scholarly journals Surface Engineering of Top7 to Facilitate Structure Determination

2022 ◽  
Vol 23 (2) ◽  
pp. 701
Author(s):  
Yuki Ito ◽  
Takuya Araki ◽  
Shota Shiga ◽  
Hiroyuki Konno ◽  
Koki Makabe
Keyword(s):  
Structure Determination ◽  
Surface Engineering ◽  
De Novo ◽  
Crystal Packing ◽  
Structure Model ◽  
X Ray ◽  
Hexahistidine Tag ◽  
Model Protein ◽  
Β Sheet ◽  
Packing Interactions

Top7 is a de novo designed protein whose amino acid sequence has no evolutional trace. Such a property makes Top7 a suitable scaffold for studying the pure nature of protein and protein engineering applications. To use Top7 as an engineering scaffold, we initially attempted structure determination and found that crystals of our construct, which lacked the terminal hexahistidine tag, showed weak diffraction in X-ray structure determination. Thus, we decided to introduce surface residue mutations to facilitate crystal structure determination. The resulting surface mutants, Top7sm1 and Top7sm2, crystallized easily and diffracted to the resolution around 1.7 Å. Despite the improved data, we could not finalize the structures due to high R values. Although we could not identify the origin of the high R values of the surface mutants, we found that all the structures shared common packing architecture with consecutive intermolecular β-sheet formation aligned in one direction. Thus, we mutated the intermolecular interface to disrupt the intermolecular β-sheet formation, expecting to form a new crystal packing. The resulting mutant, Top7sm2-I68R, formed new crystal packing interactions as intended and diffracted to the resolution of 1.4 Å. The surface mutations contributed to crystal packing and high resolution. We finalized the structure model with the R/Rfree values of 0.20/0.24. Top7sm2-I68R can be a useful model protein due to its convenient structure determination.

scholarly journals De novo determination of mosquitocidal Cry11Aa and Cry11Ba structures from naturally-occurring nanocrystals

2021 ◽  
Author(s):  
Guillaume Tetreau ◽  
Michael R. Sawaya ◽  
Elke De Zitter ◽  
Elena A. Andreeva ◽  
Anne-Sophie Banneville ◽  
...  
Keyword(s):  
De Novo ◽  
Mosquito Control ◽  
Crystal Packing ◽  
Molecular Replacement ◽  
Dispersion Method ◽  
X Ray ◽  
Naturally Occurring ◽  
Serial Femtosecond Crystallography

Cry11Aa and Cry11Ba are the two most potent toxins produced by mosquitocidal Bacillus thuringiensis subsp. israelensis and jegathesan, respectively. The toxins naturally crystallize within the host; however, the crystals are too small for structure determination at synchrotron sources. Therefore, we applied serial femtosecond crystallography at X-ray free electron lasers to in vivo-grown nanocrystals of these toxins. The structure of Cry11Aa was determined de novo using the single-wavelength anomalous dispersion method, which in turn enabled the determination of the Cry11Ba structure by molecular replacement. The two structures reveal a new pattern for in vivo crystallization of Cry toxins, whereby each of their three domains packs with a symmetrically identical domain, and a cleavable crystal packing motif is located within the protoxin rather than at the termini. The diversity of in vivo crystallization patterns suggests explanations for their varied levels of toxicity and rational approaches to improve these toxins for mosquito control.

scholarly journals Pink-beam serial femtosecond crystallography for accurate structure-factor determination at an X-ray free-electron laser

IUCrJ ◽  
2021 ◽  
Vol 8 (6) ◽  
Author(s):  
Karol Nass ◽  
Camila Bacellar ◽  
Claudio Cirelli ◽  
Florian Dworkowski ◽  
Yaroslav Gevorkov ◽  
...  
Keyword(s):  
Data Quality ◽  
Structure Determination ◽  
Structure Factor ◽  
Free Electron ◽  
Free Electron Laser ◽  
De Novo ◽  
Similar Data ◽  
X Ray ◽  
Redundant Data ◽  
Serial Femtosecond Crystallography

