scholarly journals Exploiting subtle structural differences in heavy-atom derivatives for experimental phasing

2014 ◽  
Vol 70 (7) ◽  
pp. 1873-1883 ◽  
Author(s):  
Jimin Wang ◽  
Yue Li ◽  
Yorgo Modis
Keyword(s):  
Structure Determination ◽  
Heavy Atom ◽  
Data Sets ◽  
Diarrhea Virus ◽  
Isomorphous Replacement ◽  
Experimental Phasing ◽  
Structural Differences ◽  
Structure Determinations ◽  
Weak Derivatives ◽  
Viral Diarrhea Virus

Structure determination using the single isomorphous replacement (SIR) or single-wavelength anomalous diffraction (SAD) methods with weak derivatives remains very challenging. In a recent structure determination of glycoprotein E2 from bovine viral diarrhea virus, three isomorphous uranium-derivative data sets were merged to obtain partially interpretable initial experimental maps. Small differences between them were then exploited by treating them as three independent SAD data sets plus three circular pairwise SIR data sets to improve the experimental maps. Here, how such subtle structural differences were exploited for experimental phasing is described in detail. The basis for why this approach works is also provided: the effective resolution of isomorphous signals between highly isomorphous derivatives is often much higher than the effective resolution of the anomalous signals of individual derivative data sets. Hence, the new phasing approaches outlined here will be generally applicable to structure determinations involving weak derivatives.

scholarly journals Membrane protein structure determination by SAD, SIR, or SIRAS phasing in serial femtosecond crystallography using an iododetergent

2016 ◽  
Vol 113 (46) ◽  
pp. 13039-13044 ◽  
Author(s):  
Takanori Nakane ◽  
Shinya Hanashima ◽  
Mamoru Suzuki ◽  
Haruka Saiki ◽  
Taichi Hayashi ◽  
...  
Keyword(s):  
Membrane Protein ◽  
Structure Determination ◽  
Free Electron ◽  
Heavy Atom ◽  
Anomalous Scattering ◽  
X Ray ◽  
Isomorphous Replacement ◽  
Experimental Phasing ◽  
Serial Femtosecond Crystallography

The 3D structure determination of biological macromolecules by X-ray crystallography suffers from a phase problem: to perform Fourier transformation to calculate real space density maps, both intensities and phases of structure factors are necessary; however, measured diffraction patterns give only intensities. Although serial femtosecond crystallography (SFX) using X-ray free electron lasers (XFELs) has been steadily developed since 2009, experimental phasing still remains challenging. Here, using 7.0-keV (1.771 Å) X-ray pulses from the SPring-8 Angstrom Compact Free Electron Laser (SACLA), iodine single-wavelength anomalous diffraction (SAD), single isomorphous replacement (SIR), and single isomorphous replacement with anomalous scattering (SIRAS) phasing were performed in an SFX regime for a model membrane protein bacteriorhodopsin (bR). The crystals grown in bicelles were derivatized with an iodine-labeled detergent heavy-atom additive 13a (HAD13a), which contains the magic triangle, I3C head group with three iodine atoms. The alkyl tail was essential for binding of the detergent to the surface of bR. Strong anomalous and isomorphous difference signals from HAD13a enabled successful phasing using reflections up to 2.1-Å resolution from only 3,000 and 4,000 indexed images from native and derivative crystals, respectively. When more images were merged, structure solution was possible with data truncated at 3.3-Å resolution, which is the lowest resolution among the reported cases of SFX phasing. Moreover, preliminary SFX experiment showed that HAD13a successfully derivatized the G protein-coupled A2a adenosine receptor crystallized in lipidic cubic phases. These results pave the way for de novo structure determination of membrane proteins, which often diffract poorly, even with the brightest XFEL beams.

Structure determination using poorly diffracting membrane-protein crystals: the H+-ATPase and Na+,K+-ATPase case history

2010 ◽  
Vol 66 (3) ◽  
pp. 309-313 ◽  
Author(s):  
Bjørn P. Pedersen ◽  
J. Preben Morth ◽  
Poul Nissen
Keyword(s):  
Structure Determination ◽  
Heavy Atom ◽  
Real Space ◽  
Search Model ◽  
Data Sets ◽  
Molecular Replacement ◽  
Maximum Resolution ◽  
Phase Combination ◽  
Site Identification

An approach is presented for the structure determination of membrane proteins on the basis of poorly diffracting crystals which exploits molecular replacement for heavy-atom site identification at 6–9 Å maximum resolution and improvement of the heavy-atom-derived phases by multi-crystal averaging using quasi-isomorphous data sets. The multi-crystal averaging procedure allows real-space density averaging followed by phase combination between non-isomorphous native data sets to exploit crystal-to-crystal nonisomorphism despite the crystals belonging to the same space group. This approach has been used in the structure determination of H+-ATPase and Na+,K+-ATPase using Ca2+-ATPase models and its successful application to the Mhp1 symporter using LeuT as a search model is demonstrated.

