molecular weight of the solute. The effects of changes of concentration, exposure time, flux, wavelength, sample-detector distance, detector dimensions, pixel size, and the mask as well as incident beam position can be considered for the simulation. The simulated data may be used in method development, for educational purposes, and also to determine the most suitable beamline setup for a project prior to the application and use of the actual beamtime. is available as part of the software package (3.0.0) and is freely available for academic use (http://www.embl-hamburg.de/biosaxs/download.html).
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http://dx.doi.org/10.1107/S1600576720000527DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7133063PMC
April 2020

Probing the Architecture of a Multi-PDZ Domain Protein: Structure of PDZK1 in Solution.

Structure 2018 11 13;26(11):1522-1533.e5. Epub 2018 Sep 13.

Centre for Systems Structural Biology (CSSB), DESY and European Molecular Biology Laboratory, Notkestrasse 85, Hamburg D-22607, Germany; Department of Medical Biochemistry and Biophysics, Karolinska Insititutet, Scheels väg 2, Stockholm SE-17177, Sweden. Electronic address:

The scaffolding protein PDZK1 has been associated with the regulation of membrane transporters. It contains four conserved PDZ domains, which typically recognize a 3-5-residue long motif at the C terminus of the binding partner. The atomic structures of the individual domains are available but their spatial arrangement in the full-length context influencing the binding properties remained elusive. Here we report a systematic study of full-length PDZK1 and deletion constructs using small-angle X-ray scattering, complemented with biochemical and functional studies on PDZK1 binding to known membrane protein partners. A hybrid modeling approach utilizing multiple scattering datasets yielded a well-defined, extended, asymmetric L-shaped domain organization of PDZK1 in contrast to a flexible "beads-on-string" model predicted by bioinformatics analysis. The linker regions of PDZK1 appear to play a central role in the arrangement of the four domains underlying the importance of studying scaffolding proteins in their full-length context.
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http://dx.doi.org/10.1016/j.str.2018.07.016DOI Listing
November 2018

Smaller capillaries improve the small-angle X-ray scattering signal and sample consumption for biomacromolecular solutions.

J Synchrotron Radiat 2018 Jul 26;25(Pt 4):1113-1122. Epub 2018 Jun 26.

European Molecular Biology Laboratory (EMBL), Hamburg Outstation c/o DESY, Notkestrasse 85, 22607 Hamburg, Germany.

Radiation damage by intense X-ray beams at modern synchrotron facilities is one of the major complications for biological small-angle X-ray scattering (SAXS) investigations of macromolecules in solution. To limit the damage, samples are typically measured under a laminar flow through a cell (typically a capillary) such that fresh solution is continuously exposed to the beam during measurement. The diameter of the capillary that optimizes the scattering-to-absorption ratio at a given X-ray wavelength can be calculated a priori based on fundamental physical properties. However, these well established scattering and absorption principles do not take into account the radiation susceptibility of the sample or the often very limited amounts of precious biological material available for an experiment. Here it is shown that, for biological solution SAXS, capillaries with smaller diameters than those calculated from simple scattering/absorption criteria allow for a better utilization of the available volumes of radiation-sensitive samples. This is demonstrated by comparing two capillary diameters d (d = 1.7 mm, close to optimal for 10 keV; and d = 0.9 mm, which is nominally sub-optimal) applied to study different protein solutions at various flow rates. The use of the smaller capillaries ultimately allows one to collect higher-quality SAXS data from the limited amounts of purified biological macromolecules.
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http://dx.doi.org/10.1107/S1600577518007907DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6038601PMC
July 2018

Consensus Bayesian assessment of protein molecular mass from solution X-ray scattering data.

Sci Rep 2018 05 8;8(1):7204. Epub 2018 May 8.

European Molecular Biology Laboratory (EMBL) Hamburg Outstation, DESY, Hamburg, Germany.

Molecular mass (MM) is one of the key structural parameters obtained by small-angle X-ray scattering (SAXS) of proteins in solution and is used to assess the sample quality, oligomeric composition and to guide subsequent structural modelling. Concentration-dependent assessment of MM relies on a number of extra quantities (partial specific volume, calibrated intensity, accurate solute concentration) and often yields limited accuracy. Concentration-independent methods forgo these requirements being based on the relationship between structural parameters, scattering invariants and particle volume obtained directly from the data. Using a comparative analysis on 165,982 unique scattering profiles calculated from high-resolution protein structures, the performance of multiple concentration-independent MM determination methods was assessed. A Bayesian inference approach was developed affording an accuracy above that of the individual methods, and reports MM estimates together with a credibility interval. This Bayesian approach can be used in combination with concentration-dependent MM methods to further validate the MM of proteins in solution, or as a reliable stand-alone tool in instances where an accurate concentration estimate is not available.
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http://dx.doi.org/10.1038/s41598-018-25355-2DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5940760PMC
May 2018

Integrated beamline control and data acquisition for small-angle X-ray scattering at the P12 BioSAXS beamline at PETRAIII storage ring DESY.

J Synchrotron Radiat 2018 May 25;25(Pt 3):906-914. Epub 2018 Apr 25.

Hamburg Outstation, European Molecular Biology Laboratory, Notkestrasse 85, 22607 Hamburg, Germany.

The versatility of small-angle X-ray scattering (SAXS) as a structural biology method is apparent by its compatibility with many experimental set-ups. Most advanced SAXS studies are conducted at dedicated synchrotron beamlines yielding high beam brilliance, throughput and temporal resolution. However, utilizing the full potential of the method while preserving a high degree of automation provides a challenge to any SAXS beamline. This challenge is especially pertinent at the P12 BioSAXS beamline of the EMBL at the PETRAIII Synchrotron DESY (Hamburg, Germany), optimized and dedicated to scattering of macromolecular solutions. Over 200 unique set-ups are possible at this beamline offering various functionalities, including different temporal and spatial resolutions. Presented here is a beamline control and data-acquisition software, BECQUEREL, designed to maximize flexibility and automation in the operation of P12. In the frame of a single intuitive interface the control system allows for convenient operation with all hardware set-ups available at P12 including a robotic sample changer, in-line size-exclusion chromatography, stop-flow devices, microfluidic spinning disk and various in-air settings. Additional functionalities are available to assist the data-collection procedure for novice users, and also routine operation of the support staff.
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http://dx.doi.org/10.1107/S1600577518005398DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5929361PMC
May 2018

Protein-ligand interactions investigated by thermal shift assays (TSA) and dual polarization interferometry (DPI).

Acta Crystallogr D Biol Crystallogr 2015 Jan 1;71(Pt 1):36-44. Epub 2015 Jan 1.

Chemistry Department and School of Biological and Biomedical Sciences, Durham University, South Road, Durham DH1 3LE, England.

Over the last decades, a wide range of biophysical techniques investigating protein-ligand interactions have become indispensable tools to complement high-resolution crystal structure determinations. Current approaches in solution range from high-throughput-capable methods such as thermal shift assays (TSA) to highly accurate techniques including microscale thermophoresis (MST) and isothermal titration calorimetry (ITC) that can provide a full thermodynamic description of binding events. Surface-based methods such as surface plasmon resonance (SPR) and dual polarization interferometry (DPI) allow real-time measurements and can provide kinetic parameters as well as binding constants. DPI provides additional spatial information about the binding event. Here, an account is presented of new developments and recent applications of TSA and DPI connected to crystallography.
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http://dx.doi.org/10.1107/S1399004714016617DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4304684PMC
January 2015