Serial femtosecond crystallography (SFX) at X-ray free-electron lasers (XFELs) enables essentially radiation-damage-free macromolecular structure determination using microcrystals that are too small for synchrotron studies. However, SFX experiments often require large amounts of sample in order to collect highly redundant data where some of the many stochastic errors can be averaged out to determine accurate structure-factor amplitudes. In this work, the capability of the Swiss X-ray free-electron laser (SwissFEL) was used to generate large-bandwidth X-ray pulses [Δλ/λ = 2.2% full width at half-maximum (FWHM)], which were applied in SFX with the aim of improving the partiality of Bragg spots and thus decreasing sample consumption while maintaining the data quality. Sensitive data-quality indicators such as anomalous signal from native thaumatin micro-crystals and de novo phasing results were used to quantify the benefits of using pink X-ray pulses to obtain accurate structure-factor amplitudes. Compared with data measured using the same setup but using X-ray pulses with typical quasi-monochromatic XFEL bandwidth (Δλ/λ = 0.17% FWHM), up to fourfold reduction in the number of indexed diffraction patterns required to obtain similar data quality was achieved. This novel approach, pink-beam SFX, facilitates the yet underutilized de novo structure determination of challenging proteins at XFELs, thereby opening the door to more scientific breakthroughs.

Crystal Structure Optimization and Semi-Empirical Quantum Chemical Calculations of N-(3,4-Dichlorophenyl)-3-Oxo-Butanamide

2012 ◽  
Vol 620 ◽  
pp. 82-86
Author(s):  
Mukesh M. Jotani
Keyword(s):  
Crystal Structure ◽  
Molecular Electrostatic Potential ◽  
Crystal Packing ◽  
Empirical Method ◽  
Molecular Orbital Calculations ◽  
X Ray ◽  
Semi Empirical ◽  
Packing Interactions ◽  
Optimized Geometries ◽  
Good Agreement

The crystal structure of N-(3,4-Dichlorophenyl)-3-oxobutanamide (I) is optimized by semi-empirical methods using MOPAC2009 program. The optimized geometries from both Austin Model 1 (AM1) and Parametrization Model 6 (PM6) describe the conformational discrepancy and crystal packing. The energy minimized structures from both the models are in good agreement with X-ray crystal data. The intramolecular charge transfer interactions are studied from the molecular orbital calculations. The parametric molecular electrostatic potential (PMEP) calculated by AM1 semi-empirical method shows the involvement of oxygen and chlorine atoms in the crystal packing interactions. The aromaticity of phenyl ring in the structure is determined using HOMED calculations.

Synthesis and Structure of (1,8-Diammonio-3,6,10,13,16,19-hexaazabicyclo[6.6.6]icosane)-nickel(II) Tetrachloride Monohydrate

1993 ◽  
Vol 46 (1) ◽  
pp. 127 ◽  
Author(s):  
LM Engelhardt ◽  
JM Harrowfield ◽  
AM Sargeson ◽  
AH White
Keyword(s):  
Hydrogen Bonding ◽  
Single Crystal ◽  
Structure Determination ◽  
Title Compound ◽  
Narrow Range ◽  
Crystal Packing ◽  
The Other ◽  
X Ray ◽  
The Mean

The synthesis and single-crystal X-ray structure determination of the title compound are described. Crystals are monoclinic, P 21, a 16.164(9), b 8.277(3), c 8.829(4) Ǻ, β 102.86(4)°, Z 2; 2666 independent 'observed' diffractometer data [I > 3σ(I)] were refined to a residual of 0.045. The cation is unusual amongst complexes of sarcophagine (3,6,10,13,16,19-hexaazabicyclo[6.6.6]icosane) cage amines in adopting a lel2ob conformation, seemingly in response to hydrogen bonding/crystal packing forces. In consequence, unlike the tetranitrate analogue in which Ni-N bond distances are dispersed over a narrow range (2.097(5)-2.119(5) Ǻ; mean 2.109 Ǻ], the coordination sphere is more distorted with one pair of Ni-N distances, cis to each other, being short at 2.081(5) and 2.086(5) Ǻ, while the other four are long, ranging from 2.116(5) to 2.135(5) Ǻ, the mean of this array being 2.111 Ǻ.