scholarly journals High-throughput in situ experimental phasing

2020 ◽  
Vol 76 (8) ◽  
pp. 790-801 ◽  
Author(s):  
Joshua M. Lawrence ◽  
Julien Orlans ◽  
Gwyndaf Evans ◽  
Allen M. Orville ◽  
James Foadi ◽  
...  
Keyword(s):  
Heavy Atom ◽  
Data Sets ◽  
Human Intervention ◽  
Macromolecular Crystallography ◽  
New Approach ◽  
Partial Data ◽  
Experimental Phasing ◽  
Anomalous Signal ◽  
First Time

In this article, a new approach to experimental phasing for macromolecular crystallography (MX) at synchrotrons is introduced and described for the first time. It makes use of automated robotics applied to a multi-crystal framework in which human intervention is reduced to a minimum. Hundreds of samples are automatically soaked in heavy-atom solutions, using a Labcyte Inc. Echo 550 Liquid Handler, in a highly controlled and optimized fashion in order to generate derivatized and isomorphous crystals. Partial data sets obtained on MX beamlines using an in situ setup for data collection are processed with the aim of producing good-quality anomalous signal leading to successful experimental phasing.

scholarly journals Temperature dependence of Uiso constraints in riding hydrogen treatments

2014 ◽  
Vol 70 (a1) ◽  
pp. C286-C286
Author(s):  
Jens Luebben ◽  
Simon Grabowsky ◽  
Alison Edwards ◽  
Wolfgang Morgenroth ◽  
George Sheldrick ◽  
...  
Keyword(s):  
Temperature Dependence ◽  
Structure Refinement ◽  
Heavy Atom ◽  
Data Sets ◽  
Hydrogen Atoms ◽  
X Ray ◽  
Structure Determinations ◽  
Thermal Displacements ◽  
Conventional Structure ◽  
Oniom Approach

"Anisotropic parametrisation of the thermal displacements of hydrogen atoms in single-crystal X-ray structure refinement is not possible with independent atom model (IAM) scattering factors. This is due to the weak scattering contribution of hydrogen atoms. Only when aspherical scattering factors are used can carefully measured Bragg data provide such information. For conventional structure determinations parameters of ""riding"" hydrogen atoms are frequently constrained to values of their ""parent"" heavy atom. Usually values of 1.2 and 1.5 times X-U_eq are assigned to H-U_iso in these cases. Such constraints yield reasonable structural models for room-temperature data. However, todays small molecule X-Ray diffraction experiments are usually carried out at significantly lower temperatures. To further study the temperature dependence of ADPs we have evaluated several data sets of N-Acetyl-L-4-Hydroxyproline Monohydrate at temperatures ranging from 9 K to 250 K. Methods compared were HAR [1], Invariom refinement [2], time-of-flight Neutron diffraction and the TLS+ONIOM approach [3]. In the TLS+ONIOM approach non-hydrogen ADPs from Invariom refinement provided ADPs for the TLS-fit. Hydrogen atoms in all methods were grouped and analyzed according to their Invariom name. We reach a good agreement of the temperature dependence of H-U_iso/X-U_eq. At very low temperatures the ratio H-U_iso/X-U_eq can be as high as 4, e.g. for Hydrogen attached to a sp3 carbon atom with three non-Hydrogen atom neighbors. Since all methods consistently show that the H-U_iso/X-U_eq ratio is temperature dependent, this effect should be taken into account in conventional structure determinations."

scholarly journals Alternative phasing method in macromolecular crystallography

2014 ◽  
Vol 70 (a1) ◽  
pp. C342-C342
Author(s):  
Santosh Panjikar ◽  
Daniele de Sanctis
Keyword(s):  
Crystal Structures ◽  
Uv Radiation ◽  
Absorption Edge ◽  
Heavy Atom ◽  
Anomalous Scattering ◽  
Covalent Bonds ◽  
X Ray ◽  
Isomorphous Replacement ◽  
Experimental Phasing ◽  
Radiation Induced

Selenium is the most widely used heavy atom for experimental phasing, either by single anomalous scattering (SAD) or multiple-wavelength anomalous diffraction (MAD) procedures. The use of the single isomorphous replacement (SIR) or single isomorphous replacement with anomalous scattering (SIRAS) phasing procedure with selenomethionine (Mse) containing proteins is not so commonly used, as it requires isomorphous native data. Several non-redundant X-ray diffraction data sets from various Mse derivatised protein crystals were collected at energies far below the absorption edge before and after exposing the crystal to ultraviolet (UV) radiation with 266 nm lasers. A detailed analysis revealed that significant changes in diffracted intensities were induced by ultraviolet irradiation whilst retaining crystal isomorphism. These intensity changes allowed the crystal structures to be solved by the radiation damage-induced phasing (RIP) technique [1]. These can be coupled with the anomalous signal from the dataset collected at the selenium absorption edge to obtain SIRAS phases in a UV-RIPAS phasing experiment [2]. Inspection of the crystal structures and electron-density maps demonstrated that covalent bonds between selenium and carbon at all sites located in the core of the proteins or in a hydrophobic environment were much more susceptible to UV radiation-induced cleavage than other bonds typically present in Mse proteins. The rapid UV radiation-induced bond cleavage opens a reliable new paradigm for phasing at synchrotron [1,2] and at in-house X-ray source [3].

scholarly journals A Brief History of Fourier Methods in Crystal-structure Determination

1985 ◽  
Vol 38 (3) ◽  
pp. 263 ◽  
Author(s):  
CA Beevers ◽  
H Lipson
Keyword(s):  
Crystal Structure ◽  
Crystal Structures ◽  
Structure Determination ◽  
Heavy Atom ◽  
Direct Methods ◽  
Crystal Structure Determination ◽  
Fourier Methods ◽  
Isomorphous Replacement ◽  
History Of

Fourier methods for the determination of crystal structures were first suggested by Bragg in 1929, and were then successfully used by Beevers and Lipson for determining the structure of CuS04.5H20 in 1934. It was necessary for methods of summation to be devised, and after some experimentation the Beevers-Lipson strips became established as the best device for the work. They enabled increasingly complicated structures to be derived, but ultimately more elaborate and automatic devices based on digital computers had to be introduced. At the same time, isomorphous-replacement, heavy-atom and direct methods were also developed and these have enabled structures of enormous complexity to be successfully determined.

scholarly journals Initiating heavy-atom-based phasing by multi-dimensional molecular replacement

2016 ◽  
Vol 72 (3) ◽  
pp. 440-445 ◽  
Author(s):  
Bjørn Panyella Pedersen ◽  
Pontus Gourdon ◽  
Xiangyu Liu ◽  
Jesper Lykkegaard Karlsen ◽  
Poul Nissen
Keyword(s):  
Conformational Changes ◽  
Wide Spectrum ◽  
Heavy Atom ◽  
Direct Methods ◽  
Data Sets ◽  
Molecular Replacement ◽  
Search Models ◽  
Experimental Phasing ◽  
Difference Fourier ◽  
P Type

To obtain an electron-density map from a macromolecular crystal the phase problem needs to be solved, which often involves the use of heavy-atom derivative crystals and concomitant heavy-atom substructure determination. This is typically performed by dual-space methods, direct methods or Patterson-based approaches, which however may fail when only poorly diffracting derivative crystals are available. This is often the case for, for example, membrane proteins. Here, an approach for heavy-atom site identification based on a molecular-replacement parameter matrix (MRPM) is presented. It involves ann-dimensional search to test a wide spectrum of molecular-replacement parameters, such as different data sets and search models with different conformations. Results are scored by the ability to identify heavy-atom positions from anomalous difference Fourier maps. The strategy was successfully applied in the determination of a membrane-protein structure, the copper-transporting P-type ATPase CopA, when other methods had failed to determine the heavy-atom substructure. MRPM is well suited to proteins undergoing large conformational changes where multiple search models should be considered, and it enables the identification of weak but correct molecular-replacement solutions with maximum contrast to prime experimental phasing efforts.

scholarly journals Automated MAD and MIR structure solution

1999 ◽  
Vol 55 (4) ◽  
pp. 849-861 ◽  
Author(s):  
Thomas C. Terwilliger ◽  
Joel Berendzen
Keyword(s):  
Model Building ◽  
Heavy Atom ◽  
Solution Process ◽  
Data Sets ◽  
X Ray Diffraction ◽  
Major Step ◽  
Subjective Evaluations ◽  
Structure Solution ◽  
Structure Determinations ◽  
Genomic Scale

Obtaining an electron-density map from X-ray diffraction data can be difficult and time-consuming even after the data have been collected, largely because MIR and MAD structure determinations currently require many subjective evaluations of the qualities of trial heavy-atom partial structures before a correct heavy-atom solution is obtained. A set of criteria for evaluating the quality of heavy-atom partial solutions in macromolecular crystallography have been developed. These have allowed the conversion of the crystal structure-solution process into an optimization problem and have allowed its automation. The SOLVE software has been used to solve MAD data sets with as many as 52 selenium sites in the asymmetric unit. The automated structure-solution process developed is a major step towards the fully automated structure-determination, model-building and refinement procedure which is needed for genomic scale structure determinations.

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