scholarly journals Advances in long-wavelength native phasing at X-ray free-electron lasers

IUCrJ ◽  
2020 ◽  
Vol 7 (6) ◽  
pp. 965-975 ◽  
Author(s):  
Karol Nass ◽  
Robert Cheng ◽  
Laura Vera ◽  
Aldo Mozzanica ◽  
Sophie Redford ◽  
...  
Keyword(s):  
Data Quality ◽  
Structure Determination ◽  
Free Electron ◽  
De Novo ◽  
Geometry Optimization ◽  
Protein Structure Determination ◽  
Time Resolved ◽  
X Ray ◽  
Long Wavelength ◽  
Order Of Magnitude

Long-wavelength pulses from the Swiss X-ray free-electron laser (XFEL) have been used for de novo protein structure determination by native single-wavelength anomalous diffraction (native-SAD) phasing of serial femtosecond crystallography (SFX) data. In this work, sensitive anomalous data-quality indicators and model proteins were used to quantify improvements in native-SAD at XFELs such as utilization of longer wavelengths, careful experimental geometry optimization, and better post-refinement and partiality correction. Compared with studies using shorter wavelengths at other XFELs and older software versions, up to one order of magnitude reduction in the required number of indexed images for native-SAD was achieved, hence lowering sample consumption and beam-time requirements significantly. Improved data quality and higher anomalous signal facilitate so-far underutilized de novo structure determination of challenging proteins at XFELs. Improvements presented in this work can be used in other types of SFX experiments that require accurate measurements of weak signals, for example time-resolved studies.

De novo protein crystal structure determination from X-ray free-electron laser data

Nature ◽  
2013 ◽  
Vol 505 (7482) ◽  
pp. 244-247 ◽  
Author(s):  
Thomas R. M. Barends ◽  
Lutz Foucar ◽  
Sabine Botha ◽  
R. Bruce Doak ◽  
Robert L. Shoeman ◽  
...  
Keyword(s):  
Crystal Structure ◽  
Structure Determination ◽  
Free Electron ◽  
Free Electron Laser ◽  
De Novo ◽  
Crystal Structure Determination ◽  
Protein Crystal ◽  
X Ray ◽  
Protein Crystal Structure ◽  
Laser Data

scholarly journals Protein structure determination by single-wavelength anomalous diffraction phasing of X-ray free-electron laser data

IUCrJ ◽  
2016 ◽  
Vol 3 (3) ◽  
pp. 180-191 ◽  
Author(s):  
Karol Nass ◽  
Anton Meinhart ◽  
Thomas R. M. Barends ◽  
Lutz Foucar ◽  
Alexander Gorel ◽  
...  
Keyword(s):  
Structure Determination ◽  
Free Electron ◽  
De Novo ◽  
Protein Structure Determination ◽  
Anomalous Scattering ◽  
X Ray ◽  
Sad Phasing ◽  
Anomalous Signal ◽  
Serial Femtosecond Crystallography

Serial femtosecond crystallography (SFX) at X-ray free-electron lasers (XFELs) offers unprecedented possibilities for macromolecular structure determination of systems that are prone to radiation damage. However, phasing XFEL datade novois complicated by the inherent inaccuracy of SFX data, and only a few successful examples, mostly based on exceedingly strong anomalous or isomorphous difference signals, have been reported. Here, it is shown that SFX data from thaumatin microcrystals can be successfully phased using only the weak anomalous scattering from the endogenous S atoms. Moreover, a step-by-step investigation is presented of the particular problems of SAD phasing of SFX data, analysing data from a derivative with a strong anomalous signal as well as the weak signal from endogenous S atoms.